gebhart/patrepeval huggingface dataset:
The M Protein of SARS-CoV: Basic Structural and Immunological Properties (2003)

We studied structural and immunological properties of the SARS-CoV M (membrane) protein, based on comparative analyses of sequence features, phylogenetic investigation, and experimental results. The M protein is predicted to contain a triple-spanning transmembrane (TM) region, a single N-glycosylation site near its N-terminus that is in the exterior of the virion, and a long C-terminal region in the interior. The M protein harbors a higher substitution rate (0.6% correlated to its size) among viral open reading frames (ORFs) from published data. The four substitutions detected in the M protein, which cause non-synonymous changes, can be classified into three types. One of them results in changes of pI (isoelectric point) and charge, affecting antigenicity. The second changes hydrophobicity of the TM region, and the third one relates to hydrophilicity of the interior structure. Phylogenetic tree building based on the variations of the M protein appears to support the non-human origin of SARS-CoV. To investigate its immunogenicity, we synthesized eight oligopeptides covering 69.2% of the entire ORF and screened them by using ELISA (enzyme-linked immunosorbent assay) with sera from SARS patients. The results confirmed our predictions on antigenic sites.
Finding Email in a Multi-Account, Multi-Device World (2016)

Email is far from dead; in fact the volume of messages exchanged daily, the number of accounts per user, and the number of devices on which email is accessed have been constantly growing. Most previous studies on email have focused on management and retrieval behaviour within a single account and on a single device. In this paper, we examine how people find email in today's ecosystem through an in-depth qualitative diary study with 16 participants. We found that personal and work accounts are managed differently, resulting in diverse retrieval strategies: while work accounts are more structured and thus email is retrieved through folders, personal accounts have fewer folders and users rely primarily on the built-in search option. Moreover, retrieval occurs primarily on laptops and PCs compared to smartphones. We explore the reasons, and uncover barriers and workarounds related to managing multiple accounts and devices. Finally, we consider new design possibilities for email clients to better support how email is used today.
<b>IR, 1H-NMR, UV-Vis and thermal studies on the Rhodamine 6G charge-transfer complexes</b> (2011)

Charge-transfer (CT) complexes formed between Rhodamine 6G (Rh6G) as donor with iodine, CLA and PA as acceptors have been studied spectrophotometrically. The synthesis and characterization of Rhodamine 6G CT-complexes of iodine, [(Rh6G)2]I+.I3ˉ, chloranilic acid (CLA), [(Rh6G)(CLA)] and picric acid (PA) [(Rh6G)(PA)] were described. These complexes are readily prepared from the reaction of Rh6G with I2, CLA and PA with CHCl3 solvent. Mid and far IR, 1H-NMR, UV-Vis techniques, elemental analyses (CHN) and thermal studies, characterize the three new Rhodamine 6G charge-transfer complexes. Modified Benesi-Hildebrand method was applied to the determination of association constant and molar extinction coefficient.KEY WORDS: Rhodamine 6G, Charge transfer complexes, Picric acid, Chloranilic acid, Iodine, Thermal studies Bull. Chem. Soc. Ethiop. 2011, 25(1), 137-146.
Modeling the switching dynamics of programmable-metallization-cell (PMC) memory and its application as synapse device for a neuromorphic computation system (2010)

A physical model is developed to investigate the switching dynamics of programmable-metallization-cell (PMC) memory. Both “quasi-DC” and time-dependent transient characteristics of PMC are captured by this model in good agreement with the experimental data from Cu/SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> and Ag/Ge <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.3</inf> Se <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.7</inf> cells. For the first time, the time-dependent switching process of PMC is quantified, thus paving the way for a compact SPICE model for circuit simulation. This model reveals that experimentally measured switching parameters such as threshold voltage and cell resistance are dynamic quantities that depend on the programming pulse shape and not the pulse amplitude alone. Using this model, we show that the PMC has the potential to emulate the function of a biological synapse and exhibit the spike-timing-dependent plasticity (STDP) behavior for emerging neuromorphic computation system designs.
Programmable Infusion Pumps in ICUs: An Analysis of Corresponding Adverse Drug Events (2007)

The smart pumps we evaluated are unlikely to reduce preventable IV-ADEs in ICUs because they address only 4% of them. Expanding smart-pump capabilities might prevent more IV-ADEs.
Control of Jasmonate Biosynthesis and Senescence by miR319 Targets (2008)

Considerable progress has been made in identifying the targets of plant microRNAs, many of which regulate the stability or translation of mRNAs that encode transcription factors involved in development. In most cases, it is unknown, however, which immediate transcriptional targets mediate downstream effects of the microRNA-regulated transcription factors. We identified a new process controlled by the miR319-regulated clade of TCP (TEOSINTE BRANCHED/CYCLOIDEA/PCF) transcription factor genes. In contrast to other miRNA targets, several of which modulate hormone responses, TCPs control biosynthesis of the hormone jasmonic acid. Furthermore, we demonstrate a previously unrecognized effect of TCPs on leaf senescence, a process in which jasmonic acid has been proposed to be a critical regulator. We propose that miR319-controlled TCP transcription factors coordinate two sequential processes in leaf development: leaf growth, which they negatively regulate, and leaf senescence, which they positively regulate.
A Survey of Indexing and Retrieval of Multimodal Documents: Text and Images (2006)

A document conveys information using multiple modalities, including text, layout/style and images. For example, journal articles usually have figures to illustrate experimental results, and the title in a journal article usually has a different font size than the body text. Indexing and retrieval using only text is the traditional way of IR (Information Retrieval). With the development of the Internet and Digital Libraries, it becomes increasingly important to develop IR techniques for intelligent indexing and retrieval of multimodal documents, such as web pages in HTML or XML format, scientific publications in PDF format and document images from scanned papers. In this paper, I make a survey of multimodal IR systems that combine the text and image modalities. Indexing and retrieval are two important components of an IR system. Given a collection of documents, indexing describes documents using an index language. Retrieval uses the results of indexing and finds related documents corresponding to a user’s query. Text and image modalities use different indexing and retrieval techniques. Single-modality IR, either using text or images, has limitations. Multimodal IR aims to overcome the limitations in each single modality by combining them. The following issues in multimodal IR are addressed: various techniques to combine text and images; techniques to find
Access Pattern-Aware Cache Management for Improving Data Utilization in GPU (2017)

Long latency of memory operation is a prominent performance bottleneck in graphics processing units (GPUs). The small data cache that must be shared across dozens of warps (a collection of threads) creates significant cache contention and premature data eviction. Prior works have recognized this problem and proposed warp throttling which reduces the number of active warps contending for cache space. In this paper we discover that individual load instructions in a warp exhibit four different types of data locality behavior: (1) data brought by a warp load instruction is used only once, which is classified as streaming data (2) data brought by a warp load is reused multiple times within the same warp, called intra-warp locality (3) data brought by a warp is reused multiple times but across different warps, called inter-warp locality (4) and some data exhibit both a mix of intra- and inter-warp locality. Furthermore, each load instruction exhibits consistently the same locality type across all warps within a GPU kernel. Based on this discovery we argue that cache management must be done using per-load locality type information, rather than applying warp-wide cache management policies. We propose Access Pattern-aware Cache Management (APCM), which dynamically detects the locality type of each load instruction by monitoring the accesses from one exemplary warp. APCM then uses the detected locality type to selectively apply cache bypassing and cache pinning of data based on load locality characterization. Using an extensive set of simulations we show that APCM improves performance of GPUs by 34% for cache sensitive applications while saving 27% of energy consumption over baseline GPU.
Enhanced Fluorescence Turn‐on Imaging of Hypochlorous Acid in Living Immune and Cancer Cells (2016)

Two closely related phenyl selenyl based boron-dipyrromethene (BODIPY) turn-on fluorescent probes for the detection of hypochlorous acid (HOCl) were synthesized for studies in chemical biology; emission intensity is modulated by a photoinduced electron-transfer (PET) process. Probe 2 intrinsically shows a negligible background signal; however, after reaction with HOCl, chemical oxidation of selenium forecloses the PET process, which evokes a significant increase in fluorescence intensity. The fluorescence intensity of probes 1 and 2 with HOCl involves an ∼18 and ∼50-fold enhancement compared with the respective responses from other reactive oxygen/nitrogen species (ROS/RNS) and low detection limits (30.9 nm for 1 and 4.5 nm for 2). Both probes show a very fast response with HOCl; emission intensity reached a maximum within 1 s. These probes show high selectivity for HOCl, as confirmed by confocal microscopy imaging when testing with RAW264.7 and MCF-7 cells.
A sequence analysis of the β‐glucosidase sub‐family B (1996)

This computational study is a summary of structural properties of the beta-glucosidase subfamily B. Computations were carried out using GCG package programs. All sequences used in this analysis were taken from the protein data bank. The multialignment and the phylogenetic tree of the beta-glucosidase sub-family B are shown. The conserved patterns: DGP, GRNFE, DPYL, KHF, SDW, GLD, VLLKN in the N-terminal region and FGYGLSY in the C-terminal part should be pointed out. C-terminal parts of the Butyrivibrio fibrisolvens and Ruminoccocus albus beta-glucosidase sequences can be aligned to the N-terminal region of the other members of the subfamily. A crossed homology model in sub-family B beta-glucosidases is described.
WellCON: An Early Kick Detection System (2015)

Abstract The main objective of the work is to provide an automated system of early kick detection and control system which monitors and reports the physical conditions of the inside of wellbore annulus instantaneously through time measurements of primary waves propagation through the annulus. This system is graphically modelled as virtual instruments using the software, LabVIEW and is named ‘WellCON’ by authors. Authors propose a model in which time taken for this wave propagation in the annulus reveals the physical condition of the wellbore and denotes the fluids present in the annulus. In case of an unexpected event of kick, the model instantaneously provides the type of fluid in the kick and notifies the driller. To understand the capacity of the well to take a kick, kick tolerance are calculated at every instance of drilling. Based on the severity of the kick influx, considering the tolerance level, commands are sent to BOP to shut-in, leading to complete automation of the kick handling system.
Efficient multi-user MIMO transmissions in the LTE-A uplink (2016)

Single-User Multiple-Input Multiple-Output (MIMO) transmissions are possible since Rel. 10 of 3GPP LTE-A. The Closed Loop Spatial Multiplexing (CLSM) transmission mode enables up to a four fold increase in spectral efficiency compared to Rel. 8, yet it requires complex User Equipment (UE) hardware supporting more than one transmit antenna. The closed loop spatial multiplexing transmission mode enables up to a four fold increase in spectral efficiency compared to Rel. 8, yet it requires complex UE hardware supporting more than one transmit antenna. As it is likely that the Base Station (BS) has more receive antennas than the UE transmit antennas, employing Multi-User (MU) MIMO transmissions in the uplink can lead to significant improvement in cell throughput. We formulate MU MIMO transmissions with linear receivers as a compact matrix system model. Based on our model we present a post-equalization SINR equation, allowing the calculation of a quantized feedback parameter, the Channel Quality Indicator (CQI) value. Within this framework we reveal possible MU gains through known scheduling algorithms although the frequency selective channel is approximated by its arithmetic mean.
Non-specific cholinesterase activity in mouse spinal ganglia. The usefulness of histochemical study and image analysis for simple characterization of neuron subclasses. (1990)

Non-specific cholinesterase (ChE) activity was studied histochemically at light and electron microscopical levels in dorsal root ganglia (DRG) of adult mice. The reaction staining and diameter of neuron cells perykaria were measured by using an image analysis system. The methodological approach enable to distinguish 8 subclasses of primary sensory neurons. The proportion of individual subclasses was mapping in three subsequent cervical, thoracal and lumbar DRG. The populations of small-sized neurons increased towards lumbar level similarly as medium and small neurons exhibiting high ChE reactivity. The variations in ChE-containing neurons among DRG from different area may reflect differences in modality-specific primary sensory neurons at each spinal cord level. In addition, the effect of 3 week sciatic nerve transection on the percentage of the subclasses in L4-L6 DRG has been investigated. The number of large neurons was reduced and a decrease of ChE reactivity in medium-size neurons was found in DRG on the operated side. Thus, the present results demonstrate a selective affectation of primary sensory neurons in mouse DRG by the peripheral nerve transection. Different amounts of the reaction product corresponding with ChE activity were found in the nuclear envelope and the cisternae of rough endoplasmic reticulum.
Impaired colonization by and full invasiveness of Escherichia coli K1 bearing a site-directed mutation in the type 1 pilin gene (1990)

A type 1 pilus-deficient mutant of a systemically invasive Escherichia coli K1 strain was constructed by directed mutagenesis of pilA, the gene that codes for the major structural subunit of type 1 pili. By comparing this mutant with an isogenic pilA+ strain, we were able to assess the role of type 1 piliation in alimentary tract colonization and bloodstream invasion in neonatal rats. Intestinal colonization was not significantly affected by the pilA mutation; in contrast, loss of type 1 piliation correlated with a dramatic decrease in oropharyngeal colonization. Nevertheless, development of bacteremia after oral administration of E. coli K1 was not diminished by the mutation in pilA. Thus, loss of type 1 piliation correlated with a site-dependent effect on colonization within the alimentary tract while not interfering with bloodstream invasion.
An Objective Scatter Index Based on Double-Pass Retinal Images of a Point Source to Classify Cataracts (2011)

We introduced an objective index based in the analysis of double-pass retinal images to classify cataract patients. The method is robust and fully based in objective measurements; i.e., not depending on subjective decisions. This procedure could be used in combination with standard current methods to improve cataract patient surgery scheduling.
Underwater treatment of lead‐contaminated sediment (1996)

Abstract The sediment associated with the reconstruction of a bridge pier was classifiable as hazardous by the Toxicity Characteristic Leaching Procedure (TCLP), due to elevated concentrations of lead. However, RCRA regulations do not classify the sediment as hazardous unless it is moved. RMT designed an in‐situ, underwater treatment process to render the sediment nonhazardous, using phosphate‐based chemistry before dredging. Subsequent sediment management was conducted without the additional regulatory requirements and costs associated with managing hazardous waste.
Molecular aspects of heavy-chain class switching. (1989)

Ig heavy chain class switching results from recombination that specifically joins together tandemly repeated sequences called S-regions. S-regions are located 5' of every CH gene except C delta. Recombination between S mu and a downstream S-region results in the juxtaposition of the rearranged variable region genes with C gamma, C epsilon, or C alpha genes and expression of the new isotype. Switch recombination is probably mediated by specific recombinase(s) that may be involved in other types of Ig-gene recombination. The efficiency and regulation of class-switch recombination is influenced by a number of factors, both structural and functional. Structurally, S-regions are all composed of tandemly repeated sequences that contain common pentamer sequences, but they differ in their length and their degree of sequence similarity with S mu. The mechanism of switching appears to be influenced by the accessibility of the S-region to recombinase(s). The conformational changes that result in accessibility are unknown but are correlated with transcription and hypomethylation of DNA near S-regions. Torsional stress resulting from progression of RNA polymerase through a GC-rich S-region could serve to further distort the DNA conformation and open the duplex, thus making it available for DNA strand invasion and recombinase activity. Although the mechanistic events of S-S recombination remain to be elucidated, switching is clearly influenced by protein mediators (mitogens and interleukins) which induce differential transcription of S regions.
Toward the Isolation of the Primary Genetic Defect in Von Hippel‐ Lindau Disease<sup>a</sup> (1991)

Von Hippel-Lindau disease (VHL) is a devastating hereditary tumor syndrome associated with various forms of cancer in multiple organ systems, including endothelial-derived tumors in the central nervous system, pheochromocytomas, and, a particularly frequent cause of death in VHL, renal cell carcinomas. Using DNA linkage analysis in a number of families displaying VHL, we recently showed that the primary defect in VHL maps to the short arm of chromosome 3. On the basis of the approximate knowledge of its chromosomal location, we have meanwhile bracketed this putative "tumor suppressor" gene to a small region of approximately 10 cM in chromosome 3p25-p26. The identification of closely linked flanking markers, together with the apparent genetic homogeneity of VHL, should allow for the development of a reliable diagnostic genetic test and provides the starting point for directed chromosomal "walking" and "jumping" toward the isolation of the defective gene itself. The characterization of the VHL gene should ultimately have important implications not only for patients with VHL, but also for a much larger number of cancer patients in the general population, afflicted with the sporadic counterparts of VHL-associated tumor types, such as renal cell carcinoma.
Low complexity algorithm for sub-pixel motion estimation of HEVC (2013)

The next generation video coding standard, namely HEVC(High Efficiency Video Coding) introduced many efficient algorithms to enhance the coding efficiency. However, the computational complexity of motion estimation is still the most bottle neck for its implementation. In this paper, we propose a complexity reduction algorithm for fractional-pixel motion estimation (FPME). Firstly, a fast termination algorithm is proposed to fast terminate FPME using a threshold. Next, the proposed algorithm designs several original search orders and search patterns for 1/2 pixel and 1/4 pixel motion estimation, respectively. These proposed patterns are on the basis of the probability of each search point and its surrounding integer search points. Simulation result shows that the proposed algorithm succeed in reduction of search point for up to 38% with almost no coding efficiency loss.
Induction of apoptosis in 9-nitrocamptothecin-treated DU145 human prostate carcinoma cells correlates with de novo synthesis of CD95 and CD95 ligand and down-regulation of c-FLIP(short). (2001)

Stimulation of CD95 leads to oligomerization of this receptor and the recruitment of the Fas-associated death domain (FADD) and procaspase-8 to form the death-inducing signaling complex (DISC). Subsequent proteolytic activation of caspase-8 at the DISC leads to the activation of downstream caspases and execution of apoptosis. The anticancer drug 9-nitrocamptothecin (9NC) inhibits the nuclear enzyme topoisomerase I (Top1), an event followed by apoptosis of cancer cells. We investigated whether other mechanisms downstream of the DNA-Top1-9NC complexing step regulate the apoptotic ability of 9NC in DU145 cells. We demonstrate that induction of apoptosis in DU145 cells, upon exposure to 9NC, is associated with de novo expression of CD95 and CD95L, suggesting that 9NC-induced apoptosis is mediated by the CD95 system. In this line, we observed early activation of procaspase-3, -7, and -8, but not -1, -9, and -10. Moreover, 9NC treatment resulted in the dramatic down-regulation of c-FLIP(short) expression, but not that of c-FLIP(long) or FADD. Furthermore, incubation of DU145 cells with a neutralizing antibody (NOK-1) to CD95L or transient transfection of a c-FLIP(short) expression vector into DU145 cells partially abrogated 9NC-triggered apoptosis. We propose that 9NC triggers apoptosis by driving DU145 cells from a nonapoptotic status (c-FLIP(short)(high), CD95(low), CD95L(low)) toward a proapoptotic status (c-FLIP(short)(low), CD95(high), CD95L(high)). These findings indicate that in addition to a Top1-mediated effect, 9NC can additionally activate a CD95/CD95L-dependent apoptotic pathway.
Human Body Reconstruction (2015)

This paper gives a survey of different algorithms of human body reconstruction. According to different input data and devices we introduce human body reconstruction algorithms as two classes: image-based methods and depth data-based methods. The first class reconstructs the body with images, which is fast and convenient. However, it is not so accurate as the second one. Reconstruction methods based on 3D depth data differ in the processing of depth data. Some algorithms have accurate results by using total scanning data. Other algorithms estimate human model from part of depth data by using template or fitting in the database.
Synthesis and Properties of Annulated 2-(Azaar-2-yl)- and 2,2'-Di(azaar-2-yl)-9,9'-spirobifluorenes (2013)

A series of 9,9'-spirobifluorene-derived N-heterocycles were prepared by the reactions of 8,9-dihydrospiro(benzo[b]fluorene-11,9'-fluoren)-6(7H)-one and 8,8',9,9'-tetrahydro-11,11'-spirobi(benzo[b]fluorene)-6,6'(7H,7'H)-dione with a series of 2-amino-arenecarbaldehydes such as 2-aminobenzaldehyde, 2-aminonicotinealdehyde, 1-amino-2-naphthaldehyde, and 8-aminoquinoline-7-carbaldehyde. In addition to the absorption maxima based on the parent 9,9'-spirobifluorene skeleton in the 225-234, 239-280, 296-298, and 308-328 nm regions, the absorptions due to the π-π* transitions of the heterocycles were observed in the 351-375 nm region in the UV absorption spectra. All the compounds showed strong photoluminescences in the 390-430 nm region.