gebhart/patrepeval huggingface dataset:
The matrix protein of human immunodeficiency virus type 1 is required for incorporation of viral envelope protein into mature virions (1992)

Accumulating evidence suggests that the matrix (MA) protein of retroviruses plays a key role in virus assembly by directing the intracellular transport and membrane association of the Gag polyprotein. In this report, we show that the MA protein of human immunodeficiency virus type 1 is also critical for the incorporation of viral Env proteins into mature virions. Several deletions introduced in the MA domain (p17) of human immunodeficiency virus type 1 Gag polyprotein did not greatly affect the synthesis and processing of the Gag polyprotein or the formation of virions. Analysis of the viral proteins revealed normal levels of Gag and Pol proteins in these mutant virions, but the Env proteins, gp120 and gp41, were hardly detectable in the mutant virions. Our data suggest that an interaction between the viral Env protein and the MA domain of the Gag polyprotein is required for the selective incorporation of Env proteins during virus assembly. Such an interaction appears to be very sensitive to conformational changes in the MA domain, as five small deletions in two separate regions of p17 equally inhibited viral Env protein incorporation. Mutant viruses were not infectious in T cells. When mutant and wild-type DNAs were cotransfected into T cells, the replication of wild-type virus was also hindered. These results suggest that the incorporation of viral Env protein is a critical step for replication of retroviruses and can be a target for the design of antiviral strategies.
(Invited) Nonaqueous Redoxmer Flow Batteries: New Opportunities for Size-Exclusion Using Nanoporous Separators (2020)

Nonaqueous redox flow batteries (NRFBs) are attractive devices for energy storage due to an increased potential window and the manifold possibilities they offer in terms of redox-active architectures and chemistries available for increasing energy density and battery performance. Our collaborations in the context of the Joint Center for Energy Storage Research (JCESR) have shown that pairing commercial nanoporous separators with redoxmer architectures[1] such as Redox-Active Polymers (RAPs),[2] Redox-Active Colloids (RACs),[3] and Redox-Active Oligomers (RAOs),[4] effectively prevent crossover of the active component within the flow system. The choice of redoxmer size and chemical makeup impact profoundly the electrochemical dynamics of the NRFB, and it is clear that optimal performance is only attained with a balanced pairing between redoxmer and separator membrane. In this presentation, I will discuss the design principles underlying size-exclusion NRFBs and some current directions on how nanoporous separators enable new strategies for long-term performance in the flow battery. I will highlight how the progression from high polymers to oligomers modifies the charge transfer characteristics of NRFB electrolytes and the implications of the dynamics of these redoxmer solutions on the size-exclusion approach.[5] Unlike small molecules, the electrochemical reactivity of solution-phase redoxmers is strongly modulated by the properties of both surface confined and freely diffusing species. Building from this knowledge, the recent introduction of Polymers of Intrinsic Microporosity (PIM) separators[4] into the NRFB scene area allows new opportunities in the design of redoxmers with improved charge transfer characteristics and diffusivity without sacrificing their size-exclusion performance. Finally, the use of a size-exclusion approach enables advanced concepts for long-term maintenance of a battery system. I will discuss recent results where controlled de-polymerization reactions are used for maintaining the state-of-health of NRFB components, highlighting the role of component separation using our strategy. Altogether, the combination of novel structural motifs and the use of new nanoporous materials, results in new directions to make better NRFBs that exploit the versatility of a new type of reacting redoxmer fluids for energy storage. References: [1] Acc. Chem. Res. 2016, 49, 2649. [2] J. Am. Chem. Soc. 2014, 136, 16309. [3] J. Am. Chem. Soc. 2016, 138, 13230. [4] Chem. Mater. 2018, 30, 3861. [5] J. Electrochem. Soc. 2017, 164, A1688.
Optimal Resource Capacity Management for Stochastic Networks (2016)

We develop a framework for determining the optimal resource capacity of each station composing a stochastic network, motivated by applications arising in computer capacity planning and business process management. The problem is mathematically intractable in general and therefore one typically resorts to either simplistic analytical approximations or time-consuming simulation-based optimization methods. Our solution framework includes an iterative methodology that relies only on the capability of observing the queue lengths at all network stations for a given resource capacity allocation. We theoretically investigate this proposed methodology for single-class Brownian tree networks and illustrate the use of our framework and the quality of its results through computational experiments.
Structural Basis for Metallic-Like Conductivity in Microbial Nanowires (2015)

The mechanism for long-range electron transport along the conductive pili of Geobacter sulfurreducens is of interest because these "microbial nanowires" are important in biogeochemical cycling as well as applications in bioenergy and bioelectronics. Although proteins are typically insulators, G. sulfurreducens pilus proteins possess metallic-like conductivity. The studies reported here provide important structural insights into the mechanism of the metallic-like conductivity of G. sulfurreducens pili. This information is expected to be useful in the design of novel bioelectronic materials.
Measurement of solids concentration by an ultrasonic transmission technique (1997)

Abstract An ultrasonic transmission technique is under development to determine the concentration of solids in a three‐phase slurry reactor by measuring the velocity of ultrasound in slurries. Preliminary measurements have been made on slurries consisting of water, glass beads, and air bubbles. The data show that both the sound speed and attenuation are well‐defined functions of both the solid and gas concentrations in the slurries. A simple model is proposed to correlate the concentration of solids with the measured ultrasonic signals.
Synthesis of Bioactive Glycopeptides through Endoglycosidase-Catalyzed Transglycosylation (2004)

The carbohydrate portions of glycoproteins are implicated to play a major role in modulating the structure and biological functions of glycoproteins. However, deciphering the structure and functions of glycoproteins is often hampered by the difficulties in obtaining homogeneous glycoproteins and glycopeptides. This article reviews the transglycosylation with endo-β-N-acetylglucosamindases and their application for glycopeptide synthesis. In contrast to glycosyltransferase that adds monosaccharide units one at a time, the endoglycosidase transfers an oligosaccharide moiety to a suitable acceptor in a single step. Incorporation of endoglycosidases into synthetic strategy has made available an array of homogeneous, complex glycopeptides for structural and biological studies.
A Prospective Study of Total and Ionized Serum Calcium and Fatal Prostate Cancer (2009)

These findings have implications for the potential use of serum calcium in the detection of clinically significant prostate cancer.
Nucleotide sequences of mRNAs encoding Epstein-Barr virus nuclear proteins: a probable transcriptional initiation site. (1986)

Three cDNA clones of the second Epstein-Barr virus nuclear antigen (EBNA2) mRNA and two of the EBNA1 mRNA were analyzed. Two EBNA2 clones begin 42 bases 3' to a promoter in the Epstein-Barr virus long internal repeat, which is likely to be the EBNA2 promoter. Surprisingly, the first splice creates an AUG at the beginning of the first of two nonoverlapping open reading frames. The second open reading frame encodes EBNA2. Two incomplete EBNA1 mRNA cDNA clones begin with parts of two of the EBNA2 exons and contain two other exons that map 19 and 59 kilobases 3' to the EBNA2 coding domain. The 3' exon of this mRNA encodes EBNA1. A model for regulation of transcription of these RNAs is presented.
Crosstalk behavior of cores in multi-core fiber under bent condition (2011)

Measurement results of bending diameter dependence of the crosstalk of each core in a multi-core fiber are presented. The crosstalk of cores shows different diameter dependence although the difference in core parameters is very small. The behavior is explained by taking into account the change of propagation constant caused by the fluctuation in the diameter and the refractive index of cores. The diameter dependence simulated with coupled-power theory shows the same tendency with the measured crosstalk.
CAN: Constrained Attention Networks for Multi-Aspect Sentiment Analysis (2018)

Aspect level sentiment classification is a fine-grained sentiment analysis task. To detect the sentiment towards a particular aspect in a sentence, previous studies have developed various attention-based methods for generating aspect-specific sentence representations. However, the attention may inherently introduce noise and downgrade the performance. In this paper, we propose constrained attention networks (CAN), a simple yet effective solution, to regularize the attention for multi-aspect sentiment analysis, which alleviates the drawback of the attention mechanism. Specifically, we introduce orthogonal regularization on multiple aspects and sparse regularization on each single aspect. Experimental results on two public datasets demonstrate the effectiveness of our approach. We further extend our approach to multi-task settings and outperform the state-of-the-art methods.
Constructing multi-granular and topic-focused web site maps (2001)

Site maps are essential to assist users in navigating a Web site. Most of the site maps are constructed manually and are static. However, di erent users may have di erent preferences and purposes for using a Web site. For example, a user may want to see a more detailed map while another user prefers a more abstract map. Two users looking for di erent topics at a large portal site would bene t more from two site maps with di erent focuses than a single map. In this paper, we present a technique for automatically constructing multi-granular and topic-focused site maps by utilizing directory paths, page contents, and link structures. In these site maps, the Web site topology is preserved and document importance, indicated by citation and semantic relevancy to user's topics of interest, is used for prioritizing the presentation of pages and directories. Experiments on real Web data have been conducted to validate the usefulness of the technique.
Threshold Shock Sensor Based On A Bi-Stable Mechanism (2013)

We propose a novel MEMS shock sensor based on the notion of bistability. A moving mass induces the transition of a beam from a first stable configuration to a second stable configuration when a given acceleration threshold is reached. The new device has been designed, analysed numerically and tested with encouraging results.
Engineering the color rendering index of phosphor-free InGaN/(Al)GaN nanowire white light emitting diodes grown by molecular beam epitaxy (2014)

The functional properties, such as color rendering index (CRI) and correlated color temperature (CCT) of nanowire white light emitting diodes (LEDs), have been studied. The nanowire LEDs can generate broad spectrum white light, and by controlling the growth conditions, it is easy to tailor the spectrum. This is a significant advantage over phosphor converted or nanocrystal based white light sources since it is difficult to modulate the spectrum while maintaining high efficiency using these conventional methods. The authors demonstrated that the InGaN/(Al)GaN dot-in-a-wire heterostructure LEDs can generate high CRI values of 94–98 in both warm and cool white regions. Furthermore, the generated light demonstrates relatively stable CCT, CRI, and Commission Internationale d'Eclairage coordinates at different injection currents.
Spectral contrast optical coherence tomography angiography enables single-scan vessel imaging (2019)

Optical coherence tomography angiography relies on motion for contrast and requires at least two data acquisitions per pointwise scanning location. We present a method termed spectral contrast optical coherence tomography angiography using visible light that relies on the spectral signatures of blood for angiography from a single scan using endogenous contrast. We demonstrate the molecular sensitivity of this method, which enables lymphatic vessel, blood, and tissue discrimination.
Inhibition of tumor growth by a novel approach: in situ allicin generation using targeted alliinase delivery. (2003)

Allicin (diallyl thiosulfinate), a highly active component in extracts of freshly crushed garlic, is the interaction product of non-protein amino acid alliin (S-allyl-L-cysteine sulfoxide) with the enzyme alliinase (alliin lyase; EC 4.4.1.4). Allicin was shown to be toxic in various mammalian cells in a dose-dependent manner in vitro. We made use of this cytotoxicity to develop a novel approach to cancer treatment, based on site-directed generation of allicin. Alliinase from garlic was chemically conjugated to a mAb directed against a specific tumor marker, ErbB2. After the mAb-alliinase conjugate was bound to target tumor cells, the substrate, alliin, was added. In the presence of alliin, tumor-localized alliinase produced allicin, which effectively killed N87 and CB2, both ErbB2-expressing cells in vitro, whereas 32D cells (a murine hematopoietic progenitor cell line, devoid of the ErbB2 receptors) were not affected. Moreover, using N87, a human tumor cell line xenograft in athymic nude mice, we demonstrated for the first time, a high antitumor activity of allicin that was produced in situ by the conjugate, on alliin administration in vivo, while at the same time other tissues were unharmed due to the inert nature of alliin and the high clearance rate of allicin. The effect of the treatment on tumor growth arrest became significant 2 weeks after its onset, and it continued to rise, reaching highly significant inhibition a week later. Ten days after the end of the treatment (day 18), tumor growth inhibition was still the same.
Fatiguing STDP: Learning from spike-timing codes in the presence of rate codes (2017)

Spiking neural networks (SNNs) could play a key role in unsupervised machine learning applications, by virtue of strengths related to learning from the fine temporal structure of event-based signals. However, some spike-timing-related strengths of SNNs are hindered by the sensitivity of spike-timing-dependent plasticity (STDP) rules to input spike rates, as fine temporal correlations may be obstructed by coarser correlations between firing rates. In this article, we propose a spike-timing-dependent learning rule that allows a neuron to learn from the temporally-coded information despite the presence of rate codes. Our long-term plasticity rule makes use of short-term synaptic fatigue dynamics. We show analytically that, in contrast to conventional STDP rules, our fatiguing STDP (FSTDP) helps learn the temporal code, and we derive the necessary conditions to optimize the learning process. We showcase the effectiveness of FSTDP in learning spike-timing correlations among processes of different rates in synthetic data. Finally, we use FSTDP to detect correlations in real-world weather data from the United States in an experimental realization of the algorithm that uses a neuro-morphic hardware platform comprising phase-change memristive devices. Taken together, our analyses and demonstrations suggest that FSTDP paves the way for the exploitation of the spike-based strengths of SNNs in real-world applications.
Surface Functionalization of Thermoplastic Polymers for the Fabrication of Microfluidic Devices by Photoinitiated Grafting (2003)

Abstract Photografting has been used for the surface modification of a wide range of commercial commodity polymers such as poly‐ styrene, poly(methyl methacrylate), poly(dimethyl siloxane), polycarbonate, Parylene C, polypropylene, cyclic olefin copolymer, and hydrogenated polystyrene that are useful substrate materials for the fabrication of microfluidic chips. Since the chain propagation is initiated after UV light‐activated abstraction of a hydrogen atom from the surface of channels within the materials, their permeability for UV light was tested and polyolefins were found to be the best candidates. A number of monomers with a variety of functional groups such as perfluorinated, hydrophobic, hydrophilic, reactive, acidic, basic, and zwitterionic have been successfully grafted from the surface of selected substrates, and the grafting efficiency determined using X‐ray photoemission spectroscopy. Layered surface structures were prepared by consecutive grafting of different monomers. Our approach also enables photolithographic patterning of surfaces and specific functionalization of confined areas within the microchannel.
Higher activity of polymorphic thiopurine S-methyltransferase in erythrocytes from neonates compared to adults (1995)

Thiopurine S-methyltransferase (TPMT) catalyses the S-methylation of aromatic and heterocyclic sulfhydryl compounds, including thiopurine antimetabolites (i.e. mercaptopurine and thioguanine). The activity of TPMT in erythrocytes and other tissues exhibits genetic polymorphism, which is inherited as an autosomal codominant trait. Although inheritance is the principal determinant of TPMT activity, other factors (e.g. renal function, race and thiopurine therapy) have been shown to influence erythrocyte TPMT activity. Because the TPMT polymorphism has not been established in early erythrocyte populations, and the activity of many enzymes differs in neonates, we determined the activity of TPMT in erythrocytes obtained from 60 full-term newborns. Median peripheral blood TPMT activity was 25.3 U per ml pRBC (range 9-52.8 U per ml pRBC), which was > 50% higher than race matched healthy adults (p < 0.001). Western blot analysis demonstrated higher TPMT protein content in erythrocytes from newborns compared to adults, and revealed a significant correlation between TPMT protein and TPMT activity in erythrocytes (rs = 0.63, p = 0.03). Although erythrocyte TPMT activity was significantly higher in newborns, the distribution of activity in newborns was consistent with the genetic polymorphism previously observed in adults.
A Hybrid FinFET-based Biosensor with Integrated Readout Capability (2012)

We report on two circuits built with hybrid FinFETs [1], capable of both sensing and signal conditioning. The first circuit is a ring oscillator, whose oscillating frequency depends on the analyte concentration, i.e., on the voltage drop in the liquid. The second is a pseudo-differential amplifier for differential measurements with tunable gain. To the best of our knowledge, no FinFET-based circuits featuring both, biosensing and readout have been reported on so far.
A Novel Calcium-Dependent Protein Kinase Inhibitor as a Lead Compound for Treating Cryptosporidiosis (2013)

Cryptosporidium parasites infect intestinal cells, causing cryptosporidiosis. Despite its high morbidity and association with stunting in the developing world, current therapies for cryptosporidiosis have limited efficacy. Calcium-dependent protein kinases (CDPKs) are essential enzymes in the biology of protozoan parasites. CDPK1 was cloned from the genome of Cryptosporidium parvum, and potent and specific inhibitors have been developed based on structural studies. In this study, we evaluated the anti-Cryptosporidium activity of a novel CDPK1 inhibitor, 1294, and demonstrated that 1294 significantly reduces parasite infection in vitro, with a half maximal effective concentration of 100 nM. Pharmacokinetic studies revealed that 1294 is well absorbed, with a half-life supporting daily administration. Oral therapy with 1294 eliminated Cryptosporidium parasites from 6 of 7 infected severe combined immunodeficiency-beige mice, and the parasites did not recur in these immunosuppressed mice. Mice treated with 1294 had less epithelial damage, corresponding to less apoptosis. Thus, 1294 is an important lead for the development of drugs for treatment of cryptosporidiosis.
Test Strip Platform Spin-Off for Telomerase Activity Detection: Development of an Electrochemical Biosensor (2022)

Telomerase overexpression has been associated directly with cancer, and the enzyme itself is recognized within the scientific community as a cancer biomarker. BIDEA's biosensing strip (BBS) is an innovative technology capable of detecting the presence of telomerase activity (TA) using electrochemical impedance spectroscopy (EIS). This BBS is an interdigital gold (GID) electrode array similar in size and handling to a portable glucose sensor. For the detection of the biomarker, BBS was modified by the immobilization of a telomere-like single strand DNA (ssDNA) on its surface. The sensor was exposed to telomerase-positive extract from commercially available cancer cells, and the EIS spectra were measured. Telomerase recognizes the sequence of this immobilized ssDNA probe on the BBS, and the reverse transcription process that occurs in cancer cells is replicated, resulting in the ssDNA probe elongation. This surface process caused by the presence of TA generates changes in the capacitive process on the electrode array microchip surface, which is followed by EIS as the sensing tool and correlated with the presence of cancer cells. The telomerases' total cell extraction protocol results demonstrate significant changes in the charge-transfer resistance (<i>R</i> <sub>ct</sub>) change rate after exposure to telomerase-positive extract with a detection limit of 2.94 × 10<sup>4</sup> cells/mL. Finally, a preliminary study with a small set of "blind" uterine biopsy samples suggests the feasibility of using the changes in the <i>R</i> <sub>ct</sub> magnitude change rate (Δ(Δ<i>R</i> <sub>ct</sub>/<i>R</i> <sub>cti</sub>)/Δ<i>t</i>) to distinguish positive from negative endometrial adenocarcinoma samples by the presence or absence of TA.
Painting with Polygons: A Procedural Watercolor Engine (2013)

Existing natural media painting simulations have produced high-quality results, but have required powerful compute hardware and have been limited to screen resolutions. Digital artists would like to be able to use watercolor-like painting tools, but at print resolutions and on lower end hardware such as laptops or even slates. We present a procedural algorithm for generating watercolor-like dynamic paint behaviors in a lightweight manner. Our goal is not to exactly duplicate watercolor painting, but to create a range of dynamic behaviors that allow users to achieve a similar style of process and result, while at the same time having a unique character of its own. Our stroke representation is vector based, allowing for rendering at arbitrary resolutions, and our procedural pigment advection algorithm is fast enough to support painting on slate devices. We demonstrate our technique in a commercially available slate application used by professional artists. Finally, we present a detailed analysis of the different vector-rendering technologies available.