gebhart/patrepeval huggingface dataset:
D-104 Structure, immune recognition, and conformational stabilization of the HIV-1 viral spike (2014)

The HIV-1-Env spike is a marvel of immune evasion. Despite its exposed position on the viral surface and the elicitation of narrow-breadth antibodies throughout the course of natural infection, the evolving spike manages to evade antibody-mediated neutralization. To provide an atomic-level understand of its evasion (and ways to overcome), we determined the structure of a soluble trimeric HIV-1-Env, in complex antibodies PGT122 and 35O22 at 3.5 Å resolution. The spike structure, which single molecule FRET analysis indicated to be of a prefusion mature near-native conformation, revealed the prefusion structure of the gp41 subunit, indicated structural rearrangements required for entry, and provided aggregate parameters of N-linked glycosylation and sequence variation. While N-linked glycosylation covers the membrane-distal apex of the spike, nearer the membrane, substantial “holes” can be seen in the assemble glycan shield. Serologic analysis from chronic cohorts, meanwhile, provides the prevalence and location of Env regions recognized by elicited neutralizing antibodies. Further, the atomic-level structure enabled structure-based design, which we used to stabilize the near-native state in its antibody-bound conformation. Implications of the trimer structure on HIV-1 vaccine design will be discussed.
Applications of Computation-In-Memory Architectures based on Memristive Devices (2019)

Today’s computing architectures and device technologies are unable to meet the increasingly stringent demands on energy and performance posed by emerging applications. Therefore, alternative computing architectures are being explored that leverage novel post-CMOS device technologies. One of these is a Computation-in-Memory architecture based on memristive devices. This paper describes the concept of such an architecture and shows different applications that could significantly benefit from it. For each application, the algorithm, the architecture, the primitive operations, and the potential benefits are presented. The applications cover the domains of data analytics, signal processing, and machine learning.
Cross Coupling of Bromo Sydnones: Development of a Flexible Route toward Functionalized Pyrazoles (2008)

The application of a Suzuki cross coupling approach to a range of C-4 substituted sydnones from a 4-bromosydnone is described. Moreover, the potential of this approach to prepare a diverse range of pyrazoles is demonstrated.
Cryogenic performance of double-fused 1.5-μm vertical cavity lasers (1999)

The low-temperature performance of vertical cavity lasers (VCL's) is of interest for high-speed data transmission from superconducting and cryogenic semiconductor circuits. Our double-fused 1.5 /spl mu/m lasers employ a strain-compensated InGaAsP-InP multiquantum-well (MQW) active region that is sandwiched between two AlGaAs-GaAs distributed Bragg reflectors. Continuous wave (CW) lasing at ambient temperature as low as 7 K is measured on the same type of top-emitting devices that previously lased at a record-high temperature of 337 K. The optimum temperature is found at 180 K giving minimum threshold current, maximum modulation bandwidth of 5 GHz, and more than 3 GHz/mA/sup 1/2/ modulation current efficiency. The optimum temperature agrees very well with the theoretical prediction. Further device optimization for cryogenic high-speed applications is discussed in detail.
LRRK2 A419V Is Not Associated with Parkinson's Disease in Different Chinese Populations (2012)

It has been suggested that a common LRRK2 polymorphic variant (A419V (rs34594498 C >T)) may be a risk factor among Asians (especially in Taiwan). In this study, we examined this variant in a larger and independent Taiwan cohort. We found the frequency of the variant (A419V) to be very rare in our Taiwan PD and controls (?0.6%). Further studies were conducted in two other Chinese populations (Singapore and China), comprising of a total of 3004 subjects including 1517 PD patients and 1487 control subjects. However, our multi-center Chinese study revealed that the frequency of the variant was rare (?0.4%) and was not associated with risk of PD, suggesting that the variant is not a major risk factor for PD among Chinese, at least in our study population.
Computational features of TIL architecture are differentially prognostic of uterine cancer between African and Caucasian American women. (2021)

5585 Background: Although the vast majority of endometrial cancer (EC) is early-stage and thus, curable by surgery, chemotherapy, and radiotherapy (with at least 85% 5-year OS), a fraction of them are aggressive neoplasms such as high-grade or deeply invasive lesions and thus exhibit poor prognosis. African American (AA) women are disproportionately affected by high-grade EC and have 80% higher mortality rate compared with Caucasian American (CA) women. In this work, we evaluated the prognostic ability of computational measurements of architecture of tumor-infiltrating lymphocytes (ArcTIL) from H&amp;E slide images for EC. We also investigated the presence of morphologic differences in terms of ArcTIL features between AA and CA women and whether ArcTIL based population-specific models were more prognostic of OS in AA women compared to a population-agnostic model. Methods: The study included digitized H&amp;E tissue slides from 445 post-surgery EC patients from TCGA, with further chemotherapy, or radiotherapy, including only the AA and CA patients, patients without reported race or from other populations were excluded. The dataset was divided into discovery (D1, n = 300), and a validation set (D2, n = 145), while ensuring population balance between two splits (D1(AA) = 65, D1(CA) = 235, D2(AA) = 37, D2(CA) = 108). A machine learning approach was employed to identify tumor regions, and tumor-associated stroma on the diagnostic slides and then used to automatically identify TILs within these compartments. Graph network theory based computational algorithms were used to capture 85 quantitative descriptors of the architectural patterns of intratumoral and stromal TILs. A multivariable Cox regression model (MCRM) was used to create population specific-prognostic models (M AA , M CA ) and a population-agnostic model (M AA+CA )) to predict OS. All 3 models were evaluated on D2(AA), D2(CA), and D2. Results: M AA identified 4 prognostic features relating to interaction of TIL clusters with cancer nuclei in stromal compartment and was prognostic of OS on D2(AA) (see Table) but not prognostic in D2(CA) nor D2(AA+CA). M CA and M AA+CA identified respectively 7 and 6 prognostic features relating to interaction of TIL clusters with cancer nuclei (both in the epithelial and stromal regions) and were prognostic of OS on D2(CA) and D2, but not prognostic in D2(AA). Conclusions: Our findings suggest an important role of stromal TIL architecture in prognosticating OS in AA women with EC, while epithelial TIL features were more prognostic in CA women. These findings need to be validated in larger, multi-site validation sets.[Table: see text]
Public Key Cryptography for RFID-Tags (2012)

Abstract. RFID-tags are a new generation of bar-codes with added functionality. They are becoming very popular tools for identification of products in various applications like e.g. supply-chain management. An emerging application is the use of RFID-tags for anti-counterfeiting by embedding them into a product. However, there is a risk related to naively using those tags for several applications. In particular, if no appropriate cryptographic measures are taken, the privacy of a user carrying tagged items can be severely damaged. In order to enable these applications and at the same time minimize the risks, public-key cryptography (PKC) offers attractive solutions. Whether a public-key cryptosystem can be implemented on an RFID tag or not remains an open problem. In this paper, we focus on the problem of anti-counterfeiting measures that can be provided by RFID-tags. More precisely, we investigate which PKC-based identification protocols are useful for this application. We discuss the feasibility of identification protocols based on Elliptic Curve Cryptography (ECC) and show that it is feasible on RFID tags.
Mini Review: Cytochrome P450BM-3 in the Remediation of Semi-Volatile Fatty Acids Associated with Feedlot Odors (2006)

A sound understanding of Animal Feeding Operations (AFOs) air emissions and theireffects require the expertise of many disciplines. These disciplines may include a broadrepresentation of academia, industry and local communities. Bioengineering is an emerging fieldthat can provide new remediation methodologies by addressing the problem of chemical odoremissions from CAFO's. Development of methods for the reduction of organic compounds has theability to move from monitoring and detection to air quality improvement. Utilization of metabolicpathways and the heterologous protein expression of Saccharomyces cerevisiae can yield costeffective methods for odor management at CAFOs. The metabolism of volatile fatty acids (VFAs)using Saccharomyces cerevisiae produced cytochrome P450BM-3 could possibly reduce downwindodors and assist in beneficial biogas production in wastewater effluents. The purpose of this reviewis to discuss a multiple disciplinary approach to air quality combining a variety of approaches whichcan assist federal agencies in successfully implementing a long term plan for this issue.
Ultrasound Gene Transfer into Fibroblast Cells using Microbubbles (2009)

Ultrasound is widely applied in the medical field and offers the strong advantages of non‐invasiveness and high‐selectivity. Gene transfer using ultrasound, which is called sonoporation, is one application. Ultrasound has the potential to deliver therapeutic materials such as genes, drugs or proteins into cells. Microbubbles are known to be able to improve delivery efficiency. This is attributed to therapeutic materials passing through the cell membrane after permeability is increased by destruction or oscillation of microbubbles. The present study tried to deliver the GFP plasmids into fibroblast cells. Cells were cultured in 6‐well culture plates and exposed to ultrasound (frequency, 2.1 MHz; wave pattern, duty cycle 10%; intensity, 0–26 W/cm2; time, 0–200 s) transmitted through medium containing microbubbles (Levovist® (void fraction, 8×10−5) or Sonazoid® (void fraction, 0–24×10−4)) and GFP plasmids at a concentration of 15 μg/mL. Density of microbubbles after ultrasound irradiation was measured. When ultrasound intensity was increased with Levovist® 8×10−4, transfection efficiency increased, cell viability decreased and microbubbles disappeared. With Sonazoid®, transfection efficiency and cell viability were basically unchanged and microbubbles decreased, but did not disappear. Transfection efficiency also improved with increased ultrasound irradiation time or microbubble density. Microbubble destruction appeared to have the main effect on gene transfection under Levovist® and microbubble oscillation had the main effect under Sonazoid®.
Altered miRNA-profile dependent on ART outcome in early pregnancy targets Wnt-pathway (2017)

Main goal of this study is to detect the possible alterations in microRNA (miRNA) expression and the pathway targeted in plasma at the time of embryo transfer and pregnancy testing dependent on the assisted reproductive treatment (ART) outcome after ovarian hyperstimulation for <i>in vitro</i> fertilization. Changes in miRNA expression in plasma of women, who became pregnant (<i>n</i> = 6) vs women who failed implantation (<i>n</i> = 6) following day 5 embryo transfer (ET), were investigated at the day of ET and pregnancy testing (PT). Protein expression to validate the finding was performed with a sample size of <i>n</i> = 20 (10 per group) using enzyme-linked immunosorbent assay. Enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed using DIANA-miRPath, v3.0 software based on predicted targets by DIANA-microT-CDS. 4 miRNAs could be identified as possible biomarkers for implantation success. The 11 miRNAs showing the highest significant alterations were all associated with the regulation of WNT3 and WNT7a. While WNT7a presented with a significant decrease between ET and PT in case of ongoing pregnancy, women with implantation failure showed unaltered concentrations. WNT3 presented with a significant decrease in both groups. However, the loss of WNT3 between ET and PT was significantly higher in patients who became pregnant. Main limitation of this prospective study is its small sample size, defining it as a pilot analysis. To conclude, we could demonstrate a significant change in miRNA profile dependent on the ART outcome affecting Wnt pathway. Our findings indicate a possible prospective use of miRNA as biomarkers for implantation success.
Entropy and scintillation analysis of acoustical beam propagation through ocean internal waves (2005)

Parabolic equation numerical simulations of waveguide acoustical beam propagation in an ocean of Garrett–Munk internal waves are used to examine the range evolution of beam properties such as beamwidth (both spectral and spatial), Shannon entropy, and scintillation index, as a function of beam angle. Simulations are carried out at 250- and 125-Hz acoustic frequencies. The ray trajectories associated with these beams are predominantly chaotic or exponentially sensitive to initial conditions and/or medium perturbations. At long range near saturation, the finite-frequency beams show a constant rate of change of Shannon entropy with range, independent of acoustic frequency. This full-wave rate of entropy is of the same order of magnitude as the average rate of entropy for the ray trajectories associated with this beam. Finite-range Lyapunov exponents provide the estimates of ray entropy rate or Kolmogorov–Siani entropy. The correspondence between full-wave and ray entropies suggests a full-wave manifestation of ray chaos, but only once statistical saturation is obtained. In spite of this correspondence, the simulated acoustical beams expand diffusively not exponentially (or explosively).
Concept Comparison for Underwater Power Generation (2002)

In this thesis permanent magnet direct drive generator for power conversion from water currents is studied. Water currents as a power source involves a number of constrains as well as possibilities, especially when direct drive and permanent magnets are considered. The high power fluxes and low current velocities of a water current, in combination with its natural variations, will affect the way the generator is operated and, flowingly, the appearance of the generator. The work in this thesis can, thus, be categorized into two general topics, generator technology and optimization. Under the first topic, fundamental generator technology is used to increase the efficiency of a water current generator. Under the latter topic, water current generators are optimized to a specific environment. The conclusion drawn from this work is that it is possible to design very low speed direct drive generators with good electromagnetic properties and wide efficiency peak.
Direct Measurement of Broadband FWM Induced Noise in Dispersion Uncompensated Systems (2013)

We experimentally measured nonlinear noise induced by broadband FWM over different power levels, system lengths, and transmission bandwidths in dispersion uncompensated systems. We confirmed that broadband FWM induced noise is proportional to PSD3, L1, and Log(BW).
Graph-Based Approach to Systematic Molecular Coarse-Graining (2018)

A novel methodology is introduced here to generate coarse-grained (CG) representations of molecular models for simulations. The proposed strategy relies on basic graph-theoretic principles and is referred to as graph-based coarse-graining (GBCG). It treats a given system as a molecular graph and derives a corresponding CG representation by using edge contractions to combine nodes in the graph, which correspond to atoms in the molecule, into CG sites. A key element of this methodology is that the nodes are combined according to well-defined protocols that rank-order nodes based on the underlying chemical connectivity. By iteratively performing these operations, successively coarser representations of the original atomic system can be produced to yield a systematic set of CG mappings with hierarchical resolution in an automated fashion. These capabilities are demonstrated in the context of several test systems, including toluene, pentadecane, a polysaccharide dimer, and a rhodopsin protein. In these examples, GBCG yields multiple, intuitive structures that naturally preserve the chemical topology of the system. Importantly, these representations are rendered from algorithmic implementation rather than an arbitrary ansatz, which, until now, has been the conventional approach for defining CG mapping schemes. Overall, the results presented here indicate that GBCG is efficient, robust, and unambiguous in its application, making it a valuable tool for future CG modeling.
Continuous Segmented-Flow Synthesis of Ag and Au Nanoparticles Using a Low Cost Microfluidic PTFE Tubing Reactor (2021)

We present in here a simple and low cost continuous segmented-flow process for the synthesis of Ag and Au spherical-shaped nanoparticles. Different residence times (RT) were used to perform the nanoparticle synthesis, observing that at low RT, the Ag nanoparticles production, which uses a fast reduction reaction with NaBH<sub>4</sub>, is improved due to an enhancement in the mixing of the reactants. However, the flow conditions have an opposite effect in the case of Au nanoparticles synthesis. Indeed, since the chemical reduction process (Turkevich method) exhibit a much slower kinetics, high RT (low flowrates) improve the synthesis yield and the quality of the nanoparticles. The Ag and Au nanoparticles were characterized by UV-Vis spectrophotometry (UV-Vis) and Transmission Electron Microscopy (TEM). The Ag spherical-shaped nanoparticles presented a LSPR at 400 nm (size ≈ 4 nm), while the synthesized Au nanoparticles exhibit LSPR and sizes in the range 520 - 550 nm and 14 - 17 nm, respectively.
Neutral Endopeptidase Terminates Substance P-Induced Inflammation in Allergic Contact Dermatitis (2001)

Sensory nerve-derived neuropeptides such as substance P demonstrate a number of proinflammatory bioactivities, but less is known about their role in inflammatory skin disease. The cell surface metalloprotease neutral endopeptidase (NEP) is the principal proteolytic substance P-degrading enzyme. This study tests the hypothesis that the absence of NEP results in dysregulated inflammatory skin responses. The effector phase of allergic contact dermatitis (ACD) responses was examined in NEP(-/-) knockout and NEP(+/+) wild-type mice and compared with the irritant contact dermatitis response in these animals. NEP was found to be normally immunolocalized in epidermal keratinocytes and dermal blood vessels. The ACD ear swelling response was 2.5-fold higher in animals lacking NEP and was accompanied by a significant increase in plasma extravasation and infiltration of inflammatory leukocytes. The augmented ACD response in NEP(-/-) animals was abrogated by either administration of a neurokinin receptor 1 antagonist or by repeated pretreatment with topical capsaicin. Similar to NEP(-/-) mice, the acute inhibition of NEP in NEP(+/+) animals resulted in an augmented ACD response. In contrast to the ACD responses, little differences were observed in the irritant contact dermatitis response of NEP(-/-) compared with NEP(+/+) animals after epicutaneous application of the skin irritants croton oil or SDS. Thus, these results indicate that NEP and cutaneous neuropeptides have a significant role in the pathogenesis of ACD.
Remote Store Programming: Mechanisms and Performance (2009)

This paper presents remote store programming (RSP). This paradigm combines usability and efficiency through the exploitation of a simple hardware mechanism, the remote store, which can easily be added to existing multicores.Remote store programs are marked by fine-grained and one-sided communication which results in a stream of data flowing from the registers of a sending process to the cache of a destination process. The RSP model and its hardware implementation trade a relatively high store latency for a low load latency because loads are more common than stores, and it is easier to tolerate store latency than load latency. This paper demonstrates the performance advantages of remote store programming by comparing it to both cache-coherent shared memory and direct memory access (DMA) based approaches using the TILEPro64 processor. The paper studies two applications: a two-dimensional Fast Fourier Transform (2D FFT) and an H.264 encoder for high-definition video. For a 2D FFT using 56 cores, RSP is 1.64x faster than DMA and 4.4x faster than shared memory. For an H.264 encoder using 40 cores, RSP achieves the same performance as DMA and 4.8x the performance of shared memory. Along with these performance advantages, RSP requires the least hardware support of the three. RSP's features, performance, and hardware simplicity make it well suited to the embedded processing domain.
Extraction of DNA from Whole Blood (2003)

There are many differing protocols and a large number of commercially available kits used for the extraction of DNA from whole blood. This procedure is one we use routinely in both research and clinical service provision and is cheap and robust. It can also be applied to cell pellets from dispersed tissues or cell cultures (omitting the red blood lysis step.
Probable secondary transmission of antimicrobial-resistant <i>Escherichia coli</i> between people living with and without pets (2017)

Companion animals are considered as one of the reservoirs of antimicrobial-resistant (AR) bacteria that can be cross-transmitted to humans. However, limited information is available on the possibility of AR bacteria originating from companion animals being transmitted secondarily from owners to non-owners sharing the same space. To address this issue, the present study investigated clonal relatedness among AR E. coli isolated from dog owners and non-owners in the same college classroom or household. Anal samples (n=48) were obtained from 14 owners and 34 non-owners; 31 E. coli isolates were collected (nine from owners and 22 from non-owners). Of 31 E. coli, 20 isolates (64.5%) were resistant to at least one antimicrobial, and 16 isolates (51.6%) were determined as multi-drug resistant E. coli. Six isolates (19.4%) harbored integrase genes (five harbored class I integrase gene and one harbored class 2 integrase gene, respectively). Pulsed-field gel electrophoretic analysis identified three different E. coli clonal sets among isolates, indicating that cross-transmission of AR E. coli can easily occur between owners and non-owners. The findings emphasize a potential risk of spread of AR bacteria originating from pets within human communities, once they are transferred to humans. Further studies are needed to evaluate the exact risk and identify the risk factors of secondarily transmission by investigating larger numbers of isolates from pets, their owners and non-owners in a community.