gebhart/patrepeval huggingface dataset:
S1 domain of the porcine epidemic diarrhea virus spike protein as a vaccine antigen (2016)

Of three eukaryotic expression systems tested (yeast, insect-cell, and mammalian), expression by HEK-293 T cells gave the highest yield of protein that was N-glycosylated and was the most appropriate candidate for vaccination. Administration of the subunit vaccine in a sow resulted in induction of S1-specific IgG and IgA that were passively transferred to the suckling piglets. Also, high virus neutralization titres were observed in the serum of the vaccinated sow and its piglets. After PEDV challenge, piglets born to the vaccinated sow exhibited less severe signs of disease and significantly lower mortality compared to the piglets of a control sow. However, there were no significant differences in diarrhea, body weight and virus shedding. Thus, vaccination with S1 subunit vaccine failed to provide complete protection to suckling piglets after challenge exposure, and further improvements are needed for the development of a subunit vaccine that fully protects against PEDV infection.
Modeling Blood Vessel Formation in the Mouse (2004)

Abstract Much of our current understanding of the development and maintenance of blood vessels in mammals comes from the analysis of mice. We summarize our current understanding of the developmental, cell, and molecular biology of blood vessel formation both in the mouse embryo and postnatally. The reader is provided with an understanding of how this information may impact on our ability to control blood vessel formation for the management of human cancers.
Neuromorphic Processing for Optical Microbead Arrays: Dimensionality Reduction and Contrast Enhancement (2007)

This paper presents a neuromorphic approach for sensor-based machine olfaction that combines a portable chemical detection system based on microbead array technology with a biologically inspired model of signal processing in the olfactory bulb. The sensor array contains hundreds of microbeads coated with solvatochromic dyes adsorbed in, or covalently attached on, the matrix of various microspheres. When exposed to odors, each bead sensor responds with corresponding intensity changes, spectral shifts, and time-dependent variations associated with the fluorescent sensors. The bead array responses are subsequently processed using a model of olfactory circuits that capture the following two functions: chemotopic convergence of receptor neurons and center on-off surround lateral interactions. The first circuit performs dimensionality reduction, transforming the high-dimensional microbead array response into an organized spatial pattern (i.e., an odor image). The second circuit enhances the contrast of these spatial patterns, improving the separability of odors. The model is validated on an experimental dataset containing the responses of a large array of microbead sensors to five different analytes. Our results indicate that the model is able to significantly improve the separability between odor patterns, compared to that available from the raw sensor response
Newborn Screening for Lysosomal Storage Diseases: Methodologies, Screen Positive Rates, Normalization of Datasets, Second-Tier Tests, and Post-Analysis Tools (2018)

All of the worldwide newborn screening (NBS) for lysosomal storage diseases (LSDs) is done by measurement of lysosomal enzymatic activities in dried blood spots (DBS). Substrates used for these assays are discussed. While the positive predictive value (PPV) is the gold standard for evaluating medical tests, current PPVs for NBS of LSDs cannot be used as a performance metric due to statistical sampling errors and uncertainty in the onset of disease symptoms. Instead, we consider the rate of screen positives as the only currently reliable way to compare LSD NBS results across labs worldwide. It has been suggested that the expression of enzymatic activity data as multiple-of-the-mean is a way to normalize datasets obtained using different assay platforms, so that results can be compared, and universal cutoffs can be developed. We show that this is often not the case, and normalization is currently not feasible. We summarize the recent use of pattern matching statistical analysis together with measurement of an expanded group of enzymatic activities and biomarkers to greatly reduce the number of false positives for NBS of LSDs. We provide data to show that these post-enzymatic activity assay methods are more powerful than genotype analysis for the stratification of NBS for LSDs.
All fiber Michelson-Gires-Turnois interferometer-based optical filter with programmable transfer function (2011)

We present a flexible and dynamically programmable optical filter based on an all fiber Michelson Gires-Turnois interferometer (MGTI). Arbitrary filter transfer functions can be accomplished by dynamically adjusting the reflectance of fiber loop mirrors.
Biquadratic Exchange Coupling in Epitaxial Co$_{2}$MnSi/Cr/Fe Trilayers (2008)

Interlayer exchange coupling (IEC) behavior in epitaxial Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> MnSi (20 nm)/Cr/Fe (7 nm) trilayers has been investigated against Cr spacer thickness (t <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Cr</sub> = 0.3-6.3 nm). High-quality trilayer samples have grown on a Cr (5 nm)/Au (30 nm)/Cr (15 nm) buffer layer on a MgO substrate by ultrahigh vacuum (UHV) compatible dc sputtering method. A simple numerical simulation model has been used to explain magnetization process, which shows good agreement with the experimental M-H curves. The values of bilinear and biquadratic coupling energy (J <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> and J <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ) and the cubic anisotropy energy of Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> MnSi and Fe (K <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">CMS</sub> and K <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Fe</sub> ) have been determined uniquely from the simulations. As a result, we have found a dominating contribution of biquadratic (90deg) coupling and absence of bilinear (180deg) coupling in all the samples with nonferromagnetic coupling. It has also been found that, the energetical competition between 90deg coupling energy and anisotropy energy largely affects the magnetization process due to different easy directions of bottom Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> MnSi (110) and Fe (100).
SARS-CoV-2 induces double-stranded RNA-mediated innate immune responses in respiratory epithelial-derived cells and cardiomyocytes (2021)

Coronaviruses are adept at evading host antiviral pathways induced by viral double-stranded RNA, including interferon (IFN) signaling, oligoadenylate synthetase-ribonuclease L (OAS-RNase L), and protein kinase R (PKR). While dysregulated or inadequate IFN responses have been associated with severe coronavirus infection, the extent to which the recently emerged SARS-CoV-2 activates or antagonizes these pathways is relatively unknown. We found that SARS-CoV-2 infects patient-derived nasal epithelial cells, present at the initial site of infection; induced pluripotent stem cell-derived alveolar type 2 cells (iAT2), the major cell type infected in the lung; and cardiomyocytes (iCM), consistent with cardiovascular consequences of COVID-19 disease. Robust activation of IFN or OAS-RNase L is not observed in these cell types, whereas PKR activation is evident in iAT2 and iCM. In SARS-CoV-2-infected Calu-3 and A549<sup>ACE2</sup> lung-derived cell lines, IFN induction remains relatively weak; however, activation of OAS-RNase L and PKR is observed. This is in contrast to Middle East respiratory syndrome (MERS)-CoV, which effectively inhibits IFN signaling and OAS-RNase L and PKR pathways, but is similar to mutant MERS-CoV lacking innate immune antagonists. Remarkably, OAS-RNase L and PKR are activated in <i>MAVS</i> knockout A549<sup>ACE2</sup> cells, demonstrating that SARS-CoV-2 can induce these host antiviral pathways despite minimal IFN production. Moreover, increased replication and cytopathic effect in <i>RNASEL</i> knockout A549<sup>ACE2</sup> cells implicates OAS-RNase L in restricting SARS-CoV-2. Finally, while SARS-CoV-2 fails to antagonize these host defense pathways, which contrasts with other coronaviruses, the IFN signaling response is generally weak. These host-virus interactions may contribute to the unique pathogenesis of SARS-CoV-2.
Computational modelling of tactoid dynamics in chromonic liquid crystals (2017)

Motivated by recent experiments, the isotropic–nematic phase transition in chromonic liquid crystals is studied. As temperature decreases, nematic nuclei nucleate, grow and coalesce, giving rise to tactoid microstructures in an isotropic liquid. These tactoids produce topological defects at domain junctions (disclinations in the bulk or point defects on the surface). We simulate such tactoid equilibria and their coarsening dynamics with a model using degree of order, a variable length director and an interfacial normal as state descriptors. We adopt Ericksen’s work and introduce an augmented Oseen–Frank energy, with non-convexity in both interfacial energy and the dependence of the energy on the degree of order. A gradient flow dynamics of this energy does not succeed in reproducing some simple expected feature of tactoid dynamics. Therefore, a strategy is devised based on continuum kinematics and thermodynamics to represent such features. The model is used to predict tactoid nucleation, expansion and coalescence during the process of phase transition. We reproduce observed behaviours in experiments and perform an experimentally testable parametric study of the effect of bulk elastic and tactoid interfacial energy parameters on the interaction of interfacial and bulk fields in the tactoids.
Magnetic resonance elastography measured shear stiffness as a biomarker of fibrosis in pediatric nonalcoholic fatty liver disease (2017)

2D MRE can estimate hepatic stiffness in children with NAFLD. Further refinement and validation of automated analysis techniques will be an important step in standardizing MRE. How to best integrate MRE into clinical protocols for the assessment of NAFLD in children will require prospective evaluation. (Hepatology 2017;66:1474-1485).
Insertion Force Sensor by Sidewall-Doping with Rapid Thermal Diffusion (2006)

We propose an insertion force sensor with piezoresistors fabricated by sidewall-doping with rapid thermal diffusion. The sensor consists of a main body, to which a pointed tip is installed, and supporting beams whose sidewalls are made piezoresistive. When an insertion force is applied to the tip and the silicon structure deforms, the change of the strain distribution condition on the piezoresistive sidewall varies the electrical resistance of the sensor, which is in turn transduced into output voltage signal via an outside circuitry. The beams are 250 µ m in length, 20 µ m in thickness, 8 µ m in width. By etching an appropriate pattern onto the wafer, additional exposed surfaces for doping can be created where vertical dope-sites are needed. With rapid thermal diffusion, we are able to fabricate dope-sites which are perpendicular to the surface of the wafer. Fabricated piezoresistive sensor has 20 pairs of supporting beams. The spring constant is 2500 N/m. The electrical resistance is 1.6 kΩ. The displacement sensitivity is 1.03 % per µ m. This displacement sensitivity on the insertion direction is as high as that on the vertical direction of reported sensors, which means that our proposal is an effective doping method for sidewall.
Decoupling of a double‐row 16‐element tight‐fit transceiver phased array for human whole‐brain imaging at 9.4 T (2018)

One of the major challenges in constructing multi‐channel and multi‐row transmit (Tx) or transceiver (TxRx) arrays is the decoupling of the array's loop elements. Overlapping of the surface loops allows the decoupling of adjacent elements and also helps to improve the radiofrequency field profile by increasing the penetration depth and eliminating voids between the loops. This also simplifies the design by reducing the number of decoupling circuits. At the same time, overlapping may compromise decoupling by generating high resistive (electric) coupling near the overlap, which cannot be compensated for by common decoupling techniques. Previously, based on analytical modeling, we demonstrated that electric coupling has strong frequency and loading dependence, and, at 9.4 T, both the magnetic and electric coupling between two heavily loaded loops can be compensated at the same time simply by overlapping the loops. As a result, excellent decoupling was obtained between adjacent loops of an eight‐loop single‐row (1 × 8) human head tight‐fit TxRx array. In this work, we designed and constructed a 9.4‐T (400‐MHz) 16‐loop double‐row (2 × 8) overlapped TxRx head array based on the results of the analytical and numerical electromagnetic modeling. We demonstrated that, simply by the optimal overlap of array loops, a very good decoupling can be obtained without additional decoupling strategies. The constructed TxRx array provides whole‐brain coverage and approximately 1.5 times greater Tx efficiency relative to a transmit‐only/receive‐only (ToRo) array, which consists of a larger Tx‐only array and a nested tight‐fit 31‐loop receive (Rx)‐only array. At the same time, the ToRo array provides greater peripheral signal‐to‐noise ratio (SNR) and better Rx parallel performance in the head–feet direction. Overall, our work provides a recipe for a simple, robust and very Tx‐efficient design suitable for parallel transmission and whole‐brain imaging at ultra‐high fields.
Severe COVID-19 and non-COVID-19 severe sepsis converge transcriptionally after a week in the intensive care unit, indicating common disease mechanisms (2023)

Early on, COVID-19 patients had elevated antiviral responses and suppressed heme metabolism processes compared to non-COVID-19 severe sepsis patients, although both had similar underlying immune dysfunction. However, after one week in the ICU, these diseases became indistinguishable on a gene expression level. These findings highlight the importance of early antiviral treatment for COVID-19, the potential for heme-related therapeutics, and consideration of immunomodulatory therapies for both diseases to treat shared immune dysfunction.
ChemInform Abstract: Organometallic Chemistry: Carbon—Carbon Bonds Get a Break (2010)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Ethnobotany, trade and population dynamics of Cycas circinalis L., and Cycas swamyi Singh & Radha in the Western Ghats of southern India (2014)

Harvest of Non Timber Forest Products (NTFPs) has been frequently studied as a means to conserve forests and provide income to user communities, often with the assumption that harvest has relatively little ecological impact. Cycas circinalis L. and Cycas swamyi Singh & Radha are such NTFPs extensively harvested from the Western Ghats, South India. They are harvested for bark, leaves, seeds and male cones by indigenous people for medicinal, food and ornamental purposes, while commercially harvested for the medicinal and floricultural industries. Although indigenous people have a long association with Cycas spp, harvest for sale in informal regional markets has been uncontrolled over the past 15years. Cycas circinalis is now regionally listed as 'critically endangered' and internationally listed as an 'endangered' species. In an attempt to understand the uses and responses of these species to harvest pressures, this study aims to document the trade, ethnobotany, life history, and population dynamics of Cycas spp. My study shows there is a large scale trade of leaves and pith and peak leaf sales occurs shortly after new leaf production in cycad habitats. The pith of C. circinalis and C. swamyi are collected for the herbal medicinal industry however, they are adulterants and don't provide the necessary constituents of the herbal drug, vidari. Demographical studies confirm that harvested populations are on a decline as the projected population growth rate over the long term λ, was <1 for all harvested populations. Cycas spp have ancient lineages from the Jurassic age, being long-lived and slow-growing, and this coupled with intensive extraction reduces the chances for populations to rapidly withstand the induced stress of harvest. The effects of harvest can be further compounded by other disturbances such as fire, habitat loss and climate change. Sustainable harvest practices for seed harvested populations and the discontinuation of leaf and pith harvest are imperative to conserve the last few populations of C. circinalis and C. swamyi in the Western Ghats.
Alternative Lengthening of Telomeres in Primary Pancreatic Neuroendocrine Tumors Is Associated with Aggressive Clinical Behavior and Poor Survival (2016)

<b>Purpose:</b> Alternative lengthening of telomeres (ALT), a telomerase-independent telomere maintenance mechanism, is strongly associated with ATRX and DAXX alterations and occurs frequently in pancreatic neuroendocrine tumors (PanNET).<b>Experimental Design:</b> In a Korean cohort of 269 surgically resected primary PanNETs and 19 sporadic microadenomas, ALT status and nuclear ATRX and DAXX protein expression were assessed and compared with clinicopathologic factors.<b>Results:</b> In PanNETs, ALT or loss of ATRX/DAXX nuclear expression was observed in 20.8% and 19.3%, respectively, whereas microadenomas were not altered. ALT-positive PanNETs displayed a significantly higher grade, size, and pT classification (all, <i>P</i> < 0.001). ALT also strongly correlated with lymphovascular (<i>P</i> < 0.001) and perineural invasion (<i>P</i> = 0.001) and the presence of lymph node (<i>P</i> < 0.001) and distant metastases (<i>P</i> = 0.002). Furthermore, patients with ALT-positive primary PanNETs had a shorter recurrence-free survival [HR = 3.38; 95% confidence interval (CI), 1.83-6.27; <i>P</i> < 0.001]. Interestingly, when limiting to patients with distant metastases, those with ALT-positive primary tumors had significantly better overall survival (HR = 0.23; 95% CI, 0.08-0.68; <i>P</i> = 0.008). Similarly, tumors with loss of ATRX/DAXX expression were significantly associated with ALT (<i>P</i> < 0.001), aggressive clinical behavior, and reduced recurrence-free survival (<i>P</i> < 0.001). However, similar to ALT, when limiting to patients with distant metastases, loss of ATRX/DAXX expression was associated with better overall survival (<i>P</i> = 0.003).<b>Conclusions:</b> Both primary ALT-positive and ATRX/DAXX-negative PanNETs are independently associated with aggressive clinicopathologic behavior and displayed reduced recurrence-free survival. In contrast, ALT activation and loss of ATRX/DAXX are both associated with better overall survival in patients with metastases. Therefore, these biomarkers may be used as prognostic markers depending on the context of the disease. <i>Clin Cancer Res; 23(6); 1598-606. ©2016 AACR</i>.
DVB‐H Overview (2009)

This chapter contains sections titled: Time Slicing MPE-FEC DVB-H Specific Signaling The Broadcast and Cellular Systems in DVB-H Market Needs Applications
Living Bioelectrochemical Composites (2020)

Composites, in which two or more material elements are combined to provide properties unattainable by single components, have a historical record dating to ancient times. Few include a living microbial community as a key design element. A logical basis for enabling bioelectronic composites stems from the phenomenon that certain microorganisms transfer electrons to external surfaces, such as an electrode. A bioelectronic composite that allows cells to be addressed beyond the confines of an electrode surface can impact bioelectrochemical technologies, including microbial fuel cells for power production and bioelectrosynthesis platforms where microbes produce desired chemicals. It is shown that the conjugated polyelectrolyte CPE-K functions as a conductive matrix to electronically connect a three-dimensional network of Shewanella oneidensis MR-1 to a gold electrode, thereby increasing biocurrent ≈150-fold over control biofilms. These biocomposites spontaneously assemble from solution into an intricate arrangement of cells within a conductive polymer matrix. While increased biocurrent is due to more cells in communication with the electrode, the current extracted per cell is also enhanced, indicating efficient long-range electron transport. Further, the biocomposites show almost an order-of-magnitude lower charge transfer resistance than CPE-K alone, supporting the idea that the electroactive bacteria and the conjugated polyelectrolyte work synergistically toward an effective bioelectronic composite.
Serologic Response of Individuals Infected with Para Influenza Viruses (1960)

Serologic Response of Individuals Infected with Para Influenza Viruses Robert M. Chanock, Doris C. Wong, Robert J. Huebner, and Joseph A. Bell CopyRight https://doi.org/10.2105/AJPH.50.12.1858 Published Online: August 29, 2011
Optical modes in a rectangular resonator with properties of both Gaussian and Fourier modes (2013)

We present the optical modes of a resonator with a large Fresnel number in one direction and a small Fresnel number in the other direction. The modes show properties of both the well-known Gaussian modesand the modes of the Fourier type which have been observed in laserswith a large Fresnel number.
System and method for monitoring atomic absorption during a surface modification process (2023)

A processing system monitors and/or controls a surface modification process occurring on a substrate within a processing chamber. An optical processing module having a light emission submodule to output a generated light signal and an optical detection submodule to detect a resultant light signal, is connected via fiber optic cables to light illuminating and light receiving components located within the chamber. A processor determines an amount of atomic absorption by an atomic element encountered by a probing beam passing between the illuminating and receiving components, based on the intensity of the generated light signal, the intensity of the received light signal and optionally the spontaneous emission of the atomic element in the absence of illumination by a probing beam. Based on the determined amount, the system derives a plurality of parameters of the modified substrate, their spatial and temporal uniformity, and information about process conditions in the processing chamber.