gebhart/patrepeval huggingface dataset:
Abstract 367: Extreme High-Density Lipoprotein Cholesterol Genetics: An Assortment of Large and Small Polygenic Effects (2017)

Rationale: Although HDL-C levels are known to have a complex genetic basis, most studies have focused solely on identifying rare variants with large phenotypic effects to explain extreme HDL-C phenotypes. Objective: Here we concurrently evaluate the contribution of both rare and common genetic variants, as well as large-scale copy number variations (CNVs), towards extreme HDL-C concentrations. Methods: In clinically ascertained patients with low ( N =136) and high ( N =119) HDL-C profiles, we applied our targeted next-generation sequencing panel (LipidSeq TM ) to sequence genes involved in HDL metabolism, which were subsequently screened for rare variants and CNVs. We also developed a novel polygenic trait score (PTS) to assess patients’ genetic accumulations of common variants that have been shown by genome-wide association studies to associate primarily with HDL-C levels. Two additional cohorts of patients with extremely low and high HDL-C (total N =1,746 and N =1,139, respectively) were used for PTS validation. Results: In the discovery cohort, 32.4% of low HDL-C patients carried rare variants or CNVs in primary ( ABCA1 , APOA1 , LCAT ) and secondary ( LPL , LMF1 , GPD1 , APOE ) HDL-C–altering genes. Additionally, 13.4% of high HDL-C patients carried rare variants or CNVs in primary ( SCARB1 , CETP , LIPC , LIPG ) and secondary ( APOC3 , ANGPTL4 ) HDL-C–altering genes. For polygenic effects, patients with abnormal HDL-C profiles but without rare variants or CNVs were ~2-fold more likely to have an extreme PTS compared to normolipidemic individuals, indicating an increased frequency of common HDL-C–associated variants in these patients. Similar results in the two validation cohorts demonstrate that this novel PTS successfully quantifies common variant accumulation, further characterizing the polygenic basis for extreme HDL-C phenotypes. Conclusions: Patients with extreme HDL-C levels have various combinations of rare variants, common variants, or CNVs driving their phenotypes. Fully characterizing the genetic basis of HDL-C levels must extend to encompass multiple types of genetic determinants—not just rare variants—to further our understanding of this complex, controversial quantitative trait.
Genomic identification, annotation, and comparative analysis of Vacuolar-type ATP synthase subunits in Diaphorina citri (2022)

The hemipteran insect <i>Diaphorina citri</i>, or Asian citrus psyllid, is a vector for <i>Candidatus</i> Liberibacter asiaticus (<i>C</i>Las), the bacterium causing citrus greening disease, or Huanglongbing (HLB). Millions of citrus trees have been destroyed, and every grove in Florida, USA, has been directly affected by this disease. In eukaryotes, vacuolar-type ATP synthase (V-ATPase) is an abundant heterodimeric enzyme that serves the cell with essential compartment acidification through the active processes that transport protons across the membrane. Fifteen putative <i>V-ATPase</i> genes in the <i>D. citri</i> genome were manually curated. Comparative genomic analysis revealed that <i>D. citri</i> V-ATPase subunits share domains and motifs with other insects, including the V-ATPase-A superfamily domain. Phylogenetic analysis separates <i>D. citri</i> V-ATPase subunits into expected clades with orthologous sequences. Annotation of the <i>D. citri</i> genome is a critical step towards developing directed pest management strategies to reduce the spread of HLB throughout the citrus industry.
Inter-cell interference coordination using frequency block dependent transmission power control and PF scheduling in non-orthogonal access with SIC for cellular uplink (2013)

This paper proposes an inter-cell interference coordination (ICIC) method using frequency block-dependent transmission power control (TPC) and proportional fair (PF) scheduling in non-orthogonal access with minimum mean squared error-based linear filtering followed by a successive interference canceller (MMSE-SIC) in the cellular uplink. The proposed method uses TPC coordinated among neighboring cells based on frequency block-dependent parameters. Under this transmission power setting, the use of PF scheduling achieves the ICIC effect. In conventional fractional frequency reuse (FFR) for ICIC in the uplink, users within a cell are categorized into cell-interior and cell-edge user groups and each user group can access only a portion of the frequency blocks. This degrades the multiuser diversity gain and the throughput gain due to non-orthogonal user multiplexing, which is in general increased when the users with largely different channel conditions are multiplexed into the same frequency block. Since all the users within a cell can access all frequency blocks in the proposed method, the method abates the drawbacks of conventional FFR. Simulation results show that non-orthogonal access employing an MMSE-SIC using the proposed ICIC method significantly enhances the system-level throughput performance compared to conventional FFR. We also show the performance gain of non-orthogonal access employing the MMSE-SIC compared to orthogonal access, which is widely used in 3.9 and 4G mobile communication systems.
Interaction of sulfonylurea-conjugated polymer with insulinoma cell line of MIN6 and its effect on insulin secretion (2001)

A carboxylated derivative of sulfonylurea (SU), an insulinotropic agent, was synthesized and grafted onto a water-soluble polymer as a biospecific and stimulating polymer for insulin secretion. To evaluate the effect of the SU-conjugated polymer on insulin secretion, its solution in dimethyl sulfoxide was added to the culture of insulinoma cell line of MIN6 cells to make 10 nM of SU units in the medium and incubated for 3 h at 37 degrees C. The culture medium was conditioned with glucose concentration of 3.3 or 25 mM. To verify the specific interaction between the SU (K+ channel closer)-conjugated polymer and MIN6 cells, the cells were pretreated with diazoxide, an agonist of adenosine triphosphate-sensitive K+ channel (K+ channel opener), before adding the SU-conjugated polymer to the cell culture medium. This treatment suppressed the action of SUs on MIN6 cells. Fluorescence-labeled polymer with rodamine-B isothiocyanate was used to visualize the interactions, and we found that the labeled polymer strongly absorbed to MIN6 cells, probably owing to its specific interaction mediated by SU receptors on the cell membrane. The fluorescence intensity on the cells significantly increased with an increase in incubation time and polymer concentration. A confocal laser microscopic study further confirmed this interaction. The results from this study provided evidence that SU-conjugated copolymer stimulates insulin secretion by specific interactions of SU moieties in the polymer with MIN6 cells.
Concept and experimental evaluation of a novel DC- 100MHz wireless oscilloscope (2014)

A wireless oscilloscope featuring 100MHz analog bandwidth and ultra-high isolated measurement channels is presented in this paper. In order to visualize the benefits of this potential-free measurement system, the paper starts with a revision of commonly utilized isolated voltage and current measurement concepts.With a clear understanding of the benefits given by a high-bandwidth, high-isolated and highly common mode immune measurement system laid down, the details about the wireless oscilloscope and its potential-free input channels are presented. Experimental measurements comparing the state of the art isolated voltage and current measurement concepts with the proposed wireless oscilloscope regarding common mode rejection ratio and signal-to-noise ratio are presented, showing the excellent performance of the introduced measurement system.
Organic Solvent Vapor Detection Using Holographic Photopolymer Reflection Gratings (2005)

Porous polymer colorimetric vapor- sensing elements have been produced using a holographic interferometry technique. Acetone vapor is detected by the change in the peak reflective wavelength of the resulting photonic bandgap structures (see Figure). The transmission electron microscopy image (Figure, inset) shows the voids generated in the film by adding a non-reactive solvent to the prepolymer syrup.
Noncryogenic I/Br−Mg Exchange of Aromatic Halides Bearing Sensitive Functional Groups Using i-PrMgCl−Bis[2-(N,N-dimethylamino)ethyl] Ether Complexes (2005)

[reaction: see text] Iodo- and bromoaromatics bearing sensitive carboxylic ester and cyano groups underwent a selective halide-magnesium exchange with isopropylmagnesium chloride at ambient temperature in the presence of bis[2-(N,N-dimethylamino)ethyl] ether to afford the corresponding Grignard reagents. The newly formed reactive Grignard reagents were allowed to react with electrophiles such as trimethylborate to afford arylboronic acids in good to excellent yields.
(Invited) Impact of LED Implementation on Rare-Earth Usage in Lighting (2016)

Several rare earth elements are used in phosphors for fluorescent lighting: a significant fraction of global demand for yttrium, europium, and terbium have beenfrom lighting applications. Solid-state lighting products based on InGaN light emitting diodes (LEDs) are in the process of taking over the general illumination market due to their higher energy efficiency, lifetime, and packaging flexibility. . While LED phosphors also use yttrium and europium, the quantities required are much lower than what is needed to produce an equivalent amount of light using fluorescent bulbs. This dynamic suggests that rare earth oxide demand for lighting will peak and then decline off of current usage levels. This paper presents a simple order of magnitude analysis to estimate when this peak is expected to occur, based on projected LED adoption rates in different regions. We also discuss some of the implications for the supply-demand balance for rare earth elements.
Data from Immunotherapy with a HER2-Targeting <i>Listeria</i> Induces HER2-Specific Immunity and Demonstrates Potential Therapeutic Effects in a Phase I Trial in Canine Osteosarcoma (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Recombinant &lt;i&gt;Listeria&lt;/i&gt; vaccines induce tumor-specific T-cell responses that eliminate established tumors and prevent metastatic disease in murine cancer models. We used dogs with HER2/neu&lt;sup&gt;+&lt;/sup&gt; appendicular osteosarcoma, a well-recognized spontaneous model for pediatric osteosarcoma, to determine whether a highly attenuated, recombinant &lt;i&gt;Listeria monocytogenes&lt;/i&gt; expressing a chimeric human HER2/neu fusion protein (ADXS31-164) could safely induce HER2/neu-specific immunity and prevent metastatic disease.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Eighteen dogs that underwent limb amputation or salvage surgery and adjuvant chemotherapy were enrolled in a phase I dose escalation clinical trial and received either 2 × 10&lt;sup&gt;8&lt;/sup&gt;, 5 × 10&lt;sup&gt;8&lt;/sup&gt;, 1 × 10&lt;sup&gt;9&lt;/sup&gt;, or 3.3 × 10&lt;sup&gt;9&lt;/sup&gt; CFU of ADXS31-164 intravenously every 3 weeks for 3 administrations.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Only low-grade, transient toxicities were observed. ADXS31-164 broke peripheral tolerance and induced antigen-specific IFNγ responses against the intracellular domain of HER2/neu in 15 of 18 dogs within 6 months of treatment. Furthermore, ADXS31-164 reduced the incidence of metastatic disease and significantly increased duration of survival time and 1-, 2-, and 3-year survival rates when compared with a historical control group with HER2/neu&lt;sup&gt;+&lt;/sup&gt; appendicular osteosarcoma treated with amputation and chemotherapy alone.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; These findings demonstrate that ADXS31-164 administered in the setting of minimal residual disease can induce HER2/neu-specific immunity and may reduce the incidence of metastatic disease and prolong overall survival in a clinically relevant, spontaneous, large animal model of cancer. These findings, therefore, have important translational relevance for children with osteosarcoma and adults with other HER2/neu&lt;sup&gt;+&lt;/sup&gt; cancers. &lt;i&gt;Clin Cancer Res; 22(17); 4380–90. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Identification of Trimeric Peptides That Bind Porcine Parvovirus from Mixtures Containing Human Blood Plasma (2008)

Virus contamination in human therapeutics is of growing concern as more therapeutic products from animal or human sources come into the market. All biopharmaceutical processes are required to have at least two distinct viral clearance steps to remove viruses. Most of these steps work well for enveloped viruses and large viruses, whether enveloped or not. That leaves a class of small non-enveloped viruses, like parvoviruses and hepatitis A, which are not easily removed by these typical steps. In this study, we report the identification of trimeric peptides that bind specifically to porcine parvovirus (PPV) and their potential use to remove this virus from process solutions. All of the trimeric peptides isolated completely removed all detectable PPV from buffer in the first nine column volumes, corresponding to a clearance of 4.5-5.5 log of infectious virus. When the virus was spiked into a more complex matrix consisting of 7.5% human blood plasma, one of the trimers, WRW, was able to remove all detectable PPV in the first three column volumes, after which human blood plasma began to interfere with the binding of the virus to the peptide resin. These trimer resins removed considerably more virus than weak ion exchange resins. The results of this work indicate that small peptide ligand resins have the potential to be used in virus removal processes where removal of contaminating virus is necessary to ensure product safety.
New routes to monomers and polymers for LEDs (2001)

The synthesis of poly(1,4-phenylene vinylene)s (PPVs) containing a 2,3-dialkoxy substitution pattern has been developed. Poly[2,3-bis(2-ethylhexyloxy)-1,4-phenylene vinylene] (BEH-PPV) 4 was prepared by Gilch polycondensation, and its optical properties were compared with the recently discussed poly(2,3-dibutoxy-1,4-phenylene vinylene) (DB-PPV) 1. The precursors for the Gilch method have traditionally been prepared by methods which have certain disadvantages. These can be overcome by the use of directed metallation reactions which are illustrated in the synthesis of some poly(2,5-disilyl-substituted 1,4-arylene vinylene) derivatives.
Adaptive Regularization With the Structure Tensor (2015)

Natural images exhibit geometric structures that are informative of the properties of the underlying scene. Modern image processing algorithms respect such characteristics by employing regularizers that capture the statistics of natural images. For instance, total variation (TV) respects the highly kurtotic distribution of the pointwise gradient by allowing for large magnitude outlayers. However, the gradient magnitude alone does not capture the directionality and scale of local structures in natural images. The structure tensor provides a more meaningful description of gradient information as it describes both the size and orientation of the image gradients in a neighborhood of each point. Based on this observation, we propose a variational model for image reconstruction that employs a regularization functional adapted to the local geometry of image by means of its structure tensor. Our method alternates two minimization steps: 1) robust estimation of the structure tensor as a semidefinite program and 2) reconstruction of the image with an adaptive regularizer defined from this tensor. This two-step procedure allows us to extend anisotropic diffusion into the convex setting and develop robust, efficient, and easy-to-code algorithms for image denoising, deblurring, and compressed sensing. Our method extends naturally to nonlocal regularization, where it exploits the local self-similarity of natural images to improve nonlocal TV and diffusion operators. Our experiments show a consistent accuracy improvement over classic regularization.
Surface structural changes of naturally aged silicone and EPDM composite insulators (1991)

In a long-term outdoor test with high direct and alternating voltages, silicone and ethylene propylene diene monomer (EPDM) rubber composite insulators have, at the beginning, shown a performance superior to that of glass and porcelain insulators. In the long-term test, however, the silicone rubber composite insulator has, in spite of the aging of both insulator types, kept its good performance, while the performance of the EPDM rubber composite insulator was drastically deteriorated. In order to get a better insight into the results obtained, the wettability and the surface structural changes of the insulators were studied by the drop deposition method using a goniometer and by advanced techniques such as scanning electron microscopy, electron spectroscopy for chemical analysis, Fourier-transform infrared spectroscopy, and secondary ion mass spectrometry. The results show that the differences in performance are related to the differences in the surface structural changes and in the dynamic ability of the surface to compensate the aging. Silicone rubber insulators have higher repellency than the EPDM insulators, especially when aged. The reason seems to be low silicone polymer diffusion from the bulk which covers the insulator surface, embeds the pollutants, and keeps the surface hydrophobic. Porcelain insulators with silicone elastomer coatings show lower water repellency than insulators with massive silicone rubber sheds. When aged, EPDM insulators do not, however, seen to possess the same dynamic recovery of their surface, thus becoming hydrophilic.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
An easily accessible Re-based catalyst for the selective conversion of methanol: evidence for an unprecedented active site structure through combined operando techniques (2011)

Heterogeneous Re/SiO(2) catalysts prepared using a one pot sol-gel synthesis were found to display high activity in the direct, selective methanol conversion to methylal, which is correlated to an unprecedented rhenium oxide structure.
An analysis of the role of high energy neutral bombardment in longthrow/collimated sputtering of refractory metal barrier layers (1998)

The development and optimization of sputtering techniques for the deposition of refractory metal thin films for very large scale integration (VLSI) barrier and encapsulation layers is of significant concern for the microelectronic fabrication industry. A number of directed sputtering techniques such as collimation and low pressure longthrow configurations have been applied to this problem. This paper addresses a number of issues present in the understanding and simulation of the growth of films deposited by directed sputtering techniques over VLSI topography. In particular the role of high energy neutral gas atoms reflected from the target is investigated as a source of resputtering. Also addressed is the creation of a low density porous film on the sidewalls of vias/contacts due to oblique incident fluxes on these areas. Experimentally Ti and W films are deposited at pressures varying from 0.2 to 12.0 mTorr with and without collimators present. A number of re-emission/resputtering mechanisms were investigated using a Monte Carlo growth simulator and it was found that the model most consistent with the experimental films was an assumption of resputtering due to reflected neutrals. A significant result is a dramatic increase in the resputtering rate when a collimator was present due to a relative increase in the reflected neutral flux. Finally, the paper presents an analysis of the effect of pressure on bottom and step coverage in high aspect topography.
[Perspectives on interferon research and on its therapeutic use]. (1982)

After briefly reviewing recent advances in the knowledge of various molecular species of interferon, some prospects of the basic research in this field are discussed: 1) interferon as a physiological hormone endowed with antiviral and immunomodulatory functions and possibly interacting with the neuroendocrine system; 2) interferon as an inducible protein, a model which allows a refined molecular analysis using the probes made available by cloning; 3) the various mechanisms of interferon action at the biochemical level. In the last section, the past and future of interferon as a therapeutic agent are examined. For its therapeutic evaluation, interferon needs to be compared with the best chemotherapeutic agents now available against viruses and tumors. Large scale clinical trials require a large production of interferons. Hence, a dilemma will be encountered: either pursue trials with natural preparations which are always a mixture of several types and subclasses of interferons in no defined proportions; wait for availability of the interferons produced by genetic recombinants which are cloned species, and try these various species, each one alone and in combination, or even more use hybrid molecular species. The availability of accurate markers for the action of interferon in man will be of great usefulness to study its therapeutic action and furthermore to define its indications. Finally, the possibility is raised that some non toxic interferon inducers, such as Poly A, Poly U, could also be used as well as interferon itself.
Cre recombinase specificity defined by the tau locus (2004)

We generated a transgenic mouse line (tau::Cre) by targeting the Cre to the tau locus (Mapt). Based on previous reports on the expression of Tau during development, we expected the Cre recombinase to be expressed in a neuron-specific and pan-neuronal manner. However, intercrosses between the tau::Cre and the Cre-activatable reporter animals resulted in offspring with recombination either restricted to the nervous system or throughout the entire conceptus, indicating expression of Tau early in development. The percentage of neuron-specific excision was dependent on the Cre reporter used representing different Cre target sites in the mouse genome. In spite of the observed variability, our data suggest that the tau::Cre mouse line can be used for pan-neuronal recombination of floxed alleles when it is used with caution.
Generalized Periodic Boundary Conditions for DGTD Analysis of Arbitrary Skewed Periodic Structures (2022)

An efficient discontinuous Galerkin time-domain (DGTD) method with an implementation of generalized periodic boundary conditions (PBCs) is proposed to analyze the electromagnetic scattering from arbitrary skewed periodic structures. The transformed field variable approach and the discontinuous Galerkin technique with nonconformal mesh are presented to implement the generalized PBCs for arbitrary skewed periodic structures under both normally and obliquely incident illuminations. The arbitrary high-order time-stepping scheme, which retains the DGTD feature of high-order accuracy and breaks the Butcher barrier, is extended to a transformed version of Maxwell’s equations introduced by the generalized PBCs implementation. The proposed method enables an efficient modeling of arbitrary skewed arrays with a fixed unit-cell mesh. Numerical examples for skewed periodic structures, such as an infinite gold film, 1-D and 2-D staggered dipole frequency-selective surfaces (FSSs), mechanically reconfigurable FSSs, and skewed nanohole arrays, are presented to demonstrate the accuracy and applicability of the proposed method.