gebhart/patrepeval huggingface dataset:
High-Level Expression and Purification of a Truncated Merozoite Antigen-2 of<i>Babesia equi</i>in<i>Escherichia coli</i>and Its Potential for Immunodiagnosis (2003)

The gene encoding a truncated merozoite antigen-2 (EMA-2t) of Babesia equi was cloned and highly expressed in Escherichia coli as a glutathione S-transferase fusion protein (G-rEMA-2t). Both G-rEMA-2t and rEMA-2t (after the removal of glutathione S-transferase) had good antigenicity. Either Western blot analysis with rEMA-2t or enzyme-linked immunosorbent assay (ELISA) with G-rEMA-2t clearly discriminated the sera of horses experimentally infected with B. equi from sera of horses infected with Babesia caballi and healthy horses, although rEMA-2t was not suitable for ELISA, probably owing to its poor absorbability to the plates. The specific antibodies in B. equi-infected horses were detectable during both acute and latent infection (6 to 244 days postinfection). Horse sera from Jilin Province, China, were examined by the two tests. The seroprevalence of B. equi was 49.2% (31 of 63 sera) by Western blot analysis with rEMA-2t and 47.6% (30 of 63 sera) by ELISA with G-rEMA-2t. The correspondence was 98.4% (62 of 63 sera) between the two tests. The results indicate that G-rEMA-2t and rEMA-2t proteins should be suitable antigens for the development of an effective immunodiagnostic assay due to their high sensitivity, specificity, and great yield.
Progress In The Development Of Prism Light Guides (1987)

Prism light guides are hollow structures which pipe light by means of total internal reflection (TIR). These devices are unique in their ability to combine the efficiency of TIR with the relatively low cost of a hollow structure. An important application stems from their ability to transform a point source of light such as an incandescent or discharge lamp into a linear or area source of light or illumination. We report the development of an economical, flexible prismatic film for fabricating the light guide wall. This film is adaptable to a wide variety of applications, some of which are described. Other guide geometries and films are currently under development.
Angiotensin-Converting Enzyme Inhibitory Activity of Enzymatic Hydrolysates of Crassostrea gigas (Oyster) (2012)

굴 효소 가수분해물은 굴을 alcalase, protamex, neutrase, flavourzyme, pepsin으로 각각 처리하였고, 이들의 ACE 저해활성을 측정하였다. ACE 저해활성은 가수분해 시간에 따라 증가 또는 감소하였으며, 그 중 10시간 이상 가수분해 처리한 PEH에서 가장 높은 ACE 저해활성을 나타내었다. PEH 가수분해물을 한외여과(30, 10 kDa) 하여 낮은 분자량의 분획물을 얻었다. 30 kDa와 10 kDa 이하 분자량 별 ACE 저해활성은 각각 <TEX>$69.18{\pm}0.75$</TEX>, <TEX>$83.71{\pm}1.12$</TEX>의 활성을 나타내었다. 이 결과 10 kDa 이하의 시료로부터 HPLC column (watchers 120 ODS-AP <TEX>$250{\times}4.6$</TEX> (<TEX>$5{\mu}m$</TEX>))을 이용하여 각각의 활성 분획을 분취하여 얻은 6분획의 ACE 저해 활성은 29.56~85.85% 로 나타났다. 그 중 저해활성이 가장 높게 나타나는 B fraction의 아미노산 서열을 확인한 결과 Leu-Gln-Pro 임을 확인하였고, peptide합성하여 얻은 저해활성 농도(<TEX>$IC_{50}$</TEX>)가 1.18 uM임을 확인하였다. 이러한 결과는 PEH를 이용하여 건강 기능성 식품의 개발에 도움이 될 수 있을 것으로 생각된다. The peptides of enzymatic hydrolysates from oyster were determined by inhibitory activity against angiotensin-converting enzyme. The ACE inhibitory activity of enzymatic oyster hydrolysates increases with hydrolysis time. Among enzymatic oyster hydrolysates, oyster hydrolysates incubated with Protamex showed the best ACE inhibitory activity after 10 h. Hydrolysates were filtered through a HiSep ultrafiltration membrane (M.W. cut-off 30 kDa, 10 kDa) to obtain the peptide fractions with ACE inhibition activity. These fractions were applied to an HPLC column (watchers 120 ODS-AP <TEX>$250{\times}4.6$</TEX> (<TEX>$5{\mu}m$</TEX>)). Six active fractions were collected and the range of ACE inhibition was from 29.56 to 85.85%. Peptide was purified from fraction B, showing the highest ACE inhibitory activity, and its sequence was Leu-Gln-Pro. These results suggest that PEH may be beneficial for developing antihypertensive food and drug.
Identification of Neuropeptide S Antagonists: Structure–Activity Relationship Studies, X-ray Crystallography, and in Vivo Evaluation (2014)

Modulation of the neuropeptide S (NPS) system has been linked to a variety of CNS disorders such as panic disorder, anxiety, sleeping disorders, asthma, obesity, PTSD, and substance abuse. In this study, a series of diphenyltetrahydro-1H-oxazolo[3,4-α]pyrazin-3(5H)-ones were synthesized and evaluated for antagonist activity at the neuropeptide S receptor. The absolute configuration was determined by chiral resolution of the key synthetic intermediate, followed by analysis of one of the individual enantiomers by X-ray crystallography. The R isomer was then converted to a biologically active compound (34) that had a Ke of 36 nM. The most potent compound displayed enhanced aqueous solubility compared with the prototypical antagonist SHA-68 and demonstrated favorable pharmacokinetic properties for behavioral assessment. In vivo analysis in mice indicated a significant blockade of NPS induced locomotor activity at an ip dose of 50 mg/kg. This suggests that analogs having improved drug-like properties will facilitate more detailed studies of the neuropeptide S receptor system.
Expanding the Reach of Federated Learning by Reducing Client Resource Requirements (2018)

Communication on heterogeneous edge networks is a fundamental bottleneck in Federated Learning (FL), restricting both model capacity and user participation. To address this issue, we introduce two novel strategies to reduce communication costs: (1) the use of lossy compression on the global model sent server-to-client; and (2) Federated Dropout, which allows users to efficiently train locally on smaller subsets of the global model and also provides a reduction in both client-to-server communication and local computation. We empirically show that these strategies, combined with existing compression approaches for client-to-server communication, collectively provide up to a $14\times$ reduction in server-to-client communication, a $1.7\times$ reduction in local computation, and a $28\times$ reduction in upload communication, all without degrading the quality of the final model. We thus comprehensively reduce FL's impact on client device resources, allowing higher capacity models to be trained, and a more diverse set of users to be reached.
Coded aperture structured illumination digital holographic microscopy (2018)

This work proposes and experimentally demonstrates coded aperture structured illumination digital holographic microscopy for resolution enhancement. The binary codes are applied for spatial phase shifting along with compressive sensing for retrieving the missing data.
On residual smoothing in ILUM-type preconditioning (2000)

Incomplete block factorisations are used to construct flexible preconditioners for iterative linear solvers. In practice these approaches have shown to be very effective and robust. Especially they are more suitable for parallel computer architectures when comparing to classic ILU preconditioning. In this paper we introduce residual smoothing into the forward/backward substitution in order to compensate the element dropping in the Schur complement.
Evaluation of a 3D technique for quantifying neovascularization within plaques imaged by contrast enhanced ultrasound (2013)

Intra-plaque neovascularization and inflammation are considered as important indicators of plaque vulnerability, which when ruptured, may cause stroke or acute myocardial infarction. The purpose of this research was to validate and evaluate a semi-automatic method, which allows quantification of carotid plaque neovascularization using contrast-enhanced ultrasound cines, thus enabling assessment of plaque vulnerability. The method detects contrast clusters in the images, and tracks them, to generate over time a path that portrays the neovasculature. It classifies the paths as either artifacts or `blood vessels' and reconstructs the 3D arterial tree. Software-based phantom was developed to represent volumetric structures of the carotid lumen, the plaque, and `objects' passing through the intra-plaque neovasculature. These 3D objects, which mimic microbubbles or clusters of microbubbles, were based on original 2D formations, imaged during clinical examinations using contrast-enhanced ultrasound. Within a plaque, several paths were constructed, representing flow inside blood vessels, and several isolated objects were added, representing artifacts. Different paths were generated, classified into 4 groups: separate paths, paths that merge at some point, paths that branch and intersecting paths. The phantom was used to generate sets of cines, which were then processed by the method. The method identified artifacts and different paths, which were then compared to the `true' ones. Sixty-four 'objects' in 16 movies were examined. All of them were detected. 79% of those objects were well tracked and classified to either artifacts or real blood vessels. The results of this study show that the method accurately identifies artifacts and paths, which allows reconstruction of intra-plaque vascular tree and quantification of the plaque neovasculature, which is associated with plaque vulnerability.
A zero voltage switching three-level DC/DC converter (2002)

A novel zero voltage switching (ZVS) three-level (TL) DC/DC power converter is presented in this paper. The converter uses a flying capacitor in the primary side to allow operation with phase-shift control and in this way achieves ZVS for all the switches. The principle of operation of the converter is analyzed and verified on a 6 kW, 100 kHz experimental prototype. Additionally, this paper presents improvement of the proposed converter by using different ZVS techniques.
Digital sound reconstruction using arrays of CMOS-MEMS microspeakers (2003)

We report on the generation of sound by the superposition of discrete sound pulses from arrays of micromachined membrane microspeakers or speaklets. Digital sound reconstruction (DSR) is unlike any other reconstruction approach in use, offering true, direct digital reconstruction of sound. CMOS-MEMS micromachining techniques allow the integration of hundreds to thousands of microspeakers as as well as sound optimization electronics on a single chip. Nonlinearities typically problematic for analog speakers can be controlled through membrane geometries and material properties to produce acoustic responses useful for DSR.
Synthesis of Antimicrobial Poly(guanylurea)s (2018)

Bacterial infections are serious health threats. Emerging drug resistance in bacteria further poses serious challenges to the treatment options involving traditional antibiotics. Antimicrobial polymers disrupt the physical cell membrane integrity of bacteria to address the drug resistance problems. Here, we introduce a conceptually new class of antimicrobial polymers containing positively charged guanylurea backbones for enhanced antimicrobial effects. The initial structure-activity relationship studies demonstrate that poly(guanylurea piperazine)s (PGU-Ps) exhibit excellent antimicrobial activity against different types of bacteria with high selectivity. The new design concept of using a positively charged guanylurea backbone will contribute to the development of future biocompatible, specific, and selective antimicrobial polymers.
Molecular basis for epitope recognition by non-neutralizing anti-gp41 antibody F240 (2016)

Antibody-dependent cell-mediated cytotoxicity (ADCC) by non-neutralizing antibodies (nnAbs) specific to the HIV envelope (Env) glycoproteins present at the surface of virus sensitized or infected cells plays a role in the effective adaptive immune response to HIV. Here, we explore the molecular basis for the epitope at the disulfide loop region (DLR) of the principal immunodominant domain of gp41, recognized by the well-known nnAb F240. Our structural studies reveal details of the F240-gp41 interface and describe a structure of DLR that is distinct from known conformations of this region studied in the context of either CD4-unliganded Env trimer or the gp41 peptide in the unbound state. These data coupled with binding and functional analyses indicate that F240 recognizes non-trimeric Env forms which are significantly overexpressed on intact virions but poorly represented at surfaces of cells infected with infectious molecular clones and endogenously-infected CD4 T cells from HIV-1-infected individuals. Furthermore, although we detect ADCC activities of F240 against cells spinoculated with intact virions, our data suggest that these activities result from F240 recognition of gp41 stumps or misfolded Env variants present on virions rather than its ability to recognize functional gp41 transition structures emerging on trimeric Env post CD4 receptor engagement.
Core−Shell Diamond as a Support for Solid-Phase Extraction and High-Performance Liquid Chromatography (2010)

We report the formation of core-shell diamond particles for solid-phase extraction (SPE) and high-performance liquid chromatography (HPLC) made by layer-by-layer (LbL) deposition. Their synthesis begins with the amine functionalization of microdiamond by its immersion in an aqueous solution of a primary amine-containing polymer (polyallylamine (PAAm)). The amine-terminated microdiamond is then immersed in an aqueous suspension of nanodiamond, which leads to adsorption of the nanodiamond. Alternating (self-limiting) immersions in the solutions of the amine-containing polymer and the suspension of nanodiamond are continued until the desired number of nanodiamond layers is formed around the microdiamond. Finally, the core-shell particles are cross-linked with 1,2,5,6-diepoxycyclooctane or reacted with 1,2-epoxyoctadecane. Layer-by-layer deposition of PAAm and nanodiamond is also studied on planar Si/SiO(2) surfaces, which were characterized by scanning electron microscopy (SEM), Rutherford backscattering spectrometry (RBS), and nuclear reaction analysis (NRA). Core-shell particles are characterized by diffuse reflectance infrared Fourier transform spectroscopy (DRIFT), environmental scanning electron microscopy (ESEM), and Brunauer-Emmett-Teller (BET) surface area and pore size measurements. Larger (ca. 50 microm) core-shell diamond particles have much higher surface areas and analyte loading capacities in SPE than nonporous solid diamond particles. Smaller (ca. 3 microm), normal and reversed-phase, core-shell diamond particles have been used for HPLC, with 36,300 plates/m for mesitylene in a separation of benzene and alkyl benzenes and 54,800 plates/m for diazinon in a similar separation of two pesticides on a C(18) adsorbent.
UTILIZATION OF NUCLEOTIDE PROBES FOR THE MEASUREMENT OF SPECIFIC MESSENGER RNA: APPLICATION FOR MOLECULAR DIAGNOSIS OF AUTOSOMAL RECESSIVE SPINAL MUSCULAR ATROPHY (2002)

ABSTRACT Spinal muscular atrophy (SMA) is a lethal autosomal recessive disease. SMA is characterized by degeneration of motor neurons in the spinal cord, causing progressive weakness of the limbs and trunk, followed by muscle atrophy. The gene most highly associated with SMA is the survival motor neuron (SMN) gene. This paper describes the results concerning the development of a quantitative method for the molecular diagnosis of SMA by measuring the amount of cytosolic mRNA from human muscle cells. The procedures using radioactive material and the Enzyme-Linked Immunosorbent Assay (ELISA) non-radioactive method were developed using 32P-dCTP labeled and biotinylated nucleotide probes, respectively; the results obtained demonstrate that the measurement of specific mRNA could be used as a quantitative method for the molecular diagnosis of SMA. There was a perfect concordance of the results obtained between the procedure using radioactive material, the ELISA method and the single-strand conformation polymorphism (SSCP) analysis regarding negative and positive SMA samples. All values obtained for the control group were significantly greater than the ones obtained for the SMA positive samples (33–76% in radioactive method and 38–54% in ELISA method). The methods developed in this study may be applicable to the diagnosis (detection of homozygous and heterozygous deletions in exons 7 and 8 of the SMN gene) and the control of mRNA concentrations in future gene therapy of patients with SMA.
Applications of ion implantation to integrated optical spectrum analyzers (1980)

H implantation into bulk and Ti-diffused LiNbO3 is shown to result in the creation of optically absorbing layers. The induced absorption is characterized, and application to the suppression of optical noise in Ti:LiNbO3 integrated optical spectrum analyzers is considered. Potential uses include beam dumps, spatial filters, and the absorption of substrate modes.
Celecoxib Encapsulation in β-Casein Micelles: Structure, Interactions, and Conformation (2015)

β-Casein is a 24 kDa natural protein that has an open conformation and almost no folded or secondary structure, and thus is classified as an intrinsically unstructured protein. At neutral pH, β-casein has an amphiphilic character. Therefore, in contrast to most unstructured proteins that remain monomeric in solution, β-casein self-assembles into well-defined core-shell micelles. We recently developed these micelles as potential carriers for oral administration of poorly water-soluble pharmaceuticals, using celecoxib as a model drug. Herein we present deep and precise insight into the physicochemical characteristics of the protein-drug formulation, both in bulk solution and in dry form, emphasizing drug conformation, packing properties and aggregation state. In addition, the formulation is extensively studied in terms of structure and morphology, protein/drug interactions and physical stability. Particularly, NMR measurements indicated strong drug-protein interactions and noncrystalline drug conformation, which is expected to improve drug solubility and bioavailability. Small-angle X-ray scattering (SAXS) and cryogenic transmission electron microscopy (cryo-TEM) were combined for nanostructural characterization, proving that drug-protein interactions lead to well-defined spheroidal micelles that become puffier and denser upon drug loading. Dynamice light scattering (DLS), turbidity measurements, and visual observations complemented the analysis for determining formulation structure, interactions, and stability. Additionally, it was shown that the loaded micelles retain their properties through freeze-drying and rehydration, providing long-term physical and chemical stability. Altogether, the formulation seems greatly promising for oral drug delivery.
Identification of cold‐inducible downstream genes of the <i>Arabidopsis</i> DREB1A/CBF3 transcriptional factor using two microarray systems (2004)

The transcriptional factor DREB/CBF (dehydration-responsive element/C-repeat-binding) specifically interacts with the dehydration-responsive element (DRE)/C-repeat (CRT) cis-acting element (A/GCCGAC) and controls the expression of many stress-inducible genes in Arabidopsis. Transgenic plants overexpressing DREB1A showed activated expression of many stress-inducible genes and improved tolerance to not only drought, salinity, and freezing but also growth retardation. We searched for downstream genes in transgenic plants overexpressing DREB1A using the full-length cDNA microarray and Affymetrix GeneChip array. We confirmed candidate genes selected by array analyses using RNA gel blot and identified 38 genes as the DREB1A downstream genes, including 20 unreported new downstream genes. Many of the products of these genes were proteins known to function against stress and were probably responsible for the stress tolerance of the transgenic plants. The downstream genes also included genes for protein factors involved in further regulation of signal transduction and gene expression in response to stress. The identified genes were classified into direct downstream genes of DREB1A and the others based on their expression patterns in response to cold stress. We also searched for conserved sequences in the promoter regions of the direct downstream genes and found A/GCCGACNT in their promoter regions from -51 to -450 as a consensus DRE. The recombinant DREB1A protein bound to A/GCCGACNT more efficiently than to A/GCCGACNA/G/C.
Rationalization of Intercalation Potential and Redox Mechanism for A<sub>2</sub>Ti<sub>3</sub>O<sub>7</sub> (A = Li, Na) (2013)

Na2Ti3O7 was recently reported to be highly promising as a negative electrode material for Na-ion batteries, thanks to its very low intercalation voltage (0.3 V vs Na+/Na0) and high capacity (200 mAh/g). The investigation of the redox mechanism in A2Ti3O7 (A = Li, Na) upon additional alkali ion intercalation concomitant to reduction of titanium is reported in this paper. Even if the low stability of the reduced phases (A2+xTi3O7) precluded a direct study, density functional theory (DFT) calculations allowed us to propose structural models for the reduced phases (A2+xTi3O7), which were further successfully confronted to the available experimental data. The alkali atoms are octahedrally coordinated in the reduced A2+xTi3O7 phase, so that the whole resulting structure can be considered rocksalt type. The very different potentials at which ion insertion is observed for A = Li or A = Na clearly prove that analogies between lithium and sodium systems cannot be taken for granted. In this case, such findings can be fully rationalized through DFT and arise from the differences in polarizing character between lithium and sodium ions that cause, respectively, contraction and expansion of the cell volume and the destabilization of the inserted materials derived from the larger size of sodium ions.
Epstein–Barr virus nuclear antigen 1‐specific CD4<sup>+</sup> T cells directly kill Epstein–Barr virus‐carrying natural killer and T cells (2008)

Epstein-Barr virus (EBV) nuclear antigen (EBNA)1 is expressed in every EBV-infected cell, regardless of the state of EBV infection. Although EBNA1 is thought to be a promising antigen for immunotherapy of all EBV-associated malignancies, it is less clear whether EBNA1-specific CD4(+) T cells can act as direct effectors. Herein, we investigated the ability of CD4(+) T-cell clones induced with overlapping peptides covering the C-terminal region of EBNA1, and identified minimal epitopes and their restricted major histocompatibility complex class II molecules. Of these, a novel epitope, EYHQEGGPD, was found to be presented by DRB1*0401, 0403 and 0406. Five CD4(+) T-cell clones recognized endogenously processed and presented antigens on EBV-transformed lymphoblastoid cell lines (LCL) and one example proved capable of killing EBV-carrying natural killer (NK) and T-cell lines derived from patients with chronic active EBV infection (CAEBV). Identification of minimal epitopes facilitates design of peptide-based vaccines and our data suggest that EBNA1-specific CD4(+) T cells may play roles as direct effectors for immunotherapy targeting EBV-carrying NK and T-cell malignancies.
Suppressing Alignment: Joint PAPR and Out-of-Band Power Leakage Reduction for OFDM-Based Systems (2015)

Orthogonal frequency division multiplexing (OFDM) inherently suffers from two major drawbacks: high out-of-band (OOB) power leakage and high peak-to-average power ratio (PAPR). This paper proposes a novel approach called suppressing alignment for the joint reduction of the OOB power leakage and PAPR. The proposed approach exploits the temporal degrees of freedom provided by the cyclic prefix (CP), a necessary redundancy in OFDM systems, to generate a suppressing signal, that when added to the OFDM symbol, results in marked reduction in both the OOB power leakage and PAPR. Additionally, and in order to not cause any interference to the information data carried by the OFDM symbol, the proposed approach utilizes the wireless channel to perfectly align the suppressing signal with the CP duration at the OFDM receiver. Essentially, maintaining a bit error rate (BER) performance similar to legacy OFDM without requiring any change in the receiver structure.