gebhart/patrepeval huggingface dataset:
Characterization of ShigETEC, a Novel Live Attenuated Combined Vaccine against Shigellae and ETEC (2020)

<b>Background</b>: <i>Shigella</i> spp. and enterotoxigenic <i>Escherichia coli</i> (ETEC) remain the two leading bacterial causes of diarrheal diseases worldwide. Attempts to develop preventive vaccines against Shigella and ETEC have not yet been successful. The major challenge for a broad Shigella vaccine is the serotype-specific immune response to the otherwise protective LPS O-antigen. ETEC vaccines mainly rely on the heat-labile enterotoxin (LT), while heat-stable toxin (ST) has also been shown to be an important virulence factor. <b>Methods</b>: We constructed a combined Shigella and ETEC vaccine (ShigETEC) based on a live attenuated Shigella strain rendered rough and non-invasive with heterologous expression of two ETEC antigens, LTB and a detoxified version of ST (ST<sub>N12S</sub>). This new vaccine strain was characterized and tested for immunogenicity in relevant animal models. <b>Results</b>: Immunization with ShigETEC resulted in serotype independent protection in the mouse lung shigellosis model and induced high titer IgG and IgA antibodies against bacterial lysates, and anti-ETEC toxin antibodies with neutralizing capacity. <b>Conclusions</b>: ShigETEC is a promising oral vaccine candidate against Shigella and ETEC infections and currently in Phase 1 testing.
Selective Excretion of Alkaline Xylanase by<i>Escherichia coli</i>Carrying pCX311 (1985)

Plasmid pCX311, which we constructed, has two HindlU DNA fragments (2.6 kbp and 2.0 kbp) of alkalophilic Bacillus sp. strain C-125 in the HindlU site of pBR322. These two fragments were essential not only for the xylanase production but also for the excretion of periplasmic proteins. The cloned 4.6 kbp fragment encodes some components that made the outer membrane of E. coli permeable. Some proteins such as xylanase and ²-lactamase were excreted, but alkaline phosphatase was not excreted into the culture broth.
A Compare-Aggregate Model with Latent Clustering for Answer Selection (2019)

In this paper, we propose a novel method for a sentence-level answer-selection task that is a fundamental problem in natural language processing. First, we explore the effect of additional information by adopting a pretrained language model to compute the vector representation of the input text and by applying transfer learning from a large-scale corpus. Second, we enhance the compare-aggregate model by proposing a novel latent clustering method to compute additional information within the target corpus and by changing the objective function from listwise to pointwise. To evaluate the performance of the proposed approaches, experiments are performed with the WikiQA and TREC-QA datasets. The empirical results demonstrate the superiority of our proposed approach, which achieve state-of-the-art performance for both datasets.
An Ultralinear Stress-Compensated Temperature Sensor (1987)

Stress-compensated quartz resonators having ultralinear frequency-temperature responses (NLSC cuts) have been discovered. They consist of doubly rotated cuts in which the orientations, defined in terms of the polar angles bo and eo, lie on a locus where the second- order temperature coefficients of frequency are zero in the range of bo = 20 f 2 and Bo = 20 f 5. These angles of orientation are in close proximity to, or on the locus of, zero frequency coefficients of stress. In the vicinity of the NLSC cuts, a relatively strong 1231 X-ray plane has been found to exist at the quartz crystal orientation of b,, substan- tially equal to 19.1 and eo substantially equal to +16.6. This X-ray plane makes the manufacture of NLSC cuts easier and cheaper than ones previously reported. The theoretical and experimental values of the frequency-temperature responses and some physical features for NLSC cuts are discussed. p
<title>Monte Carlo investigations of the wavelength dependence of light transport through turbid media</title> (1997)

Elastic-scattering spectroscopy examines the wavelength dependence of light that has passed through a small volume of tissue. Measurements are typically made by placing two optical fibers on the surface of the tissue to be examined. The analysis of these measurements to obtain quantitative information about scattering and absorption is important to many biomedical applications such as cancer diagnosis and measurement of bilirubin concentrations. For fiber separations large enough for the diffusion approximation to be valid, this is straight forward. However, for clinical applications such as those listed above, the separation is too small for the diffusion approximation to be applicable. To obtain insight into the question of how scattering and absorption changes affect the wavelength dependence of the elastic-scatter signal Monte Carlo simulations have been used. First, it is shown that the Monte Carlo simulations and elastic-scatter measurements of polystyrene spheres agree quite well. Monte Carlo simulations are then used to investigate how particle size and concentration affect the elastic-scatter signal. It is found that the concentration has very little effect of the wavelength dependence, but that the size of the scattering particles does affect the wavelength dependence. In general, the signal decreases more rapidly as a function of wavelength for smaller particles.
Flat optics with dielectric metasurfaces (Conference Presentation) (2018)

Miniaturized optical systems with planar form factors and low power consumption have many applications in wearable and mobile electronics, health monitoring devices, and as integral parts of medical and industrial equipment. Flat optical devices based on dielectric metasurfaces introduce a new approach for realization of such systems at low cost using conventional nanofabrication techniques. In this talk, I will present a summary of our recent work on dielectric metasurfaces that enable precise control of both polarization and phase with large transmission and high spatial resolution. Optical metasurface components such as high numerical aperture lenses, efficient wave plates, components with novel functionalities, and their potential applications will be discussed. I will also present the results of our efforts on optimizing and increasing the diffraction efficiency of metasurfaces. Furthermore, by using metasurface cameras and planar retroreflectors as examples, I will discuss a vertical on-chip integration platform that introduces a new architecture for the on-chip integration of conventional and novel optical systems and enables their low-cost manufacturing.
WALRUS: a similarity retrieval algorithm for image databases (2004)

Approaches for content-based image querying typically extract a single signature from each image based on color, texture, or shape features. The images returned as the query result are then the ones whose signatures are closest to the signature of the query image. While efficient for simple images, such methods do not work well for complex scenes since they fail to retrieve images that match the query only partially, that is, only certain regions of the image match. This inefficiency leads to the discarding of images that may be semantically very similar to the query image since they may contain the same objects. The problem becomes even more apparent when we consider scaled or translated versions of the similar objects. We propose WALRUS (wavelet-based retrieval of user-specified scenes), a novel similarity retrieval algorithm that is robust to scaling and translation of objects within an image. WALRUS employs a novel similarity model in which each image is first decomposed into its regions and the similarity measure between a pair of images is then defined to be the fraction of the area of the two images covered by matching regions from the images. In order to extract regions for an image, WALRUS considers sliding windows of varying sizes and then clusters them based on the proximity of their signatures. An efficient dynamic programming algorithm is used to compute wavelet-based signatures for the sliding windows. Experimental results on real-life data sets corroborate the effectiveness of WALRUS'S similarity model.
Retinoic Acid Regulates Hematopoietic Development from Human Pluripotent Stem Cells (2015)

The functions of retinoic acid (RA), a potent morphogen with crucial roles in embryogenesis including developmental hematopoiesis, have not been thoroughly investigated in the human setting. Using an in vitro model of human hematopoietic development, we evaluated the effects of RA signaling on the development of blood and on generated hematopoietic progenitors. Decreased RA signaling increases the generation of cells with a hematopoietic stem cell (HSC)-like phenotype, capable of differentiation into myeloid and lymphoid lineages, through two separate mechanisms: by increasing the commitment of pluripotent stem cells toward the hematopoietic lineage during the developmental process and by decreasing the differentiation of generated blood progenitors. Our results demonstrate that controlled low-level RA signaling is a requirement in human blood development, and we propose a new interpretation of RA as a regulatory factor, where appropriate control of RA signaling enables increased generation of hematopoietic progenitor cells from pluripotent stem cells in vitro.
Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-5 (2018)

Context-dependent inhibition of N-methyl-D-aspartate (NMDA) receptors has important therapeutic implications for the treatment of neurological diseases that are associated with altered neuronal firing and signaling. This is especially true in stroke, where the proton concentration in the afflicted area can increase by an order of magnitude. A class of allosteric inhibitors, the 93-series, shows greater potency against GluN1-GluN2B NMDA receptors in such low pH environments, allowing targeted therapy only within the ischemic region. Here we map the 93-series compound binding site in the GluN1-GluN2B NMDA receptor amino terminal domain and show that the interaction of the N-alkyl group with a hydrophobic cage of the binding site is critical for pH-dependent inhibition. Mutation of residues in the hydrophobic cage alters pH-dependent potency, and remarkably, can convert inhibitors into potentiators. Our study provides a foundation for the development of highly specific neuroprotective compounds for the treatment of neurological diseases.
Fully automated immunoassay for cholesterol uptake capacity to assess high-density lipoprotein function and cardiovascular disease risk (2023)

High-density lipoprotein (HDL) cholesterol efflux capacity (CEC), which is a conventional metric of HDL function, has been associated with coronary heart disease risk. However, the CEC assay requires cultured cells and takes several days to perform. We previously established a cell-free assay to evaluate cholesterol uptake capacity (CUC) as a novel measure of HDL functionality and demonstrated its utility in coronary risk stratification. To apply this concept clinically, we developed a rapid and sensitive assay system based on a chemiluminescent magnetic particle immunoassay. The system is fully automated, providing high reproducibility. Measurement of CUC in serum is completed within 20 min per sample without HDL isolation, a notably higher throughput than that of the conventional CEC assay. CUC decreased with myeloperoxidase-mediated oxidation of HDL or in the presence of N-ethylmaleimide, an inhibitor of lecithin: cholesterol acyltransferase (LCAT), whereas CUC was enhanced by the addition of recombinant LCAT. Furthermore, CUC correlated with CEC even after being normalized by ApoA1 concentration and was significantly associated with the requirement for revascularization due to the recurrence of coronary lesions. Therefore, our new assay system shows potential for the accurate measurement of CUC in serum and permits assessing cardiovascular health.
1937-P: ALK-7: A Validated Target for the Treatment of Obesity (2020)

Genetic variation in the ACVR1C gene has been reported to be associated with decreased waist-to-hip ratio and risk of type 2 diabetes in humans. However, the effect of this naturally occurring variation on ALK7 function is unclear. Here we show that the human ACVR1C variant I195T, which displays the greatest effect on waist-to-hip ratio adjusted for body mass index, fails to signal in response to ALK7 ligands in a cell-based assay. This is consistent with observations in mice that impaired ALK7 signaling increases lipolysis and decreases adiposity. As further validation of ALK7 as an obesity target, we present data showing in the naturally occurring polygenic obese TSOD mouse a specific high affinity neutralizing monoclonal anti-ALK7 antibody (ALK7 mAb) dramatically decreases leptin levels, adipose macrophages and adiposity. The specificity of the ALK7 mAb is demonstrated by its lack of effect in genetically deficient ALK7 mice. These data along with the knowledge that normal Balb/c mice harbor a homozygous ALK7 nonsense mutation suggests that targeting ALK7 in humans should decrease obesity, susceptibility to diabetes and have minimal on-target negative consequences. Disclosure Y. Bu: None. M. Zhao: None. M. Fredericks: None. M. Cannell: None. Y. Dagon: None. C.A. Emdin: None. K. Okunishi: None. H. Wang: None. D. Sako: None. R. Castonguay: Employee; Self; Acceleron Pharma. R.N.V. Suragani: None. S. Kathiresan: Advisory Panel; Self; Regeneron Genetics Center. Consultant; Self; Color Genomics, Corvia Medical, Inc., Medgenome, Pfizer Inc. Stock/Shareholder; Self; Catabasis Pharmaceuticals, Maze Therapeutics, San THerapeutics, Verve Therapeutics. A. Grinberg: None. J. Knopf: Stock/Shareholder; Self; Acceleron Phama. R.S. Pearsall: Employee; Self; Acceleron Pharma, Inc. Stock/Shareholder; Self; Acceleron Pharma, Inc. R. Kumar: Employee; Self; Acceleron Pharma. T. Izumi: Research Support; Self; Acceleron Pharma.
Strain relaxation index and diastolic function from echocardiography: the multi-ethnic study of atherosclerosis (2013)

Background A novel strain relaxation index (SRI) is introduced to assess diastolic function by CMR, using myocardial deformation during LV relaxation. We investigate how SRI relates to standard diastolic parameters by echocardiography (echo). We also relate SRI to mass to volume ratio (MVR) by CMR, which is seen to increase in diastolic dysfunction. SRI accounts for both very early myocardial relaxation and tissue compliance.
De novo 14484 mitochondrial DNA mutation in monozygotic twins discordant for Leber's hereditary optic neuropathy (1997)

Monozygotic twin brothers, clinically discordant for Leber's hereditary optic neuropathy (LHON), had a heteroplasmic point mutation at position 14484 in the mitochondrial DNA that was not detected in their mother. Moreover, the mutation occurred on the rare European haplogroup X, rather than the haplogroup J commonly associated with the 14484 mutation. These data indicate that the 14484 mutation in this family was a new mutation, indicating that it was the de novo occurrence of a common, primary LHON mutation.
Moving coil loudspeaker with heat dissipating enclosure (1979)

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New potent mitomycin derivatives: synthesis and antitumor activity of 7,7-(ethylenedioxy)mitomycins (1992)

A series of 6,7-dihydro-7,7-(ethylenedioxy)mitomycins was synthesized and evaluated for antitumor and anticellular activities. These compounds were prepared by basic treatment of 7-methoxymitomycins with ethylene glycol, and were structurally novel mitomycin derivatives containing a masked quinone moiety. 5,6-Enol or 6-chloro derivatives of 6,7-dihydro-7,7-(ethylenedioxy)mitomycins were also prepared and the (allyloxy)carbonyl group at the aziridine nitrogen has proved to be an efficient protecting group in chemical modification of mitomycins. Most of these mitomycin derivatives displayed potent antitumor activity against P388 leukemia in mice and anticellular activity against HeLa S3 cells.
LED-Based UV Absorption Detector with Low Detection Limits for Capillary Liquid Chromatography (2014)

A 260 nm deep UV LED-based absorption detector with low detection limits was developed and integrated with a small nanoflow pumping system. The detector is small in size (5.2 × 3.0 cm) and weighs only 85 g (without electronics). This detector was specifically designed and optimized for on-column detection to minimize extra-column band broadening. No optical reference was included due to the low drift in the signal. Two ball lenses, one of which was integrated with the LED, were used to increase light throughput through the capillary column. Stray light was minimized by the use of a band-pass filter and an adjustable slit. Signals down to the parts per billion level (nanomolar) were easily detected with a short-term noise level of 4.4 μAU, confirming a low limit of detection and low noise. The detection limit for adenosine-5'-monophosphate was 230 times lower than any previously reported values. Good linearities (3 orders of magnitude) were obtained using sodium anthraquinone-2-sulfonate, adenosine-5'-monophosphate, dl-tryptophan, and phenol. The LC system was demonstrated by performing isocratic separation of phenolic compounds using a monolithic capillary column (16.5 cm × 150 μm i.d.) synthesized from poly(ethylene glycol) diacrylate.
The Critical Role of pH Gradient Formation in Driving Superconformal Cobalt Deposition (2018)

Conventional damascene electroplating uses a combination of organic additives, namely, a suppressor, an accelerator, and a leveler, to achieve superconformal fill of interconnects. This work demonstrates an alternative mechanism that produces bottom-up cobalt deposition through a combination of pH and suppressor gradient formation within the patterned features. The fill mechanism was investigated using voltammetric and electrochemical quartz crystal microbalance measurements. The results show that local pH affects both the deposition rate and the current efficiency for cobalt deposition, which, combined with the kinetic effects of suppressor-type additives, drive a plating rate differential between the field and the feature-bottom. By appropriately selecting solution concentrations, organic additives, the waveform, and the mass transport conditions, void-free superconformal cobalt fill can be achieved in a variety of features.
EGFL6 Regulates the Asymmetric Division, Maintenance, and Metastasis of ALDH+ Ovarian Cancer Cells (2016)

Little is known about the factors that regulate the asymmetric division of cancer stem-like cells (CSC). Here, we demonstrate that EGFL6, a stem cell regulatory factor expressed in ovarian tumor cells and vasculature, regulates ALDH<sup>+</sup> ovarian CSC. EGFL6 signaled at least in part via the oncoprotein SHP2 with concomitant activation of ERK. EGFL6 signaling promoted the migration and asymmetric division of ALDH<sup>+</sup> ovarian CSC. As such, EGFL6 increased not only tumor growth but also metastasis. Silencing of EGFL6 or SHP2 limited numbers of ALDH<sup>+</sup> cells and reduced tumor growth, supporting a critical role for EGFL6/SHP2 in ALDH<sup>+</sup> cell maintenance. Notably, systemic administration of an EGFL6-neutralizing antibody we generated restricted tumor growth and metastasis, specifically blocking ovarian cancer cell recruitment to the ovary. Together, our results offer a preclinical proof of concept for EGFL6 as a novel therapeutic target for the treatment of ovarian cancer. Cancer Res; 76(21); 6396-409. ©2016 AACR.
Exhaled Volatile Organic Compounds as Noninvasive Early Molecular Markers in Lung Cancer: Bridging the Gap from Bench to Bedside (2013)

Lung cancer (LC) remains one of the deadliest cancers worldwide, with a 5-year survival rate as low as 13%. Reliable and cost-effective LC markers are urgently needed for early LC diagnosis through population-based screening. Certain volatile organic compounds (VOCs) (alkanes, alkenes, alcohols, aldehydes, ketones, and their collective patterns) in exhaled breath are interesting candidates as LC markers for malignancy, staging, histology, genotype, and distinction from other malignant and benign disease. VOC LC markers can be derived either as LC-specic compounds by analytical chemistry or as collective breath prints by statistical treatment of the output of sensor arrays. Direct breath printing using sensor arrays is better suited for clinical applications than chemical analysis of the breath VOCs.
Linear turbo equalization for parallel isi channels (2003)

We propose a method for exploiting transmit diversity using parallel independent intersymbol interference channels together with an iterative equalizing receiver. Linear iterative turbo equalization (LITE) employs an interleaver in the transmitter and passes a priori information on the transmitted symbols between multiple soft-input/soft-output minimum mean-square error linear equalizers in the receiver. We describe the LITE algorithm, present simulations for both stationary and fading channels, and develop a framework for analyzing the evolution of the a priori information as the algorithm iterates.
OWL-SOA: A service oriented architecture ontology useful during development time and independent from implementation technology (2010)

The implementation of service oriented architecture (SOA) has proven to be one of the main initiatives for organizations in gaining necessary agility in the area of information technology. However, in one particular area this process has presented a significant challenge: the implementation of a service catalog. Ontologies have been used to organize services in repositories, as proposed by of OWL-S (Ontology Web Service Language) and WSMO (Web Service Modeling Ontology). Meanwhile, these ontologies have two broad restrictions: they are used on runtime only, and deal only with Web Service technology for the implementation of services. This study proposes an ontology for SOA with an emphasis on the implementation of a service catalog in the development phase, and considering any type of service implementation technology. This ontology was created based on the existing ontologies and literature. The resulting ontology was instanced with services of a large multinational organization.
<title>Call progress time measurement in IP telephony</title> (1999)

Usually a voice call is established through multiple stages in IP telephony. In the first stage, a phone number is dialed to reach a near-end or call-originating IP-telephony gateway. The next stages involve user identification through delivering an m-digit user-id to the authentication and/or billing server, and then user authentication by using an n- digit PIN. After that, the caller is allowed (last stage dial tone is provided) to dial a destination phone number provided that authentication is successful. In this paper, we present a very flexible method for measuring call progress time in IP telephony. The proposed technique can be used to measure the system response time at every stage. It is flexible, so that it can be easily modified to include new `tone' or a set of tones, or `voice begin' can be used in every stage to detect the system's response. The proposed method has been implemented using scripts written in Hammer visual basic language for testing with a few commercially available IP telephony gateways.