gebhart/patrepeval huggingface dataset:
Gene expression profiles alteration after infection of virus, bacteria, and parasite in the Olive flounder (Paralichthys olivaceus) (2018)

Olive flounder (Paralichthys olivaceus) is one of economically valuable fish species in the East Asia. In comparison with its economic importance, available genomic information of the olive flounder is very limited. The mass mortality caused by variety of pathogens (virus, bacteria and parasites) is main problem in aquaculture industry, including in olive flounder culture. In this study, we carried out transcriptome analysis using the olive flounder gill tissues after infection of three types of pathogens (Virus; Viral hemorrhagic septicemia virus, Bacteria; Streptococcus parauberis, and Parasite; Miamiensis avidus), respectively. As a result, we identified total 12,415 differentially expressed genes (DEG) from viral infection, 1,754 from bacterial infection, and 795 from parasite infection, respectively. To investigate the effects of pathogenic infection on immune response, we analyzed Gene ontology (GO) enrichment analysis with DEGs and sorted immune-related GO terms per three pathogen groups. Especially, we verified various GO terms, and genes in these terms showed down-regulated expression pattern. In addition, we identified 67 common genes (10 up-regulated and 57 down-regulated) present in three pathogen infection groups. Our goals are to provide plenty of genomic knowledge about olive flounder transcripts for further research and report genes, which were changed in their expression after specific pathogen infection.
Antiviral Polymers Based on N-Halamine Polyurea (2021)

<i>N</i>-halamines are a commonly applied class of antimicrobial agents used for a variety of applications relating to human health. Here, we present the modulation of the common polymers polyurea and polyguanidine with the <i>N-</i>halamine technology. The N-H bonds in either polymer were converted to N-Cl or N-Br bonds capable of releasing Cl<sup>+</sup> or Br<sup>+</sup> cations to aqueous media as antiviral agents. Controlled release of the oxidizing agents was monitored for a period of 4 weeks. Antiviral activity was evaluated against the T4 bacteriophage as well as against the highly stable plant virus belonging to the <i>Tobamovirus</i> genus, tomato brown rugose fruit virus. The incorporation of the <i>N-</i>halamine technology on commonly used polymers has effectively introduced antiviral functionality for a wide variety of potential applications.
Parallel processing considerations for image recognition tasks (2010)

Many image recognition tasks are well-suited to parallel processing. The most obvious example is that many imaging tasks require the analysis of multiple images. From this standpoint, then, parallel processing need be no more complicated than assigning individual images to individual processors. However, there are three less trivial categories of parallel processing that will be considered in this paper: parallel processing (1) by task; (2) by image region; and (3) by meta-algorithm. Parallel processing by task allows the assignment of multiple workflows-as diverse as optical character recognition [OCR], document classification and barcode reading-to parallel pipelines. This can substantially decrease time to completion for the document tasks. For this approach, each parallel pipeline is generally performing a different task. Parallel processing by image region allows a larger imaging task to be sub-divided into a set of parallel pipelines, each performing the same task but on a different data set. This type of image analysis is readily addressed by a map-reduce approach. Examples include document skew detection and multiple face detection and tracking. Finally, parallel processing by meta-algorithm allows different algorithms to be deployed on the same image simultaneously. This approach may result in improved accuracy.
Protein-functionalized nanoparticles derived from end-functional polymers and polymer prodrugs for crossing the blood-brain barrier (2019)

Nanoparticles may provide a viable way for neuroprotective drugs to cross the blood-brain barrier (BBB), which limits the passage of most drugs from the peripheral circulation to the brain. Heterotelechelic polymer prodrugs comprising a neuroprotective model drug (adenosine) and a maleimide functionality were synthesized by the "drug-initiated" approach and subsequent nitroxide exchange reaction. Nanoparticles were obtained by nanoprecipitation and exhibited high colloidal stability with diameters in the 162-185 nm range and narrow size distributions. Nanoparticles were then covalently surface-conjugated to different proteins (albumin, α2-macroglobulin and fetuin A) to test their capability of enhancing BBB translocation. Their performances in terms of endothelial permeability and cellular uptake in an in vitro BBB model were compared to that of similar nanoparticles with surface-adsorbed proteins, functionalized or not with the drug. It was shown that bare NPs (i.e., NPs not surface-functionalized with proteins) without the drug exhibited significant permeability and cellular uptake, which were further enhanced by NP surface functionalization with α2-macroglobulin. However, the presence of the drug at the polymer chain-end prevented efficient passage of all types of NPs through the BBB model, likely due to adecrease in the hydrophobicity of the nanoparticle surface and alteration of the protein binding/coupling, respectively. These results established a new and facile synthetic approach for the surface-functionalization of polymer nanoparticles for brain delivery purposes.
ATP-binding Cassette Transporter A7 (ABCA7) Loss of Function Alters Alzheimer Amyloid Processing (2015)

The ATP-binding cassette transporter A7 (ABCA7) has been identified as a susceptibility factor of late onset Alzheimer disease in genome-wide association studies. ABCA7 has been shown to mediate phagocytosis and affect membrane trafficking. The current study examined the impact of ABCA7 loss of function on amyloid precursor protein (APP) processing and generation of amyloid-β (Aβ). Suppression of endogenous ABCA7 in several different cell lines resulted in increased β-secretase cleavage and elevated Aβ. ABCA7 knock-out mice displayed an increased production of endogenous murine amyloid Aβ42 species. Crossing ABCA7-deficient animals to an APP transgenic model resulted in significant increases in the soluble Aβ as compared with mice expressing normal levels of ABCA7. Only modest changes in the amount of insoluble Aβ and amyloid plaque densities were observed once the amyloid pathology was well developed, whereas Aβ deposition was enhanced in younger animals. In vitro studies indicated a more rapid endocytosis of APP in ABCA7 knock-out cells that is mechanistically consistent with the increased Aβ production. These in vitro and in vivo findings indicate a direct role of ABCA7 in amyloid processing that may be associated with its primary biological function to regulate endocytic pathways. Several potential loss-of-function ABCA7 mutations and deletions linked to Alzheimer disease that in some instances have a greater impact than apoE allelic variants have recently been identified. A reduction in ABCA7 expression or loss of function would be predicted to increase amyloid production and that may be a contributing factor in the associated Alzheimer disease susceptibility.
Attitudes of clinician educators towards interprofessional education and collaboration: Insights from two interprofessional scales (2017)

The increasing complexity of healthcare needs underlines the growing importance of interprofessional education and collaborative practice (IPECP) in enhancing quality of patient care. In particular, clinician educators play an influential role in advocating IPECP. The primary goal of our exploratory pilot study is to explore 34 clinician educators' attitudes towards IPECP by using the adapted 14-item Attitudes Toward Health Care Teams Scale (ATHCTS) and 15-item Readiness for Interprofessional Learning Scale (RIPLS). Mean scores of ATHCTS and RIPLS were 3.81 (SD = 0.90) and 4.02 (SD = 0.79), respectively. Using exploratory factor analysis, we identified four factors: team value (ATHCTS), team efficiency (ATHCTS), teamwork and collaboration (RIPLS), and professional socialisation (RIPLS). The "team efficiency" factor on the ATHCTS scored lowest (factor mean = 3.49) compared with other factors (factor means = 3.87-4.08). Correlation analyses revealed that the "team efficiency" factor had small correlations with other factors (r = -0.05-0.37). Our clinician educators valued IPECP in promoting teamwork and professional socialisation but they perceived IPECP to compromise efficiency. The issue of perceived inefficiency by clinician educators merits attention in order to promote wider implementation of IPECP.
Non-invasive measurement of nutrient uptake by single cultured pre-implantation mouse embryos (1986)

The uptake of pyruvate and glucose by single, cultured mouse embryos has been measured non-invasively throughout the pre-implantation period. The embryos, derived from CBA x C57F1 females and F1 males were removed from the oviducts on day 1 or day 2 following mating, and cultured to the blastocyst stage in M16 medium. Each day they were removed from culture and incubated in 20 nl medium M2 for 3 h. Serial approximately 0.5-nl samples were analysed for pyruvate and glucose by an ultramicrofluorescence technique. Pyruvate uptake exceeded that of glucose until the 8-cell/morula stage, when glucose consumption increased dramatically. The morphological development and patterns of nutrient uptake by embryos removed on day 2 resembled more closely those of freshly collected embryos than of embryos removed on day 1. These methods will enable the biochemistry of early embryos to be monitored non-invasively prior to transferring them into the uterus of recipient females.
Immobilization of functionalized alkyl-poly(ethylene oxide) surfactants on poly(ethylene) surfaces by means of an argon plasma treatment (1997)

Alkyl-poly(ethylene oxide) (PEO) surfactants containing a terminal hydroxyl, sulfate, or carboxylate group were grafted at the surface of poly(ethylene) (PE) samples to improve their blood compatibility. Grafting was achieved by immobilizing PEO surfactants on PE using an argon plasma treatment. The sulfate group containing PEO surfactant was synthesized by sulfating polyoxyethylene(20)stearylether (Brij78; B) with chlorosulfonic acid. A carboxylate-terminated surfactant was synthesized by a substitution reaction of the sodium alkoxide form of B with sodium iodoacetate. XPS analysis of the modified PE samples showed that at short plasma treatment times of up to 5 s the structure of the immobilized surfactants is largely retained. When plasma treatment times longer than 30 s were applied, the PEO chains of the surfactants were degraded. The wettability of the modified PE samples was improved compared to the unmodified PE samples. The wettability of the modified samples did not change when they were stored in air at room temperature for at least 12 weeks.
Cell Assay Development with Upconverting Chelates (2005)

This paper reports progress on performing a cell-based assay for the detection of EGFR on cell surfaces with upconverting chelates. A431 cells are labeled with europium DOTA and imaged using an upconverting microscope
3-D Data Storage in Two-Photon Photochromic Optical Memories (1996)

Rapid increases in the computer processing power available per unit cost, as well as a growing hunger for multimedia (text, audio, and image) entertainment and processing has led to heightened interest in multilayer and other volume optical storage technologies. 1 One such technology is 2-photon absorption-based storage. 2 , 3 , 4 In this approach, writing or erasure takes place only at the intersection of 2 beams of different wavelengths, thus allowing independent addressing of any point within a 3-dimensional volume. As a bit oriented (rather than holographic) memory, a unique physical location is allocated for each data bit. If individual bits are stored, volumetric densities on the order of terabits/cm 3 may be achievable, and parallel reading of the bits (e.g.-in planes or pages) can enable 100 Gb/s data transfer rates. The key principle behind 2-photon memories is the creation of a molecular change in the media by the simultaneous absorption of 2 photons from 2 different beams by the dopant molecule, as shown in Fig. 1(a). The localized change can store bits by changing the index of refraction, absorption, fluorescence, or the material’s electrical properties. In our system experiments so far we have utilized materials in which 2-photon excitation creates a new absorption peak and subsequent 1 or 2-photon illumination results in efficient fluorescence for readout. The broad readout absorption profile, and the high fluorescence efficiency enable the use of inexpensive, low power replay sources, including LEDs and filtered lamps. In addition to non-destructive memory recall, we have also demonstrated optically induced erasure, thus enabling random accessibility and erasure of bits. These two-photon 3-D memories are similar to the multilayer optical disk systems with the potential for simple media fabrication, many layers, parallel access for high data transfer rates, and low raw bit error rates (BER). As shown in Fig. 1(b), orthogonal intersection of the writing beams may be used, or if ultra-short (e.g.-&lt;100 femtosecond) pulses are used, a counter-propagating arrangement 10 , 5 is feasible. While single bits may be stored and recalled, parallel access of lines or planes of data is naturally accommodated in two-photon 3-D memories, to provide increased data transfer rates. Due to diffraction of the addressing beam as it propagates across the data image, there exists a tradeoff between the volumetric density of the memory and the parallelism, or data transfer rate. 9
Development and Implementation of a Framework for Adaptive Undergraduate Curricula in Manufacturing Engineering (2020)

ABSTRACT Advanced manufacturing, through the application of science and technology, compels an expanded view of the role of engineers in driving innovation. Advanced manufacturing requires engineers to imagine new ways of making products for smart, rapid, flexible, sustainable, and competitive production. Such manufacturing innovation is driving operational, tactical, and strategic advantages for industry while also creating a demand for a dynamic global workforce and market. The work herein supports the preparation of next-generation engineers for careers in academia and industry by developing and implementing a framework for adaptive manufacturing engineering curricula. The framework is founded upon a benchmarking study that applied the Society of Manufacturing Engineers Four Pillars of Manufacturing Knowledge Model to examine Accreditation Board for Engineering and Technology, Inc.–accredited undergraduate manufacturing engineering programs in the United States. Results of this work will enable universities, along with their industry partners, to identify topics that have garnered the attention of other curriculum developers and define opportunities for improvement. Thus, the adaptive framework can serve as a basis for defining how individual undergraduate programs can best meet the human resource needs of affiliated advanced manufacturing industry. To illustrate, a resulting revision to the manufacturing engineering curriculum at Oregon State University is described. The curriculum consists of a set of foundational courses and supporting thrusts in manufacturing systems and product development. The framework enables keystone options addressing needs for educating students in manufacturing systems, product development, smart manufacturing, and sustainable manufacturing. The framework supports local industry needs while taking advantage of faculty expertise. Initial implementation has demonstrated a positive student reception of the revised program, which also facilitates dual majors with industrial and mechanical engineering.
CHEMICALLY SELF-ASSEMBLED NANOELECTRONIC COMPUTING NETWORKS (1998)

Recent advances in chemical self-assembly will soon make it possible to synthesize extremely powerful computing machinery from metallic clusters and organic molecules. These self-organized networks can function as Boolean logic circuits, associative memory, image processors, and combinatorial optimizers. Computational or signal processing activity is elicited from simple charge interactions between clusters which are resistively/capacitively linked by conjugated molecular wires or ribbons. The resulting circuits are massively parallel, fault-tolerant, ultrafast, ultradense and dissipate very little power.
Design Method Support for Domain Specific SoC design (2006)

In this paper we introduce the idea of methodware (i.e., combination of language definitions and model transformations) as a framework for defining design methods. The approach should allow us to facilitate building of customized tools for domain specific problems. We apply our approach to the MICAS architecture, a novel SoC architecture for mobile peripherals
Maintenance of red blood cell integrity by AMP‐activated protein kinase α1 catalytic subunit (2010)

AMP-activated protein kinase (AMPK) plays a pivotal role in regulating cellular energy metabolism. We previously showed that AMPKalpha1-/- mice develop moderate anemia associated with splenomegaly and high reticulocytosis. Here, we report that splenectomy of AMPKalpha1-/- mice worsened anemia supporting evidence that AMPKalpha1-/- mice developed a compensatory response through extramedullary erythropoiesis in the spleen. Transplantation of bone marrow from AMPKalpha1-/- mice into wild-type recipients recapitulated the hematologic phenotype. Further, AMPKalpha1-/- red blood cells (RBC) showed less deformability in response to shear stress limiting their membrane flexibility. Thus, our results highlight the crucial role of AMPK to preserve RBC integrity.
Digital predistorters sensitivity to delay alignment resolution (2009)

In this paper, the effects of delay alignment between power amplifiers' input and output waveforms used to synthesize the digital predistorters (DPD) is discussed. Various delay values are applied to align the input and output waveforms; and a memory polynomial based DPD model is synthesized for each delay value. Then, the effects of the residual delay on the performance of the linearized amplifier are evaluated. This reveals that the DPD performance is altered by delay under-estimation. Conversely, the DPD is not sensitive to delay over-estimation by up to one sampling period. This overcomes the need for the signal up-sampling required for sub-sample fine resolution delay alignment, and considerably reduces the computational complexity of the digital signal processing algorithm employed for delay estimation and alignment. A low complexity coarse delay estimation and alignment algorithm is then proposed.
Horse Chestnut Extract Induces Contraction Force Generation in Fibroblasts through Activation of Rho/Rho Kinase (2006)

Contraction forces generated by non-muscle cells such as fibroblasts play important roles in determining cell morphology, vasoconstriction, and/or wound healing. However, few factors that induce cell contraction forces are known, such as lysophosphatidic acid and thrombin. Our study analyzed various plant extracts for ingredients that induce generation of cell contraction forces in fibroblasts populating collagen gels. We found that an extract of Horse chestnut (Aesculus hippocastanum) is able to induce such contraction forces in fibroblasts. The involvement of actin polymerization and stress fiber formation in the force generation was suggested by inhibition of this effect by cytochalasin D and by Rhodamine phalloidin. Rho kinase inhibitors (Y27632 and HA1077) and a Rho inhibitor (exoenzyme C3) significantly inhibited the force generation induced by the Horse chestnut extract. H7, which inhibits Rho kinase as well as other protein kinases, also significantly inhibited induction of force generation. However, inhibitors of other protein kinases such as myosin light chain kinase (ML-9), protein kinase C (Calphostin), protein kinase A (KT5720), and tyrosine kinase (Genistein, Herbimycin A) had no effect on force generation induced by Horse chestnut extract. These results suggest that the Horse chestnut extract induces generation of contraction forces in fibroblasts through stress fiber formation followed by activation of Rho protein and Rho kinase but not myosin light chain kinase or other protein kinases.
New Quinaphos Ligands for Asymmetric Hydrogenation (2010)

New members of the Quinaphos-type ligands have been synthesized by a simple protocol and fully characterized. These new Quinaphos ligands with a more flexible 1,2,3,4-tetrahydroquinoline backbone were shown to be extremely effective for asymmetric hydrogenation of functionalized olefins, dehydroamino acid derivatives as well as enamides.
GW8510 Increases Insulin Expression in Pancreatic Alpha Cells through Activation of p53 Transcriptional Activity (2012)

The induction of Ins2 by GW8510 occurred through p53 in a JNK- and p38-dependent manner. These results implicate p53 activity in modulation of Ins2 expression levels in pancreatic alpha cells, and point to a potential approach toward using small molecules to generate insulin in an alternative cell type.
ChemInform Abstract: A Practical Procedure for Iron‐Catalyzed Cross‐Coupling Reactions of Sterically Hindered Aryl‐Grignard Reagents with Primary Alkyl Halides. (2014)

Abstract The use of an iron phosphine complex as catalyst renders possible the cross‐coupling of sterically hindered arylmagnesium halides with primary alkyl halides and tosylates.
First Pd@Organo−Si(HIPE) Open-Cell Hybrid Monoliths Generation Offering Cycling Heck Catalysis Reactions (2008)

The syntheses and characterization of a new class of grafted organo−Si(HIPE) “high internal phase emulsion” open-cell matrixes is first proposed. Second, internal palladium particles heterogeneous nucleation is briefly discussed, leading finally to the generation of the new Pd@organo−Si(HIPE) series. The matrixes synthesized offer good turnovers and cycling performances For instance, the Pd@mercapto−Si(HIPE) matrix allows reaching at least 96% of Heck coupling catalysis yield during seven cycling tests. The Pd/iodobenzene molar ratio was settled at 0.004 and 0.002. The turnover number (TON) and turnover frequency (TOF) addressed with these new monolith catalysts are reaching values comparable with the ones obtained with powdered catalysts. Considering the fact that the catalysts in use are not powders but rather monoliths bearing hierarchical porosities, the series of Pd@organo−Si(HIPE) compounds combine heterogeneous catalysis efficiency and facile reusability where catalyzed species and catalyst supports can be easily separated by a simple removal of either the monolith or the solution from the reaction media.