gebhart/patrepeval huggingface dataset:
Informotion for Cell Culture Engineering (2019)

Automation of the cell culture process is one of the biggest challenges in cell therapy, including regenerative medicine, drug screening, and body-on-chip drug development. Cell culture processes that involve cell seeding, culture, detachment, and collection processes are typically performed manually by a technician. In order to establish an efficient and stable mass culture process for cells, “informotion technology” may play an important role. Using actuator / sensor technology to automate cell culture processes and network them online enables to share know-how to deal with live cells. By doing so, we can efficiently provide a large amount of cells ready to accelerate the spread of regenerative medicine. Ultrasonic actuation technology has proven its potential for use in cell culture automation.
Estimating accurate multi-class probabilities with support vector machines (2006)

In this paper, we propose a comparison of several post-processing methods for estimating multi-class probabilities with standard support vector machines. The different approaches have been tested on a real pattern recognition problem with a large number of training samples. The best results have been obtained by using a "one against air coupling strategy along with a softmax function optimized by minimizing the negative log-likelihood of the training data. Finally, the analysis of the error-reject tradeoff have shown that SVM allows to estimate probabilities more accurate than a classical MLP, which is indeed promising in the view of incorporated within pattern recognition system using probabilistic framework.
Multiple nested elements in As2S3 anti-resonant negative-curvature tube-lattice fibers (2016)

We computationally demonstrate that the inclusion of multiple nested elements in As2S3 anti-resonant fibers, as in the silica case, has no effect on the overall loss. We show the dominant loss mechanisms for both cases.
<title>KC-135 zero-G testing of a microsatellite docking mechanism</title> (2003)

Michigan Aerospace Corporation has developed a mechanism for microsatellite docking, which has been successfully demonstrated in a microgravity environment. This docking mechanism is specifically designed for soft-docking capability, tolerance to misalignment, and scalability. The current Autonomous Microsatellite Docking System (AMDS) design resulted from modifications to an earlier docking mechanism prototype that was tested at the Marshall Space Flight Center (MSFC) Flat Floor Facility. The AMDS was tested in a microgravity environment through the NASA JSC Reduced Gravity Program, where a KC-135 turbo jet flies a series of parabolic maneuvers. The test objectives of the KC-135 flight were to determine the docking mechanism cable assembly behavior in zero-g, test the full range of the docking envelope in a six degree of freedom test setup and determine the undocking capability and stability. The nature of the Michigan Aerospace docking mechanism enabled the entire docking cycle, including soft dock, auto-alignment and hard dock, to be completed within the 20 seconds of 'zero-g' time. Complete end-to-end docking and undocking was performed under a variety of initial conditions and docking parameters. The data collected during the KC-135 testing will be used to validate dynamic simulation models of the docking mechanism. The intent of these dynamic models is to examine a number of docking scenarios between a chaser and target satellite. This paper will discuss the results of the KC-135 docking tests and docking simulations.
Thickness dependence of intrinsic dielectric response and apparent interfacial capacitance in ferroelectric thin films (2007)

We studied theoretically the influence of the progressive strain relaxation and the depolarizing-field effect on the thickness dependence of the out-of-plane dielectric response of epitaxial ferroelectric thin films sandwiched between extended metal electrodes. The calculations show that the inverse of the measured capacitance varies with the film thickness almost linearly in the most part of the thickness range at the majority of temperatures. Extrapolation of this linear dependence to zero thickness usually gives considerable nonzero intercept even in the absence of nonferroelectric interfacial layers. Remarkably, such apparent “interfacial capacitance” in a certain temperature range becomes negative. The physical meaning of the effective dielectric constant, which can be extracted from the slope of the reciprocal capacitance thickness dependence, is also analyzed. The theoretical predictions are compared with the experimental data obtained for single-crystalline SrRuO3∕Ba0.7Sr0.3TiO3∕SrRuO3 and Pt∕Ba0.7Sr0.3TiO3∕SrRuO3 thin-film capacitors.
Gas Permeability and Free Volume of Highly Branched Substituted Acetylene Polymers (2001)

Gas permeation, sorption, and structural properties of two highly branched polyacetylenes, poly[1-phenyl-2-[p-(triphenylsilyl)phenyl]acetylene] (PPhSiDPA) and poly[1-phenyl-2-[p-(triisopropylsilyl)phenyl]acetylene] (PPrSiDPA), are reported. Structurally, both polymers have much in common; however, their transport properties are quite different. PPhSiDPA has dramatically lower permeability coefficients than PPrSiDPA. For example, the O2 permeability coefficients of PPhSiDPA and PPrSiDPA are 12 × 10-10 and 230 × 10-10 cm3 (STP) cm/(cm2 s cmHg), respectively, at 22 °C. Gas solubility is very high in PPrSiDPA, similar to that observed in poly(1-trimethysilyl-1-propyne) (PTMSP), the most permeable polymer known. Gas solubility coefficients of PPhSiDPA are 2−3 times lower than those of PPrSiDPA. Free volume size and size distribution were characterized using positron annihilation lifetime (PAL) spectroscopy. Results from these studies (i.e., a bimodal size distribution of free volume elements and large free volume element size) are consistent with the observed transport and sorption properties of PPrSiDPA. In contrast, the PAL spectrum of PPhSiDPA is similar to that of conventional low free volume glassy polymers.
Cytokinins in the perianth, carpels, and developing fruit of Helleborus niger L. (2006)

Reproductive development in the Christmas rose (Helleborus niger L.) differs from that in commonly investigated model plants in two important aspects: (i) the perianth develops a photosynthetic system, after fertilization, and persists until seed ripening; and (ii) the ripe seed contains an immature embryo which continues to mature off the mother plant. The possible roles of cytokinins in these processes are investigated here by analysing extracts of the perianth and the carpels/maturing fruit prepared during anthesis and four stages of post-floral development. trans-Zeatin, dihydrozeatin, N6-(Delta2-isopentenyl)adenine, and their ribosides were identified by tandem mass spectrometry. Single ion monitoring in the presence of deuterated internal standards demonstrated the additional presence of the corresponding riboside-5'-monophosphates, O-glucosides, and 9-glucosides, and afforded quantitative data on the whole set of endogenous cytokinins. Fruit cytokinins were mostly localized in the seeds. Their overall concentrations increased dramatically during early seed development and remained high for 6-8 weeks, until shortly before seed ripening (the last time point covered in this work). Overall cytokinin levels in the perianth did not change markedly in the period covered, but the level of N6-(Delta2-isopentenyl)adenine-type cytokinins appeared to increase slightly and transiently during the greening phase. The perianths of unpollinated or depistillated flowers, which survived, but did not pass through the complete greening process, contained significantly less cytokinins than observed in fruit-bearing flowers. This suggests that perianth greening requires defined cytokinin levels and supports the role of the developing fruit in their maintenance.
ChemInform Abstract: Biosynthesis of Aristeromycin: The Role of (1R,2R,3S,4S)‐1‐ Hydroxymethylcyclopentane‐2,3,4‐triol. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
We need to communicate! (2011)

Language immersion from birth is crucial to a child's language development. However, language immersion can be particularly challenging for hearing parents of deaf children to provide as they may have to overcome many difficulties while learning American Sign Language (ASL). We are in the process of creating a mobile application to help hearing parents learn ASL. To this end, we have interviewed members of our target population to gain understanding of their motivations and needs when learning sign language. We found that the most common motivation for parents learning ASL is better communication with their children. Parents are most interested in acquiring more fluent sign language skills through learning to read stories to their children.
Intravascular ultrasound identification of intraluminal embolic plaque material during carotid angioplasty with stenting (2006)

IVUS can identify intraluminal plaque material, which may be a precursor for embolism and delayed ischemic events after CAS. IVUS may allow for treatment before distal embolization of plaque material. Virtual histology IVUS software may help to identify carotid lesions at higher risk for significant embolization during CAS.
Spurious mode suppressing technique for performance enhancement of hybrid planar/NRD-guide circuits (2002)

A compact spurious mode suppresser for hybrid planar/NRD-guide integrated circuits is presented in this paper. The proposed mode suppressing technique with embedded metallic plate/film is used in the hybrid design that is compact and easy to implement. It is found through our investigation that the rejection of all the spurious modes (including TE and LSE modes) is better than -32 dB for a single transition of planar-to-NRD-guide over a broadband frequency of interest, and the performance could be further enhanced. This new technique also provides an alternative solution to the inherent problem of spurious modes (especially TE modes) in the standard design procedure of NRD-guide circuits.
Lymphotoxin Signaling Is Initiated by the Viral Polymerase in HCV-linked Tumorigenesis (2013)

Exposure to hepatitis C virus (HCV) typically results in chronic infection that leads to progressive liver disease ranging from mild inflammation to severe fibrosis and cirrhosis as well as primary liver cancer. HCV triggers innate immune signaling within the infected hepatocyte, a first step in mounting of the adaptive response against HCV infection. Persistent inflammation is strongly associated with liver tumorigenesis. The goal of our work was to investigate the initiation of the inflammatory processes triggered by HCV viral proteins in their host cell and their possible link with HCV-related liver cancer. We report a dramatic upregulation of the lymphotoxin signaling pathway and more specifically of lymphotoxin-β in tumors of the FL-N/35 HCV-transgenic mice. Lymphotoxin expression is accompanied by activation of NF-κB, neosynthesis of chemokines and intra-tumoral recruitment of mononuclear cells. Spectacularly, IKKβ inactivation in FL-N/35 mice drastically reduces tumor incidence. Activation of lymphotoxin-β pathway can be reproduced in several cellular models, including the full length replicon and HCV-infected primary human hepatocytes. We have identified NS5B, the HCV RNA dependent RNA polymerase, as the viral protein responsible for this phenotype and shown that pharmacological inhibition of its activity alleviates activation of the pro-inflammatory pathway. These results open new perspectives in understanding the inflammatory mechanisms linked to HCV infection and tumorigenesis.
A Digitally Controlled Tone&Volume Circuit for Autosound Systems (1986)

A microprocessor controlled tone and volume circuit for automotive applications has been integrated in a CMOS technology. Very few external components are required while a high level of performance is achieved. Stereo source selection, volume, tone, loudness, balance and fader functions are provided.
Cellular Cleavage and Polyadenylation Specificity Factor 6 (CPSF6) Mediates Nuclear Import of Human Bocavirus 1 NP1 Protein and Modulates Viral Capsid Protein Expression (2019)

Human bocavirus 1 (HBoV1), which belongs to the genus <i>Bocaparvovirus</i> of the <i>Parvoviridae</i> family, causes acute respiratory tract infections in young children. <i>In vitro</i>, HBoV1 infects polarized primary human airway epithelium (HAE) cultured at an air-liquid interface (HAE-ALI). HBoV1 encodes a small nonstructural protein, nuclear protein 1 (NP1), that plays an essential role in the maturation of capsid protein (VP)-encoding mRNAs and viral DNA replication. In this study, we determined the broad interactome of NP1 using the proximity-dependent biotin identification (BioID) assay combined with mass spectrometry (MS). We confirmed that two host mRNA processing factors, DEAH-box helicase 15 (DHX15) and cleavage and polyadenylation specificity factor 6 (CPSF6; also known as CFIm68), a subunit of the cleavage factor Im complex (CFIm), interact with HBoV1 NP1 independently of any DNA or mRNAs. Knockdown of CPSF6 significantly decreased the expression of capsid protein but not that of DHX15. We further demonstrated that NP1 directly interacts with CPSF6 <i>in vitro</i> and colocalizes within the virus replication centers. Importantly, we revealed a novel role of CPSF6 in the nuclear import of NP1, in addition to the critical role of CPSF6 in NP1-facilitated maturation of VP-encoding mRNAs. Thus, our study suggests that CPSF6 interacts with NP1 to escort NP1 imported into the nucleus for its function in the modulation of viral mRNA processing and viral DNA replication.<b>IMPORTANCE</b> Human bocavirus 1 (HBoV1) is one of the significant pathogens causing acute respiratory tract infections in young children worldwide. HBoV1 encodes a small nonstructural protein (NP1) that plays an important role in the maturation of viral mRNAs encoding capsid proteins as well as in viral DNA replication. Here, we identified a critical host factor, CPSF6, that directly interacts with NP1, mediates the nuclear import of NP1, and plays a role in the maturation of capsid protein-encoding mRNAs in the nucleus. The identification of the direct interaction between viral NP1 and host CPSF6 provides new insights into the mechanism by which a viral small nonstructural protein facilitates the multiple regulation of viral gene expression and replication and reveals a novel target for potent antiviral drug development.
Supplementary Figures from A Stromal Lysolipid–Autotaxin Signaling Axis Promotes Pancreatic Tumor Progression (2023)

&lt;p&gt;Figure S1-S5 with legends&lt;/p&gt;
PhiC31 integrase mediates integration in cultured synovial cells and enhances gene expression in rabbit joints (2006)

The ability of phiC31 integrase to facilitate genomic integration in synovial cells and increase transgene expression in the rabbit synovium suggests that, in combination with more efficient DNA delivery methods, this integrase system could be beneficial for treatment of rheumatoid arthritis and other joint disorders.
Clostridium jejuense sp. nov., isolated from soil (2004)

A strictly anaerobic, mesophilic, endospore-forming bacterium, designated strain HY-35-12T, was isolated from a soil sample in Jeju, Korea. Cells of this isolate were Gram-positive, motile rods that formed oval to spherical terminal spores. Strain HY-35-12T grew optimally at 30 degrees C, pH 7.0 and 0-0.5 % (w/v) NaCl. The isolate produced pyruvate, lactate, acetate, formate and hydrogen as fermentation end products from glucose. The G + C content of DNA of the isolate was 41 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism formed a monophyletic clade with Clostridium xylanovorans and Clostridium aminovalericum in cluster XIVa of the genus Clostridium. The closest phylogenetic neighbour was C. xylanovorans, with 96.65 % 16S rRNA gene sequence similarity. Several physiological and chemotaxonomic properties were identified that enable strain HY-35-12T to be distinguished from phylogenetically related clostridia. On the basis of polyphasic characteristics, it is proposed that strain HY-35-12T (= IMSNU 40003T = KCTC 5026T = DSM 15929T) represents a novel species, Clostridium jejuense sp. nov.
Adaptation of microscopy for studying cell polarization (2023)

Cell polarization, i.e. a spatial difference in the structural organization such as of membrane molecules over the cell, plays an important role in cellular functions. An example is the polarization in epithelial cells, whose disruption by Ras gene mutations leads to cancerous developments. Still, the cell depolarization mechanism remains unknown. Here, we investigate polarized cells by means of advanced fluorescence microscopy and spectroscopy approaches, such as super-resolution STED microscopy, fluorescence correlation spectroscopy, and spectral imaging, to explore the differences between apical and basal membranes regarding lipid organization and Ras-lipid interactions. Importantly, we overcome the difficulties to measure polarized membranes with light fluorescence microscopy due to the photoselection effect, i.e., the preferential excitation of membrane dyes depending on their orientation with respect to the excitation light polarization. Our results are important to the study of polarized cell membranes using advanced fluorescence microscopy, and for the understanding of the role of Ras and its interaction with lipids.
Galactoxylomannan Does Not Exhibit Cross-Reactivity in the Platelia Aspergillus Enzyme Immunoassay (2007)

Given the recent report of a false-positive result in the Platelia Aspergillus enzyme immunoassay in a patient with cryptococcosis and in yeast extracts and purified galactoxylomannan of Cryptococcus neoformans, we evaluated culture extracts, purified polysaccharides, clinical specimens, and specimens from animals following experimental infection. Our results revealed no cross-reactions.
<title>Fabrication and testing of polyimide thermo-optic switches</title> (2000)

CMOS compatible optical polyimide based thermo-optic switches have the potential use as low-power switches. These switches would have many advantages over other switches based on inorganic crystals. For one, they can be integrated into module-to-module systems using currently available VLSI fabrication techniques. Polyimide based, 1 by 2 thermo-optic switches are fabricated onto silicon wafers and tested. We report the properties and characteristics of digital thermo- optic switches designed to operate at 1.3 micrometers . Also, the switching characteristics at different heating electrode voltages are tested and compared.
The effect of paracrine/autocrine interactions on the in vitro culture of bovine preimplantation embryos (2006)

Bovine preimplantation embryos develop more successfully when cultured in groups, proibably because of the increased production of, and exposure to, embryotrophic autocrine and paracrine factors. Using a novel embryo culture technique, this study had two aims: 1. to determine the distance over which potential paracrine interactions affect bovine embryo development in terms of blastocyst and hatching rates, cell counts and carbohydrate metabolism; 2. to investigate the effect of platelet-activating factor (PAF) supplementation on bovine embryo development and metabolism. Groups of 16 presumptive zygotes were attached to the bottom of a culture dish by the cell adhesive Cell-Tak in a 4 x 4 equidistant array. The distance between individual embryos in each group was 0-689 microm. Optimal blastocyst formation rate occurred when embryos were cultured 165 microm apart compared with control non-attached zygotes (Kruskal-Wallis followed by Mann-Whitney U test post-hoc; P < 0.05). Increasing the distance between embryos resulted in a further decline in blastocyst rate, which reached zero at 540 microm apart. Blastocyst cell number, pyruvate/glucose uptake and lactate production decreased as the interembryo distance increased from 240 to 465 microm (P < 0.05). Supplementation with PAF during conventional group culture enhanced blastocyst cell number, hatching rates and the oxidative metabolism of pyruvate and glucose. The data indicate that the distance between individual bovine embryos in culture influences preimplantation development, in particular blastocyst formation, cell number and metabolism. It is suggested that diffusible paracrine/autocrine factors, such as PAF, are in part responsible for the regulation of early embryo development.
CoMP Schemes Based on Interf.-Aware Transceivers or Interf. Coord. (2011)

In this chapter, we introduce CoMP schemes where no or little information is exchanged between cooperating base stations. In Section 5.1, we observe an interference-aware downlink transmission scheme where each base station performs individual intra-cell beamforming, while the terminals are able to mitigate inter-cell interference to a certain extent through a particular interference estimation and rejection concept. The level of base station cooperation is then increased in Sections 5.2 and 5.3, where joint multi-cell scheduling and link adaptation, and multi-cell coordinated beamforming are investigated, respectively.
Analysis of Cre-mediated genetic deletion of Gdf11 in cardiomyocytes of young mice (2019)

Administration of active growth differentiation factor 11 (GDF11) to aged mice can reduce cardiac hypertrophy, and low serum levels of GDF11 measured together with the related protein, myostatin (also known as GDF8), predict future morbidity and mortality in coronary heart patients. Using mice with a loxP-flanked ("floxed") allele of <i>Gdf11</i> and <i>Myh6</i>-driven expression of Cre recombinase to delete <i>Gdf11</i> in cardiomyocytes, we tested the hypothesis that cardiac-specific <i>Gdf11</i> deficiency might lead to cardiac hypertrophy in young adulthood. We observed that targeted deletion of <i>Gdf11</i> in cardiomyocytes does not cause cardiac hypertrophy but rather leads to left ventricular dilation when compared with control mice carrying only the <i>Myh6-cre</i> or <i>Gdf11</i>-floxed alleles, suggesting a possible etiology for dilated cardiomyopathy. However, the mechanism underlying this finding remains unclear because of multiple confounding effects associated with the selected model. First, whole heart <i>Gdf11</i> expression did not decrease in <i>Myh6-cre; Gdf11</i>-floxed mice, possibly because of upregulation of <i>Gdf11</i> in noncardiomyocytes in the heart. Second, we observed Cre-associated toxicity, with lower body weights and increased global fibrosis, in Cre-only control male mice compared with flox-only controls, making it challenging to infer which changes in <i>Myh6-cre;Gdf11-</i>floxed mice were the result of Cre toxicity versus deletion of <i>Gdf11</i>. Third, we observed differential expression of <i>cre</i> mRNA in Cre-only controls compared with the cardiomyocyte-specific knockout mice, also making comparison between these two groups difficult. Thus, targeted <i>Gdf11</i> deletion in cardiomyocytes may lead to left ventricular dilation without hypertrophy, but alternative animal models are necessary to understand the mechanism for these findings. <b>NEW & NOTEWORTHY</b> We observed that targeted deletion of growth differentiation factor 11 in cardiomyocytes does not cause cardiac hypertrophy but rather leads to left ventricular dilation compared with control mice carrying only the <i>Myh6-cre</i> or growth differentiation factor 11-floxed alleles. However, the mechanism underlying this finding remains unclear because of multiple confounding effects associated with the selected mouse model.