gebhart/patrepeval huggingface dataset:
Supplementary Materials and Methods from High Frequency of <i>PIK3R1</i> and <i>PIK3R2</i> Mutations in Endometrial Cancer Elucidates a Novel Mechanism for Regulation of PTEN Protein Stability (2023)

Supplementary Materials and Methods from High Frequency of &lt;i&gt;PIK3R1&lt;/i&gt; and &lt;i&gt;PIK3R2&lt;/i&gt; Mutations in Endometrial Cancer Elucidates a Novel Mechanism for Regulation of PTEN Protein Stability
Application of Long-distance PCR to Restriction Site Mapping of a Cloned DNA Fragment on theλEMBL3 Phage Vector (1996)

Long-distance PCR was applied to rapidly map the restriction sites of long inserts cloned on lambda EMBL3 phage vector. The restriction sites of 9 of 15 enzymes were completely assigned in a model experiment within 14 h, including 8h for the PCR amplification. This method was found particularly useful for genomic DNA cloning when the partial sequence of the corresponding cDNA is known.
Characterization of Electron Traps in Gate Oxide of m-plane SiC MOS Capacitors (2022)

The electron trapping in gate oxides of SiC-MOS capacitors were studied by electron injection from the substrate. The trapped electron densities calculated using the flat-band voltage shift were analyzed. There are possibly three types of electron traps. Their capture cross sections are >2x10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-13</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , ~3x10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-14</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and <3x10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-18</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . The oxide grown by LPCVD has slightly lower electron trap density than the oxides by thermal oxidation or by TEOS-PECVD with regard to the oxide trap with capture cross section of 3x10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-14</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . Yet the obtained electron trap densities were found to be one order of magnitude higher than that of Si-MOS [4] and there may be large room for improvement of the electron trap in the gate oxide of SiC-MOSFET for better VT reliability.
High-power packages for phosphor-based white-light-emitting diode lamps (2006)

With the rapid development of high-power white light-emitting diodes (LEDs), advances in packaging are required to further improve the device performance. In this work, an optimized packaging configuration for high power LED lamps with enhanced phosphorescence efficiency is presented based on ray-tracing simulations and experimental results
A Novel puf-A Gene Predicted from Evolutionary Analysis Is Involved in the Development of Eyes and Primordial Germ-Cells (2009)

Although the human genome project has been completed for some time, the issue of the number of transcribed genes with identifiable biological functions remains unresolved. We used zebrafish as a model organism to study the functions of Ka/Ks-predicted novel human exons, which were identified from a comparative evolutionary genomics analysis.In this study, a novel gene, designated as puf-A, was cloned and functionally characterized, and its homologs in zebrafish, mouse, and human were identified as one of the three homolog clusters which were consisted of 14 related proteins with Puf repeats. Computer modeling of human Puf-A structure and a pull-down assay for interactions with RNA targets predicted that it was a RNA-binding protein. Specifically, Puf-A contained a special six Puf-repeat domain, which constituted a unique superhelix half doughnut-shaped Puf domain with a topology similar to, but different from the conventional eight-repeat Pumilio domain. Puf-A transcripts were uniformly distributed in early embryos, but became restricted primarily to eyes and ovaries at a later stage of development. In mice, puf-A expression was detected primarily in retinal ganglion and pigmented cells. Knockdown of puf-A in zebrafish embryos resulted in microphthalmia, a small head, and abnormal primordial germ-cell (PGC) migration. The latter was confirmed by microinjecting into embryos puf-A siRNA containing nanos 3' UTR that expressed in PGC only. The importance of Puf-A in the maturation of germline stem cells was also implicated by its unique expression in the most primitive follicles (stage I) in adult ovaries, followed by a sharp decline of expression in later stages of folliculogenesis. Taken together, our study shows that puf-A plays an important role not only in eye development, but also in PGC migration and the specification of germ cell lineage. These studies represent an exemplary implementation of a unique platform to uncover unknown function(s) of human genes and their roles in development regulation.
Molecule deposition in mask-shielded regions revealed by selective Mg vapor deposition (2021)

Vacuum deposition with a shadow mask has been widely used for preparing patterned organic films. We found that, during vacuum deposition of organic molecules with a shadow mask, a small amount of organic molecule was also deposited on the mask-shielded surface. This phenomenon was revealed by selective Mg-vapor deposition using photochromic diarylethenes (DAEs). With this selective Mg deposition, no Mg is deposited on the DAE surface in a colorless state with a low Tg near room temperature, even if the DAE film thickness is at a several-nm level. On the other hand, since Mg is deposited on the colored surface obtained by UV irradiation, the presence or absence of low-Tg organic film with a thickness of several-nm level can be determined by the Mg-deposition property. The Mg nondeposition areas of a mask-shielded region depended on the vacuum level, the space between a substrate and a shadow mask, and the DAE deposition quantity; a lower vacuum level (higher pressures), a thicker space, and a larger deposition quantity resulted in a larger Mg nondeposition area. Vacuum deposition in the high vacuum level (10−4–10−3 Pa) with a substrate-shadow-mask space distance of 60 μm led to an Mg nondeposition width over 100 μm from the mask-shielded edge. These results indicate that the origin is in molecular scattering by a residual gas in a vacuum chamber. When minute organic patterns are prepared using shadow masks, which are effective for obtaining satisfactory performances of organic electronics devices, the influence of small amount of deposition under mask-shielded areas should be taken into account.
Structure and Assignment of the Luminescence of a New Mixed-Ligand Copper(I) Polymer (1997)

The synthesis and crystal structure of a new copper(I) polymer, [{(Ph3P)2Cu2(μ-Cl)2(μ-pyrazine)}∞], are reported. The polymer is photoluminescent with its emission maximum at 16 340 cm-1 at a temperature of 20 K. The emitting state is assigned with the assistance of excited state distortions determined by using resonance Raman intensities. The polymer consists of (PPh3)(pyz)Cu(μ-Cl2)Cu(pyz)(PPh3) units in which pyrazine ligands bridge copper pairs to form a chain of dimers. The packing arrangement contains two inversion centers. Each dimer has an inversion center between the two coppers and the bridging chlorine atoms. A second inversion center is located in the center of the pyrazine ligand, which links the dimers in an infinite linear chain. The nitrogen atom of the pyrazine, the phosphorus atom of one triphenylphosphine, and the two chlorine atoms form a slightly distorted tetrahedron about the copper. The largest distortions in the lowest excited electronic state, determined from the resonance Raman intensities, occur along totally symmetric modes of the pyrazine ligand. The emission is assigned to copper(I) to pyrazine charge transfer.
Synthesis and properties of metal-substituted myoglobins (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and properties of metal-substituted myoglobinsJ. A. Cowan and Harry B. GrayCite this: Inorg. Chem. 1989, 28, 11, 2074–2078Publication Date (Print):May 1, 1989Publication History Published online1 May 2002Published inissue 1 May 1989https://pubs.acs.org/doi/10.1021/ic00310a013https://doi.org/10.1021/ic00310a013research-articleACS PublicationsRequest reuse permissionsArticle Views327Altmetric-Citations34LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Processor in Non-Volatile Memory (PiNVSM): Towards to Data-centric Computing in Decentralized Environment (2019)

The AI problem has no solution in the environment of existing hardware stack and OS architecture. CPU-centric model of computation has a huge number of drawbacks that originate from memory hierarchy and obsolete architecture of the computing core. The concept of mixing memory and logic has been around since 1960s. However, the concept of Processor-In-Memory (PIM) is unable to resolve the critical issues of the CPU-centric computing model because of inevitable replication of von Neumann architecture's drawbacks. The next generation of NVM/SCM memory is able to give the second birth to the data-centric computing paradigm. This paper presents a concept of Processor in Non-Volatile Memory (PiNVSM) architecture. The basis of PiNVSM architecture is the concept of DPU that contains the NVM memory and dedicated PU. All necessary PU's registers can be implemented in the space of NVM memory. NVM memory of DPU is the single space for storing and transformation of data. In the basis of PiNVSM architecture lies the DPU array is able to overcome the limitations as Turing machine model as von Neumann architecture. The DPU array hasn't a centralized computing core. Every data portion has dedicated computing core that excludes the necessity to transfer data to the place of data processing. Every DPU contains data portion that is associated with the set of keywords. Any complex data structure can be split on elementary items that can be stored into independent DPU with dedicated computing core(s). One DPU is able to apply the elementary transformation on one item. But the DPU array is able to make the transformation of complex structure by means of concurrent execution of elementary transformations in different DPUs. The PiNVSM architecture suggests a principally new architecture of the computing core that creates a new opportunity for data self-organization, data and code synthesis.
Transfer Learning Capabilities of Untrained Neural Networks for MIMO CSI Recreation (2021)

Machine learning (ML) applications for wireless communications have gained momentum on the standardization discussions for 5G advanced and beyond. One of the biggest challenges for real world ML deployment is the need for labeled signals and big measurement campaigns. To overcome those problems, we propose the use of untrained neural networks (UNNs) for MIMO channel recreation/estimation and low overhead reporting. The UNNs learn the propagation environment by fitting a few channel measurements and we exploit their learned prior to provide higher channel estimation gains. Moreover, we present a UNN for simultaneous channel recreation for multiple users, or multiple user equipment (UE) positions, in which we have a trade-off between the estimated channel gain and the number of parameters. Our results show that transfer learning techniques are effective in accessing the learned prior on the environment structure as they provide higher channel gain for neighbouring users. Moreover, we indicate how the under-parameterization of UNNs can further enable low-overhead channel state information (CSI) reporting.
143 TRANSCRIPTIONAL PROFILING BY HIGH-THROUGHPUT SEQUENCING OF PORCINE PRE- AND PERI-IMPLANTATION EMBRYOS (2011)

Significant embryo mortality occurs at or around the time of implantation or attachment in virtually all mammalian species studied to date, even in naturally conceived embryos. Embryos resulting from assisted reproductive technologies (ART) are even more susceptible to peri-implantation failure. Herein we describe our effort to characterise the transcriptomes of embryonic disc (ED) and trophoblast (TE) cells from porcine embryos derived from AI, IVF, parthenogenetic oocyte activation (PA) and somatic cell nuclear transfer (NT) on Days 10, 12 and 14 of gestation. The IVF, PA and somatic cell NT embryos were generated using in vitro–matured oocytes, cultured overnight in vitro and then transferred at the 1- to 2-cell stage into appropriately synchronized recipient gilts. On the appropriate collection day, embryos were flushed from the uterus and ED was separated from TE by mechanical dissection. Double-stranded cDNA from the collected samples was sequenced using the GAII platform from Illumina (San Diego, CA, USA). The resulting sequencing reads were aligned to a custom swine transcriptome database (see Isom et al. 2010). A generalized linear model was fit for each of 41 693 genomic regions, for ED and TE samples separately, accounting for embryo type, gestation day and their interaction and using total lane read count as a normalizing offset. Genes with significant embryo type differences (controlling the false discovery rate at 0.10) were subsequently tested for differences between IVF and each of AI, PA and NT. Those genes with significant post hoc differences (either up- or down-regulated compared with IVF) were characterised in terms of gene ontologies and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways using a gene set enrichment test. Bone morphogenetic protein signalling was down-regulated (KEGG; P = 0.0099; adjusted to control for FDR at 0.05) in the ED of IVF embryos when compared with AI embryos. In TE cells from IVF embryos, ubiquitin-mediated proteolysis and ErbB signalling (adj P = 0.031 for both pathways) were aberrantly regulated when compared with AI embryos. Of particular interest is the observation that expression of genes involved in chromatin modification (GO:BiologicalProcess; q-value = 0.00005) and epigenetic regulation of transcription (q = 0.00007) was very significantly disrupted in inner cell mass cells from NT embryos compared with IVF embryos. Surprisingly, no such disruption of the epigenetic machinery was observed in the TE cells from NT embryos. In summary, we have used high-throughput sequencing technologies to compare gene expression profiles of various ART embryo types during peri-implantation development. We expect that these data will provide important insight into the root causes of (and possible opportunities for mitigation of) suboptimal development of embryos derived from ART. Funding was received from NIH R01 RR013438 and Food for the 21st Century (RSP) and the Utah Agricultural Experiment Station (UTA00151 and UTA00560 for S. C. Isom and J. R. Stevens, respectively).
PET imaging of microglia by targeting macrophage colony-stimulating factor 1 receptor (CSF1R) (2019)

While neuroinflammation is an evolving concept and the cells involved and their functions are being defined, microglia are understood to be a key cellular mediator of brain injury and repair. The ability to measure microglial activity specifically and noninvasively would be a boon to the study of neuroinflammation, which is involved in a wide variety of neuropsychiatric disorders including traumatic brain injury, demyelinating disease, Alzheimer's disease (AD), and Parkinson's disease, among others. We have developed [<sup>11</sup>C]CPPC [5-cyano-<i>N</i>-(4-(4-[<sup>11</sup>C]methylpiperazin-1-yl)-2-(piperidin-1-yl)phenyl)furan-2-carboxamide], a positron-emitting, high-affinity ligand that is specific for the macrophage colony-stimulating factor 1 receptor (CSF1R), the expression of which is essentially restricted to microglia within brain. [<sup>11</sup>C]CPPC demonstrates high and specific brain uptake in a murine and nonhuman primate lipopolysaccharide model of neuroinflammation. It also shows specific and elevated uptake in a murine model of AD, experimental allergic encephalomyelitis murine model of demyelination and in postmortem brain tissue of patients with AD. Radiation dosimetry in mice indicated [<sup>11</sup>C]CPPC to be safe for future human studies. [<sup>11</sup>C]CPPC can be synthesized in sufficient radiochemical yield, purity, and specific radioactivity and possesses binding specificity in relevant models that indicate potential for human PET imaging of CSF1R and the microglial component of neuroinflammation.
Increasing the field of view in grating based X-ray phase contrast imaging using stitched gratings (2016)

Grating based X-ray differential phase contrast imaging (DPCI) allows for high contrast imaging of materials with similar absorption characteristics. In the last years' publications, small animals or parts of the human body like breast, hand, joints or blood vessels have been studied. Larger objects could not be investigated due to the restricted field of view limited by the available grating area. In this paper, we report on a new stitching method to increase the grating area significantly: individual gratings are merged on a carrier substrate. Whereas the grating fabrication process is based on the LIGA technology (X-ray lithography and electroplating) different cutting and joining methods have been evaluated. First imaging results using a 2×2 stitched analyzer grating in a Talbot-Lau interferometer have been generated using a conventional polychromatic X-ray source. The image quality and analysis confirm the high potential of the stitching method to increase the field of view considerably.
Investigating Multimodal Diagnostic Eye Biomarkers of Cognitive Impairment by Measuring Vascular and Neurogenic Changes in the Retina (2018)

Previous studies have demonstrated that cognitive impairment (CI) is not limited to the brain but also affects the retina. In this pilot study, we investigated the correlation between the retinal vascular complexity and neurodegenerative changes in patients with CI using a low-cost multimodal approach. Quantification of the retinal structure and function were conducted for every subject (<i>n</i> = 69) using advanced retinal imaging, full-field electroretinogram (ERG) and visual performance exams. The retinal vascular parameters were calculated using the Singapore Institute Vessel Assessment software. The Montreal Cognitive Assessment was used to measure CI. Pearson product moment correlation was performed between variables. Of the 69 participants, 32 had CI (46%). We found significantly altered microvascular network in individuals with CI (larger venular-asymmetry factor: 0.7 ± 0.2) compared with controls (0.6 ± 0.2). The vascular fractal dimension was lower in individuals with CI (capacity, information and correlation dimensions: D<sub>0</sub>, D<sub>1,</sub> and D<sub>2</sub> (mean ± SD): 1.57 ± 0.06; 1.56 ± 0.06; 1.55 ± 0.06; age 81 ± 6years) vs. controls (1.61 ± 0.03; 1.59 ± 0.03; 1.58 ± 0.03; age: 80 ± 7 years). Also, drusen-like regions in the peripheral retina along with pigment dispersion were noted in subjects with mild CI. Functional loss in color vision as well as smaller ERG amplitudes and larger peak times were observed in the subjects with CI. Pearson product moment correlation showed significant associations between the vascular parameters (artery-vein ratio, total length-diameter ratio, D<sub>0</sub>, D<sub>1</sub>, D<sub>2</sub> and the implicit time (IT) of the flicker response but these associations were not significant in the partial correlations. This study illustrates that there are multimodal retinal markers that may be sensitive to CI decline, and adds to the evidence that there is a statistical trend pointing to the correlation between retinal neuronal dysfunction and microvasculature changes suggesting that retinal geometric vascular and functional parameters might be associated with physiological changes in the retina due to CI. We suspect our analysis of combined structural-functional parameters, instead of individual biomarkers, may provide a useful clinical marker of CI that could also provide increased sensitivity and specificity for the differential diagnosis of CI. However, because of our study sample was small, the full extent of clinical applicability of our approach is provocative and still to be determined.
The expression of chemokine receptor CXCR3: relevance to disease activity of rheumatoid arthritis (2003)

Abstract CXC chemokine receptor 3 (CXCR3) is selectively expressed on T helper 1 (Th1) type T cells and has been shown to be responsible for Th1-dominant immune responses. In this study, we analyzed the expression of CXCR3 on peripheral blood T lymphocytes of patients with rheumatoid arthritis (RA) by FACS analysis using antihuman CXCR3 monoclonal antibody and determined the clinical relevance in this disease. Significantly higher expression of CXCR3 was found on peripheral blood CD4+ T lymphocytes of RA patients than healthy controls. The CXCR3 expression in RA patients with a high erythrocyte sedimentation rate was significantly higher than in those with a low erythrocyte sedimentation rate. Moreover, we found that the CXCR3 expression in RA patients with long-term disease duration was significantly higher than in those with short-term disease. On the other hand, CC chemokine receptor 4 (CCR4), which was shown to be selectively expressed on Th2-type T cells, was expressed at low levels in RA patients as well as in healthy controls. The serum level of interleukin (IL)-18 in RA patients was higher than that in healthy controls, although there was no statistically significant difference. This study suggests that the Th1 immune response is predominant in RA and that CXCR3 may have relevance in regard to the disease course in RA patients.