gebhart/patrepeval huggingface dataset:
Layer Specification of Transplanted Interneurons in Developing Mouse Neocortex (2003)

The six-layered neocortex is composed of excitatory projection neurons and inhibitory interneurons. Recent studies have established separate embryological origins for these two cellular populations. However, it remains uncertain how interneurons arising from the subcortical ganglionic eminences are able to participate in the orderly stratification of the cortical layers. A related question concerns whether or not early and late interneuron progenitors have equivalent developmental potentials. To address these issues, we performed transplantation experiments to test the fates of early-versus late-born interneuron populations using cells labeled with a genetic marker. Our results indicate that transplanted interneurons from the medial ganglionic eminence give rise to specific layers of the neocortex in an inside-out order. To test the potency of interneurons born at different ages, heterochronic transplantations were also performed. Both early- and late-born progenitors were able to switch their fates in the new environment, and, similar to projection neurons, fate-switching was dependent on progenitor receptivity to environmental cues during their last round of cell division. Our data also demonstrate, for the first time, that interneuron-layering cues are present within the medial ganglionic eminence, suggesting that, before the commencement of long-distance tangential migration, interneurons are already specified with respect to their future layer addresses. So, although the generation of diverse neuronal phenotypes in separate locations is an effective strategy to pursue separate developmental programs, our results indicate that excitatory and inhibitory neurons share similar mechanisms for integrating sequentially born neurons from two places into a single layered structure.
Self‐Wrinkling of UV‐Cured Polymer Films (2011)

One-step, highly controlled self-wrinkling of UV-cured polymer films is reported. During UV-curing a top layer of non-polymerized monomers, present due to oxygen inhibition, self-swells and wrinkles the bottom crosslinked film. Wrinkle wavelength and amplitude are controlled by controlling resin film thickness, oxygen partial pressure, and photoinitiator concentration. Patterned wrinkles are fabricated by spatial patterning of oxygen surrounding the curing film. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Semantic remote attestation: a virtual machine directed approach to trusted computing (2004)

Over 170 RNA modifications have been identified after transcriptions, involving in regulation of RNA splicing, processing, translation and decay. Growing evidence has unmasked the crucial role of N<sup>6</sup>-methyladenosine (m6A) in cancer development and progression, while, as a relative newly found RNA modification, N<sup>7</sup>-methylguanosine (m7G) is also certified to participate in tumorigenesis <i>via</i> different catalytic machinery from that of m6A. However, system analysis on m7G RNA modification-related regulator genes is lack. In this study, we first investigated the genetic alteration of m7G related regulator genes in 33 cancers, and found mRNA expression levels of most regulator genes were positively correlated with copy number variation (CNV) and negatively correlated with methylation in most cancers. We built a m7G RNA modification model based on the enrichment of the regulator gene scores to evaluate the m7G modification levels in 33 cancers, and investigated the connections of m7G scores to clinical outcomes. Furthermore, we paid close attention to the role of m7G in immunology due to the widely used immune checkpoint blockade therapy. Our results showed the higher m7G scores related to immunosuppression of tumor cells. Further confirmation with phase 3 clinical data with application of anti-PDL1/PDL indicated the impact of m7G modification level on immunotherapy effect. Relevance of m7G regulator genes and drug sensitivity was also evaluated to provide a better treatment choice when treating cancers. In summary, our study uncovered the profile of m7G RNA modification through various cancers, and figured out the connection of m7G modification levels with therapeutical outcomes, providing potential better options of cancer treatment.
Thermal Properties for Bulk Silicon Based on the Determination of Relaxation Times Using Molecular Dynamics (2009)

Molecular dynamics simulations are performed to estimate acoustical and optical phonon relaxation times, dispersion relations, group velocities, and specific heat of silicon needed to solve the Boltzmann transport equation (BTE) at 300 K and 1000 K. The relaxation times are calculated from the temporal decay of the autocorrelation function of the fluctuation of total energy of each normal mode in the ⟨100⟩ family of directions, where the total energy of each mode is obtained from the normal mode decomposition of the motion of the silicon atoms over a period of time. Additionally, silicon dispersion relations are directly determined from the equipartition theorem obtained from the normal mode decomposition. The impact of the anharmonic nature of the potential energy function on the thermal expansion of the crystal is determined by computing the lattice parameter at the cited temperatures using a NPT (i.e., constant number of atoms, pressure, and temperature) ensemble, and are compared with experimental values reported in the literature and with those computed analytically using the quasiharmonic approximation. The dependence of the relaxation times with respect to the frequency is identified with two functions that follow the functional form of the relaxation time expressions reported in the literature. From these functions a simplified version of relaxation times for each normal mode is extracted. Properties, such as group and phase velocities, thermal conductivity, and mean free path, needed to further develop a methodology for the thermal analysis of electronic devices (i.e., from nano- to macroscales) are determined once the relaxation times and dispersion relations are obtained. The thermal properties are validated by comparing the BTE-based thermal conductivity against the predictions obtained from the Green–Kubo method. It is found that the relaxation times closely resemble the ones obtained from perturbation theory at high temperatures; the contribution to the thermal conductivity of the transverse acoustic, longitudinal acoustic, and longitudinal optical modes being approximately 30%, 60%, and 10%, respectively, and the contribution of the transverse optical mode negligible.
Heralded Quantum Gate between Remote Quantum Memories (2009)

We demonstrate a probabilistic entangling quantum gate between two distant trapped ytterbium ions. The gate is implemented between the hyperfine "clock" state atomic qubits and mediated by the interference of two emitted photons carrying frequency encoded qubits. Heralded by the coincidence detection of these two photons, the gate has an average output state fidelity of 89+/-2%. This entangling gate together with single qubit operations is sufficient to generate large entangled cluster states for scalable quantum computing.
Electroporation as an effective means of introducing DNA into abalone (Haliotis rufescens) embryos. (1995)

Recombinant plasmid containing the Drosophila beta-actin promoter coupled to a beta-galactosidase cassette was linearized and introduced in fertilized eggs of the red abalone (Haliotis rufescens) by electroporation. Fertilized abalone eggs tolerated electroporation well with larval survival rates between 70% and 84% of that for non-electroporated siblings. Dot blot and Southern blot analysis were used to detect if abalone retained the foreign gene at various developmental stages. The inserted construct was retained in 70% to 100% of all abalone sampled with an average of 72% retention in the three- to seven-month-old juveniles. Maximal DNA uptake and retention was observed in abalone electroporated at 30-40 min after fertilization. Southern hybridization analysis suggested that the inserted vector was in head-to-tail concantermers integrated in the abalone genome. This preliminary study demonstrates that electroporation is an efficient means of transferring foreign DNA into abalone embryos.
Synthesis and study of silylene-diacetylene polymers (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and study of silylene-diacetylene polymersSina Ijadi-Maghsoodi and Thomas J. BartonCite this: Macromolecules 1990, 23, 20, 4485–4486Publication Date (Print):October 1, 1990Publication History Published online1 May 2002Published inissue 1 October 1990https://pubs.acs.org/doi/10.1021/ma00222a027https://doi.org/10.1021/ma00222a027research-articleACS PublicationsRequest reuse permissionsArticle Views427Altmetric-Citations109LEARN 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
Dominant-Negative Fas Mutation Is Reversed by Down-expression of c-FLIP (2007)

Fas triggering by agonistic antibodies or by its cognate ligand, FasL, induces apoptotic cell death, whereas mutation in the Fas death domain is associated with lymphoma progression. On prolonged culture in the presence of an agonistic anti-Fas antibody, we raised a Jurkat cell line resistant to agonistic antibodies but still sensitive to soluble FasL, which carried at the heterozygous state, a point mutation into the Fas death domain. Down-modulation of c-FLIP expression reversed the blockade of the Fas pathway. We show that the activation threshold for the Fas receptor is more easily overcome by multimeric FasL than by agonistic antibodies and that the increase of this threshold due to mutation in the Fas death domain can be overcome by acting on a downstream effector of the Fas signal, c-FLIP. These findings put forward a new approach to eradicate Fas-resistant tumor cells.
[MicroRNAs in neurobiology]. (2008)

MicroRNAs have emerged as a new regulatory factor of gene expression. They mediate translational repression or degradation of their target mRNAs by RNA interference (RNAi). The expression of each microRNA is tightly regulated in a development- and cell-specific manner by various mechanisms such as blockade of let-7 family expression by Lin-28 or RNA editing. They also act as regulatory switches for development, organogenesis, and cellular differentiation or for controlling distinct functions that are required for the maintenance of each tissue and cell subtypes. The abundant expression of microRNAs as well as the exclusive expression of certain microRNAs in the central nervous system highlights their biological importance at all stages of neural development and in postmitotic and differentiated neurons. Further, some microRNAs, such as miRNA-134, and miRNA-132 are localized and are synthesized in part at synaptic sites in dendrites to regulate synaptic formation and plasticity. In addition to the imparting of basic knowledge about the biogenesis and mechanism of action of microRNAs, this review focuses on the recent advances in microRNA studies in neurobiology, including the expression pattern of microRNAs in the mammalian brain, the role of microRNAs in neural differentiation and maturation, formation and plasticity of synaptic connections, and maintenance of neural function such as the synthesis of the neurotransmitters in selected neurons. Finally, the possible connection between microRNA dysfunction and neurological diseases, and future implications for diagnosis, and treatment of defects in human brain development and neurodegenerative diseases are discussed.
Autoimmune liver serology: Current diagnostic and clinical challenges (2008)

Liver-related autoantibodies are crucial for the correct diagnosis and classification of autoimmune liver diseases (AiLD), namely autoimmune hepatitis types 1 and 2 (AIH-1 and 2), primary biliary cirrhosis (PBC), and the sclerosing cholangitis variants in adults and children. AIH-1 is specified by anti-nuclear antibody (ANA) and smooth muscle antibody (SMA). AIH-2 is specified by antibody to liver kidney microsomal antigen type-1 (anti-LKM1) and anti-liver cytosol type 1 (anti-LC1). SMA, ANA and anti-LKM antibodies can be present in de-novo AIH following liver transplantation. PBC is specified by antimitochondrial antibodies (AMA) reacting with enzymes of the 2-oxo-acid dehydrogenase complexes (chiefly pyruvate dehydrogenase complex E2 subunit) and disease-specific ANA mainly reacting with nuclear pore gp210 and nuclear body sp100. Sclerosing cholangitis presents as at least two variants, first the classical primary sclerosing cholangitis (PSC) mostly affecting adult men wherein the only (and non-specific) reactivity is an atypical perinuclear antineutrophil cytoplasmic antibody (p-ANCA), also termed perinuclear anti-neutrophil nuclear antibodies (p-ANNA) and second the childhood disease called autoimmune sclerosing cholangitis (ASC) with serological features resembling those of type 1 AIH. Liver diagnostic serology is a fast-expanding area of investigation as new purified and recombinant autoantigens, and automated technologies such as ELISAs and bead assays, become available to complement (or even compete with) traditional immunofluorescence procedures. We survey for the first time global trends in quality assurance impacting as it does on (1) manufacturers/purveyors of kits and reagents, (2) diagnostic service laboratories that fulfill clinicians' requirements, and (3) the end-user, the physician providing patient care, who must properly interpret test results in the overall clinical context.
Connexin expression in homotypic and heterotypic cell coupling in the developing cerebral cortex (2002)

Intercellular communication through gap junction channels is a prominent feature of the developing cerebral cortex. In the first 2 weeks after birth, a time critical in the development of the rat neocortex, extensive cell coupling has been documented that diminishes as the cortex matures. Among the family of gap junction proteins, connexins 26, 36, and 43 are differentially expressed during cortical development. We used intracellular dye injections and connexin immunohistochemistry to investigate the coupling patterns and connexin expression between the different neuronal and glial cell types of the developing cortex of the rat. We found that neurons and glia couple homotypically and heterotypically at postnatal days 7 and 14. Although the prevalence of coupling was homotypic, there was considerable heterotypic coupling that involved pyramidal and nonpyramidal neurons, the principal neuronal cell types of the cortex, or neurons and astrocytes. Coupling between different cell types appeared to be mediated by differential expression of connexins 26, 36, and 43. It may be that coupling between cells in the developing neocortex is a function of the spatial and temporal expression of these and other connexin proteins.
Gene ompR and regulation of microcin 17 and colicin e2 syntheses (1982)

The production of microcin 17 is controlled by plasmid pRYC17. Chromosomal mutants unable to produce a normal amount of microcin were isolated in Escherichia coli. One of the mutations maps in the ompR locus, indicating that an active OmpR product is required for the synthesis of microcin 17. The same conclusion was obtained for the synthesis of colicin E2. Therefore, two new functions of the regulatory gene ompR have been revealed.
Improved instrumentation and techniques for non-invasive detection, characterization and quantification of atherosclerosis for research and diagnostic purposes. Annual report, 2 September 78-1 September 1979 (1979)

This annual report for the year 2 September 1978 through 1 September 1979 presents the work done in the second year of a three-year program to develop and assess new and improved video instrumentation and new techniques for noninvasive detection, characterization and quantification of atherosclerosis for research and diagnostic applications. The results of the first 18 months of activity are on schedule except for delays imposed by late delivery of two important pieces of equipment. However, as there is flexibility built into the schedule, the authors anticipate that the three-year program will be completed as planned.
Tactile Displays: Guidance for Their Design and Application (2008)

Tactile interfaces can support numerous functions, including spatial orientation and guidance, attention management, and sensory substitution, in a wide range of domains.
Alkylation of polyguanylic acid at the 2-amino group and phosphate by the potent mutagen (.+-.)-7.beta.,8.alpha.-dihydroxy-9.beta.,10.beta.-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAlkylation of polyguanylic acid at the 2-amino group and phosphate by the potent mutagen (.+-.)-7.beta.,8.alpha.-dihydroxy-9.beta.,10.beta.-epoxy-7,8,9,10-tetrahydrobenzo[a]pyreneMasato Koreeda, Patrick D. Moore, Haruhiko Yagi, Herman J. C. Yeh, and Donald M. JerinaCite this: J. Am. Chem. Soc. 1976, 98, 21, 6720–6722Publication Date (Print):October 1, 1976Publication History Published online1 May 2002Published inissue 1 October 1976https://pubs.acs.org/doi/10.1021/ja00437a061https://doi.org/10.1021/ja00437a061research-articleACS PublicationsRequest reuse permissionsArticle Views120Altmetric-Citations123LEARN 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
Inactivation of Wnt inhibitory factor-1 (WIF1) expression by epigenetic silencing is a common event in breast cancer (2006)

The Wnt signaling pathway is a powerful and prominent oncogenic mechanism dysregulated in numerous cancer types. While evidence from transgenic mouse models and studies of human tumors clearly indicate that this pathway is of likely importance in human breast cancer, few clues as to the exact molecular nature of Wnt dysregulation have been uncovered in this tumor type. Here, we show that the Wnt inhibitory factor-1 (WIF1) gene, which encodes a secreted protein antagonistic to Wnt-dependent signaling, is targeted for epigenetic silencing in human breast cancer. We show that cultured human breast tumor cell lines display absent or low levels of WIF1 expression that are increased when cells are cultured with the DNA demethylating agent 5-aza-2'-deoxycytidine. Furthermore, the WIF1 promoter is aberrantly hypermethylated in these cells as judged by both methylation-specific PCR and bisulfite genomic sequencing. Using a panel of patient-matched breast tumors and normal breast tissue, we show that WIF1 expression is commonly diminished in breast tumors when compared with normal tissue and that this correlates with WIF1 promoter hypermethylation. Analysis of a panel of 24 primary breast tumors determined that the WIF1 promoter is aberrantly methylated in 67% of these tumors, indicating that epigenetic silencing of this gene is a frequent event in human breast cancer. Using an isogenic panel of cell lines proficient or deficient in the DNA methyltransferases (DNMTs) DNMT1 and/or DNMT3B, we show that hypermethylation of the WIF1 promoter is attributable to the cooperative activity of both DNMT1 and DNMT3B. Our findings establish the WIF1 gene as a target for epigenetic silencing in breast cancer and provide a mechanistic link between the dysregulation of Wnt signaling and breast tumorigenesis.
Development and biological analysis of peritoneal metastasis mouse models for human scirrhous stomach cancer (2005)

The number of published studies on peritoneal dissemination of scirrhous gastric carcinoma is very small as a result of the unavailability of highly reproducible animal models. Orthotopic implantation of HSC-44PE and HSC-58 (scirrhous gastric carcinoma-derived cell lines) cells into nude mice led to dissemination of the tumor cells to the greater omentum, mesenterium, peritoneum and so on, and caused ascites in a small number of animals. Cycles of isolation of the ascitic tumor cells and orthotopic inoculation of these cells were repeated in turn to animals. This was to isolate highly metastatic cell lines with a strong capability of inducing the formation of ascites (44As3 from HSC-44PE; 58As1 and 58As9 from HSC-58). All three cell lines induced tumor formation at the site of orthotopic injection, and caused fatal cancerous peritonitis and bloody ascites in 90-100% of the animals approximately 3-5 weeks after the inoculation. When the parent cells were implanted, the animals became moribund in approximately 12-18 weeks, however, none of the animals developed ascites. Complementary DNA microarray and immunohistochemical analyses revealed differences in the expression levels of genes coding for the matrix proteinase, cell adhesion, motility, angiogenesis and proliferation between the highly metastatic- and parent-cell lines. The usefulness of this model for the evaluation of drugs was assessed by analyzing the stability of the metastatic potential of the cells and the reproducibility. Animals intravenously treated with CPT-11 and GEM showed suppressed tumor growth and significantly prolonged survival. The metastatic cell lines and the in vivo model established in the present study are expected to serve as a model of cancerous peritonitis developing from primary lesions, and as a useful means of clarifying the pathophysiology of peritoneal dissemination of scirrhous gastric carcinoma and the development of drugs for its treatment.