gebhart/patrepeval huggingface dataset:
Figure 4 from A Comparative Study of Neuroendocrine Heterogeneity in Small Cell Lung Cancer and Neuroblastoma (2023)

&lt;p&gt;NE score association with members of the Myc oncogene family in SCLC and neuroblastoma. Copy number (&lt;b&gt;A&lt;/b&gt;) and RNA expression (&lt;b&gt;B&lt;/b&gt;) of Myc family genes in SCLC and neuroblastoma cell lines. Note that although MYC amplification was higher in the high-NE-score SCLC cell lines, its gene expression was higher in the low-NE-score cell lines for both SCLC and neuroblastoma lines. Frequent &lt;i&gt;MYCL&lt;/i&gt; loss was found in neuroblastoma because &lt;i&gt;MYCL&lt;/i&gt; is located in a frequently deleted region (chromosome 1p) in neuroblastoma. &lt;b&gt;C,&lt;/b&gt; NE score versus Myc gene member expression in SCLC studies. “UTSW cell line” is a cell line dataset; “Drapkin_2018” is a PDX dataset; “Rudin_2012,” “George_2015,” “Jiang_2016,” and “Cai_2021” are all patient tumor datasets. NE score versus Myc gene member expression in neuroblastoma cell line datasets (&lt;b&gt;D&lt;/b&gt;) and tumor datasets (&lt;b&gt;E&lt;/b&gt;). Note that some of the same cell lines were profiled in multiple studies. &lt;b&gt;F,&lt;/b&gt; Forest plots visualizing meta-analysis of NE score association with Myc family genes. &lt;i&gt;MYC&lt;/i&gt; expression is consistently associated with lower NE scores in SCLC and neuroblastoma samples (left). &lt;i&gt;MYCL&lt;/i&gt; expression positively correlates with NE scores in SCLC but not neuroblastoma samples (middle). &lt;i&gt;MYCN&lt;/i&gt; expression positively correlates with NE scores in neuroblastoma but not SCLC samples. &lt;b&gt;G,&lt;/b&gt; Relationship between &lt;i&gt;MYC&lt;/i&gt; copy number and gene expression in neuroblastoma and SCLC cell lines. Note that &lt;i&gt;MYC&lt;/i&gt; amplification is only observed in SCLC cell lines. &lt;b&gt;H,&lt;/b&gt;&lt;i&gt;MYCN&lt;/i&gt; gene expression positively correlate with NE scores while controlling for &lt;i&gt;MYCN&lt;/i&gt; amplification status in neuroblastoma patient tumors.&lt;/p&gt;
The residue Lysine 231 of the capside protein VP1 is important for Encephalomyocarditis virus infection of human primary cells (2008)

National audience
478 Injuries in children with autism spectrum disorder: study to explore early development (SEED) (2016)

<h3>Background</h3> Studies of injury risk in children with autism spectrum disorder (ASD) have shown conflicting results. We examined medically-treated injuries in children with ASD vs. population (POP) controls. <h3>Methods</h3> The Study to Explore Early Development (SEED) is a multi-site ASD case-control study of children aged 30–68 months. ASD cases (n = 693) were determined using established ASD-specific diagnostic instruments. POP controls (n = 882) were ascertained from birth certificates. Each child’s primary caregiver reported if the child ever had a medically-treated injury and described each such injury. Injuries resulting in emergency department visit or hospitalisation were defined as “serious.” We describe the nature and cause of each child’s first reported injury. Associations between ASD and having at least one medically-treated injury and serious injury were examined using logistic regression, adjusted for child sex, age, and IQ; maternal race/ethnicity and education; and family income. <h3>Results</h3> Among children with ASD, 33% ever had a medically-treated injury and 25% ever had a serious injury; the most commonly specified injuries were laceration (41%), fracture (22%) and abrasion/contusion (12%). Among POP children, 30% had a medically-treated injury and 22% a serious injury; the most commonly specified injuries were laceration (46%), fracture (23%) and dislocation/sprain (12%). In both groups, the cause most often specified was a fall (56%). ASD cases and POP controls had similar odds of injury (crude odds ratio [cOR] = 1.1 [95% CI: 0.9, 1.4]; adjusted OR [aOR] = 1.2 [0.9, 1.7]) and serious injury (cOR = 1.1 [0.9, 1.4]; aOR = 1.2 [0.9, 1.6]). <h3>Conclusions</h3> Children with ASD and population control children had similar odds of any medically-treated injury and serious injury. Sociodemographic and IQ differences did not influence these results. We plan to further explore and compare specific injury types and causes, and additional injury outcomes, between the two groups.
Caged and uncaged ruthenium(II)-polypyridine complexes. Comparative study of the photochemical, photophysical, and electrochemical properties (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCaged and uncaged ruthenium(II)-polypyridine complexes. Comparative study of the photochemical, photophysical, and electrochemical propertiesFrancesco Barigelletti, Luisa De Cola, Vincenzo Balzani, Peter Belser, Alex Von Zelewsky, Fritz Voegtle, Frank Ebmeyer, and Smaragda GrammenudiCite this: J. Am. Chem. Soc. 1989, 111, 13, 4662–4668Publication Date (Print):June 1, 1989Publication History Published online1 May 2002Published inissue 1 June 1989https://pubs.acs.org/doi/10.1021/ja00195a021https://doi.org/10.1021/ja00195a021research-articleACS PublicationsRequest reuse permissionsArticle Views459Altmetric-Citations80LEARN 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
Structure of Dicer and Mechanistic Implications for RNAi (2006)

Dicer is a specialized ribonuclease that processes double-stranded RNA (dsRNA) into small RNA fragments about 25 nucleotides in length during the initiation phase of RNA interference (RNAi). We previously determined the crystal structure of a Dicer enzyme from the diplomonad Giardia intestinalis and proposed a structural model for dsRNA processing. Here, we provide evidence that Dicer is composed of three structurally rigid regions connected by flexible hinges and propose that conformational flexibility facilitates dsRNA binding and processing. We also examine the role of the accessory domains found in Dicers of higher eukaryotes but absent in Giardia Dicer. Finally, we combine the structure of Dicer with published biochemical data to propose a model for the architecture of the RNA-induced silencing complex (RISC)-loading complex.
Abstract 2062: Selective gene dependencies in MYCN-amplified neuroblastoma include the core transcriptional regulatory circuitry (2018)

Abstract Childhood neuroblastomas with MYCN gene amplification form a particularly high-risk subset of this disease and are difficult to treat effectively. This has focused attention on tumor-specific gene dependencies that reflect important pathways in tumorigenesis, and thus could provide valuable targets for the development of novel therapeutics. Using genome-scale CRISPR-Cas9 approaches that allow unbiased detection of genes critically involved in tumor cell growth and survival, we identified 147 candidate genes associated with selective vulnerabilities in nine MYCN-amplified neuroblastoma cell lines, compared to findings in over 300 other human cancer cell lines representing multiple tumor cell types. We then used genome-wide ChIP-seq analysis to test the hypothesis that a small number of transcription factors - MYCN, HAND2, ISL1, PHOX2B, GATA3, and TBX2, all represented in the selective dependency group - are members of the transcriptional core regulatory circuitry (CRC) that underlies cell state in MYCN-amplified neuroblastoma. We show that these transcription factors bind as dense clusters at defined epicentres within the enhancers of their own genes, as well as those of the other CRC transcription factor genes, creating a positive feed-forward autoregulatory loop that establishes and maintains high levels of gene expression. To disable the CRC, we tested a combination of BRD4 and CDK7 inhibitors, which we postulated would act synergistically by targeting both transcriptional initiation and elongation required to synthesize regulatory transcription factors. MYCN-amplified neuroblastoma cells treated with both drugs were killed synergistically, in vitro and in vivo, and accompanied by rapid downregulation of CRC transcription factor gene expression. This study defines a set of critical dependency genes in MYCN-amplified neuroblastoma, a subset of which comprises the oncogenic transcriptional regulatory circuitry that underlies cell state and survival in this tumor. Citation Format: Adam D. Durbin, Mark W. Zimmerman, Neekesh V. Dharia, Brian J. Abraham, Brian J. Abraham, Amanda Balboni-Iniguez, Nina Weichert-Leahey, Shuning He, John M. Krill-Burger, David E. Root, Francisca Vazquez, Aviad Tsherniak, William C. Hahn, Todd R. Golub, Richard A. Young, A. Thomas Look, Kimberly Stegmaier. Selective gene dependencies in MYCN-amplified neuroblastoma include the core transcriptional regulatory circuitry [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2062.
Frequency and spatial response of basilar membrane vibration in a three-dimensional gerbil cochlear model (2007)

The cochlea of the inner ear presents severe difficulties for measurement and computation, and controversy exists on virtually every issue.However, the first in vivo measurement of the spatial distribution of elastic response for a fixed frequency is now available.This work compares experimental results and those from calculations with a three-dimensional model.This is a standard model that consists of a long, fluid-filled box with a partition, a portion of which is the elastic BM (basilar membrane).The BM velocity at a fixed point as a function of frequency and the spatial response for a fixed frequency are calculated.The model includes the three-dimensional viscous fluid and the pectinate zone of the elastic orthotropic BM with the gerbil dimensional and material property variation along its length.The radial BM thickness variation is, however, replaced by an equivalent constant thickness.The active process is represented by adding the motility of the OHCs (outer hair cells) to the passive model with a feed-forward approximation of the organ of Corti (OC).Asymptotic and numerical methods combined with Fourier series expansions are used to provide a fast and efficient iterative procedure that requires about one second on a desktop computer for obtaining the BM response for a given frequency.Our threedimensional model results show the following agreement with the experimental measurements in various situations: (i) for map of place of maximum response to frequency -excellent; (ii) for the response at a fixed point as a function of frequency -excellent for amplitude, poor for phase; (iii) for the spatial distribution for fixed frequency -fair for amplitude and excellent for phase.The discrepancies in (ii) and (iii) remain to be clarified.
Longitudinal control of automated CHVs with significant actuator delays (2002)

One of the most critical obstacles in the automated operation of commercial heavy vehicles (CHVs) is the presence of significant delays in the fuel and brake actuators. These delays are especially important in longitudinal control of vehicle platoons which do not employ intervehicle communication, because their effect becomes cumulative as it propagates upstream, resulting in considerably degraded performance. Our objective in this paper is to design autonomous controllers which, in the presence of large delays, recover the good performance achieved when the delays are negligible. We propose two different approaches which are tailored to different performance requirements and computational resources. A backstepping-based nonlinear scheme with prediction almost recovers the original "delay-free" performance at the cost of additional controller complexity, while a simpler PID-based nonlinear scheme yields nearly as good performance.
DVB-IPTV Content Download Services - IPTV services anytime and anywhere (2009)

IPTV services have been widely deployed by network operators around the world over the last years. Real-time streaming of Linear TV and Video-on-Demand (VoD) offerings, especially in the now more and more popular High Definition quality, however puts a high burden on the network and content servers concerning bandwidth, Quality-of-Service, processing performance and scalability if 100.000s of user have to be supported simultaneously. While multicast delivery can cope with some of these problems for Linear TV services, the unicast VoD services cannot take advantage of that and especially the request for on-demand content is expected to substantially grow in the future. With the introduction of Content Download Services (CDSs), operators now have the option to provide IPTV services in innovative ways: They can provide high-quality video services to users with limited access bandwidth, offload the streaming request for blockbuster movies at peak times from the VoD servers or provided personalized advertisements for insertion into a live program event in advance to the users set-top box. The Digital Video Broadcast (DVB) Project has recently finalized its CDS specification. DVB CDS supports push and pull delivery models with unicast, multicast and peer-to-peer distribution to enable various business models and use cases. In this work we introduce the standardized technology, its architecture and map it to the use cases and business models.
All-organic non-PFOS nonionic photoacid generating compounds with functionalized fluoroorganic sulfonate motif for chemically amplified resists (2006)

Nonionic photoacid generators (PAGs) based on photosensitive fluoroorganic sulfonate esters of imide and nitrobenzyl have been prepared and characterized. These new compounds produce fluoroorganic sulfonic acids that contain very few fluorine atoms (non-PFOS), which make them attractive PAGs for all advanced and emerging lithography. The structural influence of these new PAGs on sensitivity, resolution and line edge roughness (LER) was investigated by using DUV (254 nm) and e-beam lithography with ESCAP and ACRYLIC type positive tone resists. E-beam lithography evaluation indicates that these new fluroorganic sulfonic acids are sensitive and capable of providing image profiles down to 80 nm. The variation observed in sensitivity and LER at e-beam lithography was analyzed in terms of the structures of the photogenerated acids, chromophores and resists.
Leafhopper Viral Pathogens: Ultrastructure of salivary gland infection of Taastrup-like virus in Psammotettix alienus Dahlbom; and a novel Rhabdovirus in Homalodisca vitripennis (Germar) Hemiptera: Cicadellidae (2018)

Abstract Viruses that are pathogenic to insect pests can be exploited as biological control agents. Viruses that are pathogenic to beneficial insects and other arthropods, as in honey bees, silk worms, and shrimp, cause millions of dollars of losses to those industries. Current advances in next generation sequencing technologies along with molecular and cellular biology have produced a wealth of information about insect viruses and their potential applications. Leafhoppers cause economic losses as vectors of plant pathogens which significantly reduce the worlds’ food crops. Each year more viruses are discovered primarily through the use of next generation sequencing of the leafhopper hosts. The diversity of viruses from leafhoppers demonstrates a wide range of taxonomic members that includes genomes of DNA or RNA from families like: Reoviridae, Iridoviridae, Dicistroviridae, Iflaviridae, and others yet to be classified. Discussed is a recent viral pathogen isolated from the leafhopper Psammotettix alienus , name Taastrup Virus. Taastrup virus (TV) is a novel virus with a RNA genome, a Filovirus-like morphology, being tentatively placed within the Mononegavirales . Adult Psammotettix alienus infected with TV, showed the highest concentration of virions in salivary glands, consisting of a principal gland (type I-VI-cells) and an accessory gland. Examination of thin sections revealed enveloped particles, about 1300 nm long and 62 nm in diameter, located singly or in paracrystalline arrays in canaliculi of type III- and IV-cells. In gland cells with TV particles in canaliculi, granular masses up to 15 μm in diameter were present in the cytoplasm. These masses are believed to be viroplasms, the sites for viral replication. TV particles were observed at the connection between a canaliculus and the salivary duct system. A TV-like virus with strongly similar morphology was discovered in the ornamental plant, Liriope , near Fort Pierce, Florida, USA. When the virus was inoculated to a leafhopper cell culture, HvWH, made from the glassy-winged sharpshooter, Homalodisca vitripennis (Germar), the cells rapidly degraded with 100% mortality in 48 hours. These two instances are the only reported cases of this newly discovered viral pathogen of leafhoppers.
Layer-by-Layer Growth on Ge(100) via Spontaneous Urea Coupling Reactions (2005)

We have demonstrated the layer-by-layer growth, via a urea coupling reaction between two bifunctional molecules, ethylenediamine and 1,4-phenylene diisocyanate, to form an ultrathin film on Ge(100)-2 x 1 at room temperature under vacuum conditions. The initial adsorption and subsequent growth of each layer was studied with multiple internal reflection Fourier transform infrared (MIR-FTIR) spectroscopy. Ethylenediamine reacts with Ge(100)-2 x 1 to produce a surface-bound amine group which is available for additional reaction. Subsequent exposure of 1,4-phenylene diisocyanate leads to a spontaneous urea coupling reaction between the surface-bound amine and the highly reactive isocyanate functional group. Three bands at 1665, 1512, and 1306 cm(-)(1) are characteristic of a urea linkage and provide evidence of the coupling reaction. The coupling procedure can be repeated in a binary fashion to create covalently bound ultrathin films at room temperature, and in the present work, we demonstrate the successful growth of four layers. In addition, we have found that an initial exposure of 1,4-phenylene diisocyanate to Ge(100)-2 x 1 produces an isocyanate-functionalized surface which, upon exposure to ethylenediamine, also forms urea linkages. This layer-by-layer deposition method provides a strategy with which to design and produce precisely tailored organic materials at semiconductor interfaces.
Optical Transmitters, Receivers, and Noise (2003)

Abstract This article is designed to open up the field of optical modulation and reception on an introductory level by discussing a selection of optical modulation techniques currently viewed as being most promising. Further, high‐performance optical receiver structures and their noise properties are outlined, both for the fiber channel and for the free‐space channel. Basic receiver design rules as well as important performance trade‐offs are extracted. Frequently used concepts for quantifying receiver performance, such as receiver sensitivity, quantum limit, Q‐factor, and optical signal‐to‐noise ratio (OSNR) are explained.
IBM multimodal interactive video threading (2007)

In this demo we present a novel approach for (a) automatic labeling and grouping of multimedia content using existing metadata and semantic concepts, and (b) interactive context driven tagging of clusters of multimedia content. Proposed system leverages existing metadata info in conjunction with automatically assigned semantic descriptors. One of the challenges of multimedia retrieval systems today is to organize and present the video data in such a way that allows the user to most efficiently navigate the rich index space. The information needs of users typically span a range of semantic concepts, associated metadata, and content similarity. We propose to jointly analyze and navigate metadata, semantic and visual space for the purpose of identifying new relationships among content, and allowing user to link the aggregated content to a complex event description. The advantages of the proposed system are realized in increased ability to target content delivery to users such as in the collaborative or multi-domain user environments.
Data from Novel Oligoamine Analogues Inhibit Lysine-Specific Demethylase 1 and Induce Reexpression of Epigenetically Silenced Genes (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Abnormal DNA CpG island hypermethylation and transcriptionally repressive histone modifications are associated with the aberrant silencing of tumor suppressor genes. Lysine methylation is a dynamic, enzymatically controlled process. Lysine-specific demethylase 1 (LSD1) has recently been identified as a histone lysine demethylase. LSD1 specifically catalyzes demethylation of mono– and dimethyl–lysine 4 of histone 3 (H3K4), key positive chromatin marks associated with transcriptional activation. We hypothesized that a novel class of oligoamine analogues would effectively inhibit LSD1 and thus cause the reexpression of aberrantly silenced genes.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Human colorectal cancer cells were treated with the oligoamines and changes in mono- and dimethyl-H3K4 and other chromatin marks were monitored. In addition, treated cells were evaluated for the reexpression of the aberrantly silenced secreted frizzled-related proteins (&lt;i&gt;SFRP&lt;/i&gt;) Wnt signaling pathway antagonist genes. Finally, the effects of the LSD1 inhibitors were evaluated in an &lt;i&gt;in vivo&lt;/i&gt; xenograft model.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Treatment of HCT116 human colon adenocarcinoma cells &lt;i&gt;in vitro&lt;/i&gt; resulted in increased H3K4 methylation and reexpression of silenced &lt;i&gt;SFRP&lt;/i&gt; genes. This reexpression is also accompanied by a decrease in H3K9me2 repressive mark. Importantly, cotreatment with low doses of oligoamines and a DNA methyltransferase inhibitor highly induces the reexpression of the aberrantly silenced &lt;i&gt;SFRP2&lt;/i&gt; gene and results in significant inhibition of the growth of established tumors in a human colon tumor model &lt;i&gt;in vivo&lt;/i&gt;.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; The use of LSD1-inhibiting oligoamine analogues in combination with DNA methyltransferase inhibitors represents a highly promising and novel approach for epigenetic therapy of cancer. (Clin Cancer Res 2009;15(23):7217–28)&lt;/p&gt;&lt;/div&gt;