gebhart/patrepeval huggingface dataset:
An investigation of exon repetition. (2004)

Exon repetition consists in the presence of tandemly repeated exons in mRNA. In all the cases reported so far, the trivial explanation that the phenomenon arises from a duplication of specific exons in the gene was ruled out by southern blot analysis. It is therefore assumed that exon repetition is the result of a post-transcriptional process involving two pre-mRNA molecules transcribed from the same gene. Exon repetition of SA is of particular interest, since it is both tissue and strain-specific. This at first suggested that repetition in SA might be caused by a tissue and strain-specific trans-acting factor. This work has shown that the property of exon repetition is allele-specific in the two best characterised examples, represented by the SA and COT (carnitine octanoyltransferase) genes in rat. Allele-specificity of exon repetition is therefore the underlying cause of strain-specificity of exon repetition in SA and also in COT.;The biological significance of exon repetition remains unknown. One possible function is the generation of new proteins. Quite often though, repetition of the exon that contains the AUG translational start codon creates a short upstream open reading frame (uORF) that precedes the ORF encoding the full length protein. The effect of this has been investigated and the results show that translation of the downstream open reading frame is significantly reduced by the presence of uORFs.;The mechanism that generates exon repetition is not well understood. It was initially proposed for the COT gene that the presence of a putative exonic splicing enhancer (ESE) in exon 2 conferred exon repetition. This work demonstrates that the presence of the ESE is not sufficient to cause exon repetition in-vivo..
Eficácia escolar e variáveis familiares em tempos de pandemia: um estudo a partir de dados do ENEM (2021)

Um dos objetivos de políticas públicas educacionais é o desenvolvimento de um sistema escolar que combine qualidade e equidade, sendo justo em igualdade de oportunidades para diferentes grupos sociais e alcançando excelência de desempenho. Atualmente, o impacto causado pela pandemia de covid-19 na educação afetou boa parte dos estudantes em todo o mundo. Professores, educadores, pais e gestores têm feito esforços para que o processo educacional não seja interrompido, mas ensinar em períodos de isolamento social com garantias de igualdade entre todos os indivíduos é uma atividade desafiadora. Os objetivos deste artigo são apresentar os conceitos de eficácia escolar e identificar, a partir de análises descritivas, as distribuições de variáveis como escolaridade materna e renda familiar por região, discutindo o quanto a ausência de aulas presenciais poderá interferir no desempenho de alunos de baixa renda de escolas públicas em todo o Brasil. Os resultados mostram a desigualdade social no país e os desafios que estão por vir para que não haja um abismo ainda maior do que o atual no que tange o acesso educação superior gratuita no Brasil. Os estudos aqui apresentados podem servir como base para gestores na discussão sobre políticas públicas educacionais.
Subtypes of relapsing-remitting multiple sclerosis identified by network analysis (2023)

We used network analysis to identify subtypes of relapsing-remitting multiple sclerosis subjects based on their cumulative signs and symptoms. The electronic medical records of 113 subjects with relapsing-remitting multiple sclerosis were reviewed, signs and symptoms were mapped to classes in a neuro-ontology, and classes were collapsed into sixteen superclasses by subsumption. After normalization and vectorization of the data, bipartite (subject-feature) and unipartite (subject-subject) network graphs were created using NetworkX and visualized in Gephi. Degree and weighted degree were calculated for each node. Graphs were partitioned into communities using the modularity score. Feature maps visualized differences in features by community. Network analysis of the unipartite graph yielded a higher modularity score (0.49) than the bipartite graph (0.25). The bipartite network was partitioned into five communities which were named fatigue, behavioral, hypertonia/weakness, abnormal gait/sphincter, and sensory, based on feature characteristics. The unipartite network was partitioned into five communities which were named fatigue, pain, cognitive, sensory, and gait/weakness/hypertonia based on features. Although we did not identify pure subtypes (e.g., pure motor, pure sensory, etc.) in this cohort of multiple sclerosis subjects, we demonstrated that network analysis could partition these subjects into different subtype communities. Larger datasets and additional partitioning algorithms are needed to confirm these findings and elucidate their significance. This study contributes to the literature investigating subtypes of multiple sclerosis by combining feature reduction by subsumption with network analysis.
Radiogenomic characterization of response to chemo-radiation therapy in glioblastoma is associated with PI3K/AKT/mTOR and apoptosis signaling pathways (2019)

Over 40% of Glioblastoma (GBM) patients do not respond to conventional chemo-radiation therapy (chemo-RT) and relapse within 6-9 months, suggesting that they may have been better suited for other targeted therapies. Currently, there are no biomarkers that can reliably predict patients' response to chemo-RT in GBM. We seek to evaluate the role of radiomic markers on pre-treatment MRI to predict GBM patients' response to chemo-RT. Further, to establish a biological underpinning of the radiomic markers, we identified radiogenomic correlates of the radiomic markers with signaling pathways that are known to impact chemo-RT response. A total of 49 studies with Gd-T1w, T2w, FLAIR MRI protocols and corresponding gene expression were obtained from Ivy GAP (n=29) and TCIA (n=20) databases. Responders (n=22) were patients with progression-free survival (PFS) of at least &ge; 6 months, while non-responders (n=27) had PFS &lt; 6 months. 13 molecular pathways were curated from the MSigDB Hallmark gene set. For each study, enhancing tumor on MRI was manually segmented by an expert reader. 1390 3D-radiomic features (Gabor, Haralick, and Laws energy) were extracted from this region across all MRI protocols. Joint mutual information identified the 3 most predictive radiomic features in the training set (n=29). This was followed by correlating these features with the gene set enrichment analysis (GSEA) score computed for every pathway. A support vector machine (SVM) classifier was trained using these 3 features and validated on a test set (n=20) that resulted in an Area Under Curve (AUC) of 0.71 to distinguish chemo-RT responders from non-responders. Laws energy descriptor (characterizing appearance of edges, spots, and ripples) from the enhancing region on Gd-T1w MR images were found to best predict chemo-RT response. Radiogenomic correlation with GSEA scores revealed that these radiomic features were significantly associated with PI3K/AKT/mTOR (promotes cell proliferation, survival) and apoptosis (programmed cell death) signaling pathways (p &lt; 0.03, False Discovery Rate = 5%).
Phénomènes non linéaires dans les plasmas poussiéreux : Apparition d'oscillations multimodales (2012)

Poster
Design and Predictions for High-Altitude (Low Reynolds Number) Aerodynamic Flight Experiment (2000)

A sailplane being developed at NASA Dryden Flight Research Center will support a high-altitude flight experiment. The experiment will measure the performance parameters of an airfoil at high altitudes (70,000 to 100,000 ft), low Reynolds numbers (200,000 to 700,000), and high subsonic Mach numbers (0.5 and 0.65). The airfoil section lift and drag are determined from pitot and static pressure measurements. The locations of the separation bubble, Tollmien-Schlichting boundary layer instability frequencies, and vortex shedding are measured from a hot-film strip. The details of the planned flight experiment are presented. Several predictions of the airfoil performance are also presented. Mark Drela from the Massachusetts Institute of Technology designed the APEX-16 airfoil, using the MSES code. Two-dimensional Navier-Stokes analyses were performed by Mahidhar Tatineni and Xiaolin Zhong from the University of California, Los Angeles, and by the authors at NASA Dryden.
Design of a novel 6-DoF robotic system for pituitary tumor removal under MRI guidance (2019)

Magnetic resonance imaging (MRI) provide superior visuals that might be suitable for complicated surgical procedures in complex parts of the human body like brain and heart. Brain tumor removal is one of the trickiest surgical procedures and the pituitary tumor is one of the most common type of intracranial tumors. In this paper, we present an MRI compatible robotic system for pituitary tumor removal via trans-nasal access to the surgical site. The robotic system is designed to operate in a Siemens® 3T MRI scanner. A 5mm diameter and 6-DOF design specific manipulator is developed to access the pituitary glands and remove the tumor using the commercially available tools. The actuation system is designed to fit inside the MRI bore and operate just above the nasal entry point. The manipulator is designed to work in a 20×20mm workspace of the pituitary gland and this workspace is validated by experiments. The presented robotic system is expected to decrease the complexity by accessing the surgical site through the nasal cavity and improve the quality of tumor removal by providing better image quality under MRI guidance.
Ensemble approach based on conditional random field for multi-label image and video annotation (2011)

Multi-label image/video annotation is a challenging task that allows to correlate more than one high-level semantic keyword with an image/video-clip. Previously, a single model is usually used for the annotation task, with relatively large variance in performance. The correlation among the annotation keywords should also be considered. In this paper, to reduce the performance variance and exploit the correlation between keywords, we propose the En-CRF (Ensemble based on Conditional Random Field) method. In this method, multiple models are first trained for each keyword, then the predictions of these models and the correlations between keywords are incorporated into a conditional random field. Experimental results on benchmark data set, including Corel5k and TRECVID 2005, show that the En-CRF method is superior or highly competitive to several state-of-the-art methods.
Resource control in network assisted device-to-device communications: solutions and challenges (2014)

Network assisted Device-to-Device (D2D) communications is envisioned as a promising technology to facilitate the discovery of geographically close cellular devices and reduce the communication cost between these devices. In order to fully take advantages of the freedom in resource management introduced by D2D communications, it is essential to design optimal resource control policies. In this article, we first review and classify the state-of-the-art research based on different considered network scenarios. We then introduce our preliminary studies on delay-aware resource control with bursty traffic, in which we propose an optimization framework and formulate a general queuing model for performance evaluation and optimization. Finally, the challenges and open issues are highlighted to serve as guidelines for future research.
Meta-iCVIs: Ensemble Validity Metrics for Concise Labeling of Correct, Under- or Over-Partitioning in Streaming Clustering (2022)

&lt;p&gt;Understanding the performance and validity of clustering algorithms is both challenging and crucial, particularly when clustering must be done online. Until recently, most validation methods have relied on batch calculation and have required considerable human expertise in their interpretation. Improving real-time performance and interpretability of cluster validation, therefore, continues to be an important theme in improving unsupervised learning. Building upon previous work on incremental cluster validity indices (iCVIs), this paper introduces the Meta-iCVI as a tool for explainable and concise labeling of partition quality in online clustering. Some iCVIs are better at detecting under-partition; others at over-partition. Combining them was hypothesized to improve cluster validation analysis. Experiments were conducted on generalized synthetic and real-world data sets to demonstrate the efficacy and application of this method.&lt;/p&gt; &lt;p&gt;Results of 100% accuracy were achieved in labeling partition quality on real-world data sets including MNIST and FLIR ADAS, demonstrating that the Meta-iCVI is a powerful and efficient tool for classifying partition quality in a variety of conditions. Its introduction should empower new and more efficient streaming clustering techniques. Additionally, we believe this to be the first implementation of an ensemble iCVI metric and the first time iCVI validation performance has been evaluated on randomized sample presentation.&lt;/p&gt;
Site-specifically platinated DNA, a new probe of the biological activity of platinum anticancer drugs (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSite-specifically platinated DNA, a new probe of the biological activity of platinum anticancer drugsAnn L. Pinto, Lisa J. Naser, John M. Essigmann, and Stephen J. LippardCite this: J. Am. Chem. Soc. 1986, 108, 23, 7405–7407Publication Date (Print):November 1, 1986Publication History Published online1 May 2002Published inissue 1 November 1986https://pubs.acs.org/doi/10.1021/ja00283a044https://doi.org/10.1021/ja00283a044research-articleACS PublicationsRequest reuse permissionsArticle Views173Altmetric-Citations23LEARN 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
Abstract 16443: Therapeutic Effect of Prostaglandin D2 Synthase Inhibition in Experimental Autoimmune Myocarditis (2016)

Introduction: Myocarditis is a life-threatening inflammatory cardiac disorder. Virus-triggered autoimmunity is considered to play a key role in the progression of myocarditis, however, detailed mol...
Novel and scalable approach to research grade AAV vector manufacturing and separation of distinct AAV serotypes (2009)

status: Published
[Loss of heterozygosity in the progression of tumors]. (1989)

Based on the two mutation hypothesis in the development of retinoblastoma, loss of heterozygosity (LOH) of specific chromosome has been implicated in the presence of tumor suppressor gene. Studies on the LOH in different types of tumors revealed that LOH of each chromosome might play a different role in the multistep process of carcinogenesis: LOH of some chromosomes may play an etiological role in the development of some tumors, while that of other chromosomes or the same chromosome in other tumors, may play a role in the progression of tumors. LOH of chromosome 13 is an example for the former cases, and the latter cases involve LOH of chromosome 17 in colorectal carcinoma and osteosarcoma, chromosome 10 in glioblastoma, chromosome 1 in neuroblastoma and malignant melanoma, and chromosome 11 in breast carcinoma. These studies indicates that the progressive or concerted LOH could be a measure of the highly malignant or metastatic potentiality. However, it should be borne in mind that, especially in polyploid tumors, LOH also occurs as a random event following the polyploidization-segregation process.
New ring-containing fluoropolymers (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNew ring-containing fluoropolymersZhen-Yu Yang, Andrew E. Feiring, and Bruce E. SmartCite this: J. Am. Chem. Soc. 1994, 116, 9, 4135–4136Publication Date (Print):May 1, 1994Publication History Published online1 May 2002Published inissue 1 May 1994https://doi.org/10.1021/ja00088a082RIGHTS & PERMISSIONSArticle Views257Altmetric-Citations31LEARN 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 InReddit PDF (195 KB) Get e-AlertsSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Real-Time Monitoring of Somatostatin Receptor-cAMP Signaling in Live Pituitary (2010)

sensitivity in LL DIO rats fed chow until 10 wk of age. The enhanced ARC leptin receptor binding and reduced adiposity of LL DIO rats persisted after an additional 5 wk on the HE diet. Female LL DIO rats had similar reductions in weight gain on both chow and HE diet vs. normal litter DIO rats. We postulate that LL rearing enhances DIO leptin sensitivity by lowering plasma leptin levels and thereby increasing leptin receptor availability and that this both enhances the ARC-paraventricular nucleus pathway development and protects them from becoming obese.
Behavior of Microscopic Liquid Droplets near A Strong Electrostatic Field: Droplet Electrospray (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBehavior of Microscopic Liquid Droplets near A Strong Electrostatic Field: Droplet ElectrosprayD. B. Hager and N. J. DovichiCite this: Anal. Chem. 1994, 66, 9, 1593–1594Publication Date (Print):April 1, 1994Publication History Published online1 May 2002Published inissue 1 April 1994https://pubs.acs.org/doi/10.1021/ac00081a040https://doi.org/10.1021/ac00081a040research-articleACS PublicationsRequest reuse permissionsArticle Views428Altmetric-Citations30LEARN 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
HMGA1 promotes metastatic processes in basal-like breast cancer regulating EMT and stemness (2013)

Breast cancer is a heterogeneous disease that progresses to the critical hallmark of metastasis. In the present study, we show that the High Mobility Group A1 (HMGA1) protein plays a fundamental role in this process in basal-like breast cancer subtype. HMGA1 knockdown induces the mesenchymal to epithelial transition and dramatically decreases stemness and self-renewal. Notably, HMGA1 depletion in basal-like breast cancer cell lines reduced migration and invasion in vitro and the formation of metastases in vivo. Mechanistically, HMGA1 activated stemness and key migration-associated genes which were linked to the Wnt/beta-catenin, Notch and Pin1/mutant p53 signalling pathways. Moreover, we identified a specific HMGA1 gene expression signature that was activated in a large subset of human primary breast tumours and was associated with poor prognosis. Taken together, these data provide new insights into the role of HMGA1 in the acquisition of aggressive features in breast cancer.
Surface Species Formed and Their Reactivity during the Alkylation of Toluene by Methanol and Dimethyl Ether on Zeolites As Determined by in Situ 13C MAS NMR (1997)

13C MAS NMR has been performed in situ to investigate the mechanism of toluene alkylation with methanol (MeOH) or dimethyl ether (DME) at 433 K over H−ZSM-11 catalyst. The reaction protocol used allowed to separate the main reaction stages: MeOH and DME adsorption, activation, and reaction with toluene. In both cases, five strongly bound species were identified upon activation at 433 K, namely, MeOH and DME side-on and end-on adsorption complexes and methoxy species. End-on adsorbed complexes and methoxy species were found to be reactive in toluene alkylation, the reactivity of end-on adsorbed complexes being much higher.
Traffic adaptive formation of mmWave meshed backhaul networks (2017)

MmWave meshed network is a promising architecture for cost-efficient wireless backhaul of millimeter-wave overlay heterogeneous network (mmWave overlay HetNet). As user distribution in practice is time-variant and spatially non-uniform, mmWave meshed backhaul should be controlled adaptively. This paper proposes a novel method to control mmWave meshed backhaul for efficient operation of mmWave overlay HetNet. Our algorithm is featured by two functionalities, i.e. backhauling route multiplexing for overloaded mmWave small cell base stations (SC-BSs) and mmWave SC-BSs' ON/OFF status switching for underloaded spot. Considering practical user distribution, radio backhaul resources should be concentrated on overloaded mmWave SC-BSs. Inversely, underloaded mmWave SC-BSs should be deactivated for saving power. The performance of mmWave meshed backhaul controlled by the proposed algorithm is evaluated by system level simulation. Numerical results show that the proposed algorithm can cope with the locally intensive traffic, network scalability, and can reduce energy consumption.
BetaCore, a designed water soluble four‐stranded antiparallel β‐sheet protein (2002)

BetaCore is a designed approximately 50-residue protein in which two BPTI-derived core modules, CM I and CM II, are connected by a 22-atom cross-link. At low temperature and pH 3, homo- and heteronuclear NMR data report a dominant folded ('f') conformation with well-dispersed chemical shifts, i, i+1 periodicity, numerous long-range NOEs, and slowed amide hydrogen isotope exchange patterns that is a four-stranded antiparallel beta-sheet with nonsymmetrical and specific association of CM I and CM II. BetaCore 'f' conformations undergo reversible, global, moderately cooperative, non-two-state thermal transitions to an equilibrium ensemble of unfolded 'u' conformations. There is a significant energy barrier between 'f' and 'u' conformations. This is the first designed four-stranded antiparallel beta-sheet that folds in water.