gebhart/patrepeval huggingface dataset:
Position‐specific expression of <i>Hox</i> genes along the gastrointestinal tract (2004)

Hox genes play a critical role in morphogenesis of the early embryo along the anteroposterior axis. In mammals, 39 Hox genes with extensive homology are organized into 13 paralogous groups, forming four clusters on four separate chromosomes. The genes within each cluster are arranged in a 3' to 5' direction and expressed in a temporally and spatially coordinated manner along the anteroposterior axis in the vertebrae, limbs and viscera, including the gastrointestinal tract, but little is known about their spatial expression in the adult gastrointestinal tract. We used the quantitative polymerase chain reaction (PCR) intercalater method with SYBR Green to quantify human Hox gene expression in the adult gastrointestinal tract tissue: esophagus, stomach, duodenum, jejunum, ileum, ileocecum, cecum, ascending colon, transverse colon, descending colon and rectum. Hox gene expression was normalized to glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) gene expression. The spatial expression pattern was analyzed by the multivariate method. The expression level of all 39 Hox genes could be measured in a reproducible manner. Genes with higher expression in the foregut-derived segments tended to have lower expression in hindgut-derived segments, whereas those with low expression in the former tended to have higher in the latter. Principal components analysis and permax analysis revealed a position-specific expression pattern of Hox genes along the anteroposterior axis of the adult gastrointestinal tract. The pattern recapitulates the expression pattern in the embryonic gastrointestinal tract. We suggest that Hox genes may play a pivotal role in the position-specific regenerative process of intestinal epithelial cells.
Discovery and Development of α7 Nicotinic Acetylcholine Receptor Modulators (2011)

ADVERTISEMENT RETURN TO ISSUEPerspectiveNEXTDiscovery and Development of α7 Nicotinic Acetylcholine Receptor ModulatorsAnatoly A. Mazurov*, Jason D. Speake, and Daniel YohannesView Author Information Targacept, Inc., 200 E. First Street, Winston-Salem, North Carolina 27101-4165, United StatesPhone: (336) 4802179. E-mail: [email protected]Cite this: J. Med. Chem. 2011, 54, 23, 7943–7961Publication Date (Web):September 15, 2011Publication History Received14 June 2011Published online29 September 2011Published inissue 8 December 2011https://pubs.acs.org/doi/10.1021/jm2007672https://doi.org/10.1021/jm2007672review-articleACS PublicationsCopyright © 2011 American Chemical SocietyRequest reuse permissionsArticle Views3640Altmetric-Citations52LEARN 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 SUBJECTS:Agonists,Circuits,Receptors,Rodent models,Schizophrenia Get e-Alerts
Mx1 in Hematopoietic Cells Protects against Thogoto Virus Infection (2019)

<i>Myxovirus resistance 1</i> (<i>Mx1</i>) is an interferon-induced gene that encodes a GTPase that plays an important role in the defense of mammalian cells against influenza A and other viruses. The Mx1 protein can restrict a number of viruses independently of the expression of other interferon-induced genes. <i>Mx</i> genes are therefore considered to be an important part of the innate antiviral immune response. However, the possible impact of <i>Mx</i> expression in the hematopoietic cellular compartment has not been investigated in detail in the course of a viral infection. To address this, we performed bone marrow chimera experiments using congenic B6.A2G <i>Mx1</i><sup>+/+</sup> and B6.A2G <i>Mx1<sup>-/-</sup></i> mice to study the effect of <i>Mx1</i> expression in cells of hematopoietic versus nonhematopoietic origin. <i>Mx1<sup>+/+</sup></i> mice were protected and <i>Mx1<sup>-/-</sup></i> mice were susceptible to influenza A virus challenge infection, regardless of the type of bone marrow cells (<i>Mx1</i><sup>+/+</sup> or <i>Mx1<sup>-/-</sup></i> ) the animals had received. Infection with Thogoto virus, however, revealed that <i>Mx1<sup>-/-</sup></i> mice with a functional <i>Mx1</i> gene in the bone marrow compartment showed reduced liver pathology compared with <i>Mx1<sup>-/-</sup></i> mice that had been grafted with <i>Mx1</i><sup>-/-</sup> bone marrow. The reduced pathology in these mice was associated with a reduction in Thogoto virus titers in the spleen, lung, and serum. Moreover, <i>Mx1</i><sup>+/+</sup> mice with <i>Mx1</i><sup>-/-</sup> bone marrow failed to control Thogoto virus replication in the spleen. <i>Mx1</i> in the hematopoietic cellular compartment thus contributes to protection against Thogoto virus infection.<b>IMPORTANCE</b> Mx proteins are evolutionarily conserved in vertebrates and can restrict a wide range of viruses in a cell-autonomous way. The contribution to antiviral defense of Mx1 expression in hematopoietic cells remains largely unknown. We show that protection against influenza virus infection requires <i>Mx1</i> expression in the nonhematopoietic cellular compartment. In contrast, <i>Mx1</i> in bone marrow-derived cells is sufficient to control disease and virus replication following infection with a Thogoto virus. This indicates that, in addition to its well-established antiviral activity in nonhematopoietic cells, Mx1 in hematopoietic cells can also play an important antiviral function. In addition, cells of hematopoietic origin that lack a functional <i>Mx1</i> gene contribute to Thogoto virus dissemination and associated disease.
The Antiscience Cancer (1996)

RETURN TO ISSUEPREVEditorialNEXTThe Antiscience CancerThis guest editorial by Allen J. Bard, Norman Hackerman-Welch Regents Chair in Chemistry at the University of Texas, Austin, and editor of the Journal of the American Chemical Society, is one in a series to bring the views of a broad spectrum of chemical community leaders to C&EN readers.ALLEN J. BARDView Author Information University of Texas, AustinCite this: Chem. Eng. News 1996, 74, 17, 5Publication Date (Print):April 22, 1996Publication History Published online12 November 2010Published inissue 22 April 1996https://pubs.acs.org/doi/10.1021/cen-v074n017.p005https://doi.org/10.1021/cen-v074n017.p005editorialACS PublicationsCopyright © 1996 American Chemical Society. This publication is available under these Terms of Use. This publication is free to access through this site. Learn MoreArticle Views103Altmetric-Citations-LEARN 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 PDF (86 KB) SUBJECTS:Cancer Get e-Alerts
Complex ambiguity function based on fourth-order statistics for joint estimation of frequency-delay and time-delay of arrival (2002)

The complex ambiguity function based on second-order statistics (CAF-SOS) has been used to simultaneously estimate the frequency-delay of arrival (FDOA) and time-delay of arrival (TDOA) between two signal measurements. But, its performance is sensitive do the effect due to the cross-correlation between noise sources. We develop the complex ambiguity function based on fourth-order statistics (CAF-FOS) to suppress the Gaussian noise-correlation effect. We also suggest a non-stationary estimate of the fourth-order cross-cumulants for implementing the CAF-FOS algorithm. Through simulations, we show that the CAF-FOS method can suppress the effect of spatially correlated Gaussian noise sources and produce good joint estimates of the PDOA/TDOA.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Caveolins in Signaling, Oncogenic Transformation, and Muscular Dystrophy (2001)

Conference Abstract| June 01 2001 Caveolins in Signaling, Oncogenic Transformation, and Muscular Dystrophy M. P. Lisanti M. P. Lisanti 1Albert Einstein College of Medicine, Department of Molecular Pharmacology, 1300 Morris Park Avenue, Bronx, NY, 10461, USA Search for other works by this author on: This Site PubMed Google Scholar Author and article information Publisher: Portland Press Ltd Online ISSN: 1470-8752 Print ISSN: 0300-5127 © 2001 Biochemical Society2001 Biochem Soc Trans (2001) 29 (3): A64. https://doi.org/10.1042/bst029a064b Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation M. P. Lisanti; Caveolins in Signaling, Oncogenic Transformation, and Muscular Dystrophy. Biochem Soc Trans 1 June 2001; 29 (3): A64. doi: https://doi.org/10.1042/bst029a064b Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 2001 Biochemical Society2001 Article PDF first page preview Close Modal You do not currently have access to this content.
Estimating Intersection Control Delay Using Large Data Sets of Travel Time from a Global Positioning System (2005)

Historically, stopped delay was used to characterize the operation of intersection movements because it was relatively easy to measure. During the past decade, the traffic engineering community has moved away from using stopped delay and now uses control delay. That measurement is more precise but quite difficult to extract from large data sets if strict definitions are used to derive the data. This paper evaluates two procedures for estimating control delay. The first is based on a historical approximation that control delay is 30% larger than stopped delay. The second is new and based on segment delay. The procedures are applied to a diverse data set collected in Phoenix, Arizona, and compared with control delay calculated by using the formal definition. The new approximation was observed to be better than the historical stopped delay procedure; it provided an accurate prediction of control delay. Because it is an approximation, this methodology would be most appropriately applied to large data sets collected from travel time studies for ranking and prioritizing intersections for further analysis.
Conformational properties of monosubstituted cyclohexanes in their thiourea inclusion compounds and in solution: variable-temperature one-dimensional and two-dimensional carbon-13 NMR investigations (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTConformational properties of monosubstituted cyclohexanes in their thiourea inclusion compounds and in solution: variable-temperature one-dimensional and two-dimensional carbon-13 NMR investigationsAbil E. Aliev and Kenneth D. M. HarrisCite this: J. Am. Chem. Soc. 1993, 115, 14, 6369–6377Publication Date (Print):July 1, 1993Publication History Published online1 May 2002Published inissue 1 July 1993https://pubs.acs.org/doi/10.1021/ja00067a061https://doi.org/10.1021/ja00067a061research-articleACS PublicationsRequest reuse permissionsArticle Views324Altmetric-Citations46LEARN 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
Precise Registration of Laser Mapping Data by Planar Feature Extraction for Deformation Monitoring (2018)

Quantifying near-field displacements can help enable a better understanding of earthquake physics and hazards. To date, established remote sensing techniques have failed to recover subcentimeter-level near-field displacements at the scale and resolution required for shallow fault physical investigations. In this paper, methods are developed to rapidly extract planar parameters, using fast parallel approaches and an alternative registration approach is employed to automatically match the planes extracted from pairwise temporally spaced mobile laser scanning (MLS) and Airborne laser scanning (ALS) data sets along the Napa fault. The features extracted from two temporally spaced point clouds are then used to calculate rigid-body transformation parameters. The production of robust and accurate deformation maps requires the selection of appropriate planar feature extraction and feature mapping criteria. Rigorously propagated point accuracy estimates are employed to produce realistic estimated errors for the transformation parameters. Displacements of each aggregate study area are computed separately from left and right sides of the fault and compared to be within 3 mm of alinement array displacements. Local differential displacements show distinct patterns which, compared to alinement array measurements, were found to agree within the confidence bounds. The findings demonstrate the ability to accurately estimate near-field deformations from repeated MLS or ALS scans of earthquake-prone urban areas. ALS is also used in conjunction with the MLS data sets, illustrating the algorithm's ability to accommodate different LiDAR collection modalities at subcentimeter-level accuracy. The automated planar extraction and registration is an important contribution to the study of near-field earthquake dynamics and can be used as input observations for future geological inversion models.
Tackling partial response to depression treatment. (2009)

the clinical remission of a depressive episode as a complete relief of the signs and symptoms of the presenting episode. 1 The individual should also return to his or her normal level of social and functional capacity.The Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study of 2,876 patients found that nearly 80% of patients had chronic or recurrent depression. 2 Only 33% achieved a level of symptom resolution by the end of the acute phase of treatment that would place them within the remission range according to scores on the Quick Inventory of Depressive Symptomatology (QIDS).Approximately 14% improved but had too many symptoms to be considered remitted.About 53% of patients did not improve or improved only minimally. ConsequencesDr Thase noted that remission has become the gold standard for depression treatment because patients who do not remit have a poorer prognosis than those who do achieve remission.Patients who have not fully remitted are at a greater risk of relapse and recurrence, have more chronic depressive episodes and psychiatric and medical comorbidities, and experience greater impairment in work and relationships than patients who achieved remission. 3Sustained depression may also increase the lifetime risk of suicide. 4 Risk FactorsRisk factors for incomplete remission, said Dr Thase, include high se- Tackling Partial Response to Depression Treatment
Identification of Novel Pro-Migratory, Cancer-Associated Genes Using Quantitative, Microscopy-Based Screening (2008)

In this screen we identified 4 novel genes derived from breast carcinoma related cDNA library, whose over-expression induces major alteration in the migration of the stationary MCF7 cells. This approach can serve for high throughput screening for novel ways to modulate cellular migration in pathological states such as tumor metastasis and invasion.
A Combined System for Automated Ellipsometry and for Network Analysis Based on a Microcomputer (1985)

ABSTRACT A Microcomputer has been employed for the automation of two types of measurements: Ellipsometry, and ac impedance in a wide frequency range (“network analysis”). These measurements are combined in the characterization of electrochemical interfaces. An identical simple and fast algorithm has been employed in both cases for the digital analysis of a sinusoidal signal. The rotating analyzer ellipsometer has a time resolution of 0.01 sec and a precision of 0.01 deg, following 1 sec integration time. The network analyzer generates a complex plane plot in the range of 10mHz-1kHz in 5 min. These specification have been achieved by employing only basic electrochemical instrumentation and a manual ellipsometer, in conjunction with a low cost microcomputer.
Abstract 2346: A B-RAF-MEK complex reveals a kinase-independent role for BRAF in MAPK pathway suppression. (2013)

Abstract The Ras/RAF/MEK/ERK signaling pathway (MAPK pathway) plays a major role in growth factor-mediated cell proliferation and is frequently activated by mutation in human cancers. The precise mechanism of pathway activation is dependent on the underlying mutation. Thus, the recurrent B-RAFV600E mutation, which is found in more than 60% of melanomas, promotes MAPK pathway signaling independent of RAS activation whereas activating K-RAS mutations drive MAPK signaling through C-RAF activation. The hallmarks of C-RAF activation include B and C-RAF heterodimerization, membrane localization and C-RAF phosphorylation. In this work, we have discovered that in addition to its ability to activate the pathway through B-RAF/C-RAF dimerization, B-RAF suppresses the MAPK pathway through formation of a stable B-RAF/MEK complex in the cytoplasm of B-RAFWT and K-RAS mutant (K-RASMT) tumor lines. To understand the molecular mechanism of the B-RAF/MEK interaction, we have determined the crystal structure of a heterotetrameric B-RAF:MEK1 complex in which B-RAF and MEK1 form a face-to-face dimer with B-RAF side-to-side dimers at the heart of the complex. Structural and biochemical evidence illustrate that the molecular determinants for B-RAF enzymatic activity is distinct from those required for interaction with MEK. Our work also reveals the molecular basis for the paradoxical ability of both BRAF-activating and -inactivating oncogenic mutations to stimulate the MAPK pathway. Taken together, these findings reveal a novel regulatory role for B-RAF in the MAPK pathway that is independent of its catalytic activity but dependent on the conformation of the B-RAF kinase domain. Citation Format: Malek Shiva, Jacob R. Haling, Jawahar Sudhamsu, Tony Morales, Ariana Peck, Ivana Yen, Barbara Brandhuber, Sarah Hymowitz. A B-RAF-MEK complex reveals a kinase-independent role for BRAF in MAPK pathway suppression. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2346. doi:10.1158/1538-7445.AM2013-2346
Neuroevolution of Spiking Neural Networks Using Compositional Pattern Producing Networks (2020)

Spiking neural networks (SNNs) offer tremendous potential for the future of AI, including the ability to be implemented efficiently on neuromorphic systems. One of the challenges in building functioning SNNs is the training process, as standard error back-propagation cannot be easily applied. In this work, we extend an evolutionary approach for training SNNs by implementing an indirect encoding of individuals. Specifically, we evolve SNNs using Compositional Pattern Producing Networks, which are able to learn the connectivity patterns between neurons defined in a coordinate space. We validate the approach on multiple control and classification tasks.
Group cognitive behavioural therapy with compassion training for depression in a Japanese community: a single-group feasibility study (2017)

Fourteen participants were enrolled in the trial, of which 13 completed the intervention, and 12 completed a 6-month follow-up assessment. Participants received a 1 h group-based CBT with compassion training session every week for 10 weeks. The effect of the intervention on participants' Beck Depression Inventory score was examined using a general linear mixed model. This analysis showed an effect size of d = 1.12 at post intervention and d = 0.92 at 6-month follow-up. Group cognitive behavioural therapy with compassion training for depression shows feasibility and acceptability in a Japanese community. Trial Registration UMIN000015007.