gebhart/patrepeval huggingface dataset:
Therapeutic efficacy of the bromodomain inhibitor OTX015/MK-8628 in ALK-positive anaplastic large cell lymphoma: an alternative modality to overcome resistant phenotypes (2016)

Anaplastic large cell lymphomas (ALCL) represent a peripheral T-cell lymphoma subgroup, stratified based on the presence or absence of anaplastic lymphoma kinase (ALK) chimeras. Although ALK-positive ALCLs have a more favorable outcome than ALK-negative ALCL, refractory and/or relapsed forms are common and novel treatments are needed. Here we investigated the therapeutic potential of a novel bromodomain inhibitor, OTX015/MK-8628 in ALK-positive ALCLs.The effects of OTX015 on a panel of ALK+ ALCL cell lines was evaluated in terms of proliferation, cell cycle and downstream signaling, including gene expression profiling analyses. Synergy was tested with combination targeted therapies.Bromodomain inhibition with OTX015 led primarily to ALCL cell cycle arrest in a dose-dependent manner, along with downregulation of MYC and its downstream regulated genes. MYC overexpression did not compensate this OTX015-mediated phenotype. Transcriptomic analysis of OTX015-treated ALCL cells identified a gene signature common to various hematologic malignancies treated with bromodomain inhibitors, notably large cell lymphoma. OTX015-modulated genes included transcription factors (E2F2, NFKBIZ, FOS, JUNB, ID1, HOXA5 and HOXC6), members of multiple signaling pathways (ITK, PRKCH, and MKNK2), and histones (clusters 1-3). Combination of OTX015 with the Bruton's tyrosine kinase (BTK) inhibitor ibrutinib led to cell cycle arrest then cell death, and combination with suboptimal doses of the ALK inhibitor CEP28122 caused cell cycle arrest. When OTX015 was associated with GANT61, a selective GLI1/2 inhibitor, C1156Y-resistant ALK ALCL growth was impaired.These findings support OTX015 clinical trials in refractory ALCL in combination with inhibitors of interleukin-2-inducible kinase or SHH/GLI1.
Corrections to “Super Fast Physics-Based Methodology for Accurate Memory Yield Prediction” [Mar 15 534-543] (2015)

On <xref ref-type="bibr" rid="ref1" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">[1, p. 536]</xref> , Section II-A, second paragraph, lines 5–8, [2] should be used instead of <xref ref-type="bibr" rid="ref1" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">[1]</xref> and the correct statement is as follows. “Model-to-hardware corroboration shows an excellent matching between importance-sampling-based methods yield estimation [2] and the true hardware yield. We therefore adopt the methodology in [2] as the core statistical engine for our TfM methodology.”
Healing of peri-implant tissues after flapless and flapped implant installation (2011)

The results indicate that a flapless surgical technique can be used for the installation of oral implants. In addition, using a tissue punch wider than the implant diameter should be avoided, as it can jeopardize the outcome of the implantation procedure.
An approach to capacity analysis of coarsely coordinated low power multiple access systems (2004)

We consider multiaccess problem in low power systems, where we allow each user to select its own data rate and transmit power locally and independently from other users. Here, every user has a set of low power codebooks, labeled a "policy," which accommodates a range of small spectral efficiencies, while treating instantaneous data rates of other users as an unknown compound parameter. Even with such coarse user coordination, multiuser detection enables a system, which is superior to any classic orthogonal division system. First we fully characterise the set of achievable policies, after which we demonstrate that in multiantenna systems, policies are be viewed as awarding protected receiver spatial dimensions to each user.
Mechanistic aspects of a homogeneous carbon monoxide hydrogenation catalyst - tetrairidium dodecacarbonyl in molten aluminum chloride-sodium chloride (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMechanistic aspects of a homogeneous carbon monoxide hydrogenation catalyst - tetrairidium dodecacarbonyl in molten aluminum chloride-sodium chlorideJames P. Collman, John I. Brauman, Gerald Tustin, and Grady S. Wann IIICite this: J. Am. Chem. Soc. 1983, 105, 12, 3913–3922Publication Date (Print):June 1, 1983Publication History Published online1 May 2002Published inissue 1 June 1983https://pubs.acs.org/doi/10.1021/ja00350a029https://doi.org/10.1021/ja00350a029research-articleACS PublicationsRequest reuse permissionsArticle Views261Altmetric-Citations22LEARN 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
Assembly of a freeform off-axis optical system employing three φ-polynomial Zernike mirrors (2014)

We report on the assembly of an off-axis reflective imaging system employing freeform, φ-polynomial optical surfaces. The sensitivity of the system to manufacturing errors is studied for both a passive and active alignment approach. The as-built system maintains diffraction-limited performance in the long-wave infrared.
Two-photon emission in direct-gap semiconductors (2011)

We performed a theoretical study of extreme nondegenerate two-photon stimulated emission in direct-bandgap semiconductors. We predict orders of magnitude enhancement with respect to the degenerate case. Evidence in support of this comes from 2-photon absorption measurements.
NMR structure and dynamics of the agonist dynorphin peptide bound to the human kappa opioid receptor (2015)

The structure of the dynorphin (1-13) peptide (dynorphin) bound to the human kappa opioid receptor (KOR) has been determined by liquid-state NMR spectroscopy. (1)H and (15)N chemical shift variations indicated that free and bound peptide is in fast exchange in solutions containing 1 mM dynorphin and 0.01 mM KOR. Radioligand binding indicated an intermediate-affinity interaction, with a Kd of ∼200 nM. Transferred nuclear Overhauser enhancement spectroscopy was used to determine the structure of bound dynorphin. The N-terminal opioid signature, YGGF, was observed to be flexibly disordered, the central part of the peptide from L5 to R9 to form a helical turn, and the C-terminal segment from P10 to K13 to be flexibly disordered in this intermediate-affinity bound state. Combining molecular modeling with NMR provided an initial framework for understanding multistep activation of a G protein-coupled receptor by its cognate peptide ligand.
Increased mRNA expression of CDKN2A is a transcriptomic marker of clinically aggressive meningiomas (2022)

Abstract Background Homozygous loss of CDKN2A/B is a genetic alteration found in many cancer types including meningiomas, where it is associated with poor clinical outcome. It is now also a diagnostic criterion for grade 3 meningiomas in the 2021 WHO classification for central nervous system tumors. However, as in other cancers, the relationship between copy number loss of CDKN2A/B and expression of its gene product is unclear and may be either commensurate or paradoxical in nature. Therefore, we aimed to investigate the association of CDKN2A mRNA expression with clinical prognosis, WHO grade, and other molecular biomarkers in meningiomas such as DNA methylation, molecular group, and proteomics. Methods We used multidimensional molecular data of 490 meningioma samples from 4 independent cohorts to examine the relationship between mRNA expression of CDKN2A and copy number status, its correlation to clinical outcome, the transcriptomic pathways altered in differential CDKN2A expression, and its relationship with DNA methylation, and proteomics using an integrated molecular approach. Results Meningiomas without any copy number loss were dichotomized into high (CDKN2A high ) and low (CDKN2A low ) CDKN2A mRNA expression groups. Patients with CDKN2A high meningiomas had poorer progression free survival (PFS) compared to those with CDKN2A low meningiomas. CDKN2A mRNA expression was increased in more aggressive molecular groups, and in higher WHO grade meningiomas across all cohorts. CDKN2A high meningiomas and meningiomas with CDKN2A copy number loss shared common up-regulated cell cycling pathways. CDK4 mRNA expression was increased in CDKN2A high meningiomas and both p16 and CDK4 protein were more abundant in CDKN2A high meningiomas. CDKN2A high meningiomas were frequently hypermethylated at the gene body and UTR compared to CDKN2A low meningiomas and found be more commonly Rb-deficient. Conclusions An intermediate level of CDKN2A mRNA expression appears to be optimal as significantly low (CDKN2A deleted) or high expression (CDKN2A high ) are associated with poorer outcomes clinically. Though CDK4 is elevated in CDKN2A high meningiomas, Rb-deficiency may be more common in this group, leading to lack of response to CDK inhibitors.
High-Efficiency All-Polymer Solar Cells with Poly-Small-Molecule Acceptors Having π-Extended Units with Broad Near-IR Absorption (2021)

We report two new poly-small-molecule acceptors, PYN-BDT and PYN-BDTF, which serve, by virtue of their π-extended naphthalene rings, as broad optical cross-section macromolecular absorbers (extending to ∼900 nm; ΔEopticalgap = 1.38 eV) in all-polymer solar cells (APSCs). APSCs fabricated by blending PYN-BDT or PYN-BDTF with PM6 exhibit power conversion efficiencies (PCEs) of 7.24 and 9.08%, respectively, while blends with PBDB-T exhibits far higher PCEs of 12.06 and 13.22%, respectively; the latter cell achieves Jsc = 22.28 mA cm–2, among the highest known for an APSC. The results of blend morphology, GIWAXS, charge transport, exciton and carrier dynamics, PL quenching efficiency, and impedance-based analysis indicate that the PBDB-TT:PYN-BDTF blends and their APSCs outperform the corresponding PM6:PYN-BDTF devices due to significantly suppressed bimolecular recombination. These results demonstrate that π-conjugative extension of individual polymer acceptor blocks represents an efficient strategy to broaden APSC optical cross sections, decrease bimolecular recombination, and achieve high-performance cells with enhanced Jsc metrics.
Non‐invasive integrative analysis of cardiac energetics, translation to human heart in vivo (2012)

We propose MOCA, an inovative non‐invasive clinical analysis of heart energetics, based on the combination of non‐invasive MRS &amp; MRI techniques and the analytical background of metabolic control analysis. MoCA brings new informations on the links between ATP demand and supply and delivers the description of heart function through integrated internal regulations, currently not accessible clinically. We anticipate that these informations may be of great help in the future for diagnosis and therapeutics follow‐up in human heart pathologies. By combining 31P‐NMR spectroscopy with direct measurement of heart contractile activity, we applied MoCA approach to beating Langendorf perfused rat heart and demonstrated the parallel activation of mitochondrial activity and myofibrils ATPases by Ca2+, which explains the energetic homeostasis of the heart. Further, we could describe quantitatively the global action of modulators of heart contraction (adrenaline, levosimendan) or of a pathology (hypoxia), and the relative importance of the different routes within the heart by which the effects are transmitted. Application to the study of contraction energetics in healthy and pathological heart in human may be a key to the understanding of the links between molecular events in pathologies and whole organ function/dysfunction.
NI-75 * QUANTITATIVE TEXTURE DESCRIPTORS ON BASELINE-MRI CAN PREDICT PATIENT SURVIVAL IN NEWLY DIAGNOSED GLIOBLASTOMA MULTIFORME PATIENTS (2014)

OBJECTIVE: Glioblastoma Multiforme (GBM) is the deadliest form of brain tumors with a median survival of 12 months. While methylation of the MGMT gene promoter and IDH1 status have been shown to be associated with prolonged survival in GBM patients, there is controversy about their use as prognostic markers for evaluating response in newly diagnosed patients. The underlying hypothesis of this study is that computer-extracted texture descriptors can capture subtle, multiscale morphologic attributes on baseline-MRI and thus can better predict patient survival as compared to the known molecular markers, IDH1 and MGMT. METHODS: 16 3Tesla MRI studies with Gd-T1C, FLAIR, T2w protocols with known MGMT, IDH1 status were recruited as part of ongoing IRB-approved Ohio brain tumor study. 8 patients had overall survival (OS) > 500 days (prolonged survival) and 8 had OS<200 days (poor survival). 97 computer extracted texture descriptors including intensity statistics, cooccurrence matrix homogeneity, neighboring gray level dependence matrix, Gabor, and Laws energy, were extracted from within the lesion on baseline-MRI. Kaplan-Meier survival curves were computed for every texture descriptor as well as for IDH1, and MGMT markers, where each feature was considered in a univariate fashion during analysis. RESULTS: Laws texture descriptors (specifically ripple, edge, level and spot features on T1-w, T2-w, and FLAIR MRI) were found to be the top 3 features associated with the strongest survival difference between prolonged and poor survival, with reported p-values < .01. The p-values for MGMT, IDH1, and original MRI intensities computed within the lesion were reported to be statistically insignificant (p>0.05) in separating survival outcome. CONCLUSIONS: Laws texture features appeared to capture differences in lesion heterogeneity between prolonged and poor patient population suggesting that there are subtle morphological prognostic cues on baseline-MRI that may better predict patient survival in newly diagnosed GBM patients, that the known IDH1, and MGMT molecular markers.
Cavity enhanced thin film measurements (2013)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text C. Stambaugh, U. Kemiktarak, M. Durand, and J. Lawall, "Cavity-enhanced thin film measurements," in Frontiers in Optics 2013, P. Delyett, Jr. and D. Gauthier, eds., OSA Technical Digest (online) (Optica Publishing Group, 2013), paper LTh2H.4. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Anticholinesterase Activity of Budmunchiamine Alkaloids Revealed by Comparative Chemical Profiling of Two Albizia spp., Molecular Docking and Dynamic Studies (2022)

Alzheimer's disease remains a global health challenge and an unmet need requiring innovative approaches to discover new drugs. The current study aimed to investigate the inhibitory activity of <i>Albizia lucidior</i> and <i>Albizia procera</i> leaves against acetylcholinesterase enzyme in vitro and explore their chemical compositions. Metabolic profiling of the bioactive plant, <i>A. lucidior</i>, via UHPLC/MS/MS-based Molecular Networking highlighted the richness of its ethanolic extract with budmunchiamine alkaloids, fourteen budmunchiamine alkaloids as well as four new putative ones were tentatively identified for the first time in <i>A. lucidior</i>. Pursuing these alkaloids in the fractions of <i>A. lucidior</i> extract via molecular networking revealed that alkaloids were mainly concentrated in the ethyl acetate fraction. In agreement, the alkaloid-rich fraction showed the most promising anticholinesterase activity (IC<sub>50</sub> 5.26 µg/mL) versus the ethanolic extract and ethyl acetate fraction of <i>A. lucidior</i> (IC<sub>50</sub> 24.89 and 6.90 µg/mL, respectively), compared to donepezil (IC<sub>50</sub> 3.90 µg/mL). Furthermore, deep in silico studies of tentatively identified alkaloids of <i>A. lucidior</i> were performed. Notably, normethyl budmunchiamine K revealed superior stability and receptor binding affinity compared to the two used references: donepezil and the co-crystallized inhibitor (MF2 700). This was concluded based on molecular docking, molecular dynamics simulations and molecular mechanics generalized born/solvent accessibility (MM-GBSA) calculations.
Measurements of Gulf Stream Meandering and Evidence of Seasonal Thermocline Development Using Long-Range Acoustic Transmissions (1983)

Phase-coded signals with 60 rms resolution were transmitted twice weekly for several months from acoustic sources at ∼2000 m depth in the Sargasso Sea to three bottom-mounted receives designed as West, East, and North stations at ranges approximately between 1000 and 2000 km. The transmission paths to West and East stations were entirely in the Sargasso Sea. The path to North station crossed the Gulf Stream and so traversed one of the most time- and range-dependent environments found anywhere in the ocean. Arrivals at all three stations were stable and could be identified from range-dependent ray traces. Travel times at West station clearly change is response to the warming of the seasonal thermocline from spring to summer. The travel-time change with predictions. Travel-time changes at North station primarily respond to the north-south meandering of the Gulf Stream.
A new voltage driving pixel circuit for active matrix organic light emitting diodes (2005)

A new voltage driving pixel circuit composed of five TFTs and two capacitors for AMOLED is proposed. The simulation results indicate that the proposed circuit is effective to provide a uniform output characteristic against the variation in the poly-Si TFT performances. 1.
Commentary: RBE in proton therapy – where is the experimental in vivo data? (2019)

TEST 02 - Elsevier's Scopus, the largest abstract and citation database of peer-reviewed literature. Search and access research from the science, technology, medicine, social sciences and arts and humanities fields.
Transition from spin-density-wave to layered antiferromagnetic state induced by hydrogen as a test for the origin of spin-density waves in chromium (2009)

Neutron scattering experiments of Cr/V(001) superlattices are discussed, which show that the incommensurate spin-density-wave (SDW) in thick Cr layers becomes suppressed when the V spacer layers are loaded with hydrogen. The hydrogen loading triggers a transition from the incommensurate SDW state to a commensurate antiferromagnetic state. Model Hamiltonian calculations are presented, which show that this transition is not connected with the nesting property of the Cr Fermi surface. Instead, the transition is a manifestation of the antiferromagnetic ground state of Cr, which is separated from the incommensurate SDW state by an energy barrier. Hydrogen is identified as an effective trigger for reducing the activation barrier, enabling the system to relax to the ground state.
Parallel imaging performance of 16 channels dedicated breast coils at 3T (2010)

Poster: ECR 2010 / C-3263 / Parallel imaging performance of 16 channels dedicated breast coils at 3T by: H. Momo Jeufack, L. Vidarsson, C. Piron, D. B Plewes; Toronto, ON/CA
Emerging hiPSC Models for Drug Discovery in Neurodegenerative Diseases (2021)

Neurodegenerative diseases affect millions of people worldwide and are characterized by the chronic and progressive deterioration of neural function. Neurodegenerative diseases, such as Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), and Huntington's disease (HD), represent a huge social and economic burden due to increasing prevalence in our aging society, severity of symptoms, and lack of effective disease-modifying therapies. This lack of effective treatments is partly due to a lack of reliable models. Modeling neurodegenerative diseases is difficult because of poor access to human samples (restricted in general to postmortem tissue) and limited knowledge of disease mechanisms in a human context. Animal models play an instrumental role in understanding these diseases but fail to comprehensively represent the full extent of disease due to critical differences between humans and other mammals. The advent of human-induced pluripotent stem cell (hiPSC) technology presents an advantageous system that complements animal models of neurodegenerative diseases. Coupled with advances in gene-editing technologies, hiPSC-derived neural cells from patients and healthy donors now allow disease modeling using human samples that can be used for drug discovery.
Predicting Mortality of Intensive Care Patients via Learning about Hazard (2017)

Patients in intensive care units (ICU) are acutely ill and have the highest mortality rates for hospitalized patients. Predictive models and planning system could forecast and guide interventions to prevent the hazardous deterioration of patients’ physiologies, thereby giving the opportunity of employing machine learning and inference to assist with the care of ICU patients. We report on the construction of a prediction pipeline that estimates the probability of death by inferring rates of hazard over time, based on patients’ physiological measurements. The inferred model provided the contribution of each variable and information about the influence of sets of observations on the overall risks and expected trajectories of patients.
Polarization modulation of cruciform vertical-cavity laser diodes (1994)

We demonstrate electrical switching and modulation between two orthogonal polarization modes of air-post vertical-cavity surface emitting lasers with cruciform transverse cavity geometry. The continuous-wave lasing emission is switched from one polarization mode to the orthogonal mode at frequencies up to 50 MHz by a small signal modulation of the injection current. Furthermore, a polarized output signal at twice the input frequency is generated at frequencies up to 10 MHz by a large signal modulation of the injection current from below threshold to above the polarization switching transition.
Bovine seminal ribonuclease produced from a synthetic gene (1993)

Bovine seminal ribonuclease (BS-RNase), a homolog of bovine pancreatic ribonuclease (RNase A), is isolated as a dimer in which the subunits are cross-linked by two disulfide bonds. In addition to this anomalous quaternary structure, the enzyme has extraordinary biological properties, such as antispermatogenic, antitumor, and immunosuppressive activities. The molecular bases for these properties are well-suited for exploration with the techniques of recombinant DNA. Accordingly, a gene encoding BS-RNase was designed based on criteria expected to maximize the translational efficiency of its mRNA in Escherichia coli. This gene was constructed from 12 synthetic oligonucleotides and expressed with the phage T7 system. The protein thus produced was insoluble and accumulated under optimal conditions to 15% of total cellular protein or 200 mg/liter of culture. Ribonuclease activity was generated by air oxidation of the reduced and denatured protein. Three forms of active BS-RNase were isolated by gel filtration chromatography: the well-characterized dimer and monomer and a previously uncharacterized form that migrated as a trimer. The ribonuclease activities of all three forms were equivalent to or higher than that of dimeric BS-RNase isolated from bull seminal plasma.