gebhart/patrepeval huggingface dataset:
Abstract LB-014: Targeting insulin receptor splicing as a therapeutic intervention for pediatric rhabdomyosarcoma (2016)

Abstract The insulin receptor (IN-R) alternatively spliced variant A, encoding a receptor lacking exon 11, is the predominant isoform expressed in both pediatric sarcoma cells and vascular endothelial cells. Exon 11 of the IN-R gene is composed of 36 nucleotides that encode 12-amino acids that reside at the carboxyl terminus of the alpha subunit. Though only a small change in the protein composition, deletion of these 12 amino acids results in a receptor that has increased binding affinity for the IGF-2 growth factor and is exquisitely capable of responding to autocrine and paracrine signaling. Cells expressing both the IN-R A variant and the IGF-2 growth factor are therefore programmed for growth and angiogenesis, two essential steps in tumorigenesis. Furthermore, the IGF-2 can maintain angiogenesis through IN-R A when the IGF-1 receptor is blocked. We also demonstrate that hypoxia induces IN-R alternative splicing. This finding is particularly intriguing since recent studies have shown that adaptation to hypoxic environments is a hallmark of the neoplastic phenotype. We therefore hypothesize that the expression of splicing factors is altered by hypoxia leading to the generation of the IN-R A isoform, which contributes to cancer progression beyond the micrometastatic stage. To characterize sequence elements and RNA binding proteins in the regulation of IN-R alternative splicing, we have designed a hypoxia-induced splicing system that recapitulates the IN-R splicing seen in tumors. We have shown that sequence elements flanking the regulated exon are important for the hypoxia-induced splicing changes. Furthermore, have performed an antisense oligonucleotide (ASO) walk to target these splicing enhancer and repressor sequences to interfere with IN-R splicing. We have successfully targeted the CUGBP1 negative regulator of splicing that resides in intron 10 to increase the IN-R B full-length isoform. We have shown that an ASO used to drive production of the IN-R B isoform in a rhabdomyosarcoma (RMS) cell line, which normally expresses the IN-R A isoform, affects cancer cell behavior to induce reduced motility and cell migration. We therefore postulate that modulation of the splicing of the IN-R, alone or in conjunction with IGF-1R blocking antibodies, could be used as a therapeutic intervention in pediatric RMS cells. Citation Format: Dawn S. Chandler, Chelsea Brown, Hemant Bid, Thomas Bebee, Daniel F. Comiskey, Frank Rigo, Peter J. Houghton. Targeting insulin receptor splicing as a therapeutic intervention for pediatric rhabdomyosarcoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-014.
Charged-particle multiplicities in pp interactions at s=900 GeV measured with the ATLAS detector at the LHC (2010)

The first measurements from proton–proton collisions recorded with the ATLAS detector at the LHC are presented. Data were collected in December 2009 using a minimum-bias trigger during collisions at a centre-of-mass energy of 900 GeV. The charged-particle multiplicity, its dependence on transverse momentum and pseudorapidity, and the relationship between mean transverse momentum and charged-particle multiplicity are measured for events with at least one charged particle in the kinematic range |η|<2.5 and pT>500 MeV. The measurements are compared to Monte Carlo models of proton–proton collisions and to results from other experiments at the same centre-of-mass energy. The charged-particle multiplicity per event and unit of pseudorapidity at η=0 is measured to be 1.333±0.003(stat.)±0.040(syst.), which is 5–15% higher than the Monte Carlo models predict.
Inhibition of myo-Inositol-1-phosphate Synthase by a Reaction Coordinate Intermediate (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInhibition of myo-Inositol-1-phosphate Synthase by a Reaction Coordinate IntermediateMarie E. Migaud and J. W. FrostCite this: J. Am. Chem. Soc. 1995, 117, 18, 5154–5155Publication Date (Print):May 1, 1995Publication History Published online1 May 2002Published inissue 1 May 1995https://pubs.acs.org/doi/10.1021/ja00123a019https://doi.org/10.1021/ja00123a019research-articleACS PublicationsRequest reuse permissionsArticle Views198Altmetric-Citations12LEARN 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-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Measurement of cross-correlation of fluctuations of dipolar couplings and anisotropic chemical shifts by selective spin locking (1992)

New experimental methods are presented that allow one to measure cross-correlation between the fluctuations of dipolar interactions and chemical shift anisotropy (CSA) in scalar coupled systems with two and three spins I = ½ in isotropic solution. The methods involve selective excitation of the transverse magnetization I A x of a chosen spin A, followed by selective spin locking of this magnetization. If the spin locking radiofrequency (RF) field is exactly on-resonance for spin A while leaving the other spins M and X unaffected, there is no cross-relaxation (Overhauser effect) in the rotating frame, i.e., no transfer from I A x to I M x or I X x . By contrast, cross-correlation between different relaxation mechanisms may give rise to single-quantum coherences of higher rank. In particular, CSA-dipolar cross-correlation may lead to a partial conversion of I A x into 2I A x I M z or 2I A x I X z , while interference between two dipole-dipole interactions leads to the appearance of terms such as 4I A x I M z I X z . After spin locking, selective pulses allow one to convert 2I A x I M z first into longitudinal two-spin order 2I A z I M z and, subsequently, into observable coherence 2I A z I M x . Similarly, 4I A x I M z I X z can be converted into 4I A z I M x I X z or 4I A z I M z I X x via 4I A z I M z I X z . The resulting signals, which can be recorded in one- or two-dimensional fashion, are directly proportional to the amount of 2- and 3-spin order created during the spin locking period. The cross-correlation rates may be measured from the build-up behaviour as a function of the duration of spin locking. Expressions are given for all relevant relaxation rates in 2- and 3-spin systems under arbitrary spin locking angles, including the effects of chemical shift anisotropy, thus generalizing the work of T. E. Bull (1988, J. magn. Reson., 80, 470). In the rotating frame, the effects of cross-correlation do not vanish in the slow-motion limit, in contrast to the situation in the laboratory frame, where the transformation of I A z into 2I A z I M z , 2I A z I X z or 4I A z I M z I X z only occurs if the spectral densities of cross-correlation have nonvanishing amplitudes at the Larmor frequency. Selective spin-locking experiments therefore allow one to measure cross-correlation regardless of motional correlation times.
ATP Synthase, a Target for Dementia and Aging? (2018)

Advancing age is the biggest risk factor for development for the major life-threatening diseases in industrialized nations accounting for >90% of deaths. Alzheimer's dementia (AD) is among the most devastating. Currently approved therapies fail to slow progression of the disease, providing only modest improvements in memory. Recently reported work describes mechanistic studies of J147, a promising therapeutic molecule previously shown to rescue the severe cognitive deficits exhibited by aged, transgenic AD mice. Apparently, J147 targets the mitochondrial alpha-F1-ATP synthase (ATP5A). Modest inhibition of the ATP synthase modulates intracellular calcium to activate AMP-activated protein kinase to inhibit mammalian target of rapamycin, a known mechanism of lifespan extension from worms to mammals.
Solvent‐Free Syntheses of Hierarchically Porous Aluminophosphate‐Based Zeolites with AEL and AFI Structures (2014)

Development of sustainable routes for synthesizing aluminophosphate-based zeolites are very important because of their wide applications. As a typical sustainable route, solvent-free synthesis of zeolites not only decreases polluted wastes but also increases product yields. Systematic solvent-free syntheses of hierarchically porous aluminophosphate-based zeolites with AEL and AFI structures is presented. XRD patterns and SEM images show that these samples have high crystallinity. N2 sorption isotherm tests show that these samples are hierarchically porous, and their surface areas are comparable with those of corresponding zeolites from hydrothermal route. Chosen as an example, catalytic oxidation of ethylbenzene with O2 shows that cobalt substituted APO-11 from the solvent-free route (S-CoAPO-11) is more active than conventional CoAPO-11 from hydrothermal route owing to the sample hierarchical porosity.
Inwardly rectifying potassium channels (K<sub>IR</sub>) in GtoPdb v.2023.1 (2023)

The 2TM domain family of K channels are also known as the inward-rectifier K channel family. This family includes the strong inward-rectifier K channels (Kir2.x) that are constitutively active, the G-protein-activated inward-rectifier K channels (Kir3.x) and the ATP-sensitive K channels (Kir6.x, which combine with sulphonylurea receptors (SUR1-3)). The pore-forming α subunits form tetramers, and heteromeric channels may be formed within subfamilies (e.g. Kir3.2 with Kir3.3).
Topology Identification of Directed Graphs via Joint Diagonalization of Correlation Matrices (2020)

Discovering connectivity patterns of directed networks is a crucial step to understand complex systems such as brain-, social-, and financial networks. Several existing network topology inference approaches rely on structural equation models (SEMs). These presume that exogenous inputs are available, which may be unrealistic in certain applications. Recently, an alternative line of work reformulated SEM-based topology identification as a three-way tensor decomposition task. This way, knowing the exogenous input correlation statistics (rather than the exogenous inputs themselves) suffices for network topology identification. The downside is that this approach is computationally expensive. In addition, it is hard to incorporate prior information of the network structure (e.g., sparsity and local smoothness) into this framework, while such prior information may help enhance performance when handling real-world noisy data. The present work puts forth a joint diagonalizaition (JD)-based approach to directed network topology inference. JD can be viewed as a variant of tensor decomposition, but features more efficient algorithms, and can readily account for the network structure. Different from existing alternatives, novel identifiability guarantees are derived regardless of the exogenous inputs or their statistics. Three JD algorithms tailored for network topology inference are developed, and their performance is showcased using simulated and real data tests.
SEASONAL AERATION RATES FOR THE EASTERN UNITED STATES BASED ON LONG-TERM WEATHER PATTERNS (2004)

Most aeration fans are sized to produce a minimum airflow rate of 0.1 m3/min/t (0.1 cfm/bu) in on-farm grainstorage structures. At this airflow rate a significant amount of time is required to move a cooling front completely througha bin. The desired grain temperature and prevailing weather conditions will have a significant effect on required fan size.Thirty years of weather data were analyzed for the eastern United States to determine the amount of time available intemperature windows between 0 to 15.C and 0 to 17.C. Contour maps were generated with ArcMap 8.3 for the percentageof each month within the given temperature windows. A substantial amount of time (over 4% of the month) is available withintemperature limits of 0 and 17.C between September and April. This indicates that airflow rates of at least 0.6 m3/min/t(0.5 cfm/bu) would be more adequate to completely move an aeration front through a bin for summer harvested grain inSouthern regions of the United States. However, during July and August only the northern half of the United States wouldhave a sufficient amount of time available for cooling grain below 17.C using an airflow rate of 0.1 m3/min/t (0.1 cfm/bu).The maps generated provide a starting point for sizing aeration fans in the eastern United States.
ChemInform Abstract: Hole‐Transport Materials for Perovskite Solar Cells (2016)

Abstract Review: 138 refs.
Data Supplement from Optimal Effector Functions in Human Natural Killer Cells Rely upon Autocrine Bone Morphogenetic Protein Signaling (2023)

&lt;p&gt;Supplemental Figure S4. Effects of DMH1 on NK cells IFN-y production and proliferation.&lt;/p&gt;
Drop-on-Demand Based Inkjet Printing for Making Patterned Surfaces with Controlled Surface Wetting. (2005)

Synchrotron radiation techniques have enabled us to record meridional x-ray diffraction patterns from frog sartorius muscle at resolutions ranging from approximately 2,800 to 38 nm (i.e., overlapping with the optical microscope and the region normally accessible with low angle diffraction cameras). These diffraction patterns represent the transform of the low resolution structure of muscle projected on the sarcomere axis and sampled by its repeat. Altering the sarcomere length results in the sampling of different parts of this transform, which induces changes in the positions and the integrated intensities of the diffraction maxima. This effect has been used to determine the transform of the mass projection on the muscle axis in a quasicontinuous fashion. The results reveal the existence of maxima arising from long-range periodicities in the structure. Determination of the zeroes in the transforms has been used to obtain phase information from which electron density maps have been calculated. The x-ray diffraction diagrams and the resulting electron density maps show the existence of a series of mass bands, disposed transversely to the sarcomere axis and distributed at regular intervals. A set of these transverse structures is associated with thin filaments, and their 102.0-nm repeat suggests a close structural relationship with their known molecular components. A second set, spaced by approximately 230.0 nm, is also present; from diffraction theory one has to conclude that this repeat simultaneously exists in thick and thin filament regions.
Severe COVID-19 Is Characterised by Perturbations in Plasma Amines Correlated with Immune Response Markers, and Linked to Inflammation and Oxidative Stress (2022)

The COVID-19 pandemic raised a need to characterise the biochemical response to SARS-CoV-2 infection and find biological markers to identify therapeutic targets. In support of these aims, we applied a range of LC-MS platforms to analyse over 100 plasma samples from patients with varying COVID-19 severity and with detailed clinical information on inflammatory responses (>30 immune markers). The first publication in a series reports the results of quantitative LC-MS/MS profiling of 56 amino acids and derivatives. A comparison between samples taken from ICU and ward patients revealed a notable increase in ten post-translationally modified amino acids that correlated with markers indicative of an excessive immune response: TNF-alpha, neutrophils, markers for macrophage, and leukocyte activation. Severe patients also had increased kynurenine, positively correlated with CRP and cytokines that induce its production. ICU and ward patients with high IL-6 showed decreased levels of 22 immune-supporting and anti-oxidative amino acids and derivatives (e.g., glutathione, GABA). These negatively correlated with CRP and IL-6 and positively correlated with markers indicative of adaptive immune activation. Including corresponding alterations in convalescing ward patients, the overall metabolic picture of severe COVID-19 reflected enhanced metabolic demands to maintain cell proliferation and redox balance, alongside increased inflammation and oxidative stress.
Impairment of the Retinal Nerve Fiber Integrity and Blood Flow Velocity in Multiple Sclerosis (P5.224) (2015)

OBJECTIVE: To quantify the retardation of the retinal nerve fiber layer and blood flow velocity in relapsing and remitting multiple sclerosis (RRMS). BACKGROUND: The diffuse cerebral hypoperfusion in MS is reported, but whether it contributes to neurodegeneration or is the result of decreased metabolic demand due to the neurodegeneration remains unclear. The retina has been used to study the pathophysiology of MS. The thinning of the retinal nerve fiber layer (RNFL) has been established as an ocular biomarker of neurodegeneration in MS. The vasculature in the eye and brain are similar anatomically and physiologically. Polarization-sensitive OCT (PS-OCT) is able to detect retardation changes of RNFL which represents the microtubal alteration. DESIGN/METHODS: The right eye of 6 RRMS patients and 16 healthy subjects were imaged using a custom-built PS-OCT. The thickness and retardation of the RNFL were measured. Additionally, those MS patients and 16 healthy subjects were imaged using Retinal Functional Imager (RFI, Optical Imaging, Rehovot, Israel), and the blood flow velocities in the arterioles and venules were measured. RESULTS: Measured by PS-OCT, the thickness and retardation of the RNFL in MS patients were significantly reduced (P < 0.05) compared to the healthy group. Measured by the RFI device, the velocities were 3.33 ± 0.72 mm/s (artery) and 2.73 ± 0.62 mm/s (vein), which were significantly lower than the healthy group 4.03 ± 0.92 mm/s (artery) and 3.24 ± 0.70 mm/s (vein) (P < 0.05). CONCLUSIONS: This study demonstrates that retinal hypoperfusion and the impairment of microtubal function in the retinal nerve fiber layers in MS compared to controls, indicating retinal vascular dysfunction coexists with the retinal microstructural changes in RRMS. Further studies with a larger sample and different stages of MS patients are needed to further elucidate the findings. Study Supported by: NMSS pilot grant, R01EY020607, NIH R01EY020607S.
Micromachined Chemical Reactors for Surface Catalyzed Oxidation Reactions (1996)

A micromachined chemical reactor (µ-reactor) for performing highly exothermic heterogeneous catalytic reactions has been fabricated, and successfully tested for two gas-phase model reaction systems- CO and NH3 oxidations over Pt catalyst. The results demonstrate the feasibility of chemical production on a micro-scale, and suggest that µ-reactors have the potential of safer operation as compared to conventional reactors.
Compression of Dynamic Medical CT Data Using Motion Compensated Wavelet Lifting with Denoised Update (2018)

For the lossless compression of dynamic $3-\mathrm {D}+\mathrm {t}$ volumes as produced by medical devices like Computed Tomography, various coding schemes can be applied. This paper shows that 3-D subband coding outperforms lossless HEVC coding and additionally provides a scalable representation, which is often required in telemedicine applications. However, the resulting lowpass subband, which shall be used as a downscaled representative of the whole original sequence, contains a lot of ghosting artifacts. This can be alleviated by incorporating motion compensation methods into the subband coder. This results in a high quality lowpass subband but also leads to a lower compression ratio. In order to cope with this, we introduce a new approach for improving the compression efficiency of compensated 3-D wavelet lifting by performing denoising in the update step. We are able to reduce the file size of the lowpass subband by up to 1.64%, while the lowpass subband is still applicable for being used as a downscaled representative of the whole original sequence.
Sensitivity to two major allergens (Cry j I and Cry j II) in patients with Japanese cedar (Cryptomeria japonica) pollinosis (1995)

Cry j II is an as important a major allergen as Cry j I.
Integrative model of coronary flow in anatomically based vasculature under myogenic, shear, and metabolic regulation (2017)

Coronary blood flow is regulated to match the oxygen demand of myocytes in the heart wall. Flow regulation is essential to meet the wide range of cardiac workload. The blood flows through a complex coronary vasculature of elastic vessels having nonlinear wall properties, under transmural heterogeneous myocardial extravascular loading. To date, there is no fully integrative flow analysis that incorporates global and local passive and flow control determinants. Here, we provide an integrative model of coronary flow regulation that considers the realistic asymmetric morphology of the coronary network, the dynamic myocardial loading on the vessels embedded in it, and the combined effects of local myogenic effect, local shear regulation, and conducted metabolic control driven by venous O<sub>2</sub> saturation level. The model predicts autoregulation (approximately constant flow over a wide range of coronary perfusion pressures), reduced heterogeneity of regulated flow, and presence of flow reserve, in agreement with experimental observations. Furthermore, the model shows that the metabolic and myogenic regulations play a primary role, whereas shear has a secondary one. Regulation was found to have a significant effect on the flow except under extreme (high and low) inlet pressures and metabolic demand. Novel outcomes of the model are that cyclic myocardial loading on coronary vessels enhances the coronary flow reserve except under low inlet perfusion pressure, increases the pressure range of effective autoregulation, and reduces the network flow in the absence of metabolic regulation. Collectively, these findings demonstrate the utility of the present biophysical model, which can be used to unravel the underlying mechanisms of coronary physiopathology.
Analysis of active filter behaviour by means of modified 𝒵-transform method (2005)

A calculus procedure is suggested based on integral transformations for obtaining a solution in a closed analytical form of the nonlinear mathematical model of active filters. The analytical solution expresses the reactive power and harmonic compensation of active filters as functions of filter parameters. Therefore this solution can be successfully used for obtaining design guidelines. The theoretical procedure is completed by a numerical analysis.