gebhart/patrepeval huggingface dataset:
miRNA signaling networks in cancer stem cells (2021)

Cancer stem cells (CSCs) are a small cell subpopulation in many cancer types and are involved in various processes of tumor progression, such as initiation, metastasis and recurrence. The distinguished features of CSCs include a variety of biological properties, including self-renewal, multidifferentiation, stemness marker expression, and resistance to chemotherapy and radiotherapy. Despite their great potential of clinical importance, the CSC signaling pathways are not well understood at the molecular level. MicroRNAs (miRNAs) are a class of endogenous noncoding RNAs that play an important role in the regulation of several cellular, physiological, and developmental processes. Aberrant miRNA expression is associated with many human diseases, including cancer. miRNAs have been implicated in the regulation of CSC properties; therefore, a better understanding of miRNA-induced modulation of CSC gene expression could aid in the identification of promising biomarkers and therapeutic targets. In the present review, we summarize the major findings of the impacts of miRNAs on CSC signaling networks; we then discuss the recent advances that have improved our understanding of CSC regulation by miRNA-mediated signaling networks and that may lead to the development of miRNA therapeutics specifically targeting CSCs.
Synthesis of Z-(pinacolato)allylboron and Z-(pinacolato)alkenylboron compounds through stereoselective catalytic cross-metathesis. (2013)

The first examples of catalytic cross-metathesis (CM) reactions that furnish Z-(pinacolato)allylboron and Z-(pinacolato)alkenylboron compounds are disclosed. Products are generated with high Z selectivity by the use of a W-based monoaryloxide pyrrolide (MAP) complex (up to 91% yield and >98:2 Z:E). The more sterically demanding Z-alkenylboron species are obtained in the presence of Mo-based MAP complexes in up to 93% yield and 97% Z selectivity. Z-selective CM with 1,3-dienes and aryl olefins are reported for the first time. The utility of the approach, in combination with catalytic cross coupling, is demonstrated by a concise and stereoselective synthesis of anticancer agent combretastatin A-4.
Design of a single‐stage mechanical fat separator (1997)

Abstract Thermal fractionation of highly saturated fats can address the current nutritional concerns related to the amount, type, and saturated‐fat level of lipids in foods. Separation of fats into different melting fractions allows for tailoring natural fats into functional and nutritional groups, while also allowing for the use of the less desirable fractions in nonfood applications. The single‐stage laboratory‐scale separator described herein separates fats into two gross melting fractions, termed high and low. The latter fractions can be further separated by adjusting the cooling zone temperatures, resulting in secondary fractions with different melt patterns. Thermal analysis of the hard fractions shows a 10–15°C shift to a higher melting point.
10.7 Gb/s Over 300 m GI-MMF Using a 2 × 2 MIMO System Based on Mode Group Diversity Multiplexing (2007)

We investigate experimentally the feasibility of a 2x2 MIMO system based on mode group diversity multiplexing to enlarge the bandwidth distance product of MMF. A data rate of 10.7Gb/s over 300m GI-MMF is achieved.
Trace-Gas Spectroscopy of Methane Using a Monolithically Integrated Silicon Photonic Chip Sensor (2019)

We present a monolithically integrated photonic sensor incorporating an on-chip 111- V laser, detector, sealed reference cell, and sensing waveguide capable of near-infrared absorption spectroscopy of methane near λ = 1651 nm. Sub-100 pprnv-Hz−1/2 sensitivities are demonstrated. © 2019 The Author(s)
Shear-induced ordering kinetics of a triblock copolymer melt (1998)

Disorder-to-order transitions, in which an isotropic system acquires a spatially periodic structure, are common to a number of phenomena in materials science. Here, we employ small-angle neutron scattering to probe the effects of reciprocating shear on the isotropic-to-lamellar transition of a triblock copolymer composed of poly(ethylene-co-propylene) (PEP) and poly(ethylethylene) (PEE). Prior work has shown that the transition temperature decreases with increasing shear rate, implying that the isotropic state can be produced at low temperatures through application of a flow field [T. Tepe et al., J. Rheol. 41, 1147 (1987)]. Removing this field results in a “jump” to conditions under which the lamellar phase is stable with a time scale set by the relaxation of concentration fluctuations. We describe the ordering process which results, concentrating on the possible existence of a stability limit for the initial (isotropic) state.
Abstract 13100: Genetic Ablation of Astrocyte-specific Angiotensin II Type 1 Receptors Improves Prognosis of Myocardial Infarction-Induced Heart Failure (2014)

Introduction: Abnormal sympathoexcitation worsens the prognosis of myocardial infarction (MI)-induced heart failure. We and other investigators revealed that activated brain angiotensin II type 1 receptors (AT1R) cause sympathoexcitation via oxidative stress. Previous reports, however, focused on neuronal AT1R despite the greater abundance of astrocytes than neurons in the brain, because normal astrocytes have few AT1R. Several very recent reports demonstrated that astrocytes are involved in the pathophysiology of MI-induced heart failure, but it remains unknown whether AT1R activation in the neurons or astrocytes is more crucial in MI-induced heart failure. We investigated the hypothesis that astrocytic AT1R activation plays a key role in the prognosis and left ventricular (LV) remodeling of MI-induced heart failure by genetic ablation of astrocyte-specific AT1R. Methods and Results: Using the Cre-LoxP system, we generated astrocyte-specific AT1R knockout mice (CKO-mice). At 30 days after MI, LV size and heart weight of CKO-mice were significantly smaller than those of control-MI mice (LV end-diastolic/systolic dimension: 5.0±0.1/4.5±0.1 vs. 6.1±0.1/5.6±0.1 mm, n=6, p Conclusions: Genetic ablation of astrocytic AT1R significantly improved survival prevented LV remodeling and sympathoexcitation in MI-induced heart failure. These findings indicate that astrocytic AT1R, not neuronal AT1R, have a key role in the pathophysiology of MI-induced heart failure.
Modelling Microstructures with OOF2 (2009)

OOF2 is a program designed to compute the properties and local behaviour of material microstructures, starting from a two-dimensional representation, an image, of arbitrary geometrical complexity. OOF2 uses the finite element method to resolve the local behaviour of a material, and is designed to be used by materials scientists with little or no computational background. It can solve for a wide range of physical phenomena and can be easily extended. This paper is an introduction to some of its most basic and important features.
Ligand Exchange in Tungsten−Rhenium Acetylide Complexes (C5Me5)WRe(μ-X)(CCPh)(CO)5, X = Br, I, SPh, and O2CMe, and the Conversion to Complexes LWRe(μ-SO2Ph)(CCPh)(CO)5, L = Cp and C5Me5, Bearing a Sulfinate Bridge via Oxidation Using Hydrogen Peroxide (1998)

Heterobimetallic acetylide compounds (C5Me5)WRe(μ-X)(CCPh)(CO)5, X = I and Br (1a,b), were obtained in high yields from the combination of (C5Me5)W(CO)3(CCPh) and Re(CO)5X, X = Br and I. These complexes possess a nearly symmetrical halide bridge and an acetylide ligand, linked to the W atom via σ-bonding and to the Re atom via a π-interaction. The conversion to the corresponding thiolate and acetate complexes LWRe(μ-X)(CCPh)(CO)5 [L = C5Me5, X = SPh (2a) and O2CMe (3); X = SPh, L = Cp (2b)] was realized by reactions of the halide complexes with thiophenol or with acetic acid, respectively, in the presence of triethylamine or pyridine. Related reactions of (C5Me5)W(CO)3(CCPh) with [Re(CO)4(μ-SPh)]2 or with [Re(CO)4(μ-O2CMe)]2 afforded the identical thiolate and acetate complexes through a reaction sequence involving the dissociation of these dimeric starting materials. Reactions of 1−3 with P(OMe)3 were also examined, and only the thiolate complex 2a gave the isolated monosubstituted complex (C5Me5)WRe(μ-SPh)(CCPh)(CO)4[P(OMe)3] (4) in good yield. Oxidation of the bridging thiolate ligand in 2a,b using 30% H2O2 solution yielded sulfinate complexes with the formula LWRe(μ-SO2Ph)(CCPh)(CO)5, L = C5Me5 (6) and L = Cp (7, 8). Two linkage isomers were characterized by single-crystal X-ray diffraction studies: One bears a μ-η2-SO2Ph ligand with the bridging oxygen atom coordinated to the W atom, while in the second the bridging oxygen atom is coordinated to the Re atom. The isomerization caused by the interchange of the bridging and the terminal oxygen atom of the sulfinate group is discussed.
Adverse Events Following SARS-CoV-2 mRNA Vaccination Among Patients with Inflammatory Bowel Disease (2021)

Patients with immune-mediated inflammatory diseases (IMID) such as inflammatory bowel disease (IBD) on immunosuppressive and biologic therapies were largely excluded from SARS-CoV-2 mRNA vaccine trials. We thus evaluated post-mRNA vaccination adverse events (AE) in 246 vaccinated adults with IBD participating in a longitudinal vaccine registry. In general, AE frequency was similar to that reported in the general population. As in the general population, AE were more common among younger patients, and those with prior COVID-19. We additionally found that AE were less common in individuals receiving biologic therapy. Those with IBD and other IMID on these commonly prescribed therapies can be reassured that the AE risk is likely not increased, and may be reduced, while on biologics.
Figure S1 from Impact of Prior Treatment on the Efficacy of Adoptive Transfer of Tumor-Infiltrating Lymphocytes in Patients with Metastatic Melanoma (2023)

&lt;p&gt;A CONSORT diagram of patients on trials not previously reported&lt;/p&gt;
Ultrastructural defects of collagen VI filaments in an Ullrich syndrome patient with loss of the α3(VI) N10‐N7 domains (2005)

Ultrastructural alterations of collagen VI in cultured fibroblasts and reduced collagen VI immunostaining in the papillary dermis and endomysium were detected in a patient with a mild form of Ullrich congenital muscular dystrophy caused by a COL6A3 gene mutation. The patient had been previously demonstrated to express an alpha3(VI) chain shorter than normal due to skipping of the mutated exon. We show that collagen VI filaments are not organized in a normal network in the extracellular matrix secreted by patient's cultured fibroblasts. Moreover, we demonstrate that in this patient the alpha3(VI) chain is produced in lower amounts and it is almost exclusively represented by the shorter, alternatively spliced N6-C5 isoform. These results suggest that different alpha3(VI) chain isoforms, containing also domains of the N10-N7 region, are required for assembling a proper collagen VI network in the extracellular matrix.
Learning Generative Models with Visual Attention (2013)

Attention has long been proposed by psychologists to be important for efficiently dealing with the massive amounts of sensory stimulus in the neocortex. Inspired by the attention models in visual neuroscience and the need for object-centered data for generative models, we propose a deep-learning based generative frame-work using attention. The attentional mechanism propagates signals from the region of interest in a scene to an aligned canonical representation for genera-tive modeling. By ignoring scene background clutter, the generative model can concentrate its resources on the object of interest. A convolutional neural net is employed to provide good initializations during posterior inference which uses Hamiltonian Monte Carlo. Upon learning images of faces, our model can robustly attend to the face region of novel test subjects. More importantly, our model can learn generative models of new faces from a novel dataset of large images where the face locations are not known. 1
Hypothermic cardiopulmonary bypass as a determinant of late thrombocytopenia following cardiac operations in pediatric patients (2009)

LTCP was related to a combination of factors (operation severity, degree of hypothermia during CPB, prolonged use of unfractionated heparin, and milrinone). The individual contribution of each factor seems difficult to establish. However, the degree of hypothermia during CPB and drug-associated effects were identified. HIT could be excluded in all cases.
Use of respiratory biofeedback and CLAWS for increased navigator efficiency for imaging the thoracic aorta (2011)

A novel technique to guide a subjects' breathing pattern using a respiratory biofeedback (rBF) "game" to improve respiratory efficiency is presented. The continuously adaptive windowing strategy, a fully automatic and highly efficient free-breathing navigator gated technique, is used to acquire the data as it ensures that all potential navigator acceptance windows are possible. This enables the rBF to be fully adaptable to a subject's respiratory pattern. Images of the thoracic aorta acquired using balanced steady-state free precession with continuously adaptive windowing strategy respiratory motion control, with and without rBF, were compared in 10 healthy subjects. Total scan time was reduced by using rBF. The mean scan time was reduced from 7 min 44 s (463 cardiac cycles, ± 127 cc) without rBF to 5 min 43 s (380 cardiac cycles, ± 118 cc) with the use of rBF (P < 0.05). Respiratory efficiency was increased from 45% without rBF to 56% with rBF (P < 0.01). Image quality was the same for both techniques (P = ns). In conclusion, rBF significantly improved respiratory efficiency and reduced acquisition duration without affecting image quality.
Surface Analysis of the Rear-Flank Downdraft Outflow in Two Tornadic Supercells (2008)

Abstract The rear-flank downdraft regions of two tornadic supercells were sampled on 12 June 2004 and 9 June 2005 using four “mobile mesonet” probes. These rear-flank downdraft outflows were sampled employing two different data collection routines; therefore, each case is described from a different perspective. The data samples were examined to identify variations in measured surface equivalent potential temperature, virtual potential temperature, and kinematics. In the 12 June 2004 case, the tornadic circulation was accompanied by small equivalent potential temperature deficits within the rear-flank downdraft outflow early in its life followed by increasing deficits with time. Virtual potential temperature deficits modestly increased through the duration of the sample as well. The 9 June 2005 case was highlighted by heavy precipitation near the tornado itself and relatively small negative, or even positive, equivalent and virtual potential temperature perturbations. Large horizontal variations of surface thermodynamic properties were also noted within several regions of this rear-flank downdraft outflow.
De novo design of a biologically active amyloid (2016)

Most human proteins possess amyloidogenic segments, but only about 30 are associated with amyloid-associated pathologies, and it remains unclear what determines amyloid toxicity. We designed vascin, a synthetic amyloid peptide, based on an amyloidogenic fragment of vascular endothelial growth factor receptor 2 (VEGFR2), a protein that is not associated to amyloidosis. Vascin recapitulates key biophysical and biochemical characteristics of natural amyloids, penetrates cells, and seeds the aggregation of VEGFR2 through direct interaction. We found that amyloid toxicity is observed only in cells that both express VEGFR2 and are dependent on VEGFR2 activity for survival. Thus, amyloid toxicity here appears to be both protein-specific and conditional-determined by VEGFR2 loss of function in a biological context in which target protein function is essential.
Coherent x-rays from ultrafast lasers, and applications--attosecond science meets nonlinear optics (2009)

Ultrafast short-wavelength light sources using high-harmonic generation provides a tabletop coherent EUV light source for new science. Recent rapid advances show that bright sources at soft and even hard x-ray wavelengths are now feasible.
System-Level Throughput Evaluations in Evolved UTRA (2006)

This paper presents simulation results on the achievable spectrum efficiency, user throughput, and peak data rate in the orthogonal frequency division multiplexing (OFDM) based evolved UTRA (E-UTRA) downlink and single-carrier frequency division multiple access (SC-FDMA) based uplink in order to clarify the link-level performance gain of E-UTRA compared to high-speed downlink packet access (HSDPA) and enhanced DCH (E-DCH). The simulation results show that in the OFDM based downlink, the spectrum efficiency is increased to approximately 230% compared to that for HSDPA at the activity factor of approximately 0.6-0.8, and that the user throughput at the cumulative distribution function (CDF) of 5% and the average user throughput are increased to greater than 200 and 300%, respectively, compared to those for HSDPA at the spectrum efficiency of less than 0.6 bps/Hz. Moreover, in the SC-FDMA based uplink, the spectrum efficiency of E-UTRA is improved to approximately 190% compared to that for E-DCH, and the user throughput at the CDF of 5% and average user throughput are greater than 200% that of E-DCH. In the downlink employing 2-by-2 multiple-input multiple-output (MIMO) multiplexing with a 20-MHz transmission bandwidth, the target peak data rate of 100 Mbps is achieved at the average received signal energy per symbol-to-noise power spectrum density ratio (E <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">s</sub> /N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> ) of approximately 23.5 dB using 64QAM and turbo coding with R=3/4 employing QRM-MLD, i.e., maximum likelihood detection using QR decomposition and the M-algorithm, with adaptive selection of surviving symbol replica candidates (ASESS). Furthermore, in the uplink assuming single-antenna transmission and two-branch antenna diversity reception, the target peak data rate of 50 Mbps is achieved at the average received E <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">s</sub> /N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> of approximately 23 dB using 16QAM associated with the coding rate of R=8/9
A Framework and Comparative Analysis of Control Plane Security of SDN and Conventional Networks (2017)

Software defined networking implements the network control plane in an external entity, rather than in each individual device as in conventional networks. This architectural difference implies a different design for control functions necessary for essential network properties, e.g., loop prevention and link redundancy. We explore how such differences redefine the security weaknesses in the SDN control plane and provide a framework for comparative analysis which focuses on essential network properties required by typical production networks. This enables analysis of how these properties are delivered by the control planes of SDN and conventional networks, and to compare security risks and mitigations. Despite the architectural difference, we find similar, but not identical, exposures in control plane security if both network paradigms provide the same network properties and are analyzed under the same threat model. However, defenses vary; SDN cannot depend on edge based filtering to protect its control plane, while this is arguably the primary defense in conventional networks. Our concrete security analysis suggests that a distributed SDN architecture that supports fault tolerance and consistency checks is important for SDN control plane security. Our analysis methodology may be of independent interest for future security analysis of SDN and conventional networks.
AntShield: On-Device Detection of Personal Information Exposure (2018)

Mobile devices have access to personal, potentially sensitive data, and there is a growing number of applications that transmit this personally identifiable information (PII) over the network. In this paper, we present the AntShield system that performs on-device packet-level monitoring and detects the transmission of such sensitive information accurately and in real-time. A key insight is to distinguish PII that is predefined and is easily available on the device from PII that is unknown a priori but can be automatically detected by classifiers. Our system not only combines, for the first time, the advantages of on-device monitoring with the power of learning unknown PII, but also outperforms either of the two approaches alone. We demonstrate the real-time performance of our prototype as well as the classification performance using a dataset that we collect and analyze from scratch (including new findings in terms of leaks and patterns). AntShield is a first step towards enabling distributed learning of private information exposure.
Crystal structure refinement of ferroelectric rochelle salt (1974)

The crystal structure of Rochelle salt has been refined at 0°C, where the crystal is ferroelectric. Intensity data were collected on a fully automatic four-circle neutron diffractometer. An external dc field of 90 V was applied along the ferroelectric a-axis of the specimen during the course of measurement. The R-factor of 0.102 were obtained.
Fast power network analysis with multiple clock domains (2007)

This paper proposes an efficient analysis flow and an algorithm to identify the worst case noise for power networks with multiple clock domains. First, we apply the Laplace transform on the input current sources to derive the analytical formula. Then, we calculate the circuit frequency response with logarithmic scale frequency components. The frequency domain response is approximated by a rational function using vector fitting modeling. The rational function is used to derive the natural frequency of the power ground networks, and can be converted back into time domain easily. Based on the analysis results, we then present the worst case clock gating pattern algorithm to analyze the power networks with multiple clock domains. The most expensive part of the proposed algorithm is the matrix solving: O(F(N) ldr log f ldr D). Function F is the complexity of iterative solution of complex matrix with dimension N. We assume that there are D clock domains and the frequency spans from 0 to f Hz. Experimental results show that our method is up to 60X faster than HSPICE, and can analyze large circuits which are not affordable by HSPICE.
Bacterial Cell‐Free System for Highly Efficient Protein Synthesis (2007)

This chapter contains sections titled: Overview Introduction Coupled Transcription–Translation System based on E. coli Extract DNA Template Construction Preparation of Cell Extract from E. coli Batch-mode Cell-free Reaction Dialysis-mode Cell-free Reaction Template DNA Reaction Temperature Surface Area of the Dialysis Membrane Stable-isotope Labeling for NMR Spectroscopy Selenomethionine Incorporation for X-Ray Crystallography Automation Conclusion References