gebhart/patrepeval huggingface dataset:
Identifying regulators of reversible MHC I loss in Merkel cell carcinoma through genome-scale screens (2020)

Abstract Loss of surface MHC I is an important mechanism by which cancer cells evade immune surveillance, and it can correlate with worse prognosis and resistance to immunotherapy. MHC I surface expression can be affected by genomic or transcriptional alterations to HLA-A/B/C, β2M, or the class I antigen processing machinery. In the case of transcriptional loss, we hypothesized that certain cancers might employ specific epigenetic programs to enforce downregulation of the MHC I pathway. Thus, we sought to identify novel MHC I regulators in MHC I-low cancers. In particular, we focused on Merkel cell carcinoma (MCC), a rare but aggressive neuroendocrine skin cancer that is caused by the Merkel cell polyomavirus in 80% of cases. Notably, MHC I downregulation is prevalent in MCC. We first generated and characterized a series of patient-derived MCC cell lines, in which MHC I surface expression was low but inducible with IFN-γ. We then conducted genome-scale CRISPR-KO and open reading frame (ORF) gain-of-function screens in one of our virus-positive MCC lines, using FACS to select for perturbations that upregulated surface MHC I. One of the top hits from these screens was PRC1.1, a non-canonical Polycomb repressive complex. Polycomb complexes are known to mediate gene silencing through chromatin modification and play an important role in development and cancer. These studies suggest a possible role for PRC1.1 in suppressing MHC I in MCC.
Errors In Calculating The Epicardial Potential Gradient Field From Unipolar Voltage Measurements During Cardiac Defibrillation (2005)

We examined the errors generated when calculating the magnitude of the epicardial potential gradient using voltages recorded from three unipolar electrodes in a fixed triangular geometry on the epicardial surface. The error sensitivity of the gradient calculation increases significantly with decreasing electrode separation and increasing common-mode voltage. For example, a mean error in calculated gradient magnitude of 67% results when measuring a 5 V/cm gradient at 50 V common-mode with 2 mm interelectrode spacing and random 1 % voltage error. Optimization of interelectrode spacing and common-mode voltage to reduce overall error is essential for accurate measurement of low magnitude epicardial gradients.
Velocity measurement based on bolus tracking with the aid of three‐dimensional reconstruction from digital subtraction angiography (1997)

The problem of blood flow measurement in x-ray angiography using measurements of the leading edge of the contrast bolus as it traverses the vascular bed is considered. A new technique for velocity measurement is presented based upon the ratio of the temporal derivative to the spatial derivative of the contrast bolus in the direction of flow. With the addition of a small correction factor, the value obtained is shown to reflect the transport velocity, or the velocity at which the contrast is transported down the vessel of interest. Most blood flow measurements based on bolus tracking techniques are actually using the contrast transport velocity to represent the blood flow velocity. Because of the streaming that occurs due to laminary flow conditions, the measured transport velocity is found to be somewhere between the average and the peak (central) fluid velocities for measurements taken during the traversal of the bolus leading edge. The spatial and temporal variation of the transport velocity are found to be consistent with the bolus motion expected in the presence of laminar flow. From x-ray images of contrast passage through simple tubes, we find that the derivative method measures the transport velocity during passage of the bolus leading edge. In most cases of laminar blood flow, the leading edge transport velocity can be 20%-40% higher than the average blood velocity.
Generation of broadband optical combs with high OSNR for CW-THz wave generation by photonic down-conversion (2014)

Generation of broadband optical comb with high OSNR was demonstrated by a combination of a Mach-Zehnder-modulator-based flat comb generator and a nonlinear fiber. To generate broadband combs with high OSNR, we compared three types of nonlinear fibers; a dispersion-flattened dispersion-decreasing fiber (DF-DDF), a dispersion-flattened fiber (DFF) and a highly nonlinear, dispersion-shifted fiber (HNL-DSF). As a result, we found that the HNL-DSF is suitable for THz wave generation in the range of 3 THz.
Reverse Biology Applied toMicrurus corallinus, a South American Coral Snake (1995)

Little is known about the coral snakes venom components. Clarification of the primary structure of polypeptidic toxins was hampered until now by the lack of enough venom for protein purification and chemistry. Using the Reverse Biology approach, several potential Micrurus corallinus toxins were characterized by cDNA cloning. The deduced proteins shared homology with known snake toxins, such as α-neurotoxins, phospholipase A2, natriuretic peptides and lectins. To our knowledge, these are the first complete primary structure characterization of coral snake venom toxins.
Smooth Acceleration Control of Hybrid-Vehicle Based on Constrained Model Predictive Control for Two-Inertia Systems with a Clutch (2021)

A new constrained model predictive control (MPC) based on the smooth acceleration control of a hybrid vehicle modeled as a two-inertia system with a clutch is proposed. The nonlinear characteristics of the clutch are regarded as a linear system for designing the controller. To reduce the shock caused by the clutch engagement, the MPC regulates the torsional torque of the two-inertia system through the clutch torque. The effectiveness of the acceleration control was verified via numerical simulations.
MP35-01 PROSTATE TUMOR TEXTURAL HETEROGENEITY OF 11 C-ACETATE POSITRON EMISSION TOMOGRAPHY AND T2-WEIGHTED MAGNETIC RESONANCE IMAGING CORRELATE WITH BIOCHEMICAL RECURRENCE: PRELIMINARY FINDINGS (2018)

preferences, 26/50 (54%) preferred the Rotterdam app while 24/50 (46%) preferred the Coral App.
Investigation of Heterojunctions and Multiple Quantum Well Structures Using Crystalline Organic Semiconductors (1993)

A new class of engineered materials based on crystalline organic semiconductors grown by the ultrahigh vacuum process of organic molecular beam deposition is described. The objective of this program is to investigate these materials and the conditions which lead to ordered growth between highly lattice mismatched van der Waals crystals into novel 'quasi-epitaxial' structures. During the first year of the program, considerable progress has been made in understanding and exploiting this new class of materials. In particular, a simple model has been developed which describes the physical mechanisms underlying quasi-epitaxy. The electrical and optical properties of both single and multiple heterojunction structures grown using alternating layers of two different, lattice-mismatched organic molecules have been investigated in detail. It is found that the layers can be grown sufficiently thin (10 A) to result in exciton confinement in organic multiple quantum wells. These and other quasi-epitaxially grown structures can load to an entirely new family of optoelectronic devices with exciting new electronic and nonlinear optical characteristics.
Investigation of high-Q channel drop filters using donor-type defects in two-dimensional photonic crystal slabs (2003)

This letter describes experimental investigations of surface-emitting channel drop filters using donor-type point defect cavities and line-defect waveguides in two-dimensional photonic crystal slabs. By using donor-type defect cavities with three and four linearly aligned missing air holes, filter quality factors of around 2600 and 6400, respectively, are achieved experimentally, compared to the quality factor of 400 of previous acceptor-type defect cavities. Radiation patterns and polarization properties of light emitted from the defects are also discussed. The results indicate that these donor-type defects are very useful for the development of ultrasmall high-performance channel add/drop filters.
Metal‐Ion‐Coated Graphitic Nanotubes: Controlled Self‐Assembly of a Pyridyl‐Appended Gemini‐Shaped Hexabenzocoronene Amphiphile (2009)

The assembly line: Hexabenzocoronene amphiphiles appended with pyridyl-terminated triethylene glycol side chains, in combination with trans-[Pt(PhCN)(2)Cl(2)], lead to the formation of graphitic nanotubes. The structural features and dimensions of the nanotubes depend on the assembly conditions. A platinum(II)-bridged cyclic dimer having two HBC units self-assembles into a nanotubular structure.
A policy based approach for QoS-on-demand over the Internet (2002)

This paper describes a systematic policy-based approach for offering differentiated services over a single provider's network. Emerging work in this area both in standards forums as well as in research publications, is heavily focused on the element management problem, i.e., on the specification of policy rules for managing one or more devices. However, an ISP faces the more challenging task of having to offer and deploy end-to-end services across the Internet. We take a virtual leased line service as exemplar, and describe in detail a process through which a customer's request for connectivity between multiple sites is translated into network level policies, validated, admitted, resolved into role level policies, and activated on network devices. Deliberately, this is a "big picture" paper, where we bring together various functional components (such as bandwidth brokers, directories and policy servers) and algorithms (route computation, consistency checking, admission control) to fashion a network management framework for QoS-on-demand.
Nobiletin, a Polymethoxy Flavonoid, Suppresses Bone Resorption by Inhibiting NFκB-Dependent Prostaglandin E Synthesis in Osteoblasts and Prevents Bone Loss Due to Estrogen Deficiency (2011)

Nobiletin, a polymethoxy flavonoid, prevents cancer and inflammation, but the roles of nobiletin in bone are unclear. We examined the effects of nobiletin on bone resorption in vitro and on bone mass in ovariectomized (OVX) mice in vivo. In vitro, nobiletin suppressed osteoclast formation and bone resorption induced by interleukin (IL)-1. Nobiletin suppressed the expression of cyclooxygenase-2, NFκB-dependent transcription, and prostaglandin E (PGE) production induced by IL-1 in osteoblasts. OVX mice showed severe bone loss in the femur by increased bone resorption due to estrogen deficiency, and nobiletin significantly restored the bone mass. Nobiletin could be beneficial to bone health in postmenopausal women.
The feedback capacity of degraded broadcast channels (Corresp.) (1978)

The fact that the capacity region of the discrete memoryless physically degraded broadcast channel is not increased by feedback is established.
Integration of 3D Printed and Micropatterned Polycaprolactone Scaffolds for Guidance of Oriented Collagenous Tissue Formation In Vivo (2016)

Scaffold design incorporating multiscale cues for clinically relevant, aligned tissue regeneration has potential to improve structural and functional integrity of multitissue interfaces. The objective of this preclinical study is to develop poly(ε-caprolactone) (PCL) scaffolds with mesoscale and microscale architectural cues specific to human ligament progenitor cells and assess their ability to form aligned bone-ligament-cementum complexes in vivo. PCL scaffolds are designed to integrate a 3D printed bone region with a micropatterned PCL thin film consisting of grooved pillars. The patterned film region is seeded with human ligament cells, fibroblasts transduced with bone morphogenetic protein-7 genes seeded within the bone region, and a tooth dentin segment positioned on the ligament region prior to subcutaneous implantation into a murine model. Results indicate increased tissue alignment in vivo using micropatterned PCL films, compared to random-porous PCL. At week 6, 30 μm groove depth significantly enhances oriented collagen fiber thickness, overall cell alignment, and nuclear elongation relative to 10 μm groove depth. This study demonstrates for the first time that scaffolds with combined hierarchical mesoscale and microscale features can align cells in vivo for oral tissue repair with potential for improving the regenerative response of other bone-ligament complexes.
PPAR-Induced Fatty Acid Oxidation in T Cells Increases the Number of Tumor-Reactive CD8+ T Cells and Facilitates Anti–PD-1 Therapy (2018)

Although PD-1 blockade cancer immunotherapy has shown potential for a wide range of patients with cancer, its efficacy is limited, in part, due to the loss of effector cytotoxic T lymphocytes (CTLs) via terminal differentiation-induced apoptosis. We previously demonstrated that mitochondrial activation, by the agonists of peroxisome proliferator-activated receptor γ (PPARγ) coactivator 1-α (PGC-1α)/transcription factor complexes, had synergistic effects with a PD-1-blocking monoclonal antibody in a mouse tumor model. In the current study, we examined the molecular mechanism of the synergistic effects of bezafibrate, an agonist of PGC-1α/ PPAR complexes, which enhanced the tumoricidal effects of PD-1 blockade. Bezafibrate activated CTL mitochondria and upregulated oxidative phosphorylation as well as glycolysis, resulting in more proliferation of naïve T cells and improved effector function in CTLs. Bezafibrate also increased fatty acid oxidation (FAO) and mitochondrial respiratory capacity, which supports the extra energy demands of cells in emergencies, allowing cell survival. Carnitine palmitoyl transferase 1 (Cpt1), which is needed for FAO, and Bcl2 were both upregulated. Cpt1 and Bcl2 can form a complex to prevent apoptosis of CTLs. Together, these results indicate that bezafibrate increases or maintains the number of functional CTLs by activating mitochondrial and cellular metabolism, leading in turn to enhanced antitumor immunity during PD-1 blockade. <i>Cancer Immunol Res; 6(11); 1375-87. ©2018 AACR</i>.
No benefit of continuing vs stopping 5‐aminosalicylates in patients with ulcerative colitis escalated to anti‐metabolite therapy (2020)

5-ASA are usually continued long-term even after escalating to anti-metabolite therapy in patients with UC without clinical benefit.
Aberrant Cerebellar–Cerebral Functional Connectivity in Children and Adolescents With Autism Spectrum Disorder (2018)

The cerebellum, which forms widespread functional networks with many areas in the cerebral cortices and subcortical structures, is one of the brain regions most consistently reported to exhibit neuropathological features in patients with autism spectrum disorder (ASD). However, cerebellar functional connectivity (FC) studies in patients with ASD have been very sparse. Using resting state functional connectivity (rsFC) analysis, we investigated the FC of the hemispheric/vermal subregions and the dentate nucleus of the cerebellum with the cerebral regions in 36 children and adolescents [16 participants with ASD, 20 typically developing (TD) participants, age: 6-15 years]. Furthermore, an independent larger sample population (42 participants with ASD, 88 TD participants, age: 6-15 years), extracted from the Autism Brain Imaging Data Exchange (ABIDE) II, was included for replication. The ASD group showed significantly increased or decreased FC between "hubs" in the cerebellum and cerebral cortices, when compared with the TD group. Findings of aberrant FCs converged on the posterior hemisphere, right dentate nucleus, and posterior inferior vermis of the cerebellum. Furthermore, these aberrant FCs were found to be related to motor, executive, and socio-communicative functions in children and adolescents with ASD when we examined correlations between FC and behavioral measurements. Results from the original dataset were partially replicated in the independent larger sample population. Our findings suggest that aberrant cerebellar-cerebral FC is associated with motor, socio-communicative, and executive functions in children and adolescents with ASD. These observations improve the current knowledge regarding the neural substrates that underlie the symptoms of ASD.
Data Reduction and Energy Sustenance in Multisensor Networks for Landslide Monitoring (2014)

We present extensive studies into data reduction and energy minimization in Sensor Networks for landslide detection. What started as a simple homogenous network of rainfall sensors has evolved into a complex heterogeneous network of 20 wireless probes with each probe consisting of four different types of sensors to measure rainfall, moisture, pore pressure, and movement, all of which have been in continuous operation for more than two years in the equatorial forests of Kerala, India. Each probe runs on solar power and the frequency of sensor data measurements from the probes is dynamically and adaptively throttled in real time, based on climatic conditions to minimize the total energy consumption. The probes also work together to identify who among them is sensing the maximum parameter, after which all other sensors are switched off for a predetermined duration. We present detailed analysis of data reduction and energy savings, and also relate them to the effectiveness of landslide detection. The whole system was validated by the issuance of a landslide warning in the month of July (last monsoon season), which facilitated pre-emptive action by the local government and community to prevent loss of human life.
Gate control of surface transport in MBE-grown topological insulator (Bi1−xSbx)2Te3thin films (2012)

Topological insulators are quantum materials comprised of an insulating bulk gap and topologically protected metallic surfaces with a Dirac-like band dispersion. To access the Dirac point by transport measurements is a very challenging issue faced in current investigations of these materials. Here we report the electronic state modulation in topological insulator (Bi${}_{1\ensuremath{-}x}$Sb${}_{x}$)${}_{2}$Te${}_{3}$ thin films by means of an ionic-liquid gating. The films with 20 nm thickness were grown on lattice-matched semi-insulating InP substrates by molecular beam epitaxy; the temperature dependencies of resistance of these films clearly indicate their insulating bulk and metallic surface characteristics. The surface state carriers were systematically controlled by using electric-double-layer transistor (EDLT) configurations with ionic-liquid dielectrics. It was demonstrated that the surface state in the (Bi${}_{1\ensuremath{-}x}$Sb${}_{x}$)${}_{2}$Te${}_{3}$-based EDLTs is tuned across the Dirac point, showing ambipolar transport in a topological transport regime.
Anti-counterfeiting features of artistic screening (1996)

Although Artistic Screening has been designed mainly for performing the creation of graphic designs of high artistic quality, it also incorporates several important anti-counterfeiting features. For example, bank notes or other valuable printed matters produced with Artistic Screening may incorporate both full size and microscopic letters of varying shape into the image halftoning process. In this contribution, we show that frequency modulated screen dots exhibit a strongly position-dependent reproduction behaviour, which is difficult to compensate with devices capable of applying a simple gamma correction curve to the whole image. We present a method for multidimensional gamma-correction, where the dot gain compensation is both dependent on the intensity and on the period of the screen element. This position-dependent dot gain correction can be embedded into any halftoning process capable of generating variable frequency screen elements. Position-dependent dot gain correction ensures the correct appearance of continuous tone images on the target printer for which the compensation tables have been established. Attempts to reproduce the image by electrophotographic means will fail due to the position dependent dot gain induced by the variable frequency screen dots. Correction of position-dependent dot gain would require a tremendous effort from potential counterfeiters
Vascular Remodeling in Mice Lacking the Cytoplasmic Domain of Tissue Factor (2005)

Tissue factor (TF), the cell surface receptor for the serine protease FVIIa supports cell migration by interaction with the cytoskeleton. Intracellular signaling pathways dependent on the cytoplasmic domain of TF modify cell migration and may alter vascular remodeling. Vascular remodeling was analyzed in a femoral artery injury and a blood flow cessation model in mice with a targeted deletion of the 18 carboxy-terminal intracellular amino acids of TF (TF(Deltact/Deltact)) and compared with TF wild-type mice (TF(wt/wt)). Morphometric analysis revealed a decrease in the intima/media ratio after vascular injury in arteries from TF(Deltact/Deltact) compared with TF(wt/wt) mice (femoral artery injury: 2.4+/-0.3 TF(wt/wt) versus 0.6+/-0.3 TF(Deltact/Deltact), n=9 to 10, P=0.002; carotis ligation: 0.45+0.11 TF(wt/wt) versus 0.22+0.03 TF(Deltact/Deltact), n=12 to 14, P=0.09). This was caused by an increase in the media by 54% (P=0.04) in the femoral artery model and by 32% (P=0.03) after carotis ligation and was associated with an increased number of proliferating cells. Isolated aortic smooth muscle cells (SMCs) of TF(wt/wt) mice showed an increased migratory response toward the TF ligand active site-inhibited FVIIa that was abolished in TF(Deltact/Deltact) SMC. In contrast, the unstimulated proliferation rate was increased in TF(Deltact/Deltact) SMC compared with TF(wt/wt) SMCs. Thus, retention of SMCs attributable to a migratory defect and increased proliferation results in thickening of the media and in decrease in neointima formation after arterial injury. TF cytoplasmic domain signaling alters vascular remodeling and, thereby, may play a role in the development of restenosis, atherosclerotic disease, and neovascularization.
Appendicular skeletal muscle mass assessment in dogs: a scoping literature review (2022)

Limb circumference and ultrasound are likely the main modalities that will continue to be used for serial muscle mass measurement in the clinical setting unless a new technology is developed. The reliability of limb circumference is questionable. Several key factors, including measuring tape type, body position, joint angles, and coat clipping, need to be controlled to improve the reliability of limb circumference measurements. Ultrasound may provide a reasonable alternative, but further studies are required to evaluate the reliability of this modality and identify factors that influence ultrasound measurements.
In Silico Design of Optimal Ratio for Co-Administration of Pramlintide and Insulin in Type 1 Diabetes (2013)

We can assert that a valid simulation model of pramlintide action was developed, leading to in silico estimation of optimal pramlintide:insulin co-administration ratio. Clinical trials will confirm (or adjust) this initial estimation.
Proceedings of the 22nd ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems (2014)

This is the proceedings of the 22nd ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems (ACM SIGSPATIAL GIS (2014), held in Dallas, TX USA, November 4--7, 2014. This conference is the twenty-second edition in a series of symposia and workshops that began in 1993 with the aim of promoting interdisciplinary discussions among researchers, developers, users, and practitioners and fostering research in all aspects of geographic information systems, especially in relation to novel systems based on geospatial data and knowledge. The conference provides a forum for original research contributions covering all conceptual, design, and implementation aspects of geospatial data ranging from applications, user interfaces, and visualization to data storage, query processing and indexing. The conference is the premier annual event of the ACM Special Interest Group on Spatial Information (ACM SIGSPATIAL).