gebhart/patrepeval huggingface dataset:
PIP4Kγ as a potential target for Huntington's disease (2017)

Phosphoinositide lipids provide spatial and temporal regulation of cell signaling and membrane traffic. The PI5P‐4‐kinase family is one of the less studied phosphoinositide lipid kinases. These enzymes catalyze the conversion of phosphatidylinositol 5‐phosphate to phosphatidylinositol 4,5‐bis phosphate. A recent study by Vicinanza et al., a suggested that depletion of the PI5P‐4‐kinase, PIP4Kγ promotes a non‐canonical autophagy pathway. Moreover, this depletion reduced the presence of huntingtin‐exon1‐polyglutamine aggregates. Expression of exon1 of huntingtin with an extended polyglutamine tract is a model for huntingtin protein aggregates. To further test the hypothesis that PIP4Kγ is a potential target to reduce huntingtin aggregates, we tested the depletion of PIP4Kγ in cell culture models that express full length mutant huntingtin (mHtt). We determined that depletion of PIP4Kγ, but not PIP4Kα or PIP4Kβ, lowers the levels of mHtt in patient fibroblasts and in immortalized Hdh Q111 mouse striatal neurons. We show that PIP4Kγ‐dependent depletion of mHtt requires lysosomal function because the depletion is blocked by the lysosomal inhibitor, bafilomycin A1. Moreover, we show that depletion of PIP4Kγ increases autophagic flux, as measured by an increase in LC3‐II levels by western blot analysis and an increase in LC3‐II puncta by microscopy. Our studies suggest that PIP4kγ should be further pursued as a target for Huntington's disease. Support or Funding Information This work was supported by AHA postdoctoral fellowship 14POST20480137 (Sai Srinivas Panapakkam Giridharan), NIH grants R01GM050403 and NS064015 (Lois S Weisman) and by HSS funding 1R03MH084839 (Juan Marugan)
Silicon on Lithium Niobate: A Hybrid Electro-Optical Platform for Near- and Mid-Infrared Photonics (2014)

A thin layer of silicon is transferred onto a lithium niobate substrate, forming a hybrid electro-optical platform, on which ring resonators are fabricated and characterized at 1550 nm, showing an optical loss of 3.0±0.5 dB/cm.
Residual Stress Development during Relamination of Woven Composite Circuit Boards (2001)

The manufacture of multilayer circuit boards involves relamination of alternating B-stage woven glass/epoxy prepregs, which act as bonding sheets, C-stage cores and copper foils. The high relamination temperature and mismatch of thermo-mechanical properties between the copper and woven glass/epoxy composite substrate lead to development of residual stresses in the boards. In the current work, numerical and experimental studies are performed to study residual deformation and warpage in a model multilayer circuit board construction of a common composite substrate (7628 fabric style). A numerical procedure based on classical lamination theory with non-isothermal viscoelastic constitutive relations is developed to predict the deformation and residual stress state due to relamination. Experimental values of the substrate stress relaxation modulus and coefficients of thermal expansion (CTE) are used as inputs in the numerical procedure to predict warpage of model circuit boards with a non-symmetric lay-up of 7628 style composite substrate. Boards with exactly the same construction as used in the numerical analysis were fabricated according to the prescribed pressing cycle, and the time dependent warpage measured using an ultrasonic contour scan technique. Comparison of the experimental warpage data with numerical predictions provides insight into the effects of processing cycle and substrate properties on residual stress development.
Antiangiogenic Gene Therapy of Cancer (2007)

It has been well established that tumor growth depends on angiogenesis, the process of continued expansion of endothelial cells from preexisting blood vessels (1,2). Tumors in situ, which are smaller than 3 mm in diameter, exist in a prevascular state and are limited in their ability to grow without perfusion from the blood supply. Without such a neovascularization process, these dormant tumors remain microscopic in size and quiescent for years (1,3). The recruitment of new blood vessels increases the availability of oxygen and metabolites to the tumor and removes waste products. Moreover, this newly formed vasculature facilitates the escape of tumor cells to distant regions of the body, where they may form detectable metastases (4,5). Evidence suggests that new vessel growth from bone marrow-derived endothelial precursor cells also contributes to tumor blood vessel development (6,7).
Force-Detected Magnetic Resonance Imaging of Influenza Viruses in the Overcoupled Sensor Regime (2022)

Ultrasensitive nanomechanical sensors are envisioned to enable nanoscale magnetic resonance imaging (nano-MRI) and other scanning force microscopy applications. However, their sensitivity to very small forces makes such sensors susceptible to unwanted tip-surface interactions that cause bending and instability. This study shows how these noncontact interactions affect scanning force measurements. The authors present strategies to overcome the challenges of overcoupling, which lead to the successful demonstration of faithful nano-MRI reconstruction of individual influenza viruses.
Fabrication of FinFETs by Damage-Free Neutral-Beam Etching Technology (2006)

A high aspect ratio and damage-free vertical ultrathin channel for a vertical-type double-gate MOSFET was fabricated by using low-energy neutral-beam etching (NBE). NBE can completely eliminate the charge build-up and photon-radiation damages caused by the plasma. The fabricated FinFETs realize a higher device performance (i.e., higher electron mobility) than that obtained by using a conventional reactive-ion etching. The improved mobility is well explained by the NB-etched atomically flat surface. These results strongly support the effectiveness of the NB technology for nanoscale CMOS fabrication
Quantitative Snow Stratigraphy and Stability Derived From High-Resolution Penetrometry (2014)

ABSTRACT: Precise measurements of snow structural parameters and stratigraphy are essential to understand and model snow physical processes, in particular with respect to avalanche formation. How-ever, most snow measurements are limited in spatial resolution and by extensive measurement times, and therefore lack practicability for avalanche professionals. The snow micro-penetrometer (SMP), a portable, high-resolution penetrometer allows recording vertical profiles of the penetration resistance quickly and reliably, but so far it was not possible to interpret these profiles with regard to stability. We combine a recently developed statistical model to derive the major snow structural parameters and a new method to derive snow stability parameters solely from SMP measurements. We demonstrate the poten-tial of this combined approach by analyzing a 28 m long transect through Alpine snow at the Steintälli, Davos, Switzerland. The transect consisted of 47 SMP measurements which were made perpendicular to a small ridge, thus capturing a classic terrain feature with changing snow depth. The derived structural and stability parameters were in agreement with independent measurements from snow profiles and sta-bility tests. Modeled critical cut length were smaller in the areas with larger snow depth, where the higher load of the slab appeared to be the main driver. The weak layer was located at the transition towards depth hoar at the base of the snowpack, which was consistently present throughout the whole length of the transect. Our approach provides a valuable starting point for further modeling efforts, such as finite element simulations of snow stability at the slope scale.
Parallelized Computation and Backpropagation Under Angle-Parametrized Orthogonal Matrices (2021)

We present a methodology for parallel acceleration of learning in the presence of matrix orthogonality and unitarity constraints of interest in several branches of machine learning. We show how an apparently sequential elementary rotation parametrization can be restructured into blocks of commutative operations using a well-known tool for coloring the edges of complete graphs, in turn widely applied to schedule round-robin (all-against-all) sports tournaments. The resulting decomposition admits an algorithm to compute a fully-parametrized orthogonal matrix from its rotation parameters in $O(n)$ sequential steps and one to compute the gradient of a training loss with respect to its parameters in $O(n\log n)$ steps. We discuss parametric restrictions of interest to generative modeling and present promising performance results with a prototype GPU implementation.
Transketolase-Like 1 Expression Is Modulated during Colorectal Cancer Progression and Metastasis Formation (2011)

To our knowledge, few studies have explored the association between variations in TKTL1 expression in the primary tumor and metastasis formation. Here we report downregulation of enzyme expression when metastasis appears, and a correlation between enzyme expression and regional lymph-node involvement in colon cancer. This finding may improve our understanding of metastasis and lead to new and more efficient therapies against cancer.
Perceived Quality of Recorded Music Processed through Compression Hearing Aids (2013)

Music perception with hearing aids has recently gained attention as a clinical and scientific problem. The goal of this dissertation was to examine the roles of input-signal properties, hearing-aid processing, and individual variability in the perception of recorded music. Two experiments considered music-industry compression limiting (CL) and hearing-aid wide dynamic-range compression (WDRC). The specific aims were: 1) to characterize the acoustic effects of CL on recorded music and to determine how listeners with normal hearing perceive recorded music processed by CL, 2) to quantify the acoustic and perceptual effects of CL, WDRC, and CL+WDRC on recorded music processed through simulated hearing aids, and 3) to examine the relationship between preferred compression parameters and individual perceptual characteristics of listeners with hearing loss.\nExperiment 1 investigated the effects of CL on classical and rock music. An acoustic analysis indicated reduced fidelity with increasing compression. When loudness varied due to compression, normal-hearing listeners preferred mild CL, on average. When loudness was equalized, mild compression did not affect music quality, but heavier compression was less preferred. Responses varied among individual listeners.\nExperiment 2 evaluated CL+WDRC using hearing-aid simulations and listeners with hearing loss. Acoustically, WDRC diminished amplitude contrasts and upset spectral balance, particularly for conditions with more channels (18 vs. 3) and a faster release time (50-msec vs. 1000-msec). Perceptually, linear processing and slow WDRC were equally preferred over fast WDRC for classical music. For rock music, linear processing was preferred to both slow and fast WDRC. The main effect of channels was not significant for classical music, but for rock, 3-channel processing was preferred. CL degraded music quality for classical but not for rock. For classical music, listeners with broader estimated auditory filters preferred 3 channels and linear processing, while listeners with narrower filters preferred 18 channels and slow WDRC. For rock music, the degree of preference for linear processing was greater for listeners with a larger dynamic range. The present findings have highlighted specific acoustic modifications that contribute to music quality and have identified compression parameters that are perceptually relevant for both music-industry recording and hearing-aid design.
IGNSS Computation Models and Values for GPS and GALILEO L5/E5a Civil Aviation Receivers (2020)

GNSS L5/E5a interference environment is dominated by DME/TACAN and JTIDS/MIDS pulses causing a degradation of the effective C/N0 observed by the receiver. A time-domain blanker is implemented to mitigate their impact. RTCA DO-292 proposes a model to compute the C/N0 degradation of the received useful signal by the increase of the noise PSD. This paper focuses on the computation on the max value of the I_GNSS term.
Digitized radio over fiber technology employing hardware implemented NTP technique (2010)

We introduce an outline of the digitized radio over fiber (DROF) technology that uses packet-based networks as transmission lines, and hardware-implemented NTP as synchronization technique between master and remote units. The resulting synchronization performance is sufficient for practical applications.
Thermal Versus Plasma-Enhanced ALD: Growth Kinetics and Conformality (2008)

Film purity, growth kinetics and conformality were compared for thermal and plasma-enhanced atomic layer deposition (PE-ALD) of Al2O3, AlN and TiN. The use of a plasma to enhance the activity of the reactant gas results in a significant improvement of the growth rate and film purity. However, based on experiments with an ammonia plasma for the growth AlN, the conformality of PE-ALD appears to be quite limited.
Toward filament-free semiconductor lasers (2000)

We outline physical models and simulations for suppression of self-focusing and filamentation in large aperture semiconductor lasers. The principal technical objective is to generate multi-watt CW or quasi-CW outputs with nearly diffraction limited beams, suitable for long distance free space transmission, focusing to small spots or coupling to single-mode optical fibers. The principal strategies are (1) optimization of facet damage thresholds, (2) reduction of the linewidth enhancement factor which acts as the principal nonlinear optical coefficient, and (3) design of laterally profiled propagation structures in lasers and amplifiers which suppress lateral reflections.
Test Derivation for the Software Defined Networking Platforms: Novel Fault Models and Test Completeness (2018)

Software Defined Networking (SDN) platforms are used in many applications and thus, should be thoroughly verified and tested before deployment; there are a number of research papers proposing various approaches for their verification. The next step is to test whether all the items are proceeding properly, i.e., to test the platform. As the requests can be considered as sets of paths which have to be properly implemented, the inputs of the System Under Test (SUT) are appropriate graphs (and packets traversing those graphs) while the output that can also be considered as a set of paths with appropriate parameters, is obtained via the appropriate platform monitoring. Correspondingly, for testing, we use a socalled proactive approach: check a submitted set of paths after forwarding a packet with appropriate parameters. We define several fault models (under different testing assumptions) with respect to the underlying resource connectivity graph (RNCT). Some conditions for deriving a complete test suite as well as the complexity upper bounds with respect to defined fault models are also established.
Examining the Relationship Between Nonalcoholic Fatty Liver Disease and the Metabolic Syndrome in Nondiabetic Subjects (2018)

The findings here suggest that both NAFLD and the MS very early in development have a common inciting mechanism(s)-most likely IR. Accordingly, the early concurrent temporal results are consistent with the concept that NAFLD is a hepatic manifestation of the IR associated with the MS. They do not exclude the possibility that once some liver functional adjustments take place, several aspects of the MS are bolstered further, perhaps via intensified heightening of IR.
Abstract 5494: Pharmacokinetics and Pharmacodynamics of Ticagrelor in Patients With Stable Coronary Artery Disease (2009)

Background: Ticagrelor (T), the first reversibly binding oral P2Y 12 receptor antagonist, has been evaluated in patients with ACS. Reversible inhibition is desirable for patients who experience bleeding complications or require invasive procedures. Methods: Two studies examined the pharmacokinetics (PK) of T in patients with stable coronary artery disease (CAD). In the multicenter, randomized, double-blind parallel group ONSET-OFFSET study, patients with stable CAD currently receiving aspirin (75–100 mg) were randomized to doses of T (180 mg load, 90 mg bid maintenance [n=57]), clopidogrel (C) (600 mg load, 75 mg qd maintenance [n=54]) or placebo (n=12) for 6 weeks. PK of T and AR-C124910XX (AR), an active metabolite, were evaluated following loading and last maintenance doses. In RESPOND (2-way crossover design), patients with stable CAD classified as C non-responders (n=41) and responders (n=57) were randomized to 14 days treatment with C 600 mg load/75 mg qd or T 180 mg loading/90 mg bid with no washout between treatments. On Days 1 and 14, t max , C max and AUC 0 – 8 of T and AR were evaluated. Results: In ONSET-OFFSET, C max , t max and t 1/2 values of T (733 ng/mL, 2 h, and 10.2 h, respectively) and AR (210.3 ng/mL, 2.1 h, and 12.8 h) at 90 mg bid were comparable to those seen previously in healthy subjects. E max estimates of final extent IPA (%) vs plasma concentration curves of T and AR were 98.6% and 91.8%, respectively. Trough plasma T (304.6 ng/mL) and AR (120.7 ng/mL) concentrations were 4 and 6 times higher than the respective EC 50 estimates (58.6 ng/mL and 15.7 ng/mL, respectively). In RESPOND, mean C max and AUC 0 – 8 of T following 2-week maintenance doses were similar between C responders (724.2 ng/mL and 3982.7 ng·h/mL) and non-responders (764.4 ng/mL and 3985.2 ng·h/mL). PK of T were not affected when T was administered 24 h post C dosing. Conclusions: This dosing regimen of T and AR effectively inhibited platelet aggregation; trough plasma levels of T (90 mg bid) and AR were sufficient to achieve high IPA. The pharmacodynamic response followed PK. Importantly, PK of T administered after crossover from C were unchanged and not affected by patient responsiveness to C.
Using Videos to Evaluate Image Model Robustness (2019)

Human visual systems are robust to a wide range of image transformations that are challenging for artificial networks. We present the first study of image model robustness to the minute transformations found across video frames, which we term "natural robustness". Compared to previous studies on adversarial examples and synthetic distortions, natural robustness captures a more diverse set of common image transformations that occur in the natural environment. Our study across a dozen model architectures shows that more accurate models are more robust to natural transformations, and that robustness to synthetic color distortions is a good proxy for natural robustness. In examining brittleness in videos, we find that majority of the brittleness found in videos lies outside the typical definition of adversarial examples (99.9\%). Finally, we investigate training techniques to reduce brittleness and find that no single technique systematically improves natural robustness across twelve tested architectures.
L1-optimized linear prediction for light field image compression (2016)

The advent of consumer-level plenoptic cameras has sparkled the interest towards the design of efficient compression techniques for light field images. State-of-the-art compression systems such as HEVC prove to be inefficient when directly applied on this type of data due to the inherent spatial discontinuities among neighboring microlens images. In this paper, a novel light field image compression system is proposed. The disk-shaped pixel clusters corresponding to each microlens in the light field image are efficiently predicted based on the neighboring disks. In this context, an optimized linear prediction design based on L1 minimization of the residuals is proposed. K-means clustering is employed on training data in order to determine the optimized set of predictors. The experimental results on an extensive set of light field images demonstrate that the proposed coding scheme yields an average of 2.93 dB and 3.22 dB gain in PSNR, and 52.67% and 57.27% average rate savings compared to HEVC and JPEG2000 respectively.
Cross-layer design of adaptive modulation and coding for multicast system with random network coding (2014)

Abstract This paper deals with a cross-layer design that combines link adaptation in the physical layer with random network coding for layered video multicasting in a cellular system. The objective is to design the optimum signal-to-noise ratio (SNR) threshold for adaptive modulation and coding (AMC) that can satisfy the target frame loss rate (FLS) under a delay constraint associated with real-time multicasting services. A common uplink feedback channel shared by all users is introduced to reduce the redundant transmission of the random network-coded packets, so that no unnecessarily redundant transmission can be made when the multicast packet is successful for all receivers, avoiding the overhead of the uplink wireless resource associated with each user for individual feedback. Based on our analytical results on spectral efficiency for the cellular system, we show that the aggressive AMC design approach with the common feedback channel in the multicast system outperforms all other approaches.
Phosphorylation-regulated calmodulin binding to a prominent cellular substrate for protein kinase C (1989)

We have evaluated the possibility that a major, abundant cellular substrate for protein kinase C might be a calmodulin-binding protein. We have recently labeled this protein, which migrates on sodium dodecyl sulfate-gel electrophoresis with an apparent Mr of 60,000 from chicken and 80,000-87,000 from bovine cells and tissues, the myristoylated alanine-rich C kinase substrate (MARCKS). The MARCKS proteins from both species could be cross-linked to 125I-calmodulin in a Ca2+-dependent manner. Phosphorylation of either protein by protein kinase C prevented 125I-calmodulin binding and cross-linking, suggesting that the calmodulin-binding domain might be located at or near the sites of protein kinase C phosphorylation. Both bovine and chicken MARCKS proteins contain an identical 25-amino acid domain that contains all 4 of the serine residues phosphorylated by protein kinase C in vitro. In addition, this domain is similar in sequence and structure to previously described calmodulin-binding domains. A synthetic peptide corresponding to this domain inhibited calmodulin binding to the MARCKS protein and also could be cross-linked to 125I-calmodulin in a calcium-dependent manner. In addition, protein kinase C-dependent phosphorylation of the synthetic peptide inhibited its binding and cross-linking to 125I-calmodulin. The peptide bound to fluorescently labeled 5-dimethylaminonaphthalene-1-sulfonyl-calmodulin with a dissociation constant of 2.8 nM, and inhibited the calmodulin-dependent activation of cyclic nucleotide phosphodiesterase with an IC50 of 4.8 nM. Thus, the peptide mimics the calmodulin-binding properties of the MARCKS protein and probably represents its calmodulin-binding domain. Phosphorylation of these abundant, high affinity calmodulin-binding proteins by protein kinase C in intact cells could cause displacement of bound calmodulin, perhaps leading to activation of Ca2+-calmodulin-dependent processes.
3D Ics with Embedded Microfluidic Cooling and High Aspect Ratio TSV Integration (2013)

Abstract Not Available. Outline: Introduction; Liquid Cooling in 3D ICs; Integration of Electrical TSVs in Microfluidics; and Conclusion
Multifunctional Nanoagents for the Detection and Treatment of Thromboses (2011)

The formation of a blood clot within a vessel is normally a benefi cial process, as it prevents blood loss caused by trauma. Dysregulation of this process can lead to bleeding or clotting disorders, including hemophilia and thrombophilia. There are three causal factors of clot formation: the disturbance of blood fl ow, as can occur when an individual is seated for a prolonged length of time; increased blood coagulability, as caused by genetic or autoimmune disorders; and vessel injury. The last cause can be a result of external factors, such as an injury, or pathological conditions, including atherosclerotic vascular disease.