gebhart/patrepeval huggingface dataset:
Both Vitamin D Supplementation and HIIT Boost Muscle VDR Expression, Which May Underlie Benefits for Frailty (2021)

Abstract Frailty is a condition of poor response to stressors that increases susceptibility to adverse outcomes - including disability and death. Declining physical function is an important hallmark of frailty, and we previously published that long term vitamin D insufficiency from young to middle-age leads to declines in endurance and gait disturbances. Furthermore, we report that aged mice (24-months) made vitamin D insufficient for 4 months exhibit increased frailty, whereas those made hyper-sufficient do not. Exercise, including short session high intensity interval training (HIIT - 10 minutes/3x-week), also reverses frailty in aged mice. Here we investigate the impacts of aging, vitamin D, and exercise on underlying muscle quality and muscle stem cell activity. Our preliminary data reveal muscle vitamin D receptor (VDR) expression is lower in aged mice (24-28 months) relative to young mice (6 months). Yet HIIT, either one hour after a single session or following 6 weeks, increases VDR expression. HIIT also increases myonuclear accretion in muscle fibers – an indicator of in vivo stem cell activity – and stimulates progenitor cells proliferation ex vivo. Likewise, we observe that vitamin D hyper supplementation alone also increases muscle VDR expression and the number of satellite cells. These data indicate that both vitamin D supplementation and HIIT independently enhance VDR expression in skeletal muscle with associated greater satellite and muscle progenitor cell activity. These data critically link vitamin D physiology and HIIT in muscle, and thus provide a mechanistic basis for their benefits for muscle quality, function, and health during aging.
Emerging cardiovascular molecular imaging approaches. (2009)

New molecular imaging technologies, in particular optical ones, are increasingly used to understand the complexity and heterogeneity of cardiovascular diseases. While ‘omic’ approaches can provide us with comprehensive ‘snapshots’ of biomarkers, imaging studies can be used to understand the spatiotemporal activity of these markers in vivo. Imaging has also advanced clinically, and will ultimately allow us to determine disease activity and therapy response. In addition, newer developments will likely have an impact on our understanding of biology at the systems level, promote earlier clinical diagnosis and accelerate drug development.
Expression inCaulobacter crescentusof the phosphate-starvation-inducible porin OprP ofPseudomonas aeruginosa (1991)

The gene for the phosphate-starvation-inducible outer membrane protein OprP, of Pseudomonas aeruginosa was introduced into Caulobacter crescentus CB2A on a plasmid vector. As is the case in P. aeruginosa and Escherichia coli the oprP gene was inducible under conditions of limiting phosphate in C. crescentus. However, the maximal medium concentration of phosphate which still permitted induction of OprP was lower in C. crescentus (50 μM) than in P. aeruginosa (200 μM). Induction of OprP was coincident with the process of stalk elongation, known to occur in C. crescentus under phosphate starvation conditions. When induced, OprP was localized to the cell envelope and became a major membrane protein, indicating that the Pseudomonas promoter was efficiently recognized in C. crescentus and that the gene product was targeted to the appropriate region of the cell. Our data provide support for the hypothesis that the mechanism for regulation of phosphate-starvation-inducible genes is highly conserved amongst the eubacteria.
Prevalence of Neurologic Lesions After Total Shoulder Arthroplasty (2011)

The occurrence of peripheral neurologic lesions following reverse shoulder arthroplasty is relatively common, but usually transient. Arm lengthening with a reverse shoulder arthroplasty may be responsible for these nerve injuries.
Four-band non-Abelian topological insulator and its experimental realization (2021)

Abstract Very recently, increasing attention has been focused on non-Abelian topological charges, e.g. the quaternion group Q 8 . Different from Abelian topological band insulators, these systems involve multiple tangled bulk bandgaps and support non-trivial edge states that manifest the non-Abelian topological features. Furthermore, a system with even or odd number of bands will exhibit significant difference in non-Abelian topological classifications. Up to now, there is scant research investigating the even-band non-Abelian topological insulators. Here, we both theoretically explored and experimentally realized a four-band PT (inversion and time-reversal) symmetric system, where two new classes of topological charges as well as edge states are comprehensively studied. We illustrate their difference from four-dimensional rotation senses on the stereographically projected Clifford tori. We show the evolution of bulk topology by extending the 1D Hamiltonian onto a 2D plane and provide the accompanying edge state distributions following an analytical method. Our work presents an exhaustive study of four-band non-Abelian topological insulators and paves the way to other even band systems.
Test pattern generation for multiple stuck-at faults (2002)

A new method to generate test patterns for multiple stuck-at faults in combinational circuits is presented. All multiple faults of any multiplicity are assumed present in the circuit and one does not have to resort to their explicit enumeration: the target fault is a single component of possibly several multiple faults. The authors try to generate test conditions that propagate the effect of the target fault to primary outputs regardless the effects of other faults which might be present in the circuit. When these conditions are fulfilled, the input vector is a test for the target fault and for all multiple faults containing the target fault as component. The method used a branch-and-bound technique and includes several heuristics to enhance the performance and fault detection. Experiments performed on the ISCAS'85 benchmark circuits show that high fault coverage can be obtained at a reasonable increase in cost.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Long-Term Mortality in HIV-Infected Individuals 50 Years or Older (2015)

Among HIV-infected individuals estimated median survival time from age 50 years has increased by more than 10 years from 1996-1999 to 2006-2014, but is still substantially lower than in the background population. Even among well-treated HIV-infected individuals ≥ 50 years without comorbidity or AIDS-defining events the estimated median survival time remains lower than in the general population.
Cooperative Cognitive Networks: Optimal, Distributed and Low-Complexity Algorithms (2013)

This paper considers the cooperation between a cognitive system and a primary system where multiple cognitive base stations (CBSs) relay the primary user's (PU) signals in exchange for more opportunity to transmit their own signals. The CBSs use amplify-and-forward (AF) relaying and coordinated beamforming to relay the primary signals and transmit their own signals. The objective is to minimize the overall transmit power of the CBSs given the rate requirements of the PU and the cognitive users (CUs). We show that the relaying matrices have unity rank and perform two functions: Matched filter receive beamforming and transmit beamforming. We then develop two efficient algorithms to find the optimal solution. The first one has a linear convergence rate and is suitable for distributed implementation, while the second one enjoys superlinear convergence but requires centralized processing. Further, we derive the beamforming vectors for the linear conventional zero-forcing (CZF) and prior zero-forcing (PZF) schemes, which provide much simpler solutions. Simulation results demonstrate the improvement in terms of outage performance due to the cooperation between the primary and cognitive systems.
3D angiography. Clinical interest. First applications in interventional neuroradiology. (1998)

3D angiography is a true technical revolution that allows improvement in the quality and safety of diagnostic and endovascular treatment procedures. 3D angiography images are obtained by reconstruction of a rotational angiography acquisition done on a C-arm (GE Medical Systems) spinning at 40 degrees per second. The carotid or vertebral selective injection of a total of 15 ml of non-ionic contrast media at 3 ml/sec over 5 seconds allows the selection of the "arterial phase". Four hundred sixty 3D angiographic studies were performed from December 1996 to September 1998 on 260 patients and have been analyzed in MIP (Maximum Intensity Projection) and SSD (Shaded Surface Display) views. The exploration of intracranial aneurysms is simplified and only requires, for each vascular axis, a biplane PA and Lateral run followed by a single rotational angiography run. The 3D angiography image is available on the workstation's screen (Advantage Workstation 3.1, GE Medical Systems) in less than 10 minutes after the acquisition of the rotational run. It therefore allows one to analyze, during the intervention, the aneurysm's angioarchitecture, in particular the neck, and select the best therapeutic technique. When endovascular treatment is the best indication, 3D angiography allows one to define the optimal angle of view and accurately select the microcoils dimensions. 3D angiography replaces the multiple oblique views that used to be required to analyze the complex aneurysms and therefore allows a reduction of the total contrast medium quantity, the patient X-ray dose and the length of the intervention time which is a safety factor. Also, in particular for complex cases, it brings additional elements complementing the results of standard 2D DSA and rotational angiograms. In the cervical vascular pathology, 3D angiography allows for a better assessment of the stenosis level and of dissection lesions. Our current research activities focus on the matching without stereotactic frame between 3D X-ray angiography and volumetric MR acquisition, which should allow us to improve the treatment of intracerebral arterio-venous malformations (AVMs).
Transducer placement for robustness to variations in boundary conditions for active structural acoustic control (2005)

Turbulent boundary layer (TBL) noise is considered a primary contribution to the interior noise present in commercial airliners. There are numerous investigations of interior noise control devoted to aircraft panels; however, practical realization is a potential challenge since physical boundary conditions are uncertain at best. In most prior studies, pinned or clamped boundary conditions were assumed; however, realistic panels likely display a range of boundary conditions between these two limits. Uncertainty in boundary conditions is a challenge for control system designers, both in terms of the compensator implemented and the location of transducers required to achieve the desired control. The impact of model uncertainties, specifically uncertain boundaries, on the selection of transducer locations for structural acoustic control is considered herein. The final goal of this work is the design of an aircraft panel structure that can reduce TBL noise transmission through the use of a completely adaptive, single-input, single-output control system. The feasibility of this goal is demonstrated through the creation of a detailed analytical solution, followed by the implementation of a test model in a transmission loss apparatus. Successfully realizing a control system robust to variations in boundary conditions can lead to the design and implementation of practical adaptive structures that could be used to control the transmission of sound to the interior of aircraft. Results from this research effort indicate it is possible to optimize the design of actuator and sensor location and aperture, minimizing the impact of boundary conditions on the desired structural acoustic control.
Effect of carbon contamination on the printing performance of extreme ultraviolet masks (2010)

Carbon contamination is a significant issue with extreme ultraviolet (EUV) masks because it lowers throughput and has potential effects on imaging performance. Current carbon contamination research is primarily focused on the lifetime of the multilayer surfaces, determined by reflectivity loss and reduced throughput in EUV exposure tools. However, contamination on patterned EUV masks can cause additional effects on absorbing features and can affect the printed images. In this work, various carbon contamination experiments were performed to study the impact between contamination topography and observed imaging performance. Lithographic simulation using calculated aerial images and experimentally determined resist parameters was performed and compared to the printing results to estimate the allowed carbon thickness with critical dimension compensation applied to the mask.
Silicon nano- and micro-photonic devices (2009)

Silicon VLSI plays a key role in information technology. Recent progresses in silicon photonics have significantly moved the conventional silicon VLSI to high bandwidth photonics with lower power consumption for switching and interconnects. These devices include novel waveguides, modulators and detectors that are compatible with Si CMOS fabrication process. There are two major obstacles to build a monolithic nano-photonic system on a silicon chip: 1. lack of a silicon based light source and 2. silicon does not have any electro-optic (X2) effect. The combination of these two may require a hybrid integration in the foreseeable future. In this presentation, we will present the recent results and the projection of future development.
Low frequency noise in 4H silicon carbide (1997)

The bulk low frequency noise has been investigated in the 4H silicon carbide polytype. In the temperature range of 300–550 K the noise spectral density S is proportional to f−1.5, where f is the measurement frequency. A very low noise level has been observed for the bulk noise. At 300 K, the Hooge constant α is as small as (2–4)×10−6 at f=20 Hz and α⩽5×10−7 at f=1300 Hz. At T⩾600 K, the generation-recombination noise of a local level makes the main contribution into the total low frequency noise. The electron capture cross section σ of this level depends very strongly on temperature. In the temperature range of 620–700 K, the temperature dependence of σ can be expressed as σ∼exp(−E1/kT), with an activation energy E1 as high as 2.7 eV.
Nonlinear decoding of natural images from large-scale primate retinal ganglion recordings (2020)

Abstract Decoding sensory stimuli from neural activity can provide insight into how the nervous system might interpret the physical environment, and facilitates the development of brain-machine interfaces. Nevertheless, the neural decoding problem remains a significant open challenge. Here, we present an efficient nonlinear decoding approach for inferring natural scene stimuli from the spiking activities of retinal ganglion cells (RGCs). Our approach uses neural networks to improve upon existing decoders in both accuracy and scalability. Trained and validated on real retinal spike data from &gt; 1000 simultaneously recorded macaque RGC units, the decoder demonstrates the necessity of nonlinear computations for accurate decoding of the fine structures of visual stimuli. Specifically, high-pass spatial features of natural images can only be decoded using nonlinear techniques, while low-pass features can be extracted equally well by linear and nonlinear methods. Together, these results advance the state of the art in decoding natural stimuli from large populations of neurons. Author summary Neural decoding is a fundamental problem in computational and statistical neuroscience. There is an enormous literature on this problem, applied to a wide variety of brain areas and nervous systems. Here we focus on the problem of decoding visual information from the retina. The bulk of previous work here has focused on simple linear decoders, applied to modest numbers of simultaneously recorded cells, to decode artificial stimuli. In contrast, here we develop a scalable nonlinear decoding method to decode natural images from the responses of over a thousand simultaneously recorded units, and show that this decoder significantly improves on the state of the art.
Response : Immuno-PCR with a Commercially Available Avidin System (1993)

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Low Adherence to Kidney Disease: Improving Global Outcomes 2012 CKD Clinical Practice Guidelines Despite Clear Evidence of Utility (2022)

Albuminuria monitoring is critical for optimal risk stratification in CKD, and our findings highlight an imperative for more regular UACR testing in clinical practice.
Miniaturized signal-interference planar filters (2015)

This paper addresses, for the first time, the development of miniaturized-size signal-interference planar filters. In particular, capacitive-loading and meandering-line techniques are simultaneously applied to decrease their occupied area. Footprint reduction, transfer function narrowing, and increased insertion loss caused by the capacitive loading are carefully considered for single- and multi-band bandpass filters (BPFs). Line meandering enables further size reduction in these circuits without coupled-line stages, since spurious-coupling effects become less critical. A 1-GHz miniaturized two-stage BPF prototype based on the hybrid-ring-type transversal filtering section (TFS) is built and tested to experimentally validate the presented concepts. This BPF prototype is nearly 4× smaller than its classic counterpart.
Identification of Sub-Synchronous Interaction in MMC Systems using Frequency Scanning (2020)

The interaction between the Modular Multi-level Converter (MMC) and the ac system can result in oscillation, even instability in the sub-synchronous frequency range. Rather than using an analytical model of the MMC which is complicated and often ignores details of commercial proprietary controllers, this paper proposes the application of frequency scanning of the MMC modelled on a real-time digital simulator (RTDS). The frequency response of the MMC looking from the Point of Common Coupling (PCC) bus can be extracted from the scan in either the dq0 domain or the modified PNO domain, which would be discussed in detail. The system behavior can be studied using the Generalized Nyquist stability Criterion (GNC) or equivalently, the Bode plot. The approach can predict the Critical Short Circuit Ratio (CSCR) of the ac system resulting in marginal stability, as well as the oscillation frequency. The result is then validated by real-time simulation on RTDS.
Infrared to mid-infrared non-degenerate two-photon absorption spectroscopy of bulk silicon (2022)

Non-degenerate two-photon absorption (ND-2PA) across the indirect gap of silicon is theoretically and experimentally investigated in the current work. We present measurements of the 2PA coefficient of bulk silicon using femtosecond pump and probe pulses in the IR and mid-IR range. Enhancement of ND-2PA was observed from the results of our measurements with increasing non-degeneracy. This can be utilized when designing sensitive silicon-based mid-IR detectors. Modeling of the 2PA was performed by considering three theoretical pathways across the band structure of silicon for the two photons and a phonon, and the most dominant processes are determined by comparison to our measurements.
Self-consistent simulation of very high frequency capacitively coupled plasmas (2008)

A two-dimensional plasma model that includes the full set of Maxwell equations is used to understand the physics of very high frequency capacitively coupled plasmas. The effect of radio frequency (RF) source power, inter-electrode gap and gas mixture (Ar, Ar/SF6, Ar/CF4) on the plasma characteristics is investigated. The computational results show that the plasma spatial profile is influenced by both electrostatic and electromagnetic effects. The electrostatic power deposition is stronger at the electrode edges due to electric field enhancement at corners. Therefore, when the electrostatic effects are dominant, the plasma density peaks off-axis. Due to a standing electromagnetic wave in the chamber, the electron density peak moves to the chamber center under conditions where electromagnetic effects become strong. Inductive heating due to the radial electromagnetic electric field can also influence the plasma spatial profile. The relative importance of electromagnetic and electrostatic effects is found to be a function of the RF source power, the inter-electrode gap and the plasma electronegativity. While the electron density peaks on-axis at a low source power, inductive power deposition at higher source powers shifts the electron density peak towards the electrode edge. Electrostatic power deposition makes the plasma more uniform at smaller inter-electrode gaps. Due to a lower electron density and a larger applied RF potential, electrostatic effects become more dominant in electronegative discharges.
Considerations in Making Microarray Cross-Platform Correlations (2006)

Comparison and integration of expression data derived from diverse microarray platforms is challenging. Factors affecting cross-platform comparison of microarray data include the choice of normalization method used, annotation differences, presence of splice variants, RNA degradation and probe distance from 3' end. A thorough evaluation of two commercial microarray platforms to determine an appropriate methodology for making cross-platform correlations is described here.
Role of a “Magic” Methyl: 2′-Deoxy-2′-α-F-2′-β-C-methyl Pyrimidine Nucleotides Modulate RNA Interference Activity through Synergy with 5′-Phosphate Mimics and Mitigation of Off-Target Effects (2022)

Although 2'-deoxy-2'-α-F-2'-β-<i>C</i>-methyl (2'-F/Me) uridine nucleoside derivatives are a successful class of antiviral drugs, this modification had not been studied in oligonucleotides. Herein, we demonstrate the facile synthesis of 2'-F/Me-modified pyrimidine phosphoramidites and their subsequent incorporation into oligonucleotides. Despite the C3'-<i>endo</i> preorganization of the parent nucleoside, a single incorporation into RNA or DNA resulted in significant thermal destabilization of a duplex due to unfavorable enthalpy, likely resulting from steric effects. When located at the terminus of an oligonucleotide, the 2'-F/Me modification imparted more resistance to degradation than the corresponding 2'-fluoro nucleotides. Small interfering RNAs (siRNAs) modified at certain positions with 2'-F/Me had similar or better silencing activity than the parent siRNAs when delivered via a lipid nanoparticle formulation or as a triantennary <i>N</i>-acetylgalactosamine conjugate in cells and in mice. Modification in the seed region of the antisense strand at position 6 or 7 resulted in an activity equivalent to the parent in mice. Additionally, placement of the antisense strand at position 7 mitigated seed-based off-target effects in cell-based assays. When the 2'-F/Me modification was combined with 5'-vinyl phosphonate, both <i>E</i> and <i>Z</i> isomers had silencing activity comparable to the parent. In combination with other 2'-modifications such as 2'-<i>O</i>-methyl, the <i>Z</i> isomer is detrimental to silencing activity. Presumably, the equivalence of 5'-vinyl phosphonate isomers in the context of 2'-F/Me is driven by the steric and conformational features of the <i>C</i>-methyl-containing sugar ring. These data indicate that 2'-F/Me nucleotides are promising tools for nucleic acid-based therapeutic applications to increase potency, duration, and safety.