gebhart/patrepeval huggingface dataset:
MicroRNAs 145 and 148a Are Upregulated During Congenital Zika Virus Infection (2019)

Zika virus (ZIKV) is an arthropod-borne virus (arbovirus) member of the Flaviviridae family, which has been associated with the development of the congenital Zika syndrome (CZS). RNA viruses, such as flaviviruses, have been reported to exert a profound impact on host microRNAs (miRNAs). Cellular miRNAs modulated by ZIKV may help identify cellular pathways of relevance to pathogenesis. Here, we screened 754 human cellular miRNAs modulated by ZIKV infection (Brazilian PE strain) in a neuroblastoma cell line. Seven miRNAs (miR-99a*, miR-126*, miR-190b, miR-361-3p, miR-522-3p, miR-299-5p, and miR-1267) were downregulated during ZIKV infection, while miR-145 was upregulated. Furthermore, 11 miRNAs were exclusively expressed in ZIKV-infected (miR-148a, miR-342-5p, miR-598, and miR-708-3p) or mock cells (miR-208, miR-329, miR-432-5p, miR-488, miR-518b, miR-520g, and miR-767-5p). Furthermore, in silico analysis indicated that some central nervous system, cellular migration, and adhesion function-related biological processes were overrepresented in the list of target genes of the miRNAs regulated in ZIKV-infected cells, especially for miR-145 and miR-148a. The induction of miR-145 and miR-148a was confirmed in postmortem brain samples from stillborn with severe CZS. Finally, we determined the expression regulation of microcephaly related genes through RNA interference pathway caused by ZIKV directly on neuron cells.
Robotic motion compensation for three-dimensional ultrasound-guided beating heart surgery (2009)

Beating heart surgeries offer significant health benefits to patients by removing the need for the heart-lung machine and its attendant side effects. These surgeries are challenging to perform and only feasible in certain types of procedures because of the rapid movement of the heart. Equipping the surgeon with fast, actuated, and intelligent surgical instruments that automatically compensate for heart motion could facilitate the execution of existing beating heart procedures and enable the development of new procedures that are currently not possible. These tools have particular promise for intracardiac beating heart procedures, where passive tissue stabilization techniques are not available; however, achieving motion compensation in this setting is challenging because of the sensing and space restrictions imposed from working inside of the beating heart.
This thesis investigates 3D ultrasound-guided robotic motion compensation as an assistive technology to intracardiac beating heart surgery. A number of engineering challenges are addressed to develop a viable system for in vivo experimentation: heart motion prediction to counter time delays in 3D ultrasound imaging and image processing, real-time tracking of surgical targets in noisy 3D ultrasound images, and safe force control schemes for the manipulation of tissue without exciting vibratory modes in the robot. Solutions are provided in the form of a quasiperiodic extended Kalman filter, a synergistic “flashlight” tissue tracker, and a force controller with feed-forward target motion information, respectively. Integrating these components into a system, motion compensation within the beating heart is not only shown to be feasible under in vivo conditions, but also to provide significant performance advantages in beating heart tasks. Motion and force tracking accuracies of 1.0 mm and 0.11 N are obtained in in vivo surgical tasks with the system, constituting a 70% and 75% reduction in error when compared to human performance in the same tasks.
Single crystal silicon-germanium-on-insulator for high density optical interconnects (2016)

The field of silicon photonics has seen a period of rapid technological advancement over the past decade, with significant interest and investment from both academia and industry. Progress is expected to continue, with global sales of silicon photonics products predicted to reach US$1 billion by 2020. A key motivation for silicon photonics is integration; achieved by using the CMOS compatible materials silicon and germanium. Here, we establish a silicon-germanium-on-insulator material platform using a rapid melt growth technique. We present a novel method for the fabrication of multiple, uniform composition localised silicon-germanium-on-insulator layers, demonstrating the ability to tune the composition of each layer by modifying the structural parameters of the layers, as shown in Fig. 1. This is achieved using only a single Ge growth step and a single anneal step, therefore dramatically reducing fabrication cost and complexity when compared with traditional epitaxy techniques.We investigate the regrowth mechanism exhibited by this rapid melt growth technique, and study the effects of the structural parameters of the tailored structures on the SiGe composition profiles. Using this material platform we can potentially exploit the tunable bandgap of the SiGe alloy for wavelength division multiplexing applications, with the potential to form low power electro-absorption modulators with an extremely high bandwidth density when compared to other modulator device designs. In addition, we discuss extending silicon photonic circuits into mid-infrared wavelengths, and identify the potential applications of such systems.We present some early results from passive mid-infrared photonic devices on a silicon-on-insulator platform.
Prediction and Interpretable Visualization of Retrosynthetic Reactions Using Graph Convolutional Networks (2019)

Recently, many research groups have been addressing data-driven approaches for (retro)synthetic reaction prediction and retrosynthetic analysis. Although the performances of the data-driven approach have progressed because of recent advances of machine learning and deep learning techniques, problems such as improving capability of reaction prediction and the black-box problem of neural networks persist for practical use by chemists. To spread data-driven approaches to chemists, we focused on two challenges: improvement of retrosynthetic reaction prediction and interpretability of the prediction. In this paper, we propose an interpretable prediction framework using graph convolutional networks (GCN) for retrosynthetic reaction prediction and integrated gradients (IG) for visualization of contributions to the prediction to address these challenges. As a result, from the viewpoint of balanced accuracies, our model showed better performances than the approach using an extended-connectivity fingerprint. Furthermore, IG-based visualization of the GCN prediction successfully highlighted reaction-related atoms.
Decreased Mitochondrial DNA Content in Posttreatment Salivary Rinses from Head and Neck Cancer Patients (2006)

Our data suggest that salivary mtDNA content is decreased in never smokers and in response to radiation therapy after primary surgical resection.
On estimating noncasual ARMA nonGaussian processes (2003)

The authors consider the identification of nonGaussian ARMA (autoregressive moving average) processes using columnant statistics of noisy observations. The measurement noise is allowed to be colored Gaussian or independent and identically nonGaussian distributed. It is not necessary to know whether the ARMA model is causal or noncausal, minimum phase or nonminimum phase. The unique parameter estimates of both the MA and AR parts are obtained via linear equations. The structure of the proposed algorithm facilitates asymptotic performance evaluation of the parameters estimators and model order selection using cumulant statistics. It is concluded that the method is computationally simple and can be viewed as the mean-square optimal model fitting of a sampled cumulant sequence. Simulations are presented to illustrate the proposed algorithm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Wideband Low-Sidelobe Slot Array Antenna With Compact Tapering Feeding Network for E-Band Wireless Communications (2021)

In this work, a wideband low-sidelobe slot array antenna for wireless communication system at E-band is presented. The slots are excited by a parallel feeding network where the Taylor distribution is applied. Two types of wideband unequal power divider with compact structures are designed for various output ratios to fit the limited feeding network space. One is integrated vertically inside a 2 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\times $ </tex-math></inline-formula> 1 elements subarray using a set of pins with asymmetrical offset. The other type is designed inside an E-plane T-junction with unbalance impedance at two output ports. To avoid main lobe tilt and asymmetrical radiation patterns, the feeding network is designed to be biaxially symmetrical, and the feed port is placed in the center of the back. A prototype is fabricated with brass and measured in an anechoic chamber. It achieves a peak gain of 25.8 dBi and a fractional impedance bandwidth of 19.2% with the reflection coefficient below −10 dB. The measured radiation patterns agree with the simulated patterns very well, and the sidelobe level (SLL) is lower than −21 dB.
A pie chart showing the percent relative abundance of each taxon in the McCel-adapted thermophilic bacterial consortia. (2015)

&lt;p&gt;SSU pyrosequencing was conducted to identify community members. Only members with a relative abundance greater than 1% are reported. Relative abundance is calculated as a percentage of the total number of SSU reads for the community. The closest taxon to each organism in the community is reported in the legend. The percent identity between the consortial and closest taxon SSU sequence is in parentheses.&lt;/p&gt;
Seeing around corners with a mobile phone? (2014)

Seeing around corners, in the dark, and through smoke is difficult without specialized sensors[Velten et al. 2012], and so far impossible with a mobile phone. We use an active audio system to sense objects around occluders. Current techniques perform passive localization of sound sources with a microphone array, however, we demonstrate that with one microphone and one speaker pair, such as the ones found in mobile phones, it is possible to sense the specular reflection of silent objects such as mannequins around occluding objects. We demonstrate this technique by sensing a mannequin occluded by a wall.
Abstract 1366: Computer-modeled novel cancer targeting peptides for therapy and imaging (2011)

Abstract We have recently developed practical software programs for optimization of cancer targeting peptides, including combinatorial construction of 3D peptide library (Buildpep), binding pocket analyzer (PscanMS) and high accuracy protein-ligand scoring program (HotLig). Based on these programs, a strategy of structure-based optimization of cancer targeting peptides in silico is developed to target human GRP78 which consists of 654 amino acids. The homology modeling of human GRP78 was constructed through aligning amino acid sequence and 3D structure with its homologs. This protein contains two major structural domains, the peptide-binding domain and the ATPase. Based on the results from the molecular modeling, new peptide analogs were designed and examined for optimized binding to the targeted GRP78 through in silico analysis. We had thus delineated the pharmacophore description of binding motif targeting peptide-binding domain of GRP78 as Pro-X1-Leu-X2. Peptides possessing this motif can be applied in cancer-targeted drug delivery system. We have thus designed several new tumor-targeted peptides [P-12, P-13, and P-6]. Their ability to bind target protein was confirmed in subsequent in vitro binding through Biacore analysis. We next examined their capacity to target cancer cells in the in vitro binding with various cancer cells, and in vivo tumor imaging and targeted chemotherapeutic studies. The results indicate that these peptides exhibit promising therapeutic potential by their selective binding to cancer cells, but not normal cells. Notably, these peptide analogs can bind to breast cancer stem cell (CSC) population in xenografts of primary breast cancer suggesting that they can target breast CSC enriched subpopulation. The microSPECT/CT molecular imaging of a primary human breast tumors, BC0244, xenograft with 188Re-liposome-PEG-P12 or P13 peptide showed significantly more uptake of radioactivity as compared to 188Re- liposome-PEG-L-peptide in the BC0244 breast tumors in NOD/SCID mice at 6, 24 and 48 h after intravenous injection, and even greater difference was found as compared to that of 188Re-liposome alone. To further compare P12 labeled liposome with L-peptide labeled liposome for therapeutic efficacy, mice bearing BC0244 xenografts were distributed into 4 groups for treatment with P12-Lipo-Dox, L-peptide-Lipo-Dox, Lipo-Dox, and PBS. The tumor growth of P12-lipo-Dox group was 1.57-fold slower than that of the L-peptide group; both of them showed significant increase in the therapeutic efficiency than Lipo-Dox control. These optimized cancer targeting peptides may be useful for imaging and targeted therapy of cancers. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1366. doi:10.1158/1538-7445.AM2011-1366
Theory and experiments of tire blow-out effects and hazard reduction control for automated vehicle lateral control system (2005)

This paper concentrates on the scenario of tire blow out and it's effects on lateral control of automobiles in an IVHS environment. A computer model for the tire burst phenomenon was developed to simulate the behavior of a car with a tire blow out. Based on this modeling, a control algorithm to compensate for the tire blow out was designed. Finally the tire burst experiments were conducted on a car to validate the tire burst model.
Editorial: Multifunctional Polymeric Materials for Drug and Gene Delivery (2022)

EDITORIAL article Front. Bioeng. Biotechnol., 13 May 2022Sec. Biomaterials https://doi.org/10.3389/fbioe.2022.917690
Scanning Probe Surface Modification (1993)

Nanometer-scale manipulation of surfaces is important because subtle changes in surface structure often result in new electronic, magnetic, photonic, and mechanical materials properties. In this brief article we address one aspect of nanometer-scale surface manipulation that is of both technological and fundamental interest: scanning probe microscope (SPM)-induced patterning of surfaces. We begin by discussing traditional methods for submicron patterning, then we address some general aspects of SPM surface manipulation, and finally we present some specific results from our own laboratory.
Hypertension Attenuates the Efficacy of Hypoglycemic Therapy for Preserving Coronary Flow Reserve in Patients with Type 2 Diabetes. (2002)

Impairment of coronary flow reserve (CFR) in patients with type 2 diabetes has been generally demonstrated; however, there have been few studies investigating CFR in cases of relatively well-controlled diabetes, in distinction to the influence of hypertension. The purpose of the present study was to evaluate the influence of diabetes and hypertension upon CFR in relatively well-controlled patients. This study included 12 healthy controls (C group) and 57 patients with type 2 diabetes (DM) and/or essential hypertension who were divided into three groups as follows: patients with DM (DM group; n = 24), patients with essential hypertension (HT group; n = 15), and patients with both DM and essential hypertension (DM+HT group; n = 18). We excluded patients with evidence of coronary artery disease and/or left ventricular hypertrophy. We performed transthoracic Doppler recording of diastolic coronary flow velocity (CFV) in the left anterior descending coronary artery at rest and after maximal vasodilation by adenosine infusion (140 microg/kg/min for 3 min) CFR was defined as the ratio of hyperemic to averaged basal peak CFV. The CFR (2.92 +/- 0.46) of the DM group was not decreased compared to that of the C group (2.96 +/- 0.58), although the CFR of the HT (2.33 +/- 0.25) and DM+HT (2.35 +/- 0.25) groups were significantly reduced. Left ventricular mass index, relative wall thickness, and diastolic function were worse in the HT and DM+HT groups than in the C and DM groups. Subjects with concentric left ventricular remodeling had a lower CFR than those with normal left ventricular geometry. In conclusion, adequate hyperglycemic control prevented the progression of coronary microcirculatory disturbance, but concomitant hypertension attenuated the effect.
Prim-LAfD: A Framework to Learn and Adapt Primitive-Based Skills from Demonstrations for Insertion Tasks (2022)

Learning generalizable insertion skills in a data-efficient manner has long been a challenge in the robot learning community. While the current state-of-the-art methods with reinforcement learning (RL) show promising performance in acquiring manipulation skills, the algorithms are data-hungry and hard to generalize. To overcome the issues, in this paper we present Prim-LAfD, a simple yet effective framework to learn and adapt primitive-based insertion skills from demonstrations. Prim-LAfD utilizes black-box function optimization to learn and adapt the primitive parameters leveraging prior experiences. Human demonstrations are modeled as dense rewards guiding parameter learning. We validate the effectiveness of the proposed method on eight peg-hole and connector-socket insertion tasks. The experimental results show that our proposed framework takes less than one hour to acquire the insertion skills and as few as fifteen minutes to adapt to an unseen insertion task on a physical robot.
Analog RF Performance of a CMOS Optical Filter (2006)

We have used an integrated narrowband optical filter fabricated in 0.18 micron CMOS process to optically slice a modulated broadband RF signal into an individual channel of 1 GHz bandwidth. The detected channel signal has an in-band spur-free dynamic range (SFDR) of 88 dBmiddotHz <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2/3</sup> and greater than 28 dB rejection of out-of-band signal
Progress in Ultrafast Photonics (2005)

Recent progress in ultrafast photonics is reviewed with special emphasis on the research and development activities in Japanese research institutions in the field of optical communication and related measurement technologies. After summarizing the physical natures of ultrashort optical pulses, selected topics are reviewed on such as (1) ultrahigh-bit-rate optical communication employing the combination of optical time division multiplexing (OTDM) and wavelength division multiplexing (WDM), (2) optical components for ultrafast photonics with emphasis on all optical switches including semiconductor optical amplifiers, cascaded second order frequency converters, semiconductor saturable absorber switches, organic dye saturable absorber switches and bistable semiconductor lasers, (3) microwave photonics, emphasizing millimeter-wave/photonic communication technologies, and (4) high-speed optical measurements featuring both compact femtosecond pulse source development and rf magnetic field imaging. Some comments on the future prospect of ultrafast photonics are also given. It is concluded that in order to bring the powerful and versatile capability of ultrafast photonics into the real world, further collaboration between photonics specialists and production engineers/information specialists is strongly desired.
Silver Nanoparticles Inhibit Sodium Uptake in Juvenile Rainbow Trout (Oncorhynchus mykiss) (2012)

The silver ion (Ag(+)) is well documented to be a potent inhibitor of sodium (Na(+)) transport in fish. However, it has not been determined whether silver nanoparticles (Ag NPs) elicit this same effect and, if so, if the NP itself and/or the dissociation of ionic Ag(+) causes this effect. Citrate-capped Ag NPs were dialyzed in water to determine the dissolution rate of ionic Ag(+) from the NPs and the maximum concentration of free Ag(+) released from the NPs was used as a paired Ag(+) control to distinguish NP effects from ionic metal effects. The maximum concentration of ionic Ag(+) released from these NPs over 48 h was 0.02 μg l(-1). Juvenile rainbow trout were exposed to 1.0 mg l(-1) citrate-capped Ag NPs and dialyzed citrate-capped Ag NPs or 10 μg l(-1) and 0.02 μg l(-1) ionic Ag(+) (as AgNO(3)) as controls. Both nondialyzed and dialyzed Ag NPs and 10 μg l(-1) ionic Ag(+) significantly inhibited unidirectional Na(+) influx by over 50% but had no effect on unidirectional Na(+) efflux. Na(+),K(+)-ATPase was significantly inhibited by the Ag NPs with no discernible effect on carbonic anhydrase activity. This study is the first to show that sodium regulation is disrupted by the presence of citrate-capped Ag NPs, and the results suggest that there are nanospecific effects.
[Acromegaly and pregnancy]. (2002)

Acromegaly usually results from GH hypersecretion by a somatotroph adenoma. The fertility of acromegalic patients is often impaired. Several factors may impact the course of pregnancy in acromegaly. Disturbed pituitary function might lead to infertility or spontaneous abortion. GH is a powerful insulin antagonist, and pregnant acromegalic patients are prone to added glucose intolerance and diabetes. Pregnancy itself might also impact the course of the pituitary tumor. During pregnancy, the normal pituitary increases in size due to estrogens-mediated hyperplasia. Therefore, tumors are at risk for hemorrhage due to enhanced vascularity, and might compress the optic chiasm. In this article we summarize the data on the literature on the reciprocal influences between acromegaly and pregnancy, we discuss therapeutic options and advance diagnostic and surveillance schedules of acromegaly during pregnancy.
Contact Engineering for High-Performance N-Type 2D Semiconductor Transistors (2021)

Two-dimensional (2D) semiconductors are expected to have exceptional properties for ultimately scaled transistors, but forming ohmic contact to them has been challenging, which tremendously limit the transistor performance. In this paper, we review the recent research progress on the elimination of different gap-state pinning effects, including defect-induced gap states (DIGS) and metal-induced gap states (MIGS). Specifically, an oxygen passivation method and a semimetallic contact technology were developed to reduce the DIGS and MIGS, respectively. Based on these approaches, much improved contact resistance and on-state current were observed. Key device metrics were extracted on these high-performance transistors, which reveals future directions for further improving the device performance.
Physical modeling of anisotropic domains: Ultrasonic imaging of laser‐etched fractures in glass (2011)

Physical modeling, using ultrasonic sources and receivers over scaled exploration structures, plays a useful role in wave propagation and elastic property investigations. This paper explores the anisotropic response of novel fractured glass blocks created with a laser‐etching technique. We compare transmitted and reflected signals for P‐ and S‐waves from fractured and unfractured zones in a suite of ultrasonic experiments. The unaltered glass velocities are 5801 m/s and 3448 m/s for P and S waves, respectively, with fractured zones showing a small decrease (about 1%). Signals propagating through the fractured zone have decreased amplitudes and increased coda signatures. Reflection surveys (zero‐offset and variable polarization and offset gathers) record significant scatter from the fractured zones. The glass specimens with laser‐etched fractures display a rich anisotropic response.