gebhart/patrepeval huggingface dataset:
Wireless Actuation for Soft Electronics-free Robots (2023)

This paper proposes a new primitive that allows soft robots to be physically controlled in a completely non-line-of-sight context using wireless energy - a process we call wireless actuation. Soft robots, which are composed entirely of soft materials and exclude any rigid components, are highly flexible platforms that can change their shape. This paper considers a specific class of soft robots composed of liquid-crystal elastomers (LCE) that are entirely electronics-free and engineered to change shape when heated to 60 °C. Traditionally, such robotic systems must be in line-of-sight of a light source, such as infrared to be moved, or require an external power supply for Joule heating and often take several tens of seconds to heat. We present WASER, a novel RF-based heating platform that allows electronics-free robots to be actuated rapidly (within a few seconds) and potentially in non-line-of-sight. WASER achieves this through innovations in both wireless systems and material science. On the wireless front, WASER develops a new blind beamforming solution that directs high-power wireless energy at fine spatial granularity without electronics on the robot to provide feedback. On the material science front, WASER exhibits heat-responsive shape-morphing and energy-harvesting material functionalities that allow for rapid wireless heating. We implement and evaluate WASER and demonstrate diverse shape-morphing capabilities.
Run-time detection of buffer overflow attacks without explicit sensor data objects (2004)

This paper presents two schemes for detecting buffer overflow attacks at run-time. One is sensor embedding, which hides sensor data objects inside code pointers, and the other, stack frame inversion checking, which detects attacks by inspecting processor registers. Our methods make it difficult for attackers to guess the locations of sensors so that they cannot easily bypass sensors when they attempt to access code pointers. We have implemented the schemes by extending the GCC toolchain. Experimental data shows that our schemes provide programs with powerful detection and protection capabilities at the reasonable sacrifice of execution efficiency. Operating systems would improve on the defense against buffer overflow attacks by using our toolchain when they are built.
Inductive Kernel Low-rank Decomposition with Priors: A Generalized Nystrom Method (2012)

Low-rank matrix decomposition has gained great popularity recently in scaling up kernel methods to large amounts of data. However, some limitations could prevent them from working effectively in certain domains. For example, many existing approaches are intrinsically unsupervised, which does not incorporate side information (e.g., class labels) to produce task specific decompositions; also, they typically work "transductively", i.e., the factorization does not generalize to new samples, so the complete factorization needs to be recomputed when new samples become available. To solve these problems, in this paper we propose an"inductive"-flavored method for low-rank kernel decomposition with priors. We achieve this by generalizing the Nyström method in a novel way. On the one hand, our approach employs a highly flexible, nonparametric structure that allows us to generalize the low-rank factors to arbitrarily new samples; on the other hand, it has linear time and space complexities, which can be orders of magnitudes faster than existing approaches and renders great efficiency in learning a low-rank kernel decomposition. Empirical results demonstrate the efficacy and efficiency of the proposed method.
Restoration of Lysosomal pH in RPE Cells from Cultured Human and ABCA4−/−Mice: Pharmacologic Approaches and Functional Recovery (2008)

Elevation of lysosomal pH in RPE cells interferes with the degradation of outer segments and may contribute to the pathologies associated with A2E. Pharmacologic elevation of cAMP can restore an acid pH and improve degradative function.
Predictors in the Treatment of Difficult-to-control Seizures by Electrical Stimulation of the Centromedian Thalamic Nucleus (2000)

ESCM is an efficient and safe procedure for controlling certain seizure types, if patient selection and stereotactic placement are satisfactory.
Real time femtosecond optical pulse measurement using a video-rate frequency-resolved optical gating system (2003)

We describe an improved instrument for measuring at video rate (30 frames per second) the second-harmonic frequency-resolved optical gating trace of femtosecond pulses from a mode-locked laser oscillator. The system comprises separate scanning acquisition and pulse retrieval elements which together enable the exact pulse profile to be viewed in real time with a typical refresh rate of 1 Hz. Details are given of the optical system used, the electronic synchronization circuits and the acquisition and retrieval software employed.
Biological treatment of ammonia gas at high loading (2004)

The exhaust gas from compost processing plants contains a large amount of ammonia. To treat ammonia gas at high loads, bench-scale experiments were carried out. First, nitrifying bacteria were enriched from soil and immobilized on porous ceramics. The ceramics were packed in an acrylic cylinder (diameter, 100 mm; packed height, 190 mm) and ammonia gas was introduced to the top of the cylinder. The concentration and flow rate of ammonia gas were gradually increased and finally 85 ppm was introduced at a space velocity of 800 h(-1) (empty bed residence time (EBRT), 4.5 sec). The ammonia load was 1.0 kg N/m3 day(-1). The exhaust contained 1.5-2 ppm of ammonia. Then the packed ceramics were transferred to another acrylic cylinder (diameter, 50 mm; packed height, 800 mm). A high concentration of ammonia gas (1,000 ppm) was introduced at a space velocity of 96 h(-1) (ammonia loading, 1.44 kg N/m3 day(-1); EBRT, 37.5 sec). The exhaust contained 2 ppm of ammonia (removal rate, 99.8%). The packed bed was washed with water intermittently or continuously, and the wastewater from the cylinder contained a large amount of ammonium and nitrate ions of at a 1:1 ratio. Stoichiometric analysis showed that half of the introduced ammonia was oxidized to nitrate, and the rest was converted to ammonium ion. Thus, ammonia gas was effectively treated at a high load by biofiltration with nitrifying bacteria.
Sensitivity for global shape detection (2002)

In order to understand the nature of the mechanisms responsible for global shape detection, we measured coherence thresholds in a 2IFC task where subjects judged which of two arrays of Gabors contained global circular structure. The stimulus was composed of an array of oriented Gabor patches positioned on a polar grid. Thresholds were obtained for different array parameters (e.g. different area, density, number and positions of elements) as well as for different element parameters (e.g. different carrier spatial frequencies, contrasts, polarities and orientations). Global structure was detected when ~10% of the elements were coherently oriented. Neither the properties of the array (density, area, number or position of elements), nor those of the individual elements (carrier spatial frequency, contrast, polarity) altered coherence thresholds. Varying contrast or carrier spatial frequency within individual arrays also did not alter performance. Sensitivity was invariant to positional perturbations of the array grid. Only jittering the local orientation of elements decreased sensitivity. The underlying mechanisms are broadly tuned for contrast, spatial frequency and the spatial positioning of image samples. Detecting circular structure is a robust process and, in this case, a purely global one. Sensitivity was highest for circular as opposed to radial or spiral shapes.
Validation of Genotyping-By-Sequencing Analysis in Populations of Tetraploid Alfalfa by 454 Sequencing (2015)

Genotyping-by-sequencing (GBS) is a relatively low-cost high throughput genotyping technology based on next generation sequencing and is applicable to orphan species with no reference genome. A combination of genome complexity reduction and multiplexing with DNA barcoding provides a simple and affordable way to resolve allelic variation between plant samples or populations. GBS was performed on ApeKI libraries using DNA from 48 genotypes each of two heterogeneous populations of tetraploid alfalfa (Medicago sativa spp. sativa): the synthetic cultivar Apica (ATF0) and a derived population (ATF5) obtained after five cycles of recurrent selection for superior tolerance to freezing (TF). Nearly 400 million reads were obtained from two lanes of an Illumina HiSeq 2000 sequencer and analyzed with the Universal Network-Enabled Analysis Kit (UNEAK) pipeline designed for species with no reference genome. Following the application of whole dataset-level filters, 11,694 single nucleotide polymorphism (SNP) loci were obtained. About 60% had a significant match on the Medicago truncatula syntenic genome. The accuracy of allelic ratios and genotype calls based on GBS data was directly assessed using 454 sequencing on a subset of SNP loci scored in eight plant samples. Sequencing depth in this study was not sufficient for accurate tetraploid allelic dosage, but reliable genotype calls based on diploid allelic dosage were obtained when using additional quality filtering. Principal Component Analysis of SNP loci in plant samples revealed that a small proportion (<5%) of the genetic variability assessed by GBS is able to differentiate ATF0 and ATF5. Our results confirm that analysis of GBS data using UNEAK is a reliable approach for genome-wide discovery of SNP loci in outcrossed polyploids.
Data from Monitoring Caspase-3 Activation with a Multimodality Imaging Sensor in Living Subjects (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Capsase-3 plays an important role in chemotherapy-induced apoptosis in many cancers. Herein, we applied a multimodality reporter vector to monitor caspase-3 activation indirectly in live cells and tumors of living animals undergoing apoptosis.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; A fusion protein (MTF) was constructed by combining three different reporter proteins, red fluorescent protein (mRFP1), firefly luciferase (FL), and HSV1-sr39 truncated thymidine kinase (TK), linked through a caspase-3 recognizable polypeptide linker. After cleavage by caspase-3, a significant gain in mRFP1, FL, and TK activity are observed by fluorescence-activated cell sorting and enzyme-based assays. A melanoma cell line (&lt;i&gt;B16F10-mtf-hrl&lt;/i&gt;) stably expressing &lt;i&gt;mtf&lt;/i&gt; (to measure caspase-3 activation) and &lt;i&gt;hrl-IRES-gfp&lt;/i&gt; (to determine the decrease in a number of viable cells) vectors was generated to measure two independent molecular events upon treatment.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Upon induction with 8 μmol/L staurosporine, the fusion protein showed a 2.8-fold increase in FL (&lt;i&gt;P&lt;/i&gt; = 0.03), a 1.5-fold increase in TK (&lt;i&gt;P&lt;/i&gt; = not significant), and a 2-fold increase in mRFP1 (&lt;i&gt;P&lt;/i&gt; = 0.05) activity in 293T cells. Bioluminescence and micropositron emission tomography imaging of the apoptotic &lt;i&gt;B16F10-mtf-hrl&lt;/i&gt; tumors showed a 2-fold higher FL activity (897 versus 416) and a 2-fold higher TK activity (10.3 versus 3.87) than control tumors when normalized with RL activity. Using a similar normalization approach, the time kinetics of caspase-3 activation by two protein kinase-C inhibitors was noninvasively monitored in living mice.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusion:&lt;/b&gt; This multimodality caspase sensor vector could effectively and noninvasively monitor caspase-3 activation from single live cells to a multicellular tumor environment and, thus, would be a valuable tool for drug screening in preclinical models and future patient cell based therapy.&lt;/p&gt;&lt;/div&gt;
Design of Optical Switches as Metabolic Indicators:  New Fluorogenic Probes for Monoamine Oxidases (MAO A and B) (2005)

This study describes the design of sensitive, selective, and fluorogenic reporter substrates for monoamine oxidase (MAO) enzymes. This was achieved by an iterative effort, guided by PET and TICT photophysical concepts, which led to the development of irreversible redox switches based on a facile oxidation-cyclization reporting mechanism. Specifically, enzymatic oxidation of the ethylamino group in probe 9 proceeded via a putative aldehyde intermediate, which subsequently underwent spontaneous and intramolecular condensation with the aniline amino group furnishing an indole product in an irreversible fashion. This overall change resulted in a significant change in the emission intensity. When expressed in terms of brightness, the origins of this emission switch may be rationalized by the changes in quantum yield and absorbance strength. The fluorescence readout directly correlated with the kinetics of the oxidative step (i.e., reporting mechanism was fast, the intermediate aldehyde was not detected). Probe 9 is a good substrate for MAO B (Km = 510 +/- 40 muM, kcat = 21 min-1) with the kinetic parameters comparable to physiological substrates. This probe not only allows for direct and continuous measurement of MAO activity in mitochondria and tissue homogenates, but more importantly sets the stage for future studies in intact cells and organs.
Identification of Importin 8 (IPO8) as the most accurate reference gene for the clinicopathological analysis of lung specimens (2008)

The accurate normalization of differentially expressed genes in lung cancer is essential for the identification of novel therapeutic targets and biomarkers by real time RT-PCR and microarrays. Although classical "housekeeping" genes, such as GAPDH, HPRT1, and beta-actin have been widely used in the past, their accuracy as reference genes for lung tissues has not been proven. We have conducted a thorough analysis of a panel of 16 candidate reference genes for lung specimens and lung cell lines. Gene expression was measured by quantitative real time RT-PCR and expression stability was analyzed with the softwares GeNorm and NormFinder, mean of |ΔCt| (= |Ct Normal-Ct tumor|) ± SEM, and correlation coefficients among genes. Systematic comparison between candidates led us to the identification of a subset of suitable reference genes for clinical samples: IPO8, ACTB, POLR2A, 18S, and PPIA. Further analysis showed that IPO8 had a very low mean of |ΔCt| (0.70 ± 0.09), with no statistically significant differences between normal and malignant samples and with excellent expression stability. Our data show that IPO8 is the most accurate reference gene for clinical lung specimens. In addition, we demonstrate that the commonly used genes GAPDH and HPRT1 are inappropriate to normalize data derived from lung biopsies, although they are suitable as reference genes for lung cell lines. We thus propose IPO8 as a novel reference gene for lung cancer samples.
The HIV‐1 Nef Protein Inhibits Extracellular Signal‐Regulated Kinase‐Dependent DNA Synthesis in a Human Astrocytic Cell Line (1998)

The role of nonproductive infection of astrocytes by human immunodeficiency virus type 1 (HIV-1), characterized by the overexpression of nef, in brain disease progression is largely unknown. We investigated the consequences of stable expression of nef from the HIV-1 strain LAI in the human astrocytic cell line U373. DNA synthesis induced by endothelin-1 (ET-1) was largely decreased by nef. Stable expression of nef did not affect the ET-1-induced tyrosine phosphorylation of focal adhesion kinase, an adhesion-dependent pathway known to participate in DNA synthesis in astrocytes. Conversely, the activation of extracellular signal-regulated kinase (ERK) by ET-1 was largely inhibited in cells stably or transiently expressing nef. A similar inhibitory action of nef on ERK activation was observed after direct stimulation of G proteins. Furthermore, the inhibitory action of nef did not require protein kinase C (PKC) and affected mainly the PKC-independent pathway of ERK activation. Following chemokine receptor CXCR4-mediated infection of U373 cells stably expressing CXCR4 with the T-tropic HIV-1 strain m7-NDK, ET-1-induced activation of ERK was also inhibited. Altogether, these results indicate that intracellular signaling pathways associated with the growth factor activity of ET-1 are impaired in nef-expressing and HIV-1-infected astrocytes, suggesting that infection of astrocytes may play a significant role in the neuropathogenesis of HIV-1 encephalopathy.
Nano-Targeting of Thyrointegrin αvβ3 Receptor in Solid Tumors and Impact on Radiosensitization (2021)

Tetraiodothyroacetic acid is a ligand of thyrointegrin αvβ3, a protein that is highly expressed in various solid tumors and surrounding neovascular regions. Its nano derivative, Nano-diamino-tetrac (NDAT), has anticancer properties in preclinical models, enhances radiosensitivity, and inhibits cancer cell growth in vitro after X-ray irradiation. Using a novel experimental system developed to deliver accurate radiation dose to tumors under sterile conditions, this study establishes NDAT's radiosensitizing effect in SUIT-2 pancreatic cancer and H1299 non-small cell lung carcinoma xenografts in athymic mice for tumor-targeted radiation. In this work, low-melting-point Lipowitz alloy was used to shield normal organs and allow accurate tumor-targeted irradiation. Over a three-week period, mice with SUIT-2 xenografts received daily NDAT treatment at different doses (0, 1, 3, or 10 mg/kg body weight) and tumor-targeted irradiation (1 or 5 Gy). Validation was performed with a test dose of 30 Gy to mice bearing SUIT-2 xenografts and resulted in more than 80% reduction in tumor weight, compared to nonirradiated tumor weight. The results of this work showed that NDAT had a radiosensitizing effect in a dose-dependent manner in decreasing tumor growth and viability. An enhanced anticancer effect of NDAT (1 mg/kg body weight) was observed in mice with H1299 xenografts receiving 5 Gy tumor-targeted irradiation, indicated by decreased tumor weight and increased necrosis, compared to nonirradiated tumors. This technique demonstrated accurate tumor-targeted irradiation with new shielding methodology, and combined with thyrointegrin antagonist NDAT treatment, showed anticancer efficacy in pancreatic cancer and non-small cell lung carcinoma.
OS1504 Observation of Crack Propagation Process under Rolling Contact Fatigue by using Synchrotron Radiation μCT and Compact Rolling Contact Fatigue Testing Machine (2013)

In rolling contact fatigue (RCF), cracks are usually initiated from inclusions under the surface and propagated to the surface. In the present study, the micro computed tomography (μCT) imaging and laminography using synchrotron radiation in SPring-8 is applied for observation of RCF cracks. The compact RCF testing machine is developed to observe RCF crack behavior m-situ. In this testing machine, the steel ball rolls on the specimen, linearly and reciprocally, and a specimen can be attached and removed easily. Since the size of the sample for μCT imaging has to be limited by penetrative power, the sample for μCT imaging has 500μm×500μm cross-section. On the other hand, laminography can be applied to a sheeted material. The sample, where an artificial defect is introduced, is used for observation of crack initiation and propagation. It is found from this experiment that cracks initiate and propagate in the depth direction along the artificial hole with increasing the number of cycles. Flaking and RCF crack in sheeted sample are observed by laminography. RCF cracks which initiate and propagate under contact surface can be detected. The shape and location observed by laminography coincide with that by SEM.
Putting Mobile DNA to Work: the Toolbox (2007)

This chapter reviews some mobile DNA tools currently being used in DNA sequencing for manipulating clones efficiently, and in functional analysis of more modest segments of DNA containing one or a few genes as well as entire genomes. It covers the increasing use of transposons as genetic tags and as devices for the delivery and selective destruction of genes. It also provides a brief review of some recent applications of transposons as genetic markers. Two systems have recently been developed to attack the difficulties associated with the often complex subcloning steps required to ensure efficient recombinant protein expression. The original uses of transposons as tools for genome analysis date back to Casadaban's pioneering work with Mu in Escherichia coli . A variation on the footprinting theme for analyzing the genomes of naturally transformable bacteria referred to as genomic analysis and mapping through in vitro transposition (GAMBIT) has also been described. A most powerful technology based on Cre is the activation and shutoff of the target gene in transgenic animals. In recent years, several groups have used mariner/Tc1 elements to perform mutagenesis and to deliver genes to various organisms. The transposon has many attractive features, but its main shortcoming is that it is quite specific for TA dinucleotides in every species examined. This chapter focuses on the practical application of transposons as tangible tools for the manipulation of DNA sequences and of cellular phenotypes.
N‐Heterocyclische Carbene (1997)

Abstract Lange Zeit war die Chemie der N‐heterocyclischen Carbene auf Koordinationsverbindungen beschränkt, die aus Azoliumsalz‐Vorstufen synthetisiert werden können, wie es Wanzlick und Öfele 1968 zum ersten Mal beschrieben hatten. Seit aber durch die Arbeiten von Arduengo (1991) freie Carbene zur Verfügung stehen, erlebt dieses bisher wenig beachtete Gebiet eine anhaltende Renaissance. Ein Leitmotiv sind dabei die vorteilhaften Eigenschaften der N‐heterocyclischen Carbene als Liganden in der metallorganischen Katalyse, wo sie die breite Anwendungspalette der Phosphane ergänzen und erweitern. Hier wird der gegenwärtige Wissensstand auf dem Gebiet der Synthese‐ und Strukturchemie, der Bindungstheorie, Koordinationschemie und Katalyse zusammengefaßt. Chelatisierende, funktionalisierte, chirale und immobilisierte Liganden können in einfachen Verfahren unter milden Bedingungen hergestellt und an Metallzentren fixiert werden, wodurch sich ein neues, weites Feld der Chemie eröffnet. Auch die Rolle der von Imidazol und Triazol abgeleiteten Carbene als Liganden in der Katalyse wird in dieser Übersicht beleuchtet. Es wäre denkbar, daß N‐heterocyclische Carbene die allgegenwärtigen Phosphane in manchen metallorganisch katalysierten Reaktionen als Liganden ersetzen.
Implementation of an integer wavelet transform on a parallel TI TMS320C40 platform (2003)

We present the implementation of an integer wavelet transform on a parallel TI TMS320C40-platform. The design space exploration is not driven by arithmetic optimizations, but rather by data transfer and storage estimates. The main focus of this paper lies on the detailed memory organization exploration. A number of implementation approaches is discussed. Based on the memory constraints imposed by the selected platform, the classical row-column approach was selected. By efficiently exploiting the DMA-facilities of the TMS320C40, we have realized a near real-time implementation.