gebhart/patrepeval huggingface dataset:
Heterometallic titanium–gold complexes inhibit renal cancer cells in vitro and in vivo (2015)

Following recent work on heterometallic titanocene-gold complexes as potential chemotherapeutics for renal cancer, we report here on the synthesis, characterization and stability studies of new titanocene complexes containing a methyl group and a carboxylate ligand (mba = S-C<sub>6</sub>H<sub>4</sub>-COO<sup>-</sup>) bound to gold(I)-phosphane fragments through a thiolate group ([(<i>η</i>-C<sub>5</sub>H<sub>5</sub>)<sub>2</sub>TiMe(<i>μ</i>-mba)Au(PR<sub>3</sub>)]. The compounds are more stable in physiological media than those previously reported and are highly cytotoxic against human cancer renal cell lines. We describe here preliminary mechanistic data involving studies on the interaction of selected compounds with plasmid (pBR322) DNA used as a model nucleic acid, and with selected protein kinases from a panel of 35 protein kinases having oncological interest. Preliminary mechanistic studies in Caki-1 renal cells indicate that the cytotoxic and anti-migration effects of the most active compound <b>5</b> ([(η-C<sub>5</sub>H<sub>5</sub>)<sub>2</sub>TiMe(μ-mba)Au(PPh<sub>3</sub>)] involve inhibition of thioredoxin reductase and loss of expression of protein kinases that drive cell migration (AKT, p90-RSK, and MAPKAPK3). The co-localization of both titanium and gold metals (1:1 ratio) in Caki-1 renal cells was demonstrated for <b>5</b> indicating the robustness of the heterometallic compound <i>in vitro</i>. Two compounds were selected for further <i>in vivo</i> studies on mice based on their selectivity <i>in vitro</i> against renal cancer cell lines when compared to non-tumorigenic human kidney cell lines (HEK-293T and RPTC) and the favourable preliminary toxicity profile in C57BL/6 mice. Evaluation of Caki-1 xenografts in NOD.CB17-Prkdc SCID/J mice showed an impressive tumor reduction (67%) after treatment for 28 days (3 mg/kg/every other day) with heterometallic compound <b>5</b> as compared with the previously described [(<i>η</i>-C<sub>5</sub>H<sub>5</sub>)<sub>2</sub>Ti{OC(O)-4-C<sub>6</sub>H<sub>4</sub>-P(Ph<sub>2</sub>)AuCI}<sub>2</sub>] <b>3</b> which was non-inhibitory. These findings indicate that structural modifications on the ligand scaffold affect the <i>in vivo</i> efficacy of this class of compounds.
An electronically wavelength-tunable mode-locked fiber laser using an all-fiber acoustooptic tunable filter (1996)

We have demonstrated a novel scheme of a continuously wavelength-tunable and passively mode-locked fiber laser by using the sliding frequency effect of an all-fiber acoustooptic tunable filter. Stable and nearly transform-limited pulses of 800-fs pulsewidth were produced with this laser scheme for a wavelength tuning range of 17 nm at around 1550 nm.
LEARNING SENTIMENT COMPOSITION FROM SENTIMENT LEXICONS (2018)

Sentiment composition is a fundamental sentiment analysis problem. Previous work relied on manual rules and manually-created lexical resources such as negator lists, or learned a composition function from sentiment-annotated phrases or sentences. We propose a new approach for learning sentiment composition from a large, unlabeled corpus, which only requires a word-level sentiment lexicon for supervision. We automatically generate large sentiment lexicons of bigrams and unigrams, from which we induce a set of lexicons for a variety of sentiment composition processes. The effectiveness of our approach is confirmed through manual annotation, as well as sentiment classification experiments with both phrase-level and sentence-level benchmarks.
The Optimal Dual Estimate Solution for Robust Tracking of Binary Offset Carrier (BOC) Modulation (2007)

Binary Offset Carrier (BOC) is a very different way of modulating navigation signals which has been adopted for the next generation GNSS. Unfortunately in a conventional receiver, copying the general principles of PSK demodulation (as used in current GPS), a multipeaked correlation function is generated which can lead to problems of false lock or ‘false node tracking’ on a secondary rather than a primary peak. The problem is well-known. Published remedies to the problem have not been entirely successful or optimal (in sense of least square error). A radically different approach described here generalises the correlation into two dimensions within what we name as a dual estimating receiver. Two complementary estimates of the time-delay of the input signal are generated: a lower accuracy but unambiguous estimate responding purely to the code modulation; and a higher accuracy but ambiguous estimate responding purely to the sub-carrier modulation. The two estimates are then combined in a simple arithmetic operation to a single joint estimate which fully exploits the capabilities of BOC. Implementation is by a triple loop rather than the double loop of conventional receivers.
Wavelet and Denoising Techniques for Real-Time HIF Detection in 12-kV Distribution Circuits (2019)

A new two-step technique, which combines both adaptive soft denoising algorithms and orthogonal discrete wavelet transform (DWT) algorithms for detecting the high-impedance fault (HIF), is presented in this article. Three testing events in a 12-kV distribution network are performed at Southern California Edison (SCE) and the recorded datasets are employed for this experimental study. Case #0002 is the normal condition and is employed as the baseline for making up the heuristic HIF testing threshold. Both cases #0012 and #0047 have HIF events. Based on the results from the simulation, this detection technique is capable to fast and accurately detect the HIF without making false alarms. Due to the simplicity of designed algorithms, this new technique can be implemented with a digital signal processor for real-time HIF detection.
A novel process configuration of Simultaneous Saccharification and Fermentation for bioethanol production at high solid loadings (2012)

Simultaneous saccharification and fermentation (SSF) is a process option for lignocellulosic bioethanol production that has proven to have several advantages compared to separate hydrolysis and fermentation. The economical viability and commercialization of cellulose-to-ethanol demands the process to work under high-solid loadings to result in high sugar yield and final ethanol titer in S. cerevisiae based SSF process. In a conventional batch SSF process practical limitations to high-solid loadings include, poor mixing and accessibility of enzymes to substrates and high inhibitors concentration that reduces the yeast viability and metabolism. In order to overcome these limitations, we propose a novel SSF process configuration involving feeding of substrate, enzyme and yeast. It is possible to overcome mixing issues associated with a batch SSF at high-solid loadings by a feed of substrate, enzyme and yeast. The feed of freshly cultivated yeast throughout the fermentation process ensures active metabolic state of yeast. In addition, the substrate feed ensures low inhibitors concentration at any given time point increasing the survival ability of yeast compared to a batch SSF. The enzyme feed ensures slow release of glucose providing an opportunity for xylose consuming yeast strain to co-consume xylose together with glucose. The aim of the current work is to understand how different combinations of feeding strategies influence the outcome of the SSF process. In the longer perspective, we aim at deducing an optimized SSF process that can handle very high-solid loadings with efficient hydrolysis and fermentation process at low enzyme and yeast loadings, respectively.
Data from Treating Tissue Factor–Positive Cancers with Antibody–Drug Conjugates That Do Not Affect Blood Clotting (2023)

<div>Abstract<p>The primary function of tissue factor (TF) resides in the vasculature as a cofactor of blood clotting; however, multiple solid tumors aberrantly express this transmembrane receptor on the cell surface. Here, we developed anti-TF antibody–drug conjugates (ADC) that did not interfere with the coagulation cascade and benchmarked them against previously developed anti-TF ADCs. After screening an affinity-matured antibody panel of diverse paratopes and affinities, we identified one primary paratope family that did not inhibit conversion of Factor X (FX) to activated Factor X (FXa) and did not affect conversion of prothrombin to thrombin. The rest of the antibody panel and previously developed anti-TF antibodies were found to perturb coagulation to varying degrees. To compare the anticancer activity of coagulation-inert and -inhibitory antibodies as ADCs, a selection of antibodies was conjugated to the prototypic cytotoxic agent monomethyl auristatin E (MMAE) through a protease-cleavable linker. The coagulation-inert and -inhibitory anti-TF ADCs both killed cancer cells effectively. Importantly, the coagulation-inert ADCs were as efficacious as tisotumab vedotin, a clinical stage ADC that affected blood clotting, including in patient-derived xenografts from three solid tumor indications with a need for new therapeutic treatments—squamous cell carcinoma of the head and neck (SCCHN), ovarian, and gastric adenocarcinoma. Furthermore, a subset of the anti-TF antibodies could also be considered for the treatment of other diseases associated with upregulation of membranous TF expression, such as macular degeneration. <i>Mol Cancer Ther; 17(11); 2412–26. ©2018 AACR</i>.</p></div>
Multilayer Packet Classification With Graphics Processing Units (2015)

The rapid growth of server virtualization has ignited a wide adoption of software-based virtual switches, with significant interest in speeding up their performance. In a similar trend, software-defined networking (SDN), with its strong reliance on rule-based flow classification, has also created renewed interest in multi-dimensional packet classification. However, despite these recent advances, the performance of current software-based packet classifiers is still limited, mostly by the low parallelism of general-purpose CPUs. In this paper, we explore how to accelerate packet classification using the high parallelism and latency-hiding capabilities of graphic processing units (GPUs). We implement GPU-accelerated versions for both linear and tuple search, currently deployed in virtual switches, and also introduce a novel algorithm called Bloom search. These algorithms are integrated with high-speed packet I/O to build GSwitch, a GPU-accelerated software switch, and also to extend Open vSwitch. Our experimental evaluation indicates that, under realistic rule sets, GSwitch is at least 7 × faster than an equally-priced CPU classifier. We also show that our GPU-accelerated Open vSwitch outperforms the classic Open vSwitch implementation by a factor of 10, on average.
Dicer-regulated microRNAs 222 and 339 promote resistance of cancer cells to cytotoxic T-lymphocytes by down-regulation of ICAM-1 (2009)

The RNase III endonuclease Dicer plays a key role in generation of microRNAs (miRs). We hypothesized that Dicer regulates cancer cell susceptibility to immune surveillance through miR processing. Indeed, Dicer disruption up-regulated intercellular cell adhesion molecule (ICAM)-1 and enhanced the susceptibility of tumor cells to antigen-specific lysis by cytotoxic T-lymphocytes (CTLs), while expression of other immunoregulatory proteins examined was not affected. Blockade of ICAM-1 inhibited the specific lysis of CTLs against Dicer-disrupted cells, indicating a pivotal role of ICAM-1 in the interaction between tumor cells and CTL. Both miR-222 and -339 are down-regulated in Dicer-disrupted cells and directly interacted with the 3' untranslated region (UTR) of ICAM-1 mRNA. Modulation of Dicer or these miRs inversely correlated with ICAM-1 protein expression and susceptibility of U87 glioma cells to CTL-mediated cytolysis while ICAM-1 mRNA levels remained stable. Immunohistochemical and in situ hybridization analyses of 30 primary glioblastoma tissues demonstrated that expression of Dicer, miR-222, or miR-339 was inversely associated with ICAM-1 expression. Taken together, Dicer is responsible for the generation of the mature miR-222 and -339, which suppress ICAM-1 expression on tumor cells, thereby down-regulating the susceptibility of tumor cells to CTL-mediated cytolysis. This study suggests development of novel miR-targeted therapy to promote cytolysis of tumor cells.
1700-km transmission at 40-Gb/s with 100 km amplifier-spacing enabled by higher-order-mode dispersion-compensation (2002)

We report transmission at 40 Gb/s over a record length (1700 km) of non-zero dispersion fiber with 100 km amplifier spacing. The demonstration is enabled by an all-fiber higher-order-mode dispersion-compensating module that features a high effective area and low insertion loss. The high effective area of the dispersion compensating module allows high input power, which helps maintain high optical signal-to-noise ratios throughout the transmission span.
<title>Content-based downloading for digital video</title> (1996)

In this paper we examine a content-based method to download/record digital video from networks to client stations and home VCR's. The method examined is an alternative to the conventional time-based method used for recording analogue video. Various approaches to probing the video content and to triggering the VCR operations are considered, including frame signature matching, program barcode matching, preloaded pattern searching, and annotation signal searching in a hypermedia environment. Preliminary performance studies are conducted to provide some insights into this approach.
Octamer-primed sequencing technology: effects of dNTP (2001)

Octamer-primed sequencing is a directed DNA sequencing strategy that employs the use of a presynthesized octamer primer library. Together with electronic octamer sequencing technology (eOST) it provides a faster, less expensive way to obtain DNA sequence information and can be used as a valuable tool for gap closure in large-scale genomic sequencing. In this paper we discuss the effect of dGTP/TTP supplementation on octamer sequencing. We show that addition of 75 microM dGTP and 5 microM TTP can improve the sequencing success rate by increasing the length and accuracy of generated sequence information. We also discuss the effect of template base composition immediately downstream of the octamer primer on the outcome of octamer sequencing.
Gene Targeting by Adeno-Associated Virus Vectors Is Cell-Cycle Dependent (2005)

Adeno-associated virus (AAV) vectors can be used to introduce site-specific mutations into homologous chromosomal sequences. There are many potential applications of this technique, but the process of AAV-mediated gene targeting and factors that influence targeting efficiency are not completely understood. We investigated the dependence of AAV-mediated gene targeting on the host cell-cycle status. The frequency of gene targeting by AAV vectors was compared in dividing and serum-arrested normal human fibroblast cultures. Gene targeting occurred in arrested fibroblast cultures at 0.15 to 1.1% the frequency of dividing cultures, and only took place in cells that had undergone DNA synthesis. Gene targeting was also reduced when DNA synthesis was inhibited by hydroxyurea.
Probing Keratinocyte and Differentiation Specificity of the Human K5 Promoter in Vitro and in Transgenic Mice (1993)

Keratins K5 and K14 form the extensive intermediate filament network of mitotically active basal cells in all stratified epithelia. We have explored the regulatory mechanisms governing cell-type-specific and differentiation stage-specific expression of the human K5 gene in transiently transfected keratinocytes in vitro and in transgenic mice in vivo. Six thousand base pairs of 5' upstream K5 sequence directed proper basal cell-specific expression in all stratified epithelia. Surprisingly, as few as 90 bp of the K5 promoter still directed expression to stratified epithelia, with expression predominantly in epidermis, hair follicles, and tongue. Despite keratinocyte-preferred expression, the truncated K5 promoter displayed departures from basal to suprabasal expression in epidermis and from outer root sheath to inner root sheath expression in the follicle, with some regional variations in expression as well. To begin to elucidate the molecular controls underlying the keratinocyte specificity of the truncated promoter, we examined protein-DNA interactions within this region. A number of keratinocyte nuclear proteins bind to a K5 gene segment extending from -90 to +32 bp and are functionally involved in transcriptional regulation in vitro. Interestingly, several of these factors are common to both the K5 and K14 promoters, although they appear to be distinct from those previously implicated in keratinocyte specificity. Mutagenesis studies indicate that factors binding in the vicinity of the TATA box and transcription initiation are responsible for the cell type specificity of the truncated K5 promoter.
New quadric metric for simplifiying meshes with appearance attributes (1999)

Complex triangle meshes arise naturally in many areas of computer graphics and visualization. Previous work has shown that a quadric error metric allows fast and accurate geometric simplification of meshes. This quadric approach was recently generalized to handle meshes with appearance attributes. In this paper we present an improved quadric error metric for simplifying meshes with attributes. The new metric, based on geometric correspondence in 3D, requires less storage, evaluates more quickly, and results in more accurate simplified meshes. Meshes often have attribute discontinuities, such as surface creases and material boundaries, which require multiple attribute vectors per vertex. We show that a wedge-based mesh data structure captures such discontinuities efficiently and permits simultaneous optimization of these multiple attribute vectors. In addition to the new quadric metric, we experiment with two techniques proposed in geometric simplification, memoryless simplification and volume preservation, and show that both of these are beneficial within the quadric framework. The new scheme is demonstrated on a variety of meshes with colors and normals.
Implementation of Sensor RFID: Carrying Sensor Information in the Modulation Frequency (2015)

An approach that can be used for exploiting the sensing capabilities of RF identification (RFID) is presented and formulated. In this approach, sensor information is carried through the modulation frequency of RFID. The aim of this work is to investigate the sensor concept and to characterize the sensor performance both theoretically and experimentally. Furthermore, the operation of the sensor RF parts and oscillator are described analytically, and the equations are verified by simulations and measurements. The concept is experimentally demonstrated at a single carrier frequency to test its suitability for ultra-high-frequency RFID applications, and shown to be feasible for implementing sensors that can be read across distances up to 14 m.
Spontaneously Formed Interfacial Metal Silicates and Their Effect on the Magnetism of Superparamagnetic FeCo/SiO<sub>2</sub>Core/Shell Nanoparticles (2015)

The integration of superparamagnetic core/shell nanoparticles into devices and other nanoscale technological applications requires a detailed understanding of how the intimate contact between core and shell nanophases affects the magnetism. We report how, for single-domain FeCo nanoparticles, an FeCo phase unique to the nanoscale with silica shells of increasing thicknesses spontaneously formed interfacial metal silicates between the core and shell (such as Fe2SiO4 and Co2SiO4) and altered the overall magnetism of the nanomaterial significantly. The influence of this previously overlooked phenomenon on magnetic properties is reported. Evidence of these metal silicate interfacial layers was observed by X-ray absorption spectroscopy (XAS) collected over the L3,2 absorption edges of Fe and X-ray photoelectron spectra (XPS) collected over the 2p transitions of Fe and Co. Through the correlation of magnetometry and XPS data, the evolution of nanoparticle magnetic anisotropy is shown to increase with the metal silicate.
Construction and synthesis of lactoferricin derivatives with enhanced antibacterial activity (1999)

A series of peptides derived from sequences from human, bovine, murine and caprine lactoferrin has been prepared and investigated for antibacterial effect. Among the four species investigated peptides based on the bovine sequence displayed significant activity. The bovine sequence, bovine lactoferricin, showed a MIC value of 30 μg/mL on E. coli and S. aureus, whereas the three other lactoferricins possessed MIC values above 200 μg/mL. Based on these findings, novel peptides with enhanced antibacterial activities, were prepared with sequences designed by molecular modelling and structure-activity studies. Copyright © 1999 European Peptide Society and John Wiley & Sons, Ltd.
Optically encoded phase-matched second-harmonic generation in semiconductor-microcrystallite-doped glasses (1991)

We observed that the simultaneous injection of the fundamental and second-harmonic fields (1.06 μm and 532 nm) into semiconductor-doped glasses results in the evolution of a permanent, quasi-phase-matched, second-harmonic signal that is 105 times the initial background value. Using samples as long as 5 cm, we obtained second-harmonic signals that are visible under room lights, corresponding to a conversion efficiency of 10−6 for mode-locked, Q-switched input pulses. Results are presented for a variety of experiments that shed light on the basic physics of the effect. These include polarization dependence, IR and second-harmonic preparation intensity effects, thermal erasure, and the application of external static-electric fields. The results indicate that the most likely mechanism is the encoding of a periodic internal electric field, which results in a phase-matched electric-field-induced second-harmonic generation process.
Comparative study of three-dimensional localization accuracy in conventional, confocal laser scanning and axial tomographic fluorescence light microscopy (1996)

For many biological applications, precise and accurate 3D object localizations and 3D-distance measurements are necessary. Point spread functions of artificial objects of subwavelength dimensions have been measured in order to characterize the image forming properties as well as to localize extended objects in both conventional and confocal florescence light microscopy with and without the axial tomographic technique. With the axial tomographic technique it is possible to tilt the object in such a way, that substructures are located in the same focal plane. The distance of two points measured under this optimal perspective fits best to the real 3D-distance. In this case, optical sectioning is unnecessary, if only distance measurements have to be performed.
Foreign gene products can be enhanced by introduction into low storage protein mutants (2003)

Transgenic rice expressing soybean glycinin in its endosperm was crossed with two types of low-glutelin mutants to determine how much storage the protein mutants can contribute to increases in glycinin accumulation. The glycinin level (102 microg/100 mg seed) in the parental transgenic line was enhanced to approximately 224-237 microg/100 mg seed within a genetic background deficient in glutelin (i.e. of low glutelins). The enrichment of this foreign gene product was compensated by a decrease in the expression of other endogenous prolamine and globulin storage proteins, resulting in an almost equivalent total amount of seed storage proteins. These results show that low storage protein mutants can provide potentially useful hosts for the expression of foreign genes, allowing a higher-level accumulation, because they can provide wider space for the accumulation of foreign gene products than in the normal host plant.