gebhart/patrepeval huggingface dataset:
MicroRNA1 influences cardiac differentiation in <i>Drosophila</i> and regulates Notch signaling (2005)

MicroRNAs (miRNAs) are genomically encoded small RNAs that hybridize with messenger RNAs, resulting in degradation or translational inhibition of targeted transcripts. The potential for miRNAs to regulate cell-lineage determination or differentiation from pluripotent progenitor or stem cells is unknown. Here, we show that microRNA1 (miR-1) is an ancient muscle-specific gene conserved in sequence and expression in Drosophila. Drosophila miR-1 (dmiR-1) is regulated through a serum response factor-like binding site in cardiac progenitor cells. Loss- and gain-of-function studies demonstrated a role for dmiR-1 in modulating cardiogenesis and in maintenance of muscle-gene expression. We provide in vivo evidence that dmiR-1 targets transcripts encoding the Notch ligand Delta, providing a potential mechanism for the expansion of cardiac and muscle progenitor cells and failure of progenitor cell differentiation in some dmiR-1 mutants. These findings demonstrate that dmiR-1 may "fine-tune" critical steps involved in differentiation of cardiac and somatic muscle progenitors and targets a pathway required for progenitor cell specification and asymmetric cell division.
Second-harmonic Patterned Polarization-Analyzed Reflection Confocal Microscopy of Collagen (2017)

Polarization analysis of images obtained by combining confocal microscopy with a second-harmonic mask permits traditional polarimetric metrics to be adapted to collagen imaging. This approach applies to any nonlinear scattering imaging technique.
A Probabilistic Intensity Similarity Measure based on Noise Distributions (2007)

We derive a probabilistic similarity measure between two observed image intensities that is based on the noise properties of the camera. In many vision algorithms, the effect of camera noise is either neglected or reduced in a preprocessing stage. However, noise reduction cannot be performed with high accuracy due to lack of knowledge about the true intensity signal. Our similarity metric specifically represents the likelihood that two intensity observations correspond to the same unknown noise-free scene radiance. By directly accounting for noise in the evaluation of similarity, the proposed measure makes noise reduction unnecessary and enhances many vision algorithms that involve matching of image intensities. Real-world experiments demonstrate the effectiveness of the proposed similarity measure in comparison to the standard L <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> norm.
Automatic Design of VLIW and EPIC Instruction Formats (2000)

instruction format design, template design, instruction-set architecture, abstract ISA, concrete ISA, VLIW processors, EPIC processors, HPL-PD architecture, instruction encoding, bit allocation, affinity allocation, applicationspecific processors, design space exploration Very long instruction word (VLIW), and in its generalization, explicitly parallel instruction computing (EPIC) architectures explicitly encode multiple independent operations within each instruction. The processor's instruction-set architecture (ISA) specifies the interface between hardware and software, while its instruction format specifies the precise syntax and binary encodings of all instructions in the ISA. A designer of instruction formats must make efficient use of the available hardware resources and make intelligent trade-offs between decoder complexity and instruction width. Simple encodings lead to faster and less expensive decode hardware, but increase instruction width. Wider instruction formats lead to increased code size and more expensive instruction caches and instruction data paths. In embedded systems, code size is often a major component of total system cost, since the program is stored in ROM. In this report, we present an algorithmic approach to automatic design of high-quality VLIW/EPIC instruction formats. Our design process can be used to explore a large design space to find good designs at varying cost-performance points. This is also essential for automated design-space exploration of application-specific VLIW/EPIC processors.
Polysilicon VGA active matrix OLED displays-technology and performance (2002)

The first VGA polysilicon active matrix organic light emitting diode (AM-OLED) display will be presented. The goal of this work is to investigate the technology and performance of polysilicon active matrix OLED displays along with a new driving method.
Characterization <i>of fHbp</i> , <i>nhba</i> ( <i>gna2132</i> ), <i>nadA</i> , <i>porA</i> , and Sequence Type in Group B Meningococcal Case Isolates Collected in England and Wales during January 2008 and Potential Coverage of an Investigational Group B Meningococcal Vaccine (2010)

Invasive disease caused by meningococcal capsular groups A, C, W-135, and Y is now preventable by means of glycoconjugate vaccines that target their respective polysaccharide capsules. The capsule of group B meningococci (MenB) is poorly immunogenic and may induce autoimmunity. Vaccines based on the major immunodominant surface porin, PorA, are effective against clonal epidemics but, thus far, have a limited scope of coverage against the wider MenB population at large. In an alternative approach, the first-generation, investigational, recombinant MenB (rMenB) plus outer membrane vesicle (OMV) (rMenB-OMV) vaccine contains a number of relatively conserved surface proteins, fHBP, NHBA (previously GNA2132), and NadA, alongside PorA P1.4-containing OMVs from the New Zealand MeNZB vaccine. MenB currently accounts for approximately 90% of cases of meningococcal disease in England and Wales. To assess potential rMenB-OMV vaccine coverage of pathogenic MenB isolates within this region, all English and Welsh MenB case isolates from January 2008 (n = 87) were genetically characterized with respect to fHBP, NHBA, NadA, and PorA. Alleles for fHbp, nhba, and porA were identified in all of the isolates, of which 22% were also found to harbor nadA alleles. On the basis of genotypic data and predicted immunological cross-reactivity, the potential level of rMenB-OMV vaccine coverage in England and Wales ranges from 66% to 100%.
Adaptive integrated parallel reception, excitation, and shimming (iPRES‐A) with microelectromechanical systems switches (2017)

The iPRES(N)-A design retains the ability of the iPRES(N) design to shim highly localized B<sub>0</sub> inhomogeneities, while drastically reducing its cost and complexity. Magn Reson Med 80:371-379, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
Optimal audio-visual representations for illiterate users (2007)

We present research leading toward an understanding of the optimal audio-visual representation for illustrating concepts for illiterate and semi-literate users of computers. In our user study, which to our knowledge is the first of its kind, we presented to 200 illiterate subjects each of 13 different health symptoms in one representation randomly selected among the following ten: text, static drawings, static photographs, hand-drawn animations, and video, each with and without voice annotation. The goal was to see how comprehensible these representation types were for an illiterate audience. We used a methodology for generating each of the representations tested in a way that fairly stacks one representational type against the others. Our main results are that (1) voice annotation generally helps in speed of comprehension, but bimodal audio-visual information can be confusing for the target population; (2) richer information is not necessarily better understood overall; (3) the relative value of dynamic imagery versus static imagery depends on various factors. Analysis of these statistically significant results and additional detailed results are also provided.
Abstract 4068: A novel antiglycolytic small compound inhibits cancer growth in vitro and in vivo by inhibiting glut1 (2011)

Abstract This is an anticancer mechanism and an in vivo anticancer efficacy studies of a novel antiglycolytic inhibitor. Increased aerobic glycolysis in cancer cells, known as the Warburg effect, is an important biological hallmark in tumorigenesis. However, the real mechanisms and functional significance of the effect, the switch from oxidative phosphorylation to aerobic glycolysis in cancer cells have just begun to be understood. As a result, glycolysis and cancer metabolism have become new cancer research focuses and anticancer targets. Using the glucose uptake and cell viability as well as clonogenic assays, we recently reported the identification of a group of novel small compounds that inhibit basal glucose transport and reduce cancer cell growth by inducing apoptosis and cell cycle arrest using a glucose deprivation-like mechanism. Additional analysis revealed that these two activities were correlated. Furthermore, these compounds inhibit basal glucose transport in various the cancer cell lines tested. Based on these and other results, we hypothesized that the compounds inhibit cancer growth by inhibiting Glut1 and they are efficacious in vivo as anticancer agents. To test the hypotheses, the representative compound WZB117, human red blood cells (RBC) as well as their derived plasma membrane vesicles were used in the protein target study. The results of the study showed that, at 10-30 μμ range, WZB117 inhibited glucose uptake in both RBC and the vesicles in a similar manner as the anti-Glut1 antibody, indicating that the inhibiting target of the compound is Glut1, as Glut1 is the only glucose transporter expressed in RBC. When treated with the compound, a reduced intracellular NADH concentration was observed in cancer cells, suggesting that glycolysis in the treated cancer cells was inhibited. Tested in nude mice grafted with human A549 non-small cell lung cancer, a more than 70% reduction in the tumor growth rate was observed when the tumor-bearing mice were treated with daily ip injection of WZB117 at 10 mg/kg body weight for 10 weeks and compared to the mock-treated control mice. Over the treatment period, these tumor-bearing mice demonstrated an average food intake similar to that of the control mice. Small but significant changes in body weight and in complete blood counts (CBC) were also observed, although various types of blood cells were all in the normal ranges. All these results indicate that WZB117 is both efficacious and safe in treating cancers in the nude mice. This is the first in vivo report on the anticancer efficacy of a Glut1and glucose transport inhibitor, which shows the potential as a prototypic compound for developing anticancer therapeutics targeting Glut1 and glycolysis. 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 4068. doi:10.1158/1538-7445.AM2011-4068
Experimental Measurements of Spreading of Volatile Liquid Droplets (2001)

Based on the laser shadowgraphic system used by the first author of the present paper, a simple optical system, which combined the laser shadowgraphy and the direct magnified-photography, has been developed to measure the contact angle, the spreading speed, and the evaporation rate. Additionally, the system can also visualize thermocapillary convection inside of a sessile drop simultaneously. The experimental results show that evaporation/condensation and thermocapillary convection in the sessile drop induced by the evaporation strongly affects the wetting and spreading of the drop. Condensation always promotes the wetting and spreading of the drop. Evaporation may increase or decrease the contact angle of the evaporating sessile drops, depending on the evaporation rate. The thermocapillary convection in the drop induced by the evaporation enhances the effects of evaporation to suppress the spreading.
Moving contact-line mobility measured (2018)

Contact-line mobility characterizes how fast a liquid can wet or unwet a solid support by relating the contact angle $\unicode[STIX]{x0394}\unicode[STIX]{x1D6FC}$ to the contact-line speed $U_{CL}$ . The contact angle changes dynamically with contact-line speeds during rapid movement of liquid across a solid. Speeds beyond the region of stick–slip are the focus of this experimental paper. For these speeds, liquid inertia and surface tension compete while damping is weak. The mobility parameter $M$ is defined empirically as the proportionality, when it exists, between $\unicode[STIX]{x0394}\unicode[STIX]{x1D6FC}$ and $U_{CL}$ , $M\unicode[STIX]{x0394}\unicode[STIX]{x1D6FC}=U_{CL}$ . We discover that $M$ exists and measure it. The experimental approach is to drive the contact line of a sessile drop by a plane-normal oscillation of the drop’s support. Contact angles, displacements and speeds of the contact line are measured. To unmask the mobility away from stick–slip, the diagram of $\unicode[STIX]{x0394}\unicode[STIX]{x1D6FC}$ against $U_{CL}$ , the traditional diagram, is remapped to a new diagram by rescaling with displacement. This new diagram reveals a regime where $\unicode[STIX]{x0394}\unicode[STIX]{x1D6FC}$ is proportional to $U_{CL}$ and the slope yields the mobility $M$ . The experimental approach reported introduces the cyclically dynamic contact angle goniometer. The concept and method of the goniometer are illustrated with data mappings for water on a low-hysteresis non-wetting substrate.
3D mobile augmented reality in urban scenes (2011)

In this paper, we present a large-scale mobile augmented reality system that recognizes the buildings in the mobile device's live video and registers this live view with the 3-dimensional models of the buildings. Having the camera pose estimated and tracked, the system adds relevant information about the buildings to the video in the correct perspective. We demonstrate the system on a large database of geo-tagged panoramic images of an urban environment with associated 3-dimensional planar models. The system uses the capabilities of emerging mobile platforms such as location and orientation sensors, and computational power to detect, track, and augment buildings in urban scenes.
Time-domain envelope measurement technique with application to wideband power amplifier modeling (1998)

This paper presents a new time-domain measurement technique for repetitive microwave signals that is applied to modeling wideband power amplifiers. The measurement technique concept consists of recording the microwave signal after conversion to baseband using a calibrated downconverter, which improves measurement accuracy compared to measurements at the carrier frequency. The modeling section describes how such time-domain measurements can be used to model wideband signal effects in nonlinear power amplifiers. The commonly used memory-less envelope model is limited to use on narrowband signals. A new model is developed which includes a filter before the memory-less nonlinearity to capture the memory effects associated with wideband signals. It is demonstrated that the accuracy of wideband signal simulations can be improved by optimizing the model parameters based on time-domain measurements of wideband signals.
Three related receptor-like kinases are required for optimal cell elongation in <i>Arabidopsis thaliana</i> (2009)

Cell elongation in plants is controlled by environmental cues such as light and internal growth regulators including plant steroid hormones, brassinosteroids (BRs). In this study, we found that 3 related receptor-like kinases (RLKs), HERCULES1, THESEUS1, and FERONIA, are transcriptionally induced by BRs and are down-regulated in the loss-of-function BR mutant bri1 and up-regulated in the constitutive BR-response mutant bes1-D. These RLKs belong to the CrRLK family that has 17 members in Arabidopsis. We hypothesize that these RLKs are involved in BR-regulated processes. Although 2 of the RLKs were recently found to mediate male-female interaction during pollen tube reception (FERONIA) and to sense cell wall integrity (THESEUS1), our genetic studies demonstrated that they are required for cell elongation during vegetative growth as herk1 the1 double and fer RNAi mutants displayed striking dwarf phenotypes. The herk1 the1 double mutant enhances the dwarf phenotype of bri1 and partially suppresses bes1-D phenotype, supporting a role of HERK1/THE1 in BR-mediated cell elongation. Microarray experiments demonstrated that these RLKs control the expression of a unique set of genes including those implicated in cell elongation and 16% of the genes affected in herk1 the1 are regulated by BRs. Our results, therefore, identify a previously unknown pathway that functions cooperatively with, but largely independent of the BR pathway to regulate cell elongation. The work establishes a platform to identify other signaling components in this important pathway for plant growth and provides a paradigm to study the coordination of independent pathways in the regulation of a common biological process.
Extraction and visualization of the central chest lymph-node stations (2008)

Lung cancer remains the leading cause of cancer death in the United States and is expected to account for nearly 30% of all cancer deaths in 2007. Central to the lung-cancer diagnosis and staging process is the assessment of the central chest lymph nodes. This assessment typically requires two major stages: (1) location of the lymph nodes in a three-dimensional (3D) high-resolution volumetric multi-detector computed-tomography (MDCT) image of the chest; (2) subsequent nodal sampling using transbronchial needle aspiration (TBNA). We describe a computer-based system for automatically locating the central chest lymph-node stations in a 3D MDCT image. Automated analysis methods are first run that extract the airway tree, airway-tree centerlines, aorta, pulmonary artery, lungs, key skeletal structures, and major-airway labels. This information provides geometrical and anatomical cues for localizing the major nodal stations. Our system demarcates these stations, conforming to criteria outlined for the Mountain and Wang standard classification systems. Visualization tools within the system then enable the user to interact with these stations to locate visible lymph nodes. Results derived from a set of human 3D MDCT chest images illustrate the usage and efficacy of the system.
A quick-retrieval high-speed digital framing camera (1993)

A new high-speed digital framing camera is described. The design is built around a rotating polygon mirror that provides a framing rate of 24 000 frames/s. The camera electronics digitizes an image into a 32×104 grid of pixels, where the second dimension of the grid can be varied and is determined by the 8 bit computer-aided measurement and control digitizer sampling rate. Available digitizer memory provides for 314 frames at this horizontal resolution. The advantages over other available high-speed framing cameras are (1) low cost of the system provided the digitizers are available, (2) rapid retrieval of a recorded event, and (3) the ease with which the system can be used. Sample results from an application in high-power arc photography are given to illustrate the system’s spatial and temporal resolution.
Speckle contrast optical tomography: A new method for deep tissue three-dimensional tomography of blood flow (2014)

A novel tomographic method based on the laser speckle contrast, speckle contrast optical tomography (SCOT) is introduced that allows us to reconstruct three dimensional distribution of blood flow in deep tissues. This method is analogous to the diffuse optical tomography (DOT) but for deep tissue blood flow. We develop a reconstruction algorithm based on first Born approximation to generate three dimensional distribution of flow using the experimental data obtained from tissue simulating phantoms.
Purification, Modeling, and Analysis of Botulinum Neurotoxin Subtype A5 (BoNT/A5) from Clostridium botulinum Strain A661222 (2011)

A Clostridium botulinum type A strain (A661222) in our culture collection was found to produce the botulinum neurotoxin subtype A5 (BoNT/A5). Its neurotoxin gene was sequenced to determine its degree of similarity to available sequences of BoNT/A5 and the well-studied BoNT/A1. Thirty-six amino acid differences were observed between BoNT/A5 and BoNT/A1, with the predominant number being located in the heavy chain. The amino acid chain of the BoNT/A from the A661222 strain was superimposed over the crystal structure of the known structure of BoNT/A1 to assess the potential significance of these differences--specifically how they would affect antibody neutralization. The BoNT/A5 neurotoxin was purified to homogeneity and evaluated for certain properties, including specific toxicity and antibody neutralization. This study reports the first purification of BoNTA5 and describes distinct differences in properties between BoNT/A5 and BoNT/A1.
Guided fluorescence diagnosis of childhood caries: preliminary measures correlate with depth of carious decay (2014)

The current rise in childhood caries worldwide has increased the demand for portable technologies that can quickly and accurately detect and diagnose early stage carious lesions. These lesions, if identified at an early stage, can be reversed with remineralization treatments, education, and improvements in home care. A multi-modal optical prototype for detecting and diagnosing occlusal caries demineralization in vivo has been developed and pilot tested. The device uses a 405-nm laser as a scanned illumination source to obtain high resolution and high surface contrast reflectance images, which allows the user to quickly image and screen for any signs of demineralized enamel. When a suspicious region is located, the device can be switched to perform dual laser fluorescence spectroscopy using 405-nm and 532-nm laser excitations. These spectra are used to compute an auto-fluorescence (AF) ratio of the suspicious region and the percent difference of AF ratios from a healthy region of the same tooth. The device was tested on 7 children’s teeth in vivo with clinically diagnosed carious lesions. Lesion depth was then visually estimated from the video image using the 405-nm scanned light source, and within a month the maximum drill depth was assessed by a clinician. The researcher and clinicians were masked from previous measurements in a blinded study protocol. Preliminary results show that the ratiometric percent difference measurement of the AF spectrum of the tooth correlates with the severity of the demineralization as assessed by the clinician after drilling.
Applying Convolutional Neural Networks concepts to hybrid NN-HMM model for speech recognition (2012)

Convolutional Neural Networks (CNN) have showed success in achieving translation invariance for many image processing tasks. The success is largely attributed to the use of local filtering and max-pooling in the CNN architecture. In this paper, we propose to apply CNN to speech recognition within the framework of hybrid NN-HMM model. We propose to use local filtering and max-pooling in frequency domain to normalize speaker variance to achieve higher multi-speaker speech recognition performance. In our method, a pair of local filtering layer and max-pooling layer is added at the lowest end of neural network (NN) to normalize spectral variations of speech signals. In our experiments, the proposed CNN architecture is evaluated in a speaker independent speech recognition task using the standard TIMIT data sets. Experimental results show that the proposed CNN method can achieve over 10% relative error reduction in the core TIMIT test sets when comparing with a regular NN using the same number of hidden layers and weights. Our results also show that the best result of the proposed CNN model is better than previously published results on the same TIMIT test sets that use a pre-trained deep NN model.