gebhart/patrepeval huggingface dataset:
The Vinculin Binding Sites of Talin and α-Actinin Are Sufficient to Activate Vinculin (2006)

Vinculin regulates both cell-cell and cell-matrix junctions and anchors adhesion complexes to the actin cytoskeleton through its interactions with the vinculin binding sites of alpha-actinin or talin. Activation of vinculin requires a severing of the intramolecular interactions between its N- and C-terminal domains, which is necessary for vinculin to bind to F-actin; yet how this occurs in cells is not resolved. We tested the hypothesis that talin and alpha-actinin activate vinculin through their vinculin binding sites. Indeed, we show that these vinculin binding sites have a high affinity for full-length vinculin, are sufficient to sever the head-tail interactions of vinculin, and they induce conformational changes that allow vinculin to bind to F-actin. Finally, microinjection of these vinculin binding sites specifically targets vinculin in cells, disrupting its interactions with talin and alpha-actinin and disassembling focal adhesions. In their native (inactive) states the vinculin binding sites of talin and alpha-actinin are buried within helical bundles present in their central rod domains. Collectively, these results support a model where the engagement of adhesion receptors first activates talin or alpha-actinin, by provoking structural changes that allow their vinculin binding sites to swing out, which are then sufficient to bind to and activate vinculin.
Polarization behavior and mode structure of elliptical surface relief VCSELs (2004)

Summary form only given. We investigate the polarization behavior and the mode structure of elliptical surface relief vertical-cavity surface-emitting lasers. The polarization direction is governed by the orientation of the index ellipsoid, whereas the lasing mode is determined by the losses anisotropy.
Detection of Bartonella bacilliformis in cultures, blood, and formalin preserved skin biopsies by use of the polymerase chain reaction. (1992)

A polymerase chain reaction (PCR) is described for the detection of Bartonella bacilliformis, the etiologic agent of bartonellosis, which cannot be identified biochemically. Amplification of a genomic 231 bp Bartonella DNA sequence permitted specific identification of 12 Bartonella isolates from Peruvian bartonellosis patients as well as detection of Bartonella DNA in blood samples and formaldehyde preserved skin biopsies. Specificity of amplification products was confirmed by restriction fragment analysis. No positive results were obtained with Brucella abortus, phylogenetically closely related to B. bacilliformis, and several other bacterial, fungal, and protozoal species. PCR appears as a promising technique for specific identification of B. bacilliformis in cultures and in clinical materials with further applications in taxonomic studies and in the investigation of Bartonella-like isolates obtained outside South America.
Epidermal growth factor increases insulin secretion and lowers blood glucose in diabetic mice (2008)

Epidermal growth factor (EGF) is synthesized in the pancreas and diabetic animals have low levels of EGF. However, the role of EGF in regulating the major function of the pancreas, insulin secretion, has not been studied. Here, we show that EGF rapidly increased insulin secretion in mouse pancreatic islets, as well as in a pancreatic beta-cell line. These events were dependent on a Ca(2+) influx and phospholipase D (PLD) activity, particularly PLD2, as determined using pharmacological blockers and molecular manipulations such as over-expression and siRNA of PLD isozymes. In addition, EGF also increased plasma insulin levels and mediated glucose lowering in normal and diabetic mice. Here, for the first time, we provide evidence that EGF is a novel secretagogue that regulates plasma glucose levels and a candidate for the development of therapeutics for diabetes.
Lost Metal Detector Robot (2012)

Low Tian Chuan, pelajar Pusat Pengajian Kejuruteraan Mekatronik, Universiti Malaysia Perlis (UniMAP) telah memenangi pingat emas dan Taiwan Special Award pada Pameran Penyelidik Muda Antarabangsa (IYIE 2012). Pameran ini anjuran bersama Universiti Far East dan Persatuan Rekacipta & Harta Intelek Taiwan, 11 - 13 Februari 2012 di Universiti Far East, Tainan, Taiwan.
Identification of p63+ keratinocyte progenitor cells in circulation and their matrix-directed differentiation to epithelial cells (2013)

Circulating KPCs were identified with p63, which differentiated into keratinocytes with expression of the cytokeratins, involucrin and filaggrin. Components of the specifically designed matrix favored KPC attachment, directed differentiation, and may turn out to be a potential vehicle for cell transplantation.
Low linkage disequilibrium indicative of recombination in foot-and-mouth disease virus gene sequence alignments (2004)

We have applied tests for detecting recombination to genes of foot-and-mouth disease virus (FMDV). Our approach estimated summary statistics of linkage disequilibrium (LD), which are sensitive to recombination. Using the genealogical relationships, rate heterogeneity and mutation parameters estimated from individual sets of aligned gene sequences, we simulated matching RNA sequence datasets without recombination. These simulated datasets allowed for recurrent mutations at any site to mimic homoplasy in virus sequence data and allow construction of null distributions for LD parameters expected in the absence of recombination. We tested for recombination in two ways: by comparing LD in observed data with corresponding null distributions obtained from simulated data; and by testing for a negative relationship between observed LD between pairs of polymorphic nucleotide sites and inter-site distance. We applied these tests to six FMDV datasets from four serotypes and found some evidence for recombination in all of them.
Large-image CNN hardware processing using a time multiplexing scheme (2002)

The state of the art work in cellular neural networks (CNN) has concentrated on VLSI implementations without really addressing the "systems level". While efficient implementations have been reported, no reports have been presented on the use of these implementations for processing large complex images. The work hereby presented introduces a strategy to process large images using small CNN arrays. The approach, time-multiplexing, is prompted by the need to simulate hardware models and test hardware implementations of CNN. For practical size applications, due to hardware limitations, it is impossible to have a one-on-one mapping between the CNN hardware processors and all the pixels in the image involved. This paper presents a practical solution by processing the input image block by block, with the number of pixels in a block being the same as the number of CNN processors in the hardware. Image processing results obtained from an actual IC test-chip prototype using this scheme are presented.
Influence of Fluorescence of Bacteria Stained with Acridine Orange on the Enumeration of Microorganisms in Raw Milk (2000)

The staining of gram-positive and gram-negative cultures with acridine orange in metabolically active and inactive states was investigated using a Bactoscan, direct epifluorescent filter technique (DEFT), and standard plate count as the reference method. The evaluation of the bacterial cultures in the Bactoscan revealed a linear relationship between Bactoscan counts (pulses) and the quantity of pure culture suspension used. But the proper detection of bacteria with the fluorescence optic methods was dependent on the type of microorganism and the physiological state of the cells. The Bactoscan and DEFT underestimated the bacterial counts of gram-negative cultures as compared with standard plate counting. When stained with acridine orange, metabolically active bacteria showed more orange fluorescence and a lower percentage of green fluorescent cells as compared with inactive bacteria. Bactoscan pulse height analysis (PHA) diagrams, graphs of the detected pulses and their intensity, showed low pulses of inactive bacteria. Many of these weak pulses were eliminated from counting because of their faint fluorescent staining. In contrast, PHA diagrams of metabolically active microorganisms showed bright staining and, therefore, high pulses. A complete count of these bacteria was possible. These investigations point out that discrepancies between the fluorescence optical counting methods and the standard plate count depend strongly on the staining of the cultures with acridine orange and, therefore, on the type of microorganism and the metabolic state of the cells measured.
Online handwritten signature verification system based on DWT features extraction and neural network classification (2010)

Handwritten signature is the most widely accepted biometric to identity verification. The target of research is to present online handwritten signature verification system based on discrete wavelet transform (DWT) features extraction and feed forward back propagation error neural network recognition. Steps for verifying online handwritten signature in this system start with extracting pen position data (x and y positions) of points that forming the signature. Pen-movement angles are then derived from pen position data. To reduce variations in pen-position and pen-movement angles dimensionality, data are normalized and resampled. To enhance the difference between a genuine signature and its forgery, the signature is verified in DWT domain. Low frequency sub-band signals (approximations) of pen-position parameter and pen-movement angle parameter are considered as intrapersonal features. These are used for suppressing variations between different genuine signatures and enhancing the interpersonal variations, hence are given higher scores within total recognition process. Both of pen-position and pen-movement angle features are then associated for obtaining a decision about online handwritten signature verification. A multi-matcher consists of six neural networks which use multiple representations and matching for the same input biometric signal is used to verify signature. The recognition rate for each of these neural network recognizers is discussed and a comparison of those rates is performed. Experiments are carried on signature database for five users each of 20 genuine and 20 skilled forgery signatures. Recognition success rate for genuine signatures is 95%.
BrowseLine: 2D Timeline Visualization of Web Browsing Histories (2009)

Re-finding previously viewed Web pages in browsing histories is often a difficult task, due to the incomplete and vague knowledge people have about the information they are seeking. In this paper, we present a visual interface for the task of re-finding Web pages within browsing histories. BrowseLine employs a novel two-dimensional timeline metaphor, allowing users to visually identify temporal patterns within their browsing histories. These visual patterns can be matched to the users' recollection of their browsing activities, allowing them to jump to a time interval in their browsing history for further investigation. Preliminary evaluations of BrowseLine have found that users can readily grasp the two-dimensional timeline representation, and can use the system effectively to re-find previously viewed pages.
Transient Nucleolar Localization Of U6 Small Nuclear RNA In<i>Xenopus Laevis</i>Oocytes (2000)

Recent studies on the 2'-O-methylation and pseudouridylation of U6 small nuclear RNA (snRNA) hypothesize that these posttranscriptional modifications might occur in the nucleolus. In this report, we present direct evidence for the nucleolar localization of U6 snRNA and analyze the kinetics of U6 nucleolar localization after injection of in vitro transcribed fluorescein-labeled transcripts into Xenopus laevis oocytes. In contrast to U3 small nucleolar RNA (snoRNA) which developed strong nucleolar labeling over 4 h and maintained strong nucleolar signals through 24 h, U6 snRNA localized to nucleoli immediately after injection, but nucleolar staining decreased after 4 h. By 24 h after injection of U6 snRNA, only weak nucleolar signals were observed. Unlike the time-dependent profile of strong nucleolar localization of U6 snRNA or U3 snoRNA, injection of fluorescein-labeled U2 snRNA gave weak nucleolar staining at all times throughout a 24-h period; U2 snRNA modifications are believed to occur outside of the nucleolus. The notion that the decrease of U6 signals over time was due to its trafficking out of nucleoli and not to transcript degradation was supported by the demonstration of U6 snRNA stability over time. Therefore, in contrast to snoRNAs like U3, U6 snRNA transiently passes through nucleoli.
<i>N</i>‐[4‐(3<i>H</i>‐1,3,4‐Oxadiazoline‐2‐thion‐5‐yl)phenyl]‐<i>N</i>′‐substituted Thioureas: Synthesis and Antimicrobiological Activities (1991)

Abstract Diverse pharmacological properties are associated with 3 H ‐1,3,4‐oxadiazoline‐2‐thione derivatives. These include anticonvulsant 1—4) and fungicidal 5) properties. On the other hand thiourea derivatives possess antiphytoviral 6) , virucidal 7) , growth inhibitory 8—10) , and herbicide 11) activities. All these data prompted us to combine these moieties into a single molecule. The compounds synthesized were tested for their antimicrobial activities against seven microorganisms.
IRILD: An Information Retrieval Based Method for Information Leak Detection (2011)

The traditional approach for detecting information leaks is to generate fingerprints of sensitive data, by partitioning and hashing it, and then comparing these fingerprints against outgoing documents. Unfortunately, this approach incurs a high computation cost as every part of document needs to be checked. As a result, it is not applicable to systems with a large number of documents that need to be protected. Additionally, the approach is prone to false positives if the fingerprints are common phrases. In this paper, we propose an improvement for this approach to offer a much faster processing time with less false positives. The core idea of our solution is to eliminate common phrases and non-sensitive phrases from the fingerprinting process. Non-sensitive phrases are identified by looking at available public documents of the organization that we want to protect from information leaks and common phrases are identified with the help of a search engine. In this way, our solution both accelerates leak detection and increases the accuracy of the result. Experiments were conducted on real-world data to prove the efficiency and effectiveness of the proposed solution.
HOS based algorithm for autofocusing of spotlightSAR images (1997)

The authors propose a novel SAR (synthetic aperture radar) image autofocusing technique based on higher order statistics (HOS) analysis. The SAR imaging system has been modelled as a bandlimited complex linear time invariant (LTI) filter, so the autofocusing problem is equivalent to the problem of reconstructing the phase of a bandlimited complex LTI system. The complex transfer function of the imaging system is recovered from the estimated bispectrum of the received data by means of an ad-hoc algorithm.
An improved <i>tet</i>O promoter replacement system for regulating the expression of yeast genes (2003)

Regulatable promoters are commonly used to control the expression of, especially, essential genes in a conditional manner. Integration of such promoters upstream of an ORF using one-step PCR-mediated homologous recombination should be particularly efficient. However, integration of the original KanMX4-tetO promoter cassette (Belli et al., 1998a) into the relatively short upstream regions of many yeast genes is often problematic, presumably due to the size (3.9 kb) of the replacement cassette. We have created a new, shorter, KanMX4-tetO cassette by removing the transactivator (tTA) sequence from the original cassette. The transactivator (tTA) has been integrated into the yeast genome to create a new strain for use with the new system, which has a greatly increased efficiency of promoter substitution. With it, we have been able to create strains that could not be made with the original cassette. To increase the throughput of promoter substitutions, we have developed a new assay for testing doxycycline sensitivity, based on liquid culture using microtitre trays. Altogether, the components of this new 'tool kit' greatly increase the efficiency of systematic promoter substitutions.
Higher-order finite-difference schemes for electromagnetic radiation, scattering, and penetration .1. Theory (2002)

Higher-order schemes for the finite-difference time-domain (FDTD) method are presented, in particular, a second-order-in-time, fourth-order-in-space method: FDTD(2,4). This method is compared to the original Yee (1966) FDTD scheme. One-dimensional update equations are presented, and the characteristics of the FDTD(2,4) scheme are investigated. Theoretical results for numerical stability and dispersion are presented, with numerical results for the latter, as well. The use of the perfectly matched layer for the FDTD(2,4) scheme is discussed, and numerical results are shown.
Sticking Probabilities in Adsorption from Liquid Solutions: Alkylthiols on Gold (2000)

The sticking probability, defined as the rate of adsorption per molecular collision with the surface, directly expresses the difficulty encountered by a molecule in scaling the barrier to adsorption. Its prior use has been restricted to adsorption of gases. A method extending this concept to adsorption from liquid solutions is applied to transient measurements of alkylthiol adsorption onto gold from ethanol solutions. The initial sticking probability increases from approximately 10(-8) to approximately 10(-6) with alkyl chain length, implying a stabilization of the transition state by approximately 0.65 kJ/mol per CH2. Since their sticking probabilities in the gas phase are approximately 1.0, the solvent increases the activation free energy by approximately 40 kJ/mol.
Use of wild relatives to improve salt tolerance in wheat (2006)

There is considerable variability in salt tolerance amongst members of the Triticeae, with the tribe even containing a number of halophytes. This is a review of what is known of the differences in salt tolerance of selected species in this tribe of grasses, and the potential to use wild species to improve salt tolerance in wheat. Most investigators have concentrated on differences in ion accumulation in leaves, describing a desirable phenotype with low leaf Na+ concentration and a high K+/Na+ ratio. Little information is available on other traits (such as "tissue tolerance" of accumulated Na+ and Cl-) that might also contribute to salt tolerance. The sources of Na+ "exclusion" amongst the various genomes that make up tetraploid (AABB) durum wheat (Triticum turgidum L. ssp. durum), hexaploid (AABBDD) bread wheat (Triticum aestivum L. ssp. aestivum), and wild relatives (e.g. Aegilops spp., Thinopyrum spp., Elytrigia elongata syn. Lophopyrum elongatum, Hordeum spp.) are described. The halophytes display a capacity for Na+ "exclusion", and in some cases Cl- "exclusion", even at relatively high salinity. Significantly, it is possible to hybridize several wild species in the Triticeae with durum and bread wheat. Progenitors have been used to make synthetic hexaploids. Halophytic relatives, such as tall wheatgrass spp., have been used to produce amphiploids, disomic chromosome addition and substitution lines, and recombinant lines in wheat. Examples of improved Na+ "exclusion" and enhanced salt tolerance in various derivatives from these various hybridization programmes are given. As several sources of improved Na+ "exclusion" are now known to reside on different chromosomes in various genomes of species in the Triticeae, further work to identify the underlying mechanisms and then to pyramid the controlling genes for the various traits, that could act additively or even synergistically, might enable substantial gains in salt tolerance to be achieved.
Ultrasonically activated chemotherapeutic drug delivery in a rat model. (2002)

Systemic delivery of anticancer agents is accompanied by many unwanted side effects that can be mitigated by encapsulation of antineoplastic agents. However, encapsulation necessitates a technique for controlled delivery to the cancerous tissue. We have developed a novel drug delivery system that releases drug from stabilized micelles upon application of low-frequency ultrasound and that demonstrates efficacy using doxorubicin (Dox) to treat tumors in vivo. Forty-two BDIX rats were inoculated in each hind leg with a DHD/K12/TRb tumor cell line. Dox was encapsulated within stabilized Pluronic micelles and administered weekly i.v. to the rats starting 6 weeks after the tumor inoculations. One of the two tumors was exposed to low-frequency ultrasound for 1 h. Dox concentrations of 1.33, 2.67, and 8 mg/kg and ultrasound frequencies of 20 and 70 kHz were used for treatment. Tumor volume was measured with calipers and observed over the treatment time. Administration of encapsulated Dox at concentrations of 1.33 and 2.67 mg/kg was not lethal to the rats. Application of low-frequency ultrasound (both 20 and 70 kHz) significantly reduced the tumor size when compared with noninsonated controls (P = 0.0062) in the other leg for rats receiving encapsulated Dox. Significant tumor reduction was also noted for those rats receiving ultrasound and encapsulated Dox at 2.67 mg/kg (P = 0.017) and rats receiving Dox and ultrasound at 70 kHz (P = 0.029). We postulate that ultrasound releases the Dox from the micelles as they enter the insonated volume, and ultrasound could also assist the drug and/or carriers to extravasate and enter the tumor cells. Encapsulation of Dox using stabilized Pluronic micelles and localized release using low-frequency ultrasound show promise in offering controlled drug delivery in the treatment of tumors in a rat model.
A networkwide backup system with inter‐memory autonomic copy mechanism (2003)

Abstract We propose a networkwide backup system for a system composed of multiple primary nodes connected by a wide‐area network. The system enables us to implement the backup node physically far from the primary nodes. In this system, we can implement a replica of the primary node with low overhead, and the replica can start up when the primary node stops. The replica is made by serially transferring memory update information of a primary node to a backup node, by using a hardware‐based memory copying mechanism. In addition, our system is transparent for application programs, that is, the applications are not aware of the switchover. Thus, we need no modification to the application software, and we can build a highly reliable system using existing software. In the evaluation of a prototype system, the overhead for checkpoint processing was about 1.6 ms, and the processing time for switching to the backup node from the time fault detection was about 165 µs. This result means that our system is superior to the ordinary active replication system in terms of the overhead when the distance between a primary node and a backup node is larger than 160 km. © 2003 Wiley Periodicals, Inc. Syst Comp Jpn, 34(8): 89–99, 2003; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/scj.1211
Characteristics and Explanations of Interference Fading of a $\phi $-OTDR With a Multi-Frequency Source (2013)

The characteristics of interference fading in a phase sensitive optical time domain reflectometer (φ-OTDR) system with a three optical frequency source are described in this paper. It is observed in the experiments that the fading appearance is quite stable over 400 different pulse scans for each of frequencies, but different for the three frequencies. A model is proposed to explain the experimental phenomena, in which the fading waveform is expressed by an integral of propagation phase factor, taking non-uniform index distributions along the sensing fiber into account, multiplied by the random Rayleigh scattering coefficient summed within the detector response period. Simulations show that the basic characteristics of experimental observations can be explained by the model.