gebhart/patrepeval huggingface dataset:
Dimers of Silver Nanospheres: Facile Synthesis and Their Use as Hot Spots for Surface-Enhanced Raman Scattering (2008)

This paper describes a simple, one-pot method that generates dimers of silver nanospheres in one step without any additional assembly steps. The dimers are consisted of single-crystal silver nanospheres approximately 30 nm in diameter and separated by a gap of 1.8 nm wide. The key to the success of this method lies in the control of colloidal stability and oxidative etching by optimizing the amount of chloride added to a polyol synthesis. The dimers provide a well-defined system for studying the hot spot phenomenon (hot spot: the gap region of a pair of strongly coupled silver or gold nanoparticles), an extremely important but poorly understood subject in surface-enhanced Raman scattering (SERS). Because of the relatively small size of the silver nanospheres, only those molecules trapped in the hot spot region are expected to contribute to the detected SERS signals. By correlating SERS measurements with SEM imaging, we found that the SERS enhancement factor within the hot spot region of such a dimer was on the order of 2 x 10(7).
Estimation of the spatial profile of neuromodulation and the temporal latency in motor responses induced by focused ultrasound brain stimulation (2014)

This study investigates the spatial profile and the temporal latency of the brain stimulation induced by the transcranial application of pulsed focused ultrasound (FUS). The site of neuromodulation was detected using 2-deoxy-2-[¹⁸F]fluoro-D-glucose PET immediately after FUS sonication on the unilateral thalamic area of Sprague-Dawley rats. The latency of the stimulation was estimated by measuring the time taken from the onset of the stimulation of the appropriate brain motor area to the corresponding tail motor response. The brain area showing elevated glucose uptake from the PET image was much smaller (56±10% in diameter, 24±6% in length) than the size of the acoustic focus, which is conventionally defined by the full-width at half-maximum of the acoustic intensity field. The spatial dimension of the FUS-mediated neuromodulatory area was more localized, approximated to be full-width at 90%-maximum of the acoustic intensity field. In addition, the time delay of motor responses elicited by the FUS sonication was 171±63 (SD) ms from the onset of sonication. When compared with latencies of other nonultrasonic neurostimulation techniques, the longer time delay associated with FUS-mediated motor responses is suggestive of the nonelectrical modes of neuromodulation, making it a distinctive brain stimulation method.
HIBROWSE for bibliographic databases (1994)

The HIBROWSE (High Resolution Interface for Database Specific Browsing and Searching) design offers improved searching functionality for users of bibliographic databases. The interface provides a multi-windowed view of data stored on a relational database management system, using layered attribute value aggregation and classification. The user interrogates the database by invoking automatically formulated SQL (structured query language) queries that fil ter the contents of each window according to user-selected attribute values. The interface is described using 'hand crafted' screens to create realistic examples of HIBROWSE systems for EPOQUE, the European Parliament Online Query System, INSPEC, MEDLINE and EMBASE.
Global differential gene expression in response to growth temperature alteration in group A Streptococcus (2001)

Pathogens are exposed to different temperatures during an infection cycle and must regulate gene expression accordingly. However, the extent to which virulent bacteria alter gene expression in response to temperatures encountered in the host is unknown. Group A Streptococcus (GAS) is a human-specific pathogen that is responsible for illnesses ranging from superficial skin infections and pharyngitis to severe invasive infections such as necrotizing fasciitis and streptococcal toxic shock syndrome. GAS survives and multiplies at different temperatures during human infection. DNA microarray analysis was used to investigate the influence of temperature on global gene expression in a serotype M1 strain grown to exponential phase at 29 degrees C and 37 degrees C. Approximately 9% of genes were differentially expressed by at least 1.5-fold at 29 degrees C relative to 37 degrees C, including genes encoding transporter proteins, proteins involved in iron homeostasis, transcriptional regulators, phage-associated proteins, and proteins with no known homologue. Relatively few known virulence genes were differentially expressed at this threshold. However, transcription of 28 genes encoding proteins with predicted secretion signal sequences was altered, indicating that growth temperature substantially influences the extracellular proteome. TaqMan real-time reverse transcription-PCR assays confirmed the microarray data. We also discovered that transcription of genes encoding hemolysins, and proteins with inferred roles in iron regulation, transport, and homeostasis, was influenced by growth at 40 degrees C. Thus, GAS profoundly alters gene expression in response to temperature. The data delineate the spectrum of temperature-regulated gene expression in an important human pathogen and provide many unforeseen lines of pathogenesis investigation.
A two-layer model for behavior and dialogue planning in conversational service robots (2005)

This paper presents a model for the behavior and dialogue planning module of conversational service robots. Most of the previously built conversational robots cannot perform dialogue management necessary for accurately recognizing human intentions and providing information to humans. This model integrates robot behavior planning models with spoken dialogue management that is robust enough to engage in mixed-initiative dialogues in specific domains. It has two layers; the upper layer is responsible for global task planning using hierarchical planning and the lower layer engages in local planning by utilizing modules called experts, which are specialized for performing certain kind of tasks by performing physical actions and engaging in dialogues. This model enables switching and canceling tasks based on recognized human intentions. A preliminary implementation of the model, which has been integrated with Honda ASIMO, has shown its effectiveness.
Contribution of carbohydrate antigens sialyl Lewis A and sialyl Lewis X to adhesion of human cancer cells to vascular endothelium. (1993)

The carbohydrate antigen, sialyl Lex, is known to be a ligand for the cell adhesion molecule called ELAM-1 (E-selectin, endothelial cell leukocyte adhesion molecule-1), which is present on cytokine-activated human endothelial cells. Recently, we reported that another carbohydrate antigen, sialyl Lea, can also serve as a ligand for ELAM-1 (A. Takada, K. Ohmori, N. Takahashi, K. Tsuyuoka, K. Yago, K. Zenita, A. Hasegawa, and R. Kannagi, Biochem. Biophys. Res. Commun., 179: 713-719, 1991). Both sialyl Lex and sialyl Lea are expressed in many human malignant cells. In order to assess the contribution of these carbohydrate antigens to the adhesion of human malignant cells to vascular endothelium, we selected a panel of 12 cultured human epithelial cancer cell lines and a panel of 12 human leukemia cell lines which express sialyl Lex and/or sialyl Lea antigens. All 12 epithelial cancer cell lines exhibited a clearly ELAM-1-dependent adhesion to cytokine-activated human umbilical vein endothelial cells, while only 3 of the 12 leukemia cell lines exhibited significant participation of ELAM-1 in the adhesion. With regard to epithelial cancer cells, the adhesion of 6 cancer cell lines, mostly of colon and pancreas origin, was dependent almost exclusively on sialyl Lea. A significant contribution of the sialyl Lex antigen was noted in the adhesion of the other 6 cell lines, including cancers of lung and liver origin. These results imply that the sialyl Lea/ELAM-1 adhesion system, as well as the sialyl Lex/ELAM-1 adhesion system, plays an important role in the adhesion of human cancer cells to human umbilical vein endothelial cells. With regard to leukemia cells, on the other hand, adhesion of the 3 leukemia cell lines that showed ELAM-1-dependent adhesion was mediated by the sialyl Lex antigen, and none of these leukemia cell lines expressed sialyl Lea or exhibited sialyl Lea-dependent adhesion.
A modular haptic rendering algorithm for stable and transparent 6-DOF manipulation (2006)

This paper presents a modular algorithm for six-degree-of-freedom (6-DOF) haptic rendering. The algorithm is aimed to provide transparent manipulation of rigid models with a high polygon count. On the one hand, enabling a stable display is simplified by exploiting the concept of virtual coupling and employing passive implicit integration methods for the simulation of the virtual tool. On the other hand, transparency is enhanced by maximizing the update rate of the simulation of the virtual tool, and thereby the coupling impedance, and allowing for stable simulation with small mass values. The combination of a linearized contact model that frees the simulation from the computational bottleneck of collision detection, with penalty-based collision response well suited for fixed time-stepping, guarantees that the motion of the virtual tool is simulated at the same high rate as the synthesis of feedback force and torque. Moreover, sensation-preserving multiresolution collision detection ensures a fast update of the linearized contact model in complex contact scenarios, and a novel contact clustering technique alleviates possible instability problems induced by penalty-based collision response
Efficient generation of a biallelic knockout in pigs using zinc-finger nucleases (2011)

Zinc-finger nucleases (ZFNs) are powerful tools for producing gene knockouts (KOs) with high efficiency. Whereas ZFN-mediated gene disruption has been demonstrated in laboratory animals such as mice, rats, and fruit flies, ZFNs have not been used to disrupt an endogenous gene in any large domestic species. Here we used ZFNs to induce a biallelic knockout of the porcine α1,3-galactosyltransferase (GGTA1) gene. Primary porcine fibroblasts were treated with ZFNs designed against the region coding for the catalytic core of GGTA1, resulting in biallelic knockout of ∼1% of ZFN-treated cells. A galactose (Gal) epitope counter-selected population of these cells was used in somatic cell nuclear transfer (SCNT). Of the resulting six fetuses, all completely lacked Gal epitopes and were phenotypically indistinguishable from the starting donor cell population, illustrating that ZFN-mediated genetic modification did not interfere with the cloning process. Neither off-target cleavage events nor integration of the ZFN-coding plasmid was detected. The GGTA1-KO phenotype was confirmed by a complement lysis assay that demonstrated protection of GGTA1-KO fibroblasts relative to wild-type cells. Cells from GGTA1-KO fetuses and pooled, transfected cells were used to produce live offspring via SCNT. This study reports the production of cloned pigs carrying a biallelic ZFN-induced knockout of an endogenous gene. These findings open a unique avenue toward the creation of gene KO pigs, which could benefit both agriculture and biomedicine.
Butanol fermentation research: upstream and downstream manipulations (2004)

An overview of advances in acetone-butanol fermentation research is presented with specific reference to the history of acetone-butanol fermentation, genetic manipulation of the butanol-producing Clostridium beijerinckii NCIMB 8052, as well as upstream and downstream processing. Specific reference is made to the development of the hyperamylolytic, hyper-"butanolagenic" C. beijerinckii BA101 strain. Amylolytic enzyme production by C. beijerinckii BA101 was 1.8- and 2.5-fold greater than that of the C. beijerinckii NCIMB 8052 strain grown in starch and glucose, respectively. We confirmed the presence of a phosphoenolpyruvate (PEP)-dependent phosphotransferase system (PTS) associated with cell extracts of C. beijerinckii BA101 by glucose phosphorylation by PEP and ATP-dependent glucose phosphorylation. It was found that C. beijerinckii BA101 was defective in PTS activity and that it compensates for this defect with enhanced glucokinase activity, resulting in an ability to transport and utilize glucose during the solventogenic stage. The principal problem associated with acetone-butanol fermentation by C. beijerinckii or C. acetobutylicum is butanol toxicity/inhibition to the culture. To solve this problem, we have attempted various alternative in situ/online techniques of butanol removal including membrane-based systems such as pervaporation, liquid-liquid extraction, and gas stripping. We found that gas stripping and pervaporation appear to be the most promising of the in situ acetone-butanol fermentation and recovery techniques but, in terms of cost-effective industrial applications, gas stripping appears to be the most promising.
Simian virus 40 large tumor antigen is unable to transform mouse embryonic fibroblasts lacking type 1 insulin-like growth factor receptor. (1993)

Fibroblast cell lines were established from mouse embryos homozygous for a targeted disruption of the Igf1r gene, encoding the type 1 receptor for insulin-like growth factor I (IGF-I) and from their wild-type littermates. The cells from the wild-type embryos (W cells) grow in serum-free medium supplemented with platelet-derived growth factor, epidermal growth factor, and IGF-I, whereas the cells from Igf1r(-/-) embryos (R- cells) do not, although they grow at a reduced rate in 10% fetal calf serum. The simian virus 40 (SV40) large T antigen, expressed from a transfected plasmid, can transform W cells, which form foci in monolayer cultures and colonies in soft agar (anchorage-independent growth). In contrast, the SV40 large tumor antigen, although normally expressed from the transfected template, is unable to transform R- cells, which remain contact-inhibited and fail to grow in soft agar. The transformed phenotype is restored if the R- cells carrying the SV40 large tumor antigen are stably transfected with a plasmid expressing the human IGF-I receptor. These results demonstrate that signaling via the IGF-I receptor is an indispensable component of the SV40 transformation pathway. This conclusion is further supported from the results of antisense RNA experiments with tumor cell lines showing that interference with the function of the IGF-I receptor has a profound effect on anchorage-independent growth, even under conditions that only modestly affect growth in monolayers.
Targeting BCL2-Proteins for the Treatment of Solid Tumours (2014)

Due to their central role in the regulation of apoptosis, the antiapoptotic BCL2-proteins are highly promising targets for the development of novel anticancer treatments. To this end, several strategies have been developed to inhibit BCL2, BCL-XL, BCL-w, and MCL1. While early clinical trials in haematological malignancies demonstrated exciting single-agent activity of BCL2-inhibitors, the response in solid tumours was limited, indicating that, in solid tumours, different strategies have to be developed in order to successfully treat patients with BCL2-inhibitors. In this review, the function of the different antiapoptotic BCL2-proteins and their role in solid tumours will be discussed. In addition, a comprehensive analysis of current small molecules targeting these antiapoptotic BCL2-proteins (e.g., ABT-737, ABT-263, ABT-199, TW-37, sabutoclax, obatoclax, and MIM1) will be provided including a discussion of the results of any clinical trials. This analysis will summarise the potential of BCL2-inhibitors for the treatment of solid tumours and will unravel novel approaches to utilise these inhibitors in clinical applications.
Regulation of Hermissenda K+ Channels by Cytoplasmic and Membrane‐Associated C‐Kinase (1988)

Pharmacologic activation of endogenous protein kinase C (PKC) together with elevation of the intracellular Ca2+ level was previously shown to cause reduction of two voltage-dependent K+ currents (IA and ICa2+-K+) across the soma membrane of the type B photoreceptor within the eye of the mollusc Hermissenda crassicornis. Similar effects were also found to persist for days after acquisition of a classically conditioned response. Also, the state of phosphorylation of a low-molecular-weight protein was changed only within the eyes of conditioned Hermissenda. To examine the role of PKC in causing K+ current changes as well as changes of phosphorylation during conditioning (and possibly other physiologic contexts), we studied here the effects of endogenous PKC activation and exogenous PKC injection on phosphorylation and K+ channel function. Several phosphoproteins (20, 25, 56, and 165 kilodaltons) showed differences in phosphorylation in response to PKC activators applied to intact nervous systems or to isolated eyes. Specific differences were observed for membrane and cytosolic fractions in response to both the phorbol ester 12-deoxyphorbol 13-isobutyrate 20-acetate (DPBA) or exogenous PKC in the presence of Ca2+ and phosphatidylserine/diacylglycerol. Type B cells pretreated with DPBA responded to PKC injection with a persistent reduction of K+ currents. In the absence of DPBA, PKC injection also caused K+ current reduction only following Ca2+ loading conditions. However, the direct effect of PKC injection in the absence of DPBA was only to increase ICa2+-K+. According to a proposed model, the amplitude of the K+ currents would depend on the steady-state balance of effects mediated by PKC within the cytoplasm and membrane-associated PKC. The model further specifies that the effects on K+ currents of cytoplasmic PKC require an intervening proteolytic step. Such a model predicts that increasing the concentration of cytoplasmic protease, e.g., with trypsin, will increase K+ currents, whereas blocking endogenous protease, e.g., with leupeptin, will decrease K+ currents. These effects should be opposed by preexposure of the cells to DPBA. Furthermore, prior injection of leupeptin should block or reverse the effects of subsequent injection of PKC into the type B cell. All of these predictions were confirmed by results reported here. Taken together, the results of this and previous studies suggest that PKC regulation of membrane excitability critically depends on its cellular locus. The implications of such function for long-term physiologic transformations are discussed.
3G interworking with wireless LANs (2002)

Recently, the use of wireless LANs (WLAN) as a complementary technology to 3G systems has been identified. WLANs can be used to supplement the available bandwidth and capacity of a 3G network in hotspot areas, such as railway stations and airports, without sacrificing the capacity provided to cellular users. It provides support for data intensive applications and enables smooth on-line access to corporate data services, while still allowing users to roam from the private picocell network to wide area 3G networks. The paper addresses some of the current thinking within the ETSI BRAN (broadband radio access network) project regarding the interworking of the HIPERLAN/2 wireless LAN system into a 3G cellular system. Of the two initial solutions investigated (tight and loose coupling), current work has concentrated on the loose variant, producing viable solutions for security, mobility and QoS. The standardisation activity thus hopes to ensure that HIPERLAN/2 can provide a value added service within hotspot environments for both customers and operators of 3G systems.
The evolutionary biology of viruses (1994)

This volume provides researchers with a coherent theoretical framework for understanding the evolutionary biology of viruses - a subject of crucial importance to scientists investigating emerging viruses, viral transmission, and geographic variations in viral epidemics. The book defines key concepts concerning the origins and relatedness of viruses, the processes producing genetic variation among viruses, and the role of virus-host interactions and natural selection in governing viral evolution. Special emphasis is on the relationship between genetic variation and natural selection, and on the evolutionary constraints imposed by the interaction of the virus with its host.
The MADS Box Transcription Factor ZmMADS2 Is Required for Anther and Pollen Maturation in Maize and Accumulates in Apoptotic Bodies during Anther Dehiscence (2004)

The maize (Zea mays) late pollen gene ZmMADS2 belongs to the MIKC type of MADS box transcription factor genes. Here, we report that ZmMADS2, which forms a homodimer in yeast (Saccharomyces cerevisiae), is required for anther dehiscence and pollen maturation. Development of anthers and pollen was arrested at 1 d before dehiscence in transgenic plants expressing the ZmMADS2-cDNA in antisense orientation. Temporal and spatial expression analyses showed high amounts of ZmMADS2 transcripts in endothecium and connective tissues of the anther at 1 d before dehiscence and in mature pollen after dehiscence. Transient transformation of maize and tobacco (Nicotiana tabacum) pollen with the luciferase reporter gene under the control of different ZmMADS2 promoter deletion constructs demonstrated the functionality and tissue specificity of the promoter. Transgenic maize plants expressing a ZmMADS2-green fluorescent protein fusion protein under control of the ZmMADS2 promoter were used to monitor protein localization during anther maturation and pollen tube growth. High amounts of the fusion protein accumulate in degenerating nuclei of endothecial and connective cells of the anther. A possible function of ZmMADS2 during anther dehiscence and pollen maturation and during pollen tube growth is discussed.
Fast variable-size block motion estimation using merging procedure with an adaptive threshold (2003)

A merging procedure for variable-size block motion estimation is proposed to reduce the computation for block-size decision. A smaller block-size is initially used for motion estimation. An adaptive threshold, which depends on the information obtained from the motion estimation, quantization parameter, and rate distortion cost function is used to determine if the motion vectors of the neighboring blocks should be merged or not. We simulate the proposed merging procedure using an H.264 video encoder to determine if 16x16, 16x8, 8x16, or 8x8 blocksize should be used for each macroblock. Based on the simulations, performance of the proposed method is close to that of H.264 JM2.1 when 16x16, 16x8, 8x16 and 8x8 block modes are enabled and the exhaustive search method is used to determine the block-sizes. Computational complexity can be significantly reduced by the proposed algorithm since it only performs the motion search for one block-size.