gebhart/patrepeval huggingface dataset:
Alternative splicing in the C‐terminus of Ca <sub>V</sub> 2.2 controls expression and gating of N‐type calcium channels (2006)

N-type Ca(V)2.2 calcium channels localize to presynaptic nerve terminals of nociceptors where they control neurotransmitter release. Nociceptive neurons express a unique set of ion channels and receptors important for optimizing their role in transmission of noxious stimuli. Included among these is a structurally and functionally distinct N-type calcium channel splice isoform, Ca(V)2.2e[37a], expressed in a subset of nociceptors and with limited expression in other parts of the nervous system. Ca(V)2.2[e37a] arises from the mutually exclusive replacement of e37a for e37b in the C-terminus of Ca(V)2.2 mRNA. N-type current densities in nociceptors that express a combination of Ca(V)2.2e[37a] and Ca(V)2.2e[37b] mRNAs are significantly larger compared to cells that express only Ca(V)2.2e[37b]. Here we show that e37a supports increased expression of functional N-type channels and an increase in channel open time as compared to Ca(V)2.2 channels that contain e37b. To understand how e37a affects N-type currents we compared macroscopic and single-channel ionic currents as well as gating currents in tsA201 cells expressing Ca(V)2.2e[37a] and Ca(V)2.2e[37b]. When activated, Ca(V)2.2e[37a] channels remain open for longer and are expressed at higher density than Ca(V)2.2e[37b] channels. These unique features of the Ca(V)2.2e[37a] isoform combine to augment substantially the amount of calcium that enters cells in response to action potentials. Our studies of the e37a/e37b splice site reveal a multifunctional domain in the C-terminus of Ca(V)2.2 that regulates the overall activity of N-type calcium channels in nociceptors.
Solution and Surface Charge Properties of Shell Cross-Linked Knedel Nanoparticles (1999)

Solution-state characterizations of poly(4-vinylpyridine):polystyrene (PVP:PS) shell cross-linked knedel nanoparticles (SCK's) are described. A combination of techniques, including dynamic light scattering, electrophoretic light scattering, and analytical ultracentrifugation, are used to determine the hydrodynamic diameter, surface charge characteristics, molecular weight, and aggregation number of the SCK's and their micelle precursors. The use of analytical ultracentrifugation is highlighted because of the wealth of information it provides in characterizing SCK solution behavior. The analysis of SCK's indicates that particle diameter, molecular weight, and aggregation increase with increasing PS chain length of the PVP:PS block copolymer used to prepare the SCK. Measurements of electrophoretic mobility and zeta potential via electrophoretic light scattering point to partial burial of charge below the particle surface of quaternized PVP units comprising the shell of the SCK. By contrast, the characterization of corresponding solution properties for the non-cross-linked micelle precursors is problematic due to significant particle heterogeneity and nonideal solution behavior. The comparison of solution data for SCK's and micelle precursors clearly indicates stabilization of SCK particles is achieved through shell cross-linking.
Measurement and Analysis of Adhesion Property of Lithium-Ion Battery Electrodes with SAICAS<sup>®</sup> (2014)

The adhesion strength of lithium-ion battery (LIB) electrodes consisting of active material, nano-sized electric conductor and polymeric binder is measured by a new analysis tool, called the Surface and Interfacial Cutting Analysis System (SAICAS ® ). Compared to the conventional peel test with the same electrode, SAICAS ® gives higher adhesion strength owing to its elaborate cutting-based measurement system. In addition, the effects on adhesion property of the polymeric binder type and content, electrode density and measuring point are also investigated to determine whether SAICAS® provides reliable results. The findings confirm SAICAS ® as an effective and promising tool to measure and analyze the adhesion properties of LIB electrodes. References [1] B. Son et al., ACS Applied Materials & Interfaces, 6 (2014) 526-531
Cost-effectiveness of treating deep diabetic foot ulcers with Promogran in four European countries (2002)

This study was funded by Ethicon Gmbh (Johnson and Johnson), Germany.
Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors (2013)

This study reveals that the information on kinase activation encoded in phosphoproteomics data correlates remarkably well with the phenotypic responses of cancer cells to compounds that target kinase signaling and could be useful for the identification of novel markers of resistance or sensitivity to drugs that target the signaling network.
New tools for the analysis and validation of cryo-EM maps and atomic models (2018)

Recent advances in the field of electron cryomicroscopy (cryo-EM) have resulted in a rapidly increasing number of atomic models of biomacromolecules that have been solved using this technique and deposited in the Protein Data Bank and the Electron Microscopy Data Bank. Similar to macromolecular crystallography, validation tools for these models and maps are required. While some of these validation tools may be borrowed from crystallography, new methods specifically designed for cryo-EM validation are required. Here, new computational methods and tools implemented in PHENIX are discussed, including d<sub>99</sub> to estimate resolution, phenix.auto_sharpen to improve maps and phenix.mtriage to analyze cryo-EM maps. It is suggested that cryo-EM half-maps and masks should be deposited to facilitate the evaluation and validation of cryo-EM-derived atomic models and maps. The application of these tools to deposited cryo-EM atomic models and maps is also presented.
Vitamin D receptor genotypes influence the success of calcitriol therapy for recurrent vertebral fracture in osteoporosis (2005)

Osteoporosis is a complex multi-factorial disease where environment, diet and genetics play a role in determining susceptibility. Patients with existing vertebral fracture have a heightened risk of further recurrent vertebral fracture. The efficacy of new osteoporosis therapies is often compared to calcium supplementation. 1,25-dihydroxyvitamin D3 (calcitriol) acts through the vitamin D receptor (VDR) and is effective at reducing recurrent vertebral fracture risk. Because the VDR controls calcium metabolism, we hypothesized that genetic variation at the VDR locus may influence response to both calcium and calcitriol therapy. Postmenopausal women with osteoporosis from a 3-year study comparing calcitriol versus calcium for prevention of vertebral fractures were genotyped for VDR alleles detected by FokI, BsmI, ApaI and TaqI. Data were analysed by hierarchical log-linear analysis and robust analysis of variance for relationships to fracture outcomes. Significant differences in the vertebral fracture rate in response to calcium therapy were observed between VDR genotypes (P<0.001). Calcium appeared to be equally effective as calcitriol in particular genotypes. The response to calcitriol therapy was most pronounced in patients carrying the TaqI t allele in combination with the FokI f initiation codon variant: f+t+ carriers were 11.3-fold less likely to sustain recurrent vertebral fracture in the last 2 years of the trial while on calcitriol therapy compared to calcium (P=1.4x10(-5)). Response to both calcium and calcitriol therapy is dependent on genetic variation at the VDR locus and two loci in the VDR gene may contribute to this effect.
Gossip-based resource management for cloud environments (2010)

We address the problem of resource management for a large-scale cloud environment that hosts sites. Our contribution centers around outlining a distributed middleware architecture and presenting one of its key elements, a gossip protocol that meets our design goals: fairness of resource allocation with respect to hosted sites, efficient adaptation to load changes and scalability in terms of both the number of machines and sites. We formalize the resource allocation problem as that of dynamically maximizing the cloud utility under CPU and memory constraints. While we can show that an optimal solution without considering memory constraints is straightforward (but not useful), we provide an efficient heuristic solution for the complete problem instead. We evaluate the protocol through simulation and find its performance to be well-aligned with our design goals.
Black tea polyphenols restrict benzopyrene-induced mouse lung cancer progression through inhibition of Cox-2 and induction of caspase-3 expression. (2007)

Lung cancer is one of the leading causes of cancer related death in most developed and many developing countries of the world. Due to lack of validated screening methods and poor prognosis, treatment of lung cancer has not improved significantly over the last two decades. Therefore the risk of the disease needs to be minimized by preventive measures. One approach for lung cancer prevention envisages reversal or restriction of precancerous lesions by chemopreventive intervention. It demands a deeper understanding of the pathogenesis of the disease and identification of the ideal point of intervention. In the present investigation, tea components, epigallocatechin gallate (EGCG) and theaflavins (TF) were assessed for their chemopreventive potential when administered in the post initiation phase of lung carcinogenesis in an experimental mouse model. Histopathological changes in lungs of mice administered benzo(a)pyrene (BP) were followed serially and correlated with the expression of Cox-2, caspase-3 and caspase-7, which play key roles in histopathogenesis of neoplasia. The observations strongly indicate that both EGCG and TF can influence the expression of these genes to modulate the process of carcinogenesis, resulting in delayed onset and lowered incidence of pre-invasive lung lesions.
Security Infrastructure for On-demand Provisioned Cloud Infrastructure Services (2011)

Providing consistent security services in on-demand provisioned Cloud infrastructure services is of primary importance due to multi-tenant and potentially multi-provider nature of Clouds Infrastructure as a Service (IaaS) environment. Cloud security infrastructure should address two aspects of the IaaS operation and dynamic security services provisioning: (1) provide security infrastructure for secure Cloud IaaS operation, (2) provisioning dynamic security services, including creation and management of the dynamic security associations, as a part of the provisioned composite services or virtual infrastructures. The first task is a traditional task in security engineering, while dynamic provisioning of managed security services in virtualised environment remains a problem and requires additional research. In this paper we discuss both aspects of the Cloud Security and provide suggestions about required security mechanisms for secure data management in dynamically provisioned Cloud infrastructures. The paper refers to the architectural framework for on-demand infrastructure services provisioning, being developed by authors, that provides a basis for defining the proposed Cloud Security Infrastructure. The proposed SLA management solution is based on the WS-Agreement and allows dynamic SLA management during the whole provisioned services lifecycle. The paper discusses conceptual issues, basic requirements and practical suggestions for dynamically provisioned access control infrastructure (DACI). The paper proposes the security mechanisms that are required for consistent DACI operation, in particular security tokens used for access control, policy enforcement and authorisation session context exchange between provisioned infrastructure services and Cloud provider services. The suggested implementation is based on the GAAA Toolkit Java library developed by authors that is extended with the proposed Common Security Services Interface (CSSI) and additional mechanisms for binding sessions and security context between provisioned services and virtualised platform.
Lamb wave reflection for the quick nondestructive evaluation of large composite laminates (1994)

Urethane copolymer sorbent materials that incorporate β-cyclodextrin (CD) have been prepared and their sorption properties with chlorinated aromatic compounds (i.e., pentachlorophenol, 2,4-dichlorophenol and 2,4-dichlorophenoxy acetic acid) have been evaluated. The sorption properties of granular activated carbon (GAC) were similarly compared in aqueous solution at variable pH conditions. The sorbents displayed variable BET surface areas as follows: MDI-X copolymers (< 10¹ m²/g), CDI-X copolymers (< 10¹ m²/g), and granular activated carbon (GAC ~10³ m²/g). The sorption capacities for the copolymers sorbents are listed in descending order, as follows: GAC > CDI-3 copolymer ≈ MDI-3 copolymer. The sorption capacity for the aromatic adsorbates with each sorbent are listed in descending order, as follows: 2,4-dichlorophenol > 2,4-dichlorophenoxy acetic acid > pentachlorophenol. In general, the differences in the sorption properties of the copolymer sorbents with the chlorinated organics were related to the following factors: (i) surface area of the sorbent; (ii) CD content and accessibility; and (iii) and the chemical nature of the sorbent material.
Automated Selection of DAB-labeled Tissue for Immunohistochemical Quantification (2003)

The increased use of immunohistochemistry (IHC) in both clinical and basic research settings has led to the development of techniques for acquiring quantitative information from immunostains. Staining correlates with absolute protein levels and has been investigated as a clinical tool for patient diagnosis and prognosis. For these reasons, automated imaging methods have been developed in an attempt to standardize IHC analysis. We propose a novel imaging technique in which brightfield images of diaminobenzidene (DAB)-labeled antigens are converted to normalized blue images, allowing automated identification of positively stained tissue. A statistical analysis compared our method with seven previously published imaging techniques by measuring each one's agreement with manual analysis by two observers. Eighteen DAB-stained images showing a range of protein levels were used. Accuracy was assessed by calculating the percentage of pixels misclassified using each technique compared with a manual standard. Bland-Altman analysis was then used to show the extent to which misclassification affected staining quantification. Many of the techniques were inconsistent in classifying DAB staining due to background interference, but our method was statistically the most accurate and consistent across all staining levels.
Drug driving from a user's perspective (2005)

AbstractThe bulk of research into drug driving in Australia has been undertaken from a road safety orientation where drug driving is viewed within the broader context of road safety and driver behaviour. Such a specific focus precludes the broader behavioural, contextual and cultural issues associated with substance use. This study aimed to address this issue by focusing on drug driving behaviour within the context of illicit substance use. A series of focused interviews were conducted with 211 illicit drug users from urban and regional centres. A consistent theme identified in the interviews was that drug driving was not necessarily viewed as risky behaviour but rather as an outcome of illicit substance use. Further, some interviewees saw their drug use as enhancing their driving skills and frequently the motor vehicle was viewed as a safe place to use. Overall there was agreement among interviewees that the likelihood of being apprehended for drug driving by police was minimal; this perception was reinforced by past experience. The lack of concern for detection of drug driving behaviour suggests that research should continue into the development and implementation of enforcement programs and roadside detection.
Advanced Glycation End Products of the Maillard Reaction and Their Relation to Aging (1994)

Long-term incubation of proteins with glucose leads to advanced glycation end products (AGE). Demonstration of AGE in vivo as well as determination of its main structure are crucial to elucidate its potential link to aging processes and diabetic complications. We prepared polyclonal and monoclonal anti-AGE antibodies and used them to identify and quantitate AGE in human lens proteins. Results suggest that there occurs a common AGE structure and provide the direct evidence for the presence of AGE in human lens crystallins and its age-related increase.
Phylogenetic trees: an information visualisation perspective (2004)

The development of powerful visualisation tools is a major challenge in bioinformatics. Phylogenetics, a field with a growing impact on a variety of life science areas, is experiencing an increasing but poorly met requirement for software supporting the advanced visualisation of phylogenetic trees. Visualisation problems within the domain are commonly experienced by its researchers, but are poorly documented. Furthermore, the applications in the domain have not been reviewed from an information visualisation perspective. In this paper, the problems are defined and the methods employed by phylogenetic applications are reviewed with respect to related research within information visualisation. The results of a survey of the visualisation needs of phylogenetics researchers are also presented.The full version of this report is available at http://www.it.usyd.edu.au/~scarrizo.
Welcome to SIGSPATIAL Australia (2010)

Australia has a long history of research excellence and technological innovation in spatial database systems, geographical information systems, and their advanced applications. In early December 2009, eleven members of our community got together and submitted an application for forming an ACM SIGSPATIAL chapter in Australia. The application was officially chartered by ACM on 23 December 2009. ACM SIGSPATIAL Australia Chapter is the second and the most recent chapter for SIGSPATIAL, following the formation of the Chinese Chapter in October 2009.
Microvascular Decompression of the Eighth Cranial Nerve for Disabling Tinnitus without Vertigo: A Case Report (1984)

We report a patient with disabling tinnitus that responded dramatically to microvascular decompression of the 8th cranial nerve. The most annoying, episodic, high pitched tinnitus disappeared immediately after the operation. Two types of constant tinnitus either persisted or recurred after the procedure. Nevertheless, the remaining tinnitus is much reduced compared to the preoperative level. The patient was able to return to his previous work 2 months after operation.
Prognostic Value of MMP-9 in Ovarian Cancer: A Meta-analysis (2013)

Increased expression of MMP- 9 was associated with poor prognosis in ovarian cancer patients. Down-regulation of MMP-9 is an attractive therapeutic approach which might improve outcome of ovarian cancer.
Aeroacoustic liner applications of the broadband special acoustic absorber concept (2013)

Aircraft exterior noise reduction is a major task for manufacturer and carrier. However, optimum sound absorption over a broad frequency range at engine level is still a challenging aspect for acoustic liner. This paper presents the special acoustic absorber concept as broadband working liner with limited space needed. Experimental as well as numerical work is presented for different applications as there are hot stream liner for exhaust integration, broadband liner for bypass integration and low frequency broadband liner for integration into a shrouded fan.
Enhanced 4D cone‐beam CT with inter‐phase motion model (2007)

Four-dimensional (4D) cone-beam CT (CBCT) is commonly obtained by respiratory phase binning of the projections, followed by independent reconstructions of the rebinned data in each phase bin. Due to the significantly reduced number of projections per reconstruction, the quality of the 4DCBCT images is often degraded by view-aliasing artifacts easily seen in the axial view. Acquisitions using multiple gantry rotations or slow gantry rotation can increase the number of projections and substantially improve the 4D images. However, the extra cost of the scan time may set fundamental limits to their applications in clinics. Improving the trade-off between image quality and scan time is the key to making 4D onboard imaging practical and more useful. In this article, we present a novel technique toward high-quality 4DCBCT imaging without prolonging the acquisition time, referred to as the "enhanced 4DCBCT". The method correlates the data in different phase bins and integrates the internal motion into the 4DCBCT image formulation. Several strategies of the motion derivation are discussed, and the resultant images are assessed with numerical simulations as well as a clinical case.
Palladium-Catalyzed <i>α</i>-Arylation of Esters (2001)

A new and simple one-pot procedure for the palladium-catalyzed intermolecular alpha-arylation of esters is described. A number of esters can be functionalized with a wide range of aryl bromides using Pd(OAc)(2) or Pd(2)(dba)(3) and bulky electron-rich o-biphenyl phosphines 1-3. Under the reaction conditions, using LiHMDS as base, alpha-arylation proceeds at room temperature or at 80 degrees C with very good yields and high selectivities for monoarylation. Important nonsteroidal antiinflammatory drug derivatives such as (+/-)-naproxen tert-butyl ester and (+/-)-flurbiprofen tert-butyl ester can be prepared in 79% and 86% yield, respectively. The catalyst system based on the di-tert-butylphosphine (2) is also active for the alpha-arylation of esters using aryl chlorides. Furthermore, using (3) the alpha-arylation of trisubstituted ester enolates can be accomplished to provide compounds that have quaternary centers.
Peptides derived from specific interaction sites of the fibroblast growth factor 2 – FGF receptor complexes induce receptor activation and signaling (2010)

Basic fibroblast growth factor (FGF2, bFGF) is the most extensively studied member of the FGF family and is involved in neurogenesis, differentiation, neuroprotection, and synaptic plasticity in the CNS. FGF2 executes its pleiotropic biologic actions by binding, dimerizing, and activating FGF receptors (FGFRs). The present study reports the physiologic impact of various FGF2-FGFR1 contact sites employing three different synthetic peptides, termed canofins, designed based on structural analysis of the interactions between FGF2 and FGFR1. Canofins mimic the cognate ligand interaction with the receptor and preserve the neuritogenic and neuroprotective properties of FGF2. Canofins were shown by surface plasmon resonance analysis to bind to FGFR1 and promote receptor activation. However, FGF2-induced receptor phosphorylation was inhibited by canofins, indicating that canofins are partial FGFR agonists. Furthermore, canofins were demonstrated to induce neuronal differentiation determined by neurite outgrowth from cerebellar granule neurons, and this effect was dependent on FGFR activation. Additionally, canofins acted as neuroprotectants, promoting survival of cerebellar granule neurons induced to undergo apoptosis. Our results suggest that canofins mirror the effect of specific interaction sites in FGF2 for FGFR. Thus, canofins are valuable pharmacological tools to study the functional roles of specific molecular interactions of FGF2 with FGFR.