gebhart/patrepeval huggingface dataset:
Potent response of QS-21 as a vaccine adjuvant in the skin when delivered with the Nanopatch, resulted in adjuvant dose sparing (2016)

Adjuvants play a key role in boosting immunogenicity of vaccines, particularly for subunit protein vaccines. In this study we investigated the induction of antibody response against trivalent influenza subunit protein antigen and a saponin adjuvant, QS-21. Clinical trials of QS-21 have demonstrated the safety but, also a need of high dose for optimal immunity, which could possibly reduce patient acceptability. Here, we proposed the use of a skin delivery technology - the Nanopatch - to reduce both adjuvant and antigen dose but also retain its immune stimulating effects when compared to the conventional needle and syringe intramuscular (IM) delivery. We have demonstrated that Nanopatch delivery to skin requires only 1/100(th) of the IM antigen dose to induce equivalent humoral response. QS-21 enhanced humoral response in both skin and muscle route. Additionally, Nanopatch has demonstrated 30-fold adjuvant QS-21 dose sparing while retaining immune stimulating effects compared to IM. QS-21 induced localised, controlled cell death in the skin, suggesting that the danger signals released from dead cells contributed to the enhanced immunogenicity. Taken together, these findings demonstrated the suitability of reduced dose of QS-21 and the antigen using the Nanopatch to enhance humoral responses, and the potential to increase patient acceptability of QS-21 adjuvant.
Analysis of the HLA class I associated peptide repertoire in a hepatocellular carcinoma cell line reveals tumor‐specific peptides as putative targets for immunotherapy (2007)

HLA class I molecules present peptides on the cell surface to CD8(+) T cells. The repertoire of peptides that associate to class I molecules represents the cellular proteome. Therefore, cells expressing different proteomes could generate different class I-associated peptide repertoires. A large number of peptides have been sequenced from HLA class I alleles, mostly from lymphoid cells. On the other hand, T cell immunotherapy is a goal in the fight against cancer, but the identification of T cell epitopes is a laborious task. Proteomic techniques allow the definition of putative T cell epitopes by the identification of HLA natural ligands in tumor cells. In this study, we have compared the HLA class I-associated peptide repertoire from the hepatocellular carcinoma (HCC) cell line SK-Hep-1 with that previously described from lymphoid cells. The analysis of the peptide pool confirmed that, as expected, the peptides from SK-Hep-1 derive from proteins localized in the same compartments as in lymphoid cells. Within this pool, we have identified 12 HLA class I peptides derived from HCC-related proteins. This confirms that tumor cell lines could be a good source of tumor associated antigens to be used, together with MS, to define putative epitopes for cytotoxic T cells from cancer patients.
The Analysis of Some Corticosteroids and Corticosteroid Esters by Liquid Chromatography Coupled with Frit Fast-atom Bombardment Mass Spectrometry (1997)

A method utilizing a liquid chromatography/mass spectrometry method based on a Frit-fast atom bombardment (FAB) interface was developed for the analysis of corticosteroids and corticosteroid esters. The method used a microbore octadecylsilane column with methanol + water as the mobile phase; 0.5% glycerol was incorporated into the mobile phase as the FAB matrix. Separation of a mixture, containing five corticosteroids was achieved. Full-scan spectra were readily obtained for 20 ng of each steroid introduced into the instrument. © 1997 John Wiley & Sons, Ltd.
A machine learning framework for TCP round-trip time estimation (2014)

Abstract In this paper, we explore a novel approach to end-to-end round-trip time (RTT) estimation using a machine-learning technique known as the experts framework . In our proposal, each of several ‘experts’ guesses a fixed value. The weighted average of these guesses estimates the RTT, with the weights updated after every RTT measurement based on the difference between the estimated and actual RTT. Through extensive simulations, we show that the proposed machine-learning algorithm adapts very quickly to changes in the RTT. Our results show a considerable reduction in the number of retransmitted packets and an increase in goodput, especially in more heavily congested scenarios. We corroborate our results through ‘live’ experiments using an implementation of the proposed algorithm in the Linux kernel. These experiments confirm the higher RTT estimation accuracy of the machine learning approach which yields over 40% improvement when compared against both standard transmission control protocol (TCP) as well as the well known Eifel RTT estimator. To the best of our knowledge, our work is the first attempt to use on-line learning algorithms to predict network performance and, given the promising results reported here, creates the opportunity of applying on-line learning to estimate other important network variables.
Mobile sensing and network analytics for realizing smart automated systems towards health Internet of Things (2015)

Internet of Things (IoT) provides an unprecedented opportunity to realize smart automated systems such as smart manufacturing, smart city and smart home in the past few years. Pervasive sensing and mobile technology deployed in large-scale IoT systems lead to the accumulation of big data. In particular, wearable biosensing accelerates human-centered computing for smart health management. However, limited work has been done to develop advanced IoT technologies for smart monitoring and control of heart health. There is an urgent need to develop a new IoT technology specific to the heart, namely Internet of Hearts (IOH) that will enable and assist (1) the acquisition of electrocardiogram (ECG) signals pertinent to space-time cardiac dynamics at anytime anywhere; (2) real-time management and compact representation of multi-sensor signals; (3) big data analytics in large-scale IoT contexts. This paper presents a new technology of Mobile and E-Network Smart Health (MESH), which is composed of 4 components as follows: 1) Mobile-based ECG sensing device; 2) Space-time representation of cardiac electrical activity; 3) Optimal model-based representation of ECG signals; 4) Dynamic network embedding for disease pattern recognition. Our preliminary experimental results demonstrated that network analytics is efficient and effective for smart health management in IoT contexts. The MESH technology shows strong potentials to provide an indispensable and enabling tool for realizing smart heart health and wellbeing for the population worldwide.
A novel antimicrobial central venous catheter impregnated with benzalkonium chloride (1993)

Catheter-related sepsis is a common complication associated with the use of central venous catheters (CVC). In an attempt to overcome this problem benzalkonium chloride was incorporated into a CVC polymer. The effect of the presence of benzalkonium chloride on microbial colonization of the CVC was then assessed in vitro. MICs and MBCs of benzalkonium chloride for a range of organisms were performed and good activity against Gram-positive organisms was confirmed. In order to assess the antimicrobial activity of the benzalkonium-chloride-impregnated catheter, 2 cm lengths were placed on to nutrient agar plates inoculated with various micro-organisms. Zones of inhibition against five strains of Staphylococcus epidermidis and two strains of Staphylococcus aureus were demonstrated. Smaller zones of inhibition was also produced with Gram-negative species and Candida albicans. The zone sizes correlated with the MICs. Bacterial adherence to the benzalkonium-chloride-impregnated catheters was determined in both static and dynamic models and was significantly reduced compared with control catheters, containing no antimicrobial agent (P < 0.01). Inhibition of microbial adherence to benzalkonium-chloride-impregnated catheters placed in 25% human blood in phosphate-buffered saline (PBS), for up to seven days or PBS alone for 14 days was detected. The findings indicate that benzalkonium-chloride-impregnated catheters exhibit reduced microbial colonization by a range of organisms in vitro. The incorporation of benzalkonium chloride into a CVC may thus offer an effective method for the prevention of catheter related sepsis.
Stoichiometry of Active Smad-Transcription Factor Complexes on DNA (2002)

Transforming growth factor (TGF)-beta signals through a heteromeric complex of serine/threonine kinase receptors. The type I receptor phosphorylates and activates the receptor-regulated Smads (R-Smads), Smad2 and Smad3, which form hetero-oligomeric complexes with the co-Smad, Smad4, and translocate to the nucleus. Smad3 and Smad4 can bind directly to consensus DNA-binding elements in the promoters of target genes, whereas Smad2/Smad4 complexes are targeted to DNA by interacting with sequence-specific DNA-binding transcription factors that contain a well-defined Smad interaction motif (SIM). The exact stoichiometry of Smad homo- and hetero-oligomers both before and after ligand stimulation is controversial. Here we determine the stoichiometry of TGF-beta-induced Smad-transcription factor complexes on DNA. We show that complexes of Smad2/Smad4 with the transcription factors Fast-1 or Fast-3 contain one Fast, two Smad2s, and one Smad4. In contrast, Smad3/Smad4 complexes that bind the Smad-binding element from the c-jun promoter, are heterodimers. Furthermore, these Smad3/Smad4 complexes contain at least two additional components essential for complex formation, one of which contains a SIM. Our data suggest that the R-Smads can form heterodimers or heterotrimers with Smad4, and we propose that the exact stoichiometries of active Smad complexes on DNA may be determined by the transcription factors with which they associate.
Wayfinding techniques for multiScale virtual environments (2009)

Wayfinding in multiscale virtual environments can be rather complex, as users can and sometimes have to change their scale to access the entire environment. Hence, this work focuses on the understanding and classification of information needed for travel, as well as on the design of navigation techniques that provide this information. To this end, we first identified two kinds of information necessary for traveling effectively in this kind of environment: hierarchical information, based on the hierarchical structure formed by the levels of scale; and spatial information, related to orientation, distance between objects in different levels of scale and spatial localization. Based on this, we designed and implemented one technique for each kind of information. The developed techniques were evaluated and compared to a baseline set of travel and wayfinding aid techniques for traveling through multiple scales. Results show that the developed techniques perform better and provide a better solution for both travel and wayfinding aid.
Application of optical fibres in power systems (1993)

Optical fibres offer important advantages for power systems: they are cheap, of low weight, dielectric, insulating and immune from the effects of electromagnetic interference. With these features, high bandwidth secure communications along power transmission systems is an attractive option. In addition, fibres may be used for shorter path telemetry and for specialised diagnostic monitoring. Optical-fibre sensors may be used conveniently to measure power system parameters such as current, voltage, temperature, strain and displacement. These measurements may be either discrete or distributed. This paper discusses the above applications and indicates some future possibilities.
Conjugated Polymer with Intrinsic Alkyne Units for Synergistically Enhanced Raman Imaging in Living Cells (2017)

Development of Raman-active materials with enhanced and distinctive Raman vibrations in the Raman-silent region (1800-2800 cm<sup>-1</sup> ) is highly required for specific molecular imaging of living cells with high spatial resolution. Herein, water-soluble cationic conjugated polymers (CCPs), poly(phenylene ethynylene) (PPE) derivatives, are explored for use as alkyne-state-dependent Raman probes for living cell imaging due to synergetic enhancement effect of alkyne vibrations in Raman-silent region compared to alkyne-containing small molecules. The enhanced alkyne signals result from the integration of alkyne groups into the rigid backbone and the delocalized π-conjugated structure. PPE-based conjugated polymer nanoparticles (CPNs) were also prepared as Raman-responsive nanomaterials for distinct imaging application. This work opens a new way into the development of conjugated polymer materials for enhanced Raman imaging.
Characterization of the in vitro reconstituted cyclin A or B1-dependent cdk2 and cdc2 kinase activities. (1993)

Human cyclins A and B1 were assembled with the cdk2 or cdc2 protein to reconstitute their respective kinase activities in vitro. Both cyclins complemented either cdk2 or cdc2, yielding kinase activities that supported the phosphorylation of histone H1. Activation of cdk2-catalyzed H1 kinase activity by cyclin A required a 10-min preincubation of the two components, whereas cdc2 kinase supported phosphate incorporation without a detectable time lag upon the addition of cyclin B1, suggesting a slower association rate of cdk2 with cyclin A compared with cdc2 and cyclin B1. Both cdk2 and cyclin A, as well as cdc2 and cyclin B1, formed stable complexes in the absence of ATP and substrate that could be isolated after glycerol gradient centrifugation. Incubation of the isolated complexes with ATP and histone H1 supported the phosphorylation of the substrate. Cyclin A-activated cdk2 or cdc2 phosphorylated p107, a pRB-related cellular protein, 10 times more effectively than the cyclin B1-complexed kinases. This was most likely due to a direct association of cyclin A with p107 (Ewen, M. E., Faha, B., Harlow, E., and Livingston, D. (1992) Science 255, 85-87; Faha, B., Ewen, M. E., Tsai, L.-H., Livingston, D., and Harlow, E. (1992) Science 255, 87-90). The reconstituted cdc2-cyclin B1 complex incorporated 4-5-fold more phosphate into the p34 subunit of the three-subunit (p70, p34, and p14) human single-stranded DNA-binding protein (also called RP-A), a DNA replication and DNA repair factor, than cdc2-cyclin A. No detectable phosphorylation of the p34 protein was observed with cdk2 complexed with either cyclin B1 or A. These data indicate that both cyclins as well as the catalytic subunits are important factors in controlling the rate of phosphorylation of a given substrate. The cyclin-activated cdc2 family kinases may target their cellular substrates through cyclin-mediated protein-protein interactions.
The Intriguing Interplay Between Therapies Targeting the Epidermal Growth Factor Receptor, the Hypoxic Microenvironment and Hypoxia-inducible Factors (2012)

Despite their individual key roles in promoting cancer progression and treatment resistance, our knowledge about the impact of tumor hypoxia on the activity of the epidermal growth factor receptor (EGFR) pathway in cancer and vice versa remains limited. Preclinical and clinical studies support an important link between hypoxia and upregulation of EGFR in cancers that do not display genetic alterations of the receptor. Subsequent EGFR signaling stimulates hypoxia-inducible factor (HIF) signaling and thus augments induction of proteins that promote cellular survival in a hostile microenvironment. Considering the effects of EGFR-targeting agents under reduced oxygen conditions, it is now accepted that, together with their demonstrated antiproliferative and proapoptotic effects, the antiangiogenic activity of these drugs also contributes to their overall antitumor activity in vivo. Treatment of human tumor cells with EGFR inhibitors leads to decreased HIF-1α and VEGF secretion by tumor cells, resulting in vascular normalization, improved blood flow and thus improved oxygenation. These findings may have major implications with respect to the efficacy of both radiotherapy and subsequent chemotherapy when combined with EGFR inhibitors. A major challenge remains to assess which sequence of these drugs with radiation or chemotherapy is optimal. Moreover, recent data suggest that the lack of clinical responses to EGFR-directed therapy may be circumvented by supplementation of the anti-EGFR therapy with additional approaches targeting HIF-1α or VEGF. Further studies thus are warranted to define the precise mechanistic and therapeutic implications of the hypoxic response relative to the EGFR signaling pathway in cancer. Keywords: EGFR, hypoxia, hypoxia-inducible factor, cetuximab, panitumumab, gefitinib, erlotinib, cancer progression, treatment resistance, microenvironment
Motivational enhancement and coping skills training for cocaine abusers: effects on substance use outcomes (2004)

MET is more beneficial for patients with lower initial motivation than for patients with high initial motivation. CST reduced cocaine and alcohol use for women only and reduced alcohol relapses, in contrast to results with lengthier individual CST.
Learning user preferences of route choice behaviour for adaptive route guidance (2007)

As the use of navigation systems becomes more widespread, the demand for advanced functions of navigation systems also increases. In the light of user satisfaction, personalisation of route guidance by incorporating user preferences is one of the most desired features. A user model applied to personalised route guidance is presented. The user model adaptively updates route selection rules when it discovers the predicted choice differs from the actual choice of the driver. This study employs a decision tree learning algorithm, the C4.5 algorithm, which has advantages over other data mining methods in terms of its comprehensible model structure. Simulation experiments with a real-world network were conducted to analyse the applicability of the model to adaptive route guidance and the accuracy of its prediction.
Modes of cell:cell communication in the immune system (1985)

Different cell types in the immune system appear to mediate their effects by markedly different means. B lymphocytes couple information for specificity with information for function in a single long-range molecule, antibody. Major histocompatibility complex (MHC)-restricted T cells, which we have analyzed in detail, appear to recognize antigen only on the surface of cells bearing the appropriate MHC gene product. This interaction provokes the T cell to release short-range, non-antigen-specific mediators (lymphokines) that preferentially act on the target cell bearing the antigen and stimulating the T cell. Regulatory T cells appear to make antigen-specific long-range molecules that, like antibody, combine specificity with information for function. However, unlike antibody molecules, these regulatory T cell products display recognition for particular target cells in the form of genetic restrictions. These behaviors are compared to strategies of cell:cell communication in the nervous system.
Security enhanced multi-hop over the air reprogramming with Fountain Codes (2009)

Recently, several code update approaches for multi-hop sensor networks have been proposed basically addressing two orthogonal problems: security and efficient over the air reprogramming. Unfortunately, the proposed security solutions for code update mechanisms are only considering early proposed over the air reprogramming solutions like e.g. Deluge or MOAP. Therefore, currently available symmetric key based secure code update schemes are not per se suited to support advanced coding techniques such as Fountain Codes. In this work, we provide means to secure this promising technique mainly with efficient symmetric cryptographic primitives and demonstrate its applicability for efficient and robust over the air reprogramming.
Plasmid Content of Some Oral Microorganisms Isolated from Subgingival Plaque (1982)

Eighty-five strains of bacterial species selected from the predominant cultivable dental plaque flora of patients with different periodontal pathologies were examined for their plasmid content. Microorganisms studied included: Actinomyces viscosus, A. odontolyticus, Bacteroides asaccharolyticus (B. gingivalis), B. melaninogenicus subspecies intermedius, and subspecies melaninogenicus, Capnocytophaga ochracea (B. ochraceus), and Fusobacterium nucleatum. Three B. melaninogenicus isolates showed plasmids of approximately 2.7-2.9 Mdalton (mega-dalton) molecular size. Restriction enzyme digests of the plasmids demonstrated dissimilar patterns when electrophoresed on agarose gels. In other microorganisms, including the Actinomyces species, plasmids were not observed.
Transformation of <i>Salmonella typhimurium</i> by Plasmid Deoxyribonucleic Acid (1974)

A modified transformation procedure that is effective for the introduction of plasmid deoxyribonucleic acid at high frequency into Salmonella typhimurium, as well as into Escherichia coli, is described. Transformed bacteria acquire a circular deoxyribonucleic acid species having the genetic and molecular characteristics of the transforming plasmid.
Optimizing Energy Consumption of Mobile Nodes in Heterogeneous Kademlia-Based Distributed Hash Tables (2008)

This paper presents a novel mechanism that enables mobile devices to efficiently participate in Distributed Hash Tables (DHTs). By selectively dropping messages, we can significantly reduce traffic and thus the energy consumption of mobile nodes with only minor performance degradation. The protocol extension preserves compatibility with existing widely used DHT systems. We evaluate the solution by measuring the energy-consumption of mobile phones participating in the Kademlia-based Mainline BitTorrent DHT, which consists of over one million nodes. We further analyze the impact of our mechanism on the performance of the DHT by means of an analytical model.
Optical flow equation based imaging condition for elastic reverse time migration (2014)

Summary We present a new elastic reverse time migration implementation. The elastic wave propagation is simulated using a nonsplit-field complex frequency-shifted (CFS) recursive integration perfectly matched layer (PML) implementation (RIPML) with the auxiliary differential equations (ADEs) for elastic wave modeling. Here, RIPMLcan overcome the spurious reflection for waves incident on the PML interface at near-grazing angles, and evanescent waves within PML where the classic PML algorithm fails. For the imaging condition, we use Poynting vectors as a means to attenuate low-frequency cross correlation noise. This approach has been widely studied by numerous authors in acoustic imaging. We calculate the Poynting vector for elastic waves with a least squares formulation based on an optical flow equation in local windows to improve robustness. The effectiveness of our new implementation is demonstrated using a two layer synthetic model and a complicated SEG/EAGE salt dome elastic model.