1,094 research outputs found
Phonon-assisted radiofrequency absorption by gold nanoparticles resulting in hyperthermia
It is suggested that in gold nanoparticles (GNPs) of about 5 nm sizes used in
the radiofrequency (RF) hyperthermia, an absorption of the RF photon by the
Fermi electron occurs with involvement of the longitudinal acoustic vibrational
mode (LAVM), the dominating one in the distribution of vibrational density of
states (VDOS). This physical mechanism helps to explain two observed phenomena:
the size dependence of the heating rate (HR) in GNPs and reduced heat
production in aggregated GNPs. The argumentation proceeds within the
one-electron approximation, taking into account the discretenesses of energies
and momenta of both electrons and LAVMs. The heating of GNPs is thought to
consist of two consecutive processes: first, the Fermi electron absorbs
simultaneously the RF photon and the LAVM available in the GNP; hereafter the
excited electron gets relaxed within the GNP's boundary, exciting a LAVM with
the energy higher than that of the previously absorbed LAVM. GNPs containing
the Ta and/or Fe impurities are proposed for the RF hyperthermia as promising
heaters with enhanced HRs, and GNPs with rare-earth impurity atoms are also
brought into consideration. It is shown why the maximum HR values should be
expected in GNPs with about 5-7 nm size.Comment: proceedings at the NATO Advanced Research workshop FANEM-2015 (Minsk,
May 25-27, 2015). To be published in the final form in: "Fundamental and
Applied NanoElectroMagnetics" (Springer Science + Business Media B.V.
Listen to genes : dealing with microarray data in the frequency domain
Background: We present a novel and systematic approach to analyze temporal microarray data. The approach includes
normalization, clustering and network analysis of genes.
Methodology: Genes are normalized using an error model based uniform normalization method aimed at identifying and
estimating the sources of variations. The model minimizes the correlation among error terms across replicates. The
normalized gene expressions are then clustered in terms of their power spectrum density. The method of complex Granger
causality is introduced to reveal interactions between sets of genes. Complex Granger causality along with partial Granger
causality is applied in both time and frequency domains to selected as well as all the genes to reveal the interesting
networks of interactions. The approach is successfully applied to Arabidopsis leaf microarray data generated from 31,000
genes observed over 22 time points over 22 days. Three circuits: a circadian gene circuit, an ethylene circuit and a new
global circuit showing a hierarchical structure to determine the initiators of leaf senescence are analyzed in detail.
Conclusions: We use a totally data-driven approach to form biological hypothesis. Clustering using the power-spectrum
analysis helps us identify genes of potential interest. Their dynamics can be captured accurately in the time and frequency
domain using the methods of complex and partial Granger causality. With the rise in availability of temporal microarray
data, such methods can be useful tools in uncovering the hidden biological interactions. We show our method in a step by
step manner with help of toy models as well as a real biological dataset. We also analyse three distinct gene circuits of
potential interest to Arabidopsis researchers
Quasi-particle interference and superconducting gap in a high-temperature superconductor Ca2-xNaxCuO2Cl2
High-transition-temperature (high-Tc) superconductivity is ubiquitous in the
cuprates containing CuO2 planes but each cuprate has its own character. The
study of the material dependence of the d-wave superconducting gap (SG) should
provide important insights into the mechanism of high-Tc. However, because of
the 'pseudogap' phenomenon, it is often unclear whether the energy gaps
observed by spectroscopic techniques really represent the SG. Here, we report
spectroscopic imaging scanning tunneling microscopy (SI-STM) studies of
nearly-optimally-doped Ca2-xNaxCuO2Cl2 (Na-CCOC) with Tc = 25 ~ 28 K. They
enable us to observe the quasi-particle interference (QPI) effect in this
material, through which unambiguous new information on the SG is obtained. The
analysis of QPI in Na-CCOC reveals that the SG dispersion near the gap node is
almost identical to that of Bi2Sr2CaCu2Oy (Bi2212) at the same doping level,
while Tc of Bi2212 is 3 times higher than that of Na-CCOC. We also find that SG
in Na-CCOC is confined in narrower energy and momentum ranges than Bi2212. This
explains at least in part the remarkable material dependence of TcComment: 13pages, 4fig
DR6 as a Diagnostic and Predictive Biomarker in Adult Sarcoma
The Death Receptor 6 (DR6) protein is elevated in the serum of ovarian cancer patients. We tested DR6 serum protein levels as a diagnostic/predictive biomarker in several epithelial tumors and sarcomas.DR6 gene expression profiles were screened in publically available arrays of solid tumors. A quantitative immunofluorescent western blot analysis was developed to test the serum of healthy controls and patients with sarcoma, uterine carcinosarcoma, bladder, liver, and pancreatic carcinomas. Change in DR6 serum levels was used to assay the ability of DR6 to predict the response to therapy of sarcoma patients.DR6 mRNA is highly expressed in all tumor types assayed. Western blot analysis of serum DR6 protein demonstrated high reproducibility (r = 0.97). Compared to healthy donor controls, DR6 serum levels were not elevated in patients with uterine carcinosarcoma, bladder, liver, or pancreatic cancers. Serum DR6 protein levels from adult sarcoma patients were significantly elevated (p<0.001). This was most evident for patients with synovial sarcoma. Change in serum DR6 levels during therapy correlated with clinical benefit from therapy (sensitivity 75%, and positive predictive value 87%).DR6 may be a clinically useful diagnostic and predictive serum biomarker for some adult sarcoma subtypes.Diagnosis of sarcoma can be difficult and can lead to improper management of these cancers. DR6 serum protein may be a tool to aid in the diagnosis of some sarcomatous tumors to improve treatment planning. For patients with advanced disease, rising DR6 levels predict non-response to therapy and may expedite therapeutic decision making and reduce reliance on radiologic imaging
Design principles for riboswitch function
Scientific and technological advances that enable the tuning of integrated regulatory components to match network and system requirements are critical to reliably control the function of biological systems. RNA provides a promising building block for the construction of tunable regulatory components based on its rich regulatory capacity and our current understanding of the sequence–function relationship. One prominent example of RNA-based regulatory components is riboswitches, genetic elements that mediate ligand control of gene expression through diverse regulatory mechanisms. While characterization of natural and synthetic riboswitches has revealed that riboswitch function can be modulated through sequence alteration, no quantitative frameworks exist to investigate or guide riboswitch tuning. Here, we combined mathematical modeling and experimental approaches to investigate the relationship between riboswitch function and performance. Model results demonstrated that the competition between reversible and irreversible rate constants dictates performance for different regulatory mechanisms. We also found that practical system restrictions, such as an upper limit on ligand concentration, can significantly alter the requirements for riboswitch performance, necessitating alternative tuning strategies. Previous experimental data for natural and synthetic riboswitches as well as experiments conducted in this work support model predictions. From our results, we developed a set of general design principles for synthetic riboswitches. Our results also provide a foundation from which to investigate how natural riboswitches are tuned to meet systems-level regulatory demands
Regulation of neutrophil senescence by microRNAs
Neutrophils are rapidly recruited to sites of tissue injury or infection, where they protect against invading pathogens. Neutrophil functions are limited by a process of neutrophil senescence, which renders the cells unable to respond to chemoattractants, carry out respiratory burst, or degranulate. In parallel, aged neutrophils also undergo spontaneous apoptosis, which can be delayed by factors such as GMCSF. This is then followed by their subsequent removal by phagocytic cells such as macrophages, thereby preventing unwanted inflammation and tissue damage. Neutrophils translate mRNA to make new proteins that are important in maintaining functional longevity. We therefore hypothesised that neutrophil functions and lifespan might be regulated by microRNAs expressed within human neutrophils. Total RNA from highly purified neutrophils was prepared and subjected to microarray analysis using the Agilent human miRNA microarray V3. We found human neutrophils expressed a selected repertoire of 148 microRNAs and that 6 of these were significantly upregulated after a period of 4 hours in culture, at a time when the contribution of apoptosis is negligible. A list of predicted targets for these 6 microRNAs was generated from http://mirecords.biolead.org and compared to mRNA species downregulated over time, revealing 83 genes targeted by at least 2 out of the 6 regulated microRNAs. Pathway analysis of genes containing binding sites for these microRNAs identified the following pathways: chemokine and cytokine signalling, Ras pathway, and regulation of the actin cytoskeleton. Our data suggest that microRNAs may play a role in the regulation of neutrophil senescence and further suggest that manipulation of microRNAs might represent an area of future therapeutic interest for the treatment of inflammatory disease
Phylogeography of Japanese encephalitis virus:genotype is associated with climate
The circulation of vector-borne zoonotic viruses is largely determined by the overlap in the geographical distributions of virus-competent vectors and reservoir hosts. What is less clear are the factors influencing the distribution of virus-specific lineages. Japanese encephalitis virus (JEV) is the most important etiologic agent of epidemic encephalitis worldwide, and is primarily maintained between vertebrate reservoir hosts (avian and swine) and culicine mosquitoes. There are five genotypes of JEV: GI-V. In recent years, GI has displaced GIII as the dominant JEV genotype and GV has re-emerged after almost 60 years of undetected virus circulation. JEV is found throughout most of Asia, extending from maritime Siberia in the north to Australia in the south, and as far as Pakistan to the west and Saipan to the east. Transmission of JEV in temperate zones is epidemic with the majority of cases occurring in summer months, while transmission in tropical zones is endemic and occurs year-round at lower rates. To test the hypothesis that viruses circulating in these two geographical zones are genetically distinct, we applied Bayesian phylogeographic, categorical data analysis and phylogeny-trait association test techniques to the largest JEV dataset compiled to date, representing the envelope (E) gene of 487 isolates collected from 12 countries over 75 years. We demonstrated that GIII and the recently emerged GI-b are temperate genotypes likely maintained year-round in northern latitudes, while GI-a and GII are tropical genotypes likely maintained primarily through mosquito-avian and mosquito-swine transmission cycles. This study represents a new paradigm directly linking viral molecular evolution and climate
Neuroendocrine (Merkel cell) carcinoma of the retroperitoneum with no identifiable primary site
<p>Abstract</p> <p>Background</p> <p>Neuroendocrine carcinoma is an aggressive neoplasm that mainly affects elderly Caucasians and typically arises in sun-exposed areas of the skin. The disease is rather rare and only a relatively few cases present with no apparent primary lesion.</p> <p>Case presentation</p> <p>We report a case of an 81-year-old Caucasian male with neuroendocrine carcinoma, which initially presented as a large retroperitoneal mass. Pathological and immunohistochemical analysis of the transabdominal CT-guided biopsy specimen revealed tissue consistent with neuroendocrine carcinoma. The patient underwent exploratory laparotomy and the mass was successfully excised along with an associated mesenteric lymph node.</p> <p>Discussion</p> <p>There are currently two possible explanations for what occurred in our patient. First, the retroperitoneal mass could be a massively enlarged lymph node where precursor cells became neoplastic. This would be consistent with a presumptive diagnosis of primary nodal disease. Alternatively, an initial skin lesion could have spontaneously regressed and the retroperitoneal mass represents a single site of metastasis. Since Merkel cell precursors have never been identified within lymph nodes, the latter theory seems more befitting. Moreover, metastasis to the retroperitoneal lymph nodes has been reported as relatively common when compared to other sites such as liver, bone, brain and skin.</p> <p>Conclusion</p> <p>Wide local excision of the primary tumor is the surgical treatment of choice for localized disease. We propose that further studies are needed to elucidate the true efficacy of chemotherapy in conventional as well as unconventional patients with neuroendocrine carcinoma.</p
Penta-O-galloyl-β-D-glucose induces G1 arrest and DNA replicative S-phase arrest independently of P21 cyclin-dependent kinase inhibitor 1A, P27 cyclin-dependent kinase inhibitor 1B and P53 in human breast cancer cells and is orally active against triple-negative xenograft growth
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