623 research outputs found
Epstein-Barr virus infection and chronic lymphocytic leukemia: a possible progression factor?
Epstein-Barr virus is pathogenically associated with a well defined group of lymphoid and epithelial tumors in which the virus directly drives transformation of infected cells. Recent evidence however indicates that this virus may infect a subpopulation of tumor cells in patients with chronic lymphocytic leukemia (CLL) and EBV infection has been also associated with Richter transformation in a fraction of cases. We herein review available data suggesting a possible role of EBV as a direct or micro-environmental progression factor in a subset of CLL
Linear, Deterministic, and Order-Invariant Initialization Methods for the K-Means Clustering Algorithm
Over the past five decades, k-means has become the clustering algorithm of
choice in many application domains primarily due to its simplicity, time/space
efficiency, and invariance to the ordering of the data points. Unfortunately,
the algorithm's sensitivity to the initial selection of the cluster centers
remains to be its most serious drawback. Numerous initialization methods have
been proposed to address this drawback. Many of these methods, however, have
time complexity superlinear in the number of data points, which makes them
impractical for large data sets. On the other hand, linear methods are often
random and/or sensitive to the ordering of the data points. These methods are
generally unreliable in that the quality of their results is unpredictable.
Therefore, it is common practice to perform multiple runs of such methods and
take the output of the run that produces the best results. Such a practice,
however, greatly increases the computational requirements of the otherwise
highly efficient k-means algorithm. In this chapter, we investigate the
empirical performance of six linear, deterministic (non-random), and
order-invariant k-means initialization methods on a large and diverse
collection of data sets from the UCI Machine Learning Repository. The results
demonstrate that two relatively unknown hierarchical initialization methods due
to Su and Dy outperform the remaining four methods with respect to two
objective effectiveness criteria. In addition, a recent method due to Erisoglu
et al. performs surprisingly poorly.Comment: 21 pages, 2 figures, 5 tables, Partitional Clustering Algorithms
(Springer, 2014). arXiv admin note: substantial text overlap with
arXiv:1304.7465, arXiv:1209.196
Production of phi mesons at mid-rapidity in sqrt(s_NN) = 200 GeV Au+Au collisions at RHIC
We present the first results of meson production in the K^+K^- decay channel
from Au+Au collisions at sqrt(s_NN) = 200 GeV as measured at mid-rapidity by
the PHENIX detector at RHIC. Precision resonance centroid and width values are
extracted as a function of collision centrality. No significant variation from
the PDG accepted values is observed. The transverse mass spectra are fitted
with a linear exponential function for which the derived inverse slope
parameter is seen to be constant as a function of centrality. These data are
also fitted by a hydrodynamic model with the result that the freeze-out
temperature and the expansion velocity values are consistent with the values
previously derived from fitting single hadron inclusive data. As a function of
transverse momentum the collisions scaled peripheral.to.central yield ratio RCP
for the is comparable to that of pions rather than that of protons. This result
lends support to theoretical models which distinguish between baryons and
mesons instead of particle mass for explaining the anomalous proton yield.Comment: 326 authors, 24 pages text, 23 figures, 6 tables, RevTeX 4. To be
submitted to Physical Review C as a regular article. Plain text data tables
for the points plotted in figures for this and previous PHENIX publications
are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm
Effect of apoptosis in neural stem cells treated with sevoflurane
BACKGROUND: At present, sevoflurane inhalation anesthesia used on infants is well-known. But long-time exposure to inhalation anesthetic could cause neurologic disorder, especially nerve degeneration in infant and developing brain. The central nervous system degeneration of infants could affect the memory and cognitive function. γ-Aminobutyric acid (GABA) is a known inhibitory neurotransmitter in central nervous system. Inhalation anesthetic sevoflurane may activate GABA(A) receptor to inhibit central nervous system, leading to apoptosis of neural degeneration, cognitive dysfunction in the critical period of brain development. METHODS: Neural stem cells were derived from Wistar embryos, cultured in vitro. Third generation of neural stem cells were randomly divided into four groups according to cultured suspension: Sevoflurane group (Group S), GABA(A) receptor antagonists, Bicuculline group (Group B), Sevoflurane + GABA(A) receptor antagonists, Bicuculline group (Group S + B), dimethyl sulphoxide (DMSO) group (Group D). Group B and Group D did not receive sevoflurane preconditioning. Group S and Group S + B were pretreated with 1 minimum alveolar concentration (MAC) sevoflurane for 0 h, 3 h, 6 h, and 12 h. Group S + B and Group B were pretreated with bicuculline (10 uM). Group D was treated with DMSO (10 uL/mL). After treatments above, all groups were cultured for 48 h. Then we measured the cells viability by Cell Counting Kit (CCK-8) assay, cytotoxicity by Lactate Dehydrogenase (LDH) assay, apoptosis ratio with Annexin V/propidium iodide (PI) staining by flow cytometry, and the expression of GABA(A)R, anti-apoptotic protein Bcl-2, pro-apoptotic protein Bax and Caspase-3 by western blotting. RESULTS: After exposing to sevoflurane for 0 h, 3 h, 6 h, and 12 h with 1MAC, we found that cell viability obviously decreased and cytotoxicity increased in time-dependent way. And Annexin V/PI staining indicated increased apoptosis ratio by flow cytometry. The protein level of GABA(A) receptor, pro-apoptotic protein Bax and apoptosis protein Caspase-3 increased; while anti-apoptotic protein Bcl-2 decreased. And bicuculline could reverse all detrimental results caused by sevoflurane. CONCLUSION: Sevoflurane can inhibit the central nervous system by activating GABA(A), resulting in apoptosis of neural stem cells, thus leading to the NSCs degeneration
The association of APE1 −656T > G and 1349 T > G polymorphisms and cancer risk: a meta-analysis based on 37 case-control studies
<p>Abstract</p> <p>Background</p> <p>APE1 (apurinic/apyrimidinic endonuclease 1) is an important DNA repair protein in the base excision repair pathway. Polymorphisms in <it>APE1 </it>have been implicated in susceptibility to cancer; however, results from the published studies remained inconclusive. The objective of this study was to conduct a meta-analysis investigating the association between polymorphisms in <it>APE1 </it>and the risk for cancer.</p> <p>Methods</p> <p>The PubMed and Embase databases were searched for case-control studies published up to June, 2011 that investigated <it>APE1 </it>polymorphisms and cancer risk. Odds ratios (ORs) and 95% confidence intervals (CIs) were used to assess the strength of the associations.</p> <p>Results</p> <p>Two polymorphisms (−656 T > G, rs1760944 and 1349 T > G, rs1130409) in 37 case-control studies including 15, 544 cancer cases and 21, 109 controls were analyzed. Overall, variant genotypes (GG and TG/GG) of −656 T > G polymorphism were associated with significantly decreased cancer risk in homozygote comparison (OR = 0.81, 95%CI: 0.67-0.97), dominant model comparison (OR = 0.89, 95%CI: 0.81-0.97) and recessive model comparison (OR = 0.90, 95%CI: 0.82-0.98), whereas the 1349 T > G polymorphism had no effects on overall cancer risk. In the stratified analyses for −656 T > G polymorphism, there was a significantly decreased risk of lung cancer and among Asian populations.</p> <p>Conclusions</p> <p>Although some modest bias could not be eliminated, the meta-analysis suggests that <it>APE1 −</it>656 T > G polymorphism has a possible protective effect on cancer risk particularly among Asian populations whereas 1349 T > G polymorphism does not contribute to the development of cancer.</p
Age-standardized incidence and mortality rates of oral and pharyngeal cancer in Puerto Rico and among Non-Hispanics Whites, Non-Hispanic Blacks, and Hispanics in the USA
<p>Abstract</p> <p>Background</p> <p>In the American region, Puerto Rico (PR) has the highest incidence of oral and pharyngeal cancer (OPC), but racial/ethnic differences have never been assessed and compared with other groups in the United States of America (USA). We compared the age-adjusted incidence and mortality rates of OPC between PR and among USA Hispanics (USH), Non-Hispanic Whites (NHW), and Non-Hispanic Blacks (NHB) to assess the burden of this cancer in PR.</p> <p>Methods</p> <p>Analysis of the age-standardized rates (per 100,000) was performed using the direct method with the world standard population (ASR(World)) from 1998–2002. Annual percent change (APC) and Relative Risks (RR) were calculated using the Poisson regression model.</p> <p>Results</p> <p>The incidence ASR(World) for men in PR was constant (APC ≈ 0.0%), in contrast, a decrease was observed among NHW, NHB, and USH men, although only USH showed statistical significance (APC = -4.9%, p < 0.05). In women, the highest increase in incidence (APC = 5.3%) and the lowest decrease in mortality (APC = -1.4%) was observed in PR. The ratio of the ASR(World) showed that in all racial/ethnic groups, men had approximately 2–4 fold increased incidence and mortality risk of OPC than women (p < 0.05). Men in PR had a higher mortality risk (p < 0.05) of OPC as compared to USH, NHW, and NHB; but among women, PR showed a significant excess of mortality only as compared to USH (est. SRR = 1.82, 95% CI = 1.41, 2.33).</p> <p>Conclusion</p> <p>The overall higher incidence of OPC in men in PR as compared to USH, NHB, and NHW could be explained by the effect of gene-environment interactions. Meanwhile, the higher mortality from OPC in PR suggests limitations in the health-care access within this population. Further research is warranted to elucidate these findings.</p
Global Regulation of Nucleotide Biosynthetic Genes by c-Myc
The c-Myc transcription factor is a master regulator and integrates cell proliferation, cell growth and metabolism through activating thousands of target genes. Our identification of direct c-Myc target genes by chromatin immunoprecipitation (ChIP) coupled with pair-end ditag sequencing analysis (ChIP-PET) revealed that nucleotide metabolic genes are enriched among c-Myc targets, but the role of Myc in regulating nucleotide metabolic genes has not been comprehensively delineated.Here, we report that the majority of genes in human purine and pyrimidine biosynthesis pathway were induced and directly bound by c-Myc in the P493-6 human Burkitt's lymphoma model cell line. The majority of these genes were also responsive to the ligand-activated Myc-estrogen receptor fusion protein, Myc-ER, in a Myc null rat fibroblast cell line, HO.15 MYC-ER. Furthermore, these targets are also responsive to Myc activation in transgenic mouse livers in vivo. To determine the functional significance of c-Myc regulation of nucleotide metabolism, we sought to determine the effect of loss of function of direct Myc targets inosine monophosphate dehydrogenases (IMPDH1 and IMPDH2) on c-Myc-induced cell growth and proliferation. In this regard, we used a specific IMPDH inhibitor mycophenolic acid (MPA) and found that MPA dramatically inhibits c-Myc-induced P493-6 cell proliferation through S-phase arrest and apoptosis.Taken together, these results demonstrate the direct induction of nucleotide metabolic genes by c-Myc in multiple systems. Our finding of an S-phase arrest in cells with diminished IMPDH activity suggests that nucleotide pool balance is essential for c-Myc's orchestration of DNA replication, such that uncoupling of these two processes create DNA replication stress and apoptosis
A high-efficiency CRISPR/Cas9 system for targeted mutagenesis in Cotton (Gossypium hirsutum L.)
The complex allotetraploid genome is one of major challenges in cotton for repressing gene expression.
Developing site-specific DNA mutation is the long-term dream for cotton breeding scientists. The
clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system is emerging as a robust biotechnology for targeted-DNA mutation. In this study, two sgRNAs, GhMYB25-like-sgRNA1 and GhMYB25-like-sgRNA2, were designed in the identical genomic regions of GhMYB25-like A and GhMYB25-like D, which were encoded by cotton A subgenome and the D subgenome, respectively, was assembled to direct Cas9-mediated allotetraploid cotton genome
editing. High proportion (14.2–21.4%) CRISPR/Cas9-induced specific truncation events, either from GhMYB25-like A DNA site or from GhMYB25-like D DNA site, were detected in 50% examined transgenic cotton through PCR amplification assay and sequencing analyses. Sequencing results also demonstrated that 100% and 98.8% mutation frequency were occurred on GhMYB25-like-sgRNA1
and GhMYB25-like-sgRNA2 target site respectively. The off-target effect was evaluated by sequencing
two putative off-target sites, which have 3 and 1 mismatched nucleotides with GhMYB25-like-sgRNA1
and GhMYB25-like-sgRNA2, respectively; all the examined samples were not detected any off-targetcaused mutation events. Thus, these results demonstrated that CRISPR/Cas9 is qualified for generating DNA level mutations on allotetraploid cotton genome with high-efficiency and high-specificity.ECU Open Access Publishing Support Fun
Mu-Opioid Receptors Transiently Activate the Akt-nNOS Pathway to Produce Sustained Potentiation of PKC-Mediated NMDAR-CaMKII Signaling
BACKGROUND: In periaqueductal grey (PAG) matter, cross-talk between the Mu-opioid receptor (MOR) and the glutamate N-methyl-D-Aspartate receptor (NMDAR)-CaMKII pathway supports the development of analgesic tolerance to morphine. In neurons, histidine triad nucleotide binding protein 1 (HINT1) connects the regulators of G protein signaling RGSZ1 and RGSZ2 to the C terminus of the MOR. In response to morphine, this HINT1-RGSZ complex binds PKCgamma, and afterwards, the interplay between PKCgamma, Src and Gz/Gi proteins leads to sustained potentiation of NMDAR-mediated glutamate responses. METHODOLOGY/PRINCIPAL FINDINGS: Following an intracerebroventricular (icv) injection of 10 nmol morphine, Akt was recruited to the synaptosomal membrane and activated by Thr308 and Ser473 phosphorylation. The Akt activation was immediately transferred to neural Nitric Oxide Synthase (nNOS) Ser1417. Afterwards, nitric oxide (NO)-released zinc ions recruited PKCgamma to the MOR to promote the Src-mediated phosphorylation of the Tyr1325 NMDAR2A subunit. This action increased NMDAR calcium flux and CaMKII was activated in a calcium-calmodulin dependent manner. CaMKII then acted on nNOS Ser847 to produce a sustained reduction in NO levels. The activation of the Akt-nNOS pathway was also reduced by the binding of these proteins to the MOR-HINT1 complex where they remained inactive. Tolerance to acute morphine developed as a result of phosphorylation of MOR cytosolic residues, uncoupling from the regulated G proteins which are transferred to RGSZ2 proteins. The diminished effect of morphine was prevented by LNNA, an inhibitor of nNOS function, and naltrindole, a delta-opioid receptor antagonist that also inhibits Akt. CONCLUSIONS/SIGNIFICANCE: Analysis of the regulatory phosphorylation of the proteins included in the study indicated that morphine produces a transient activation of the Akt/PKB-nNOS pathway. This activation occurs upstream of PKCgamma and Src mediated potentiation of NMDAR activity, ultimately leading to morphine tolerance. In summary, the Akt-nNOS pathway acts as a primer for morphine-triggered events which leads to the sustained potentiation of the NMDAR-CaMKII pathway and MOR inhibition
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