Bayes estimators for phylogenetic reconstruction

Tree reconstruction methods are often judged by their accuracy, measured by how close they get to the true tree. Yet, most reconstruction methods like maximum likelihood (ML) do not explicitly maximize this accuracy. To address this problem, we propose a Bayesian solution. Given tree samples, we propose finding the tree estimate that is closest on average to the samples. This "median" tree is known as the Bayes estimator (BE). The BE literally maximizes posterior expected accuracy, measured in terms of closeness (distance) to the true tree. We discuss a unified framework of BE trees, focusing especially on tree distances that are expressible as squared euclidean distances. Notable examples include Robinson-Foulds (RF) distance, quartet distance, and squared path difference. Using both simulated and real data, we show that BEs can be estimated in practice by hill-climbing. In our simulation, we find that BEs tend to be closer to the true tree, compared with ML and neighbor joining. In particular, the BE under squared path difference tends to perform well in terms of both path difference and RF distances.

Repeated but not single isoflurane exposure improved the spatial memory of young adult mice

BACKGROUND

Exposure to general anesthesia damages the spatial memory of aged rodents, but its role in the young adult has not been well investigated. This study was conducted to determine the effects of single and repeated isoflurane exposure on spatial memory in young adult mice.

METHODS

The experimental design comprised three series of experiments. In the first series, animals (2 months old) were randomly exposed to 1.4% isoflurane for 2 or 6 h or vehicle gas for 6 h (n=15 in each group). The Morris water maze (MWM) test was performed at 48 h after anesthetic exposure to evaluate spatial memory. In the second part, animals were randomly exposed to 1.4% isoflurane (isoflurane group, n=15) or vehicle gas only (control group, n=15) for 2 h/day on 5 consecutive days. Forty-eight hours later, the MWM was performed. In the third part, animals were randomized into an isoflurane group (n=15) and a control group (n=15) as in the second part of the experiment. Two weeks later, the MWM was performed.

RESULTS

The mean escape latency time and the mean pathway length measured at 48 h after repeated isoflurane exposure decreased significantly compared with the control. However, there was no difference between the two groups when tested at 2 weeks after repeated isoflurane exposure. A single exposure to isoflurane lasting 2 or 6 h had no effect on the performance of mice in the MWM as compared with the control.

CONCLUSION

Repeated but not single isoflurane exposure temporarily improved the spatial memory of young adult mice.

Dijet azimuthal decorrelations in pp collisions at √s=7 TeV

Measurements of dijet azimuthal decorrelations in pp collisions at √s=7 TeV using the CMS detector at the CERN LHC are presented. The analysis is based on an inclusive dijet event sample corresponding to an integrated luminosity of 2.9 pb⁻¹. The results are compared to predictions from perturbative QCD calculations and various Monte Carlo event generators. The dijet azimuthal distributions are found to be sensitive to initial-state gluon radiation.

Facile Deposition Processes for Semiconducting Molecular Solids

Films of end-substituted dihexyl-α-sexithiophene and –quinquethiophene were cast from solutions in aromatic solvents onto SiO2 and polyimide dielectrics at moderately elevated temperatures and reduced pressure. X-ray diffraction showed perpendicular orientation for most samples, while electron and optical microscopy revealed considerable variations in grain sizes, spacings, and uniformity depending on deposition conditions. For favorable morphologies, thin film transistor (TFT) mobilities were as high as those typically obtained from vacuum-deposited films, in the range of 0.01-0.2 cm2/Vs, with on/off ratios >1000 in accumulation mode.

Measurement of the B(+) production cross section in pp collisions at sqrt[s]=7 TeV

Measurements of the total and differential cross sections dσ/dp(T)(B) and dσ/dy(B) for B(+) mesons produced in pp collisions at sqrt[s]=7  TeV are presented. The data correspond to an integrated luminosity of 5.8  pb(-1) collected by the CMS experiment operating at the LHC. The exclusive decay B(+)→J/ψK(+), with J/ψ→μ(+)μ(-), is used to detect B(+) mesons and to measure the production cross section as a function of p(T)(B) and y(B). The total cross section for p(T)(B)>5  GeV and |y(B)|<2.4 is measured to be 28.1±2.4±2.0±3.1  μb, where the first uncertainty is statistical, the second is systematic, and the last is from the luminosity measurement.

Understanding the population structure of North American patients with cystic fibrosis

It is generally presumed that the cystic fibrosis (CF) population is relatively homogeneous, and predominantly of European origin. The complex ethnic make-up observed in the CF patients collected by the North American CF Modifier Gene Consortium has brought this assumption into question, and suggested the potential for population substructure in the three CF study samples collected from North America. It is well appreciated that population substructure can result in spurious genetic associations. To understand the ethnic composition of the North American CF population, and to assess the need for population structure adjustment in genetic association studies with North American CF patients, genome-wide single-nucleotide polymorphisms on 3076 unrelated North American CF patients were used to perform population structure analyses. We compared self-reported ethnicity to genotype-inferred ancestry, and also examined whether geographic distribution and cystic fibrosis transmembrane regulator (CFTR) mutation type could explain the population structure observed. Although largely Caucasian, our analyses identified a considerable number of CF patients with admixed African-Caucasian, Mexican-Caucasian and Indian-Caucasian ancestries. Population substructure was present and comparable across the three studies of the consortium. Neither geographic distribution nor CFTR mutation type explained the population structure. Given the ethnic diversity of the North American CF population, it is essential to carefully detect, estimate and adjust for population substructure to guard against potential spurious findings in CF genetic association studies. Other Mendelian diseases that are presumed to predominantly affect single ethnic groups may also benefit from careful analysis of population structure.

Headspace measurements of irradiated in vitro cultured cells using PTR-MS

A pilot study was performed to evaluate a new concept for a radiation biodosimetry method. Proton transfer reaction-mass spectrometry (PTR-MS) was used to find out whether radiation induces changes in the composition of volatile organic compounds (VOCs) in the headspace of in vitro cultured cells. Two different cell lines, retinal pigment epithelium cells hTERT-RPE1 and lung epithelium cells A-549, were irradiated with gamma radiation at doses of 4 Gy and 8 Gy. For measuring the cell-specific effects, the VOC concentrations in the headspace of flasks containing cells plus medium, as well as of flasks containing pure medium were analyzed for changes before and after irradiation. No significant radiation-induced alterations in VOC concentrations in the headspace could be observed after irradiation.

Measurement of the isolated prompt photon production cross section in pp collisions at √s=7 TeV

The differential cross section for the inclusive production of isolated prompt photons has been measured as a function of the photon transverse energy E(T)(γ) in pp collisions at √s=7  TeV using data recorded by the CMS detector at the LHC. The data sample corresponds to an integrated luminosity of 2.9  pb(-1). Photons are required to have a pseudorapidity |η(γ)|<1.45 and E(T)(γ)>21  GeV, covering the kinematic region 0.006<x(T)<0.086. The measured cross section is found to be in agreement with next-to-leading-order perturbative QCD calculations.

Structure, Diffraction and Energetic Stability of the Spinel form of LiCoO2

A recently reported new phase of LiCoO2, called LT-LiCoO2 (LT stands for Low Temperature) by the discoverers, was synthesized at 400°C and studied using X-ray diffraction and electrochemical de-intercalation of lithium. The first reports of LT-LiCoO2 give convincing evidence that the compound is layered with the same structure type as LiCoO2 prepared at 850°C (HT-LiCoO2). However, the electrochemical properties of LT and HT LiCoO2 are markedly different, which is hard to understand if the crystal structures are almost the same. A better understanding of the diffraction and electrochemical data is attained if the LT structure is assumed to be spinel related analogous to Li2Ti2O4. We show that the layered structure (with suitable lattice constants and layer spacings) and spinel structure give identical powder diffraction patterns. We also show that the formation energies of the layered and spinel structures are also identical using a lattice gas model with pair-wise atom-atom interactions.

Combination of hsa-miR-375 and hsa-miR-142-5p as a predictor for recurrence risk in gastric cancer patients following surgical resection

BACKGROUND

Recurrence is a major factor leading to treatment failure and death in gastric cancer (GC) patients following surgical resection. Importantly, the prediction of recurrence is critical in improving clinical outcomes. We isolated a group of microRNAs (miRNAs) and evaluated their usefulness as prognostic markers for the recurrence of GC.

PATIENTS AND METHODS

A total of 65 GC patients were selected for systematic analysis, 29 patients with recurrence and 36 patients without recurrence. Firstly, miRNAs microarray and bioinformatics methods were used to characterize classifiers from primary tumor samples (n = 8). Following, we validated these predictors both in frozen fresh and paraffin-embedded tissue samples (n = 57) using quantitative PCR.

RESULTS

We have identified 17 differential miRNAs including 10 up-regulated and 7 down-regulated miRNAs in recurrence group. Using k-top scoring pairs (k-TSP) method, we further ascertained hsa-miR-375 and hsa-miR-142-5p as a classifier to recognize recurrence and nonrecurrence cases both in the training and test samples. Moreover, we validated this classifier in 34 frozen fresh tissues and 38 paraffin-embedded tissues with consistent sensitivity and specificity with training set; among them, 15 cases were matched. A high frequency recurrence and poor survival were observed in GC cases with high level of hsa-miR-375 and low level of hsa-miR-142-5p (P < 0.001). In addition, we evaluated that hsa-miR-375 and hsa-miR-142-5p were involved in regulating target genes in several oncogenic signal pathways, such as TP53, MAPK, Wnt and vascular endothelial growth factor.

CONCLUSION

Our results indicate that the combination of hsa-miR-375 and hsa-miR-142-5p as a predictor of disease progression has the potential to predict recurrence risk for GC patients.

3D visualization of subcellular structures of Schizosaccharomyces pombe by hard X-ray tomography

Cellular structures of the fission yeast, Schizosaccharomyces pombe, were examined by using hard X-ray tomography. Since cells are nearly transparent to hard X-rays, Zernike phase contrast and heavy metal staining were introduced to improve image contrast. Through using such methods, images taken at 8 keV displayed sufficient contrast for observing cellular structures. The cell wall, the intracellular organelles and the entire structural organization of the whole cells were visualized in three-dimensional at a resolution better than 100 nm. Comparison between phase contrast and absorption contrast was also made, indicating the obvious advantage of phase contrast for cellular imaging at this energy. Our results demonstrate that hard X-ray tomography with Zernike phase contrast is suitable for cellular imaging. Its unique abilities make it have potential to become a useful tool for revealing structural information from cells, especially thick eukaryotic cells.

Measurement of the parity-violating longitudinal single-spin asymmetry for W± boson production in polarized proton-proton collisions at sqrt[s] = 500 GeV

We report the first measurement of the parity-violating single-spin asymmetries for midrapidity decay positrons and electrons from W+ and W- boson production in longitudinally polarized proton-proton collisions at sqrt[s] = 500 GeV by the STAR experiment at RHIC. The measured asymmetries, A(L)(W+) = -0.27 ± 0.10(stat.) ± 0.02(syst.) ± 0.03(norm.) and A(L)(W-) = 0.14 ± 0.19(stat.) ± 0.02(syst.) ± 0.01(norm.), are consistent with theory predictions, which are large and of opposite sign. These predictions are based on polarized quark and antiquark distribution functions constrained by polarized deep-inelastic scattering measurements.

Differential expression of small ubiquitin-like modifier family of proteins in patients with colorectal adenocarcinoma

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Background: The cytotoxic effects of radiation and chemotherapy are mediated in part by DNA damage. The small ubiquitin-like modifier (SUMO) family of proteins regulates DNA repair pathways by activating factors involved in homologous recombination (HR) or non- homologous end joining (NHEJ). Our objective was to determine the potential role of SUMO proteins in patients with colorectal cancer.

Methods: We first assessed two established colorectal cancer cell lines (HCT116 and HT29) and two normal colonic mucosa cell populations utilizing ultra high-throughput expression analysis (Solexa) to examine differential expression of genes involved in SUMOylation (SAE1, SAE2, PIAS-1, and DNAPKcs). To verify the clinical relevance of SUMOylation in colorectal cancer, we obtained archived specimens from patients with colorectal cancer (n=51) and examined the expression of these proteins in both benign and malignant tissue by immunohistochemistry (IHC).

Results: Ultra high-throughput expression analysis of cancer and normal cells revealed a 10 to 15-fold upregulation of SAE2 (heterodimer of the E1 activation enzyme in SUMOylation), a 10 to 11-fold upregulation of DNAPKcs (catalytic subunit in NHEJ repair pathway), and a 6-fold upregulation of SAE1 in cancer cells. In contrast, PIAS-1 showed similar expression levels between cancer and normal colonic cells. By IHC, SAE1 and SAE2 were highly expressed in 65% and 53% of tumor specimens, respectively; but only in 7% and 0% of normal tissues, respectively. DNAPKcs was also highly expressed in tumor tissues (63%) with corresponding low expression (0%) in normal tissues. Corroborating the cell line results, PIAS-1 was infrequently expressed in both tumor (10%) and normal tissues (0%).

Conclusions: We are the first to demonstrate the differential expression of SUMO proteins in colorectal cancer cell lines and in clinical specimens. SUMO proteins have a role in DNA repair and their expression in colorectal cancer may modify tumor response to chemoradiotherapy.

No significant financial relationships to disclose.

The CKLF1-C19 peptide attenuates allergic lung inflammation by inhibiting CCR3- and CCR4-mediated chemotaxis in a mouse model of asthma

BACKGROUND

  Human chemokine-like factor 1 (CKLF1) is a functional ligand for human CCR4, which is highly expressed on Th2 lymphocytes and plays an important role in the pathogenesis of asthma. The expression and function of CKLF1 are associated with asthma. The CKLF1 C-terminal peptides C19 and C27 also interact with human CCR4. Albeit with weaker chemotactic activity, C19 can inhibit chemotaxis induced by both CKLF1 and CCL17. Here, we explore whether C19 can act as an antagonist in the development of asthma.

METHODS

  A mouse model of asthma and in vitro and in vivo chemotaxis assays were used.

RESULTS

  Using a mouse model of asthma, we demonstrate here that C19 reduces airway eosinophilia, lung inflammation and airway hyperresponsiveness; in contrast, C27 has little effect on these parameters. The inhibitory effects of C19 on CCR4-mediated chemotaxis could be observed in human Th2 lymphocytes and in the splenocytes from ovalbumin-sensitized mice. Furthermore, we show that C19 can inhibit CCL11-induced chemotaxis of mouse eosinophils and human CCR3-transfected or mouse Ccr3-transfected HEK293 cells. In vivo chemotaxis assays revealed that C19 and C27 can reduce CCL11-mediated recruitment of eosinophils into the peritoneal cavity and that this inhibitory effect is stronger for C19 than for C27.

CONCLUSIONS

  Thus, C19 can attenuate airway eosinophilia and lung inflammation by inhibiting CCR3- and CCR4-mediated chemotaxis in a mouse model of asthma. Given its ability to inhibit human CCR3- and CCR4-meditated chemotaxis, C19 has great therapeutic potential for use in the treatment and control of allergic asthma.

Use of the XRCC1 single nucleotide polymorphism to predict pathologic complete response to neoadjuvant chemoradiation in stage II/III rectal cancer

409

Background: The X-ray repair cross-complementing protein 1 (XRCC1) gene plays an important role in DNA damage repair; and the R194W and R399Q single nucleotide polymorphisms (SNPs) are associated with attenuated DNA repair activity. Our objective was to determine whether XRCC1 SNPs were associated with response to neoadjuvant chemoradiation therapy (CRT) in rectal cancer patients.

Methods: We conducted a prospective multicenter phase II trial to investigate the effect of additional chemotherapy with a longer CRT-to-surgery interval on treatment response in patients with rectal cancer. Paired normal and rectal cancer tissues were prospectively collected from enrolled patients (n=110). DNA was extracted from normal rectal mucosa and analyzed for XRCC1 R194W and R399Q by polymerase chain reaction and sequencing. Each SNP was compared to response to CRT. Response to CRT was determined by a central pathologist.

Results: Of the 110 patients, 25% (n=27) achieved a pathologic complete response (pCR). We examined the XRCC1 R194W SNP and observed that the allelic frequency of patients with the R/R genotype was 84% (n=92), the R/W genotype was 14% (n=16), the W/W genotype was 1% (n=2). By Fisher's Exact test, patients harboring either the R/W or W/W genotype, had a significantly higher rate of pCR compared to patients with the R/R genotype (44% vs. 21%, respectively; p=0.04). We then examined the R399Q SNP and observed that the allelic frequency of patients with the R/R genotype was 34% (n=37), the R/Q genotype was 49% (n=54), and the Q/Q genotype was 17% (n=19). In contrast, the detection of XRCC1 R399Q SNPs was not associated with pCR.

Conclusions: We demonstrate that XRCC1 R194W SNP is associated with increased rate of pCR in our prospective multi-center trial. Although the detection of XRCC1 R399Q SNP is not associated with pCR, the detection of XRCC1 SNPs that predict treatment response may help identify patients who are unlikely to respond to CRT and therefore may potentially avoid treatment-associated morbidities.

No significant financial relationships to disclose.

Adjuvant chemotherapy for gastric cancer: Less drug, same efficacy

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Background: Adjuvant chemotherapy is proved to improve survival in gastric cancer by meta-analyses. However, no evidence showed the best regimen. We conducted a retrospective analysis to compare triplets with doublets in the adjuvant setting.

Methods: We collected data from January 2004 to December 2008 from patients performed radical surgery and adjuvant chemotherapy. Doublets were defined as 5-FU 750 mg/m2 (d1- 5) or capecitabine 1,000 mg/m2 (d1-14) plus cisplatin 60 mg/m2 (d1) or oxaliplatin 130 mg/m2 (d1), while triplets had epirubicin 50 mg/m2 (d1) added. Chemotherapy was initiated within 6 weeks after surgery, repeated every three weeks and planned for 6 cycles. Patients were followed up in the outpatient clinic until death or April 30, 2010. Cox proportional-hazard model and chi-square test were used to test statistical difference.

Results: A total of 316 patients (210 in doublets, 106 in triplets) had a median follow-up time of 47 months. 77 patients died at the end of follow-up (3-year survival of 67.4%).Two groups were well balanced except age (median age of 57 in doublets, 51 in triplets, p < 0.001). All the patients tolerated well, with few grade 3/4 side effects (21.9% in doublets, 30.2% in triplets, p = 0.107). Two groups had similar disease-free survival (median DFS, 16 months vs. 23 months, p = 0.656) and overall survival (3-year survival rate, 59.6% vs. 64.8%, p = 0.293). Subgroup analysis showed the same benefit on survival between the two groups.

Conclusions: Our study suggested doublets and triplets had the same efficacy as the adjuvant chemotherapy. Furthermore, doublets seem more cost-effective.

[Table: see text]

No significant financial relationships to disclose.

Use of genetic variations to predict toxicity associated with neoadjuvant chemoradiation for AJCC stage II/III rectal cancer

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Background: Genetic polymorphisms have been associated with toxicity from chemotherapeutic agents for colon cancer, but none has been identified for rectal cancer. We examined the association between polymorphisms in genes for DNA repair, cell cycle progression, angiogenesis, and drug metabolism with toxicity from neoadjuvant chemoradiation treatment (CRT) for rectal cancer.

Methods: Patients with AJCC stage II/III rectal adenocarcinoma were enrolled in a phase II multicenter trial examining timing of rectal cancer response to neoadjuvant CRT. There were two treatment arms: (I) radiation (XRT) and 5-FU followed by surgery and (II) XRT/5-FU and FOLFOX followed by surgery. Treatment toxicity, classified by the NCI Common Terminology Criteria guidelines as grade 3 and above, was recorded. DNA was extracted from normal rectal mucosa and analyzed for 22 polymorphisms in 17 genes.

Results: We evaluated 110 patients (group I, n = 52; group II, n = 58). A total of 19 patients experienced grade 3+ adverse events (AE) [group I, n = 10 (19%); group II, n = 9 (16%)]. Gastrointestinal symptoms were the most common AE [group I, n = 5 (10%); group II, n = 4 (7%)]. The detection of lys allele (lys/lys or lys/gln genotypes) at codon 751 of the Xeroderma pigmentosum group D (XPD) gene was associated with increased toxicity in group II (p = 0.03), whereas homozygosity for the arg allele (i.e., arg/arg genotype) at codon 399 of the X-ray cross-complementing protein 1 (XRCC1) gene was associated with a significant increase in toxicity in both treatment groups (p = 0.009).

Conclusions: Genetic polymorphisms in DNA damage repair genes XPD and XRCC1 are associated with toxicity in rectal cancer patients receiving CRT. The identification of gene polymorphisms that predict adverse events may help to optimize patient therapy while minimizing morbidities.

No significant financial relationships to disclose.