Network Analysis of Breast Cancer Progression and Reversal Using a Tree-Evolving Network Algorithm

The HMT3522 progression series of human breast cells have been used to discover how tissue architecture, microenvironment and signaling molecules affect breast cell growth and behaviors. However, much remains to be elucidated about malignant and phenotypic reversion behaviors of the HMT3522-T4-2 cells of this series. We employed a "pan-cell-state" strategy, and analyzed jointly microarray profiles obtained from different state-specific cell populations from this progression and reversion model of the breast cells using a tree-lineage multi-network inference algorithm, Treegl. We found that different breast cell states contain distinct gene networks. The network specific to non-malignant HMT3522-S1 cells is dominated by genes involved in normal processes, whereas the T4-2-specific network is enriched with cancer-related genes. The networks specific to various conditions of the reverted T4-2 cells are enriched with pathways suggestive of compensatory effects, consistent with clinical data showing patient resistance to anticancer drugs. We validated the findings using an external dataset, and showed that aberrant expression values of certain hubs in the identified networks are associated with poor clinical outcomes. Thus, analysis of various reversion conditions (including non-reverted) of HMT3522 cells using Treegl can be a good model system to study drug effects on breast cancer. © 2014 Parikh et al

Chinese herbal medicine for symptom management in cancer palliative care systematic review and meta-analysis

© 2016 Wolters Kluwer Health, Inc. All rights reserved. Use of Chinese herbal medicines (CHM) in symptom management for cancer palliative care is very common in Chinese populations but clinical evidence on their effectiveness is yet to be synthesized. To conduct a systematic review with meta-analysis to summarize results from CHM randomized controlled trials (RCTs) focusing on symptoms that are undertreated in conventional cancer palliative care. Five international and 3 Chinese databases were searched. RCTs evaluating CHM, either in combination with conventional treatments or used alone, in managing cancer-related symptoms were considered eligible. Effectiveness was quantified by using weighted mean difference (WMD) using random effect model meta-analysis. Fourteen RCTs were included. Compared with conventional intervention alone, meta-analysis showed that combined CHM and conventional treatment significantly reduced pain (3 studies, pooled WMD:-0.90, 95% CI:-1.69 to-0.11). Six trials comparing CHM with conventional medications demonstrated similar effect in reducing constipation. One RCT showed significant positive effect of CHM plus chemotherapy for managing fatigue, but not in the remaining 3 RCTs. The additional use of CHM to chemotherapy does not improve anorexia when compared to chemotherapy alone, but the result was concluded from 2 small trials only. Adverse events were infrequent and mild. CHM may be considered as an add-on to conventional care in the management of pain in cancer patients. CHM could also be considered as an alternative to conventional care for reducing constipation. Evidence on the use of CHM for treating anorexia and fatigue in cancer patients is uncertain, warranting further research

Acupuncture and related therapies for symptom management in palliative cancer care: Systematic review and meta-analysis

Copyright © 2016 Wolters Kluwer Health, Inc. All rights reserved. Available systematic reviews showed uncertainty on the effectiveness of using acupuncture and related therapies for palliative cancer care. The aim of this systematic review and meta-analysis was to summarize current best evidence on acupuncture and related therapies for palliative cancer care. Five international and 3 Chinese databases were searched. Randomized controlled trials (RCTs) comparing acupuncture and related therapies with conventional or sham treatments were considered. Primary outcomes included fatigue, paresthesia and dysesthesias, chronic pain, anorexia, insomnia, limb edema, constipation, and health-related quality of life, of which effective conventional interventions are limited. Thirteen RCTs were included. Compared with conventional interventions, meta-analysis demonstrated that acupuncture and related therapies significantly reduced pain (2 studies, n=175, pooled weighted mean difference: -0.76, 95% confidence interval: -0.14 to -0.39) among patients with liver or gastric cancer. Combined use of acupuncture and related therapies and Chinese herbal medicine improved quality of life in patients with gastrointestinal cancer (2 studies, n=111, pooled standard mean difference: 0.75, 95% confidence interval: 0.36-1.13). Acupressure showed significant efficacy in reducing fatigue in lung cancer patients when compared with sham acupressure. Adverse events for acupuncture and related therapies were infrequent and mild. Acupuncture and related therapies are effective in reducing pain, fatigue, and in improving quality of life when compared with conventional intervention alone among cancer patients. Limitations on current evidence body imply that they should be used as a complement, rather than an alternative, to conventional care. Effectiveness of acupuncture and related therapies for managing anorexia, reducing constipation, paresthesia and dysesthesia, insomnia, and limb edema in cancer patients is uncertain, warranting future RCTs in these areas

An Intact Kidney Slice Model to Investigate Vasa Recta Properties and Function in situ

Background: Medullary blood flow is via vasa recta capillaries, which possess contractile pericytes. In vitro studies using isolated descending vasa recta show that pericytes can constrict/dilate descending vasa recta when vasoactive substances are present. We describe a live kidney slice model in which pericyte-mediated vasa recta constriction/dilation can be visualized in situ. Methods: Confocal microscopy was used to image calcein, propidium iodide and Hoechst labelling in ‘live’ kidney slices, to determine tubular and vascular cell viability and morphology. DIC video-imaging of live kidney slices was employed to investigate pericyte-mediated real-time changes in vasa recta diameter. Results: Pericytes were identified on vasa recta and their morphology and density were characterized in the medulla. Pericyte-mediated changes in vasa recta diameter (10–30%) were evoked in response to bath application of vasoactive agents (norepinephrine, endothelin-1, angiotensin-II and prostaglandin E2) or by manipulating endogenous vasoactive signalling pathways (using tyramine, L-NAME, a cyclo-oxygenase (COX-1) inhibitor indomethacin, and ATP release). Conclusions: The live kidney slice model is a valid complementary technique for investigating vasa recta function in situ and the role of pericytes as regulators of vasa recta diameter. This technique may also be useful in exploring the role of tubulovascular crosstalk in regulation of medullary blood flow

Effect of water vapor on the spallation of thermal barrier coating systems during laboratory cyclic oxidation testing.

The effect of water and water vapor on the lifetime of Ni-based superalloy samples coated with a typical thermal barrier coating system—b-(Ni,Pt)Al bond coat and yttria stabilized zirconia (YSZ) top coat deposited by electron beam physical vapor deposition (EB-PVD) was studied. Samples were thermally cycled to 1,150 C and subjected to a water-drop test in order to elucidate the effect of water vapor on thermal barrier coating (TBC) spallation. It was shown that the addition of water promotes spallation of TBC samples after a given number of cycles at 1,150 C. This threshold was found to be equal to 170 cycles for the present system. Systems based on b-NiAl bond coat or on Pt-rich c/c0 bond coat were also sensitive to the water-drop test. Moreover, it was shown that water vapor in ambient air after minutes or hours at room temperature, promotes also TBC spallation once the critical number of cycles has been reached. This desktop spalling (DTS) can be prevented by locking up the cycled samples in a dry atmosphere box. These results for TBC systems confirm and document Smialek’s theory about DTS and moisture induced delayed spalling (MIDS) being the same phenomenon. Finally, the mechanisms implying hydrogen embrittlement or surface tension modifications are discussed

Temporal Model Adaptation for Person Re-Identification

Person re-identification is an open and challenging problem in computer vision. Majority of the efforts have been spent either to design the best feature representation or to learn the optimal matching metric. Most approaches have neglected the problem of adapting the selected features or the learned model over time. To address such a problem, we propose a temporal model adaptation scheme with human in the loop. We first introduce a similarity-dissimilarity learning method which can be trained in an incremental fashion by means of a stochastic alternating directions methods of multipliers optimization procedure. Then, to achieve temporal adaptation with limited human effort, we exploit a graph-based approach to present the user only the most informative probe-gallery matches that should be used to update the model. Results on three datasets have shown that our approach performs on par or even better than state-of-the-art approaches while reducing the manual pairwise labeling effort by about 80%

DNA end resection by Dna2–Sgs1–RPA and its stimulation by Top3–Rmi1 and Mre11–Rad50–Xrs2

The repair of DNA double-strand breaks (DSBs) by homologous recombination requires processing of broken ends. For repair to start, the DSB must first be resected to generate a 3′-single-stranded DNA (ssDNA) overhang, which becomes a substrate for the DNA strand exchange protein, Rad51 (ref. 1). Genetic studies have implicated a multitude of proteins in the process, including helicases, nucleases and topoisomerases. Here we biochemically reconstitute elements of the resection process and reveal that it requires the nuclease Dna2, the RecQ-family helicase Sgs1 and the ssDNA-binding protein replication protein-A (RPA). We establish that Dna2, Sgs1 and RPA constitute a minimal protein complex capable of DNA resection in vitro. Sgs1 helicase unwinds the DNA to produce an intermediate that is digested by Dna2, and RPA stimulates DNA unwinding by Sgs1 in a species-specific manner. Interestingly, RPA is also required both to direct Dna2 nucleolytic activity to the 5′-terminated strand of the DNA break and to inhibit 3′ to 5′ degradation by Dna2, actions that generate and protect the 3′-ssDNA overhang, respectively. In addition to this core machinery, we establish that both the topoisomerase 3 (Top3) and Rmi1 complex and the Mre11–Rad50–Xrs2 complex (MRX) have important roles as stimulatory components. Stimulation of end resection by the Top3–Rmi1 heterodimer and the MRX proteins is by complex formation with Sgs1 (refs 5, 6), which unexpectedly stimulates DNA unwinding. We suggest that Top3–Rmi1 and MRX are important for recruitment of the Sgs1–Dna2 complex to DSBs. Our experiments provide a mechanistic framework for understanding the initial steps of recombinational DNA repair in eukaryotes

Spectral Line-by-Line Pulse Shaping of an On-Chip Microresonator Frequency Comb

We report, for the first time to the best of our knowledge, spectral phase characterization and line-by-line pulse shaping of an optical frequency comb generated by nonlinear wave mixing in a microring resonator. Through programmable pulse shaping the comb is compressed into a train of near-transform-limited pulses of \approx 300 fs duration (intensity full width half maximum) at 595 GHz repetition rate. An additional, simple example of optical arbitrary waveform generation is presented. The ability to characterize and then stably compress the frequency comb provides new data on the stability of the spectral phase and suggests that random relative frequency shifts due to uncorrelated variations of frequency dependent phase are at or below the 100 microHertz level.Comment: 18 pages, 4 figure