EPiK-a Workflow for Electron Tomography in Kepler.

Scientific workflows integrate data and computing interfaces as configurable, semi-automatic graphs to solve a scientific problem. Kepler is such a software system for designing, executing, reusing, evolving, archiving and sharing scientific workflows. Electron tomography (ET) enables high-resolution views of complex cellular structures, such as cytoskeletons, organelles, viruses and chromosomes. Imaging investigations produce large datasets. For instance, in Electron Tomography, the size of a 16 fold image tilt series is about 65 Gigabytes with each projection image including 4096 by 4096 pixels. When we use serial sections or montage technique for large field ET, the dataset will be even larger. For higher resolution images with multiple tilt series, the data size may be in terabyte range. Demands of mass data processing and complex algorithms require the integration of diverse codes into flexible software structures. This paper describes a workflow for Electron Tomography Programs in Kepler (EPiK). This EPiK workflow embeds the tracking process of IMOD, and realizes the main algorithms including filtered backprojection (FBP) from TxBR and iterative reconstruction methods. We have tested the three dimensional (3D) reconstruction process using EPiK on ET data. EPiK can be a potential toolkit for biology researchers with the advantage of logical viewing, easy handling, convenient sharing and future extensibility

LiY(SO4_4)2_2: A Superionic Material Synthesized by Superionic State Hidden in no-Superionic Literature

A potential superionic material LiY(SO$_4$)$_2$ has been excavated from the published literatures because its synthesis method and experiment data implied it exists the superionic state. We use \textit{ab initio} calculation to analyzing the differences between solid state and superionic state. We found the diffusion of Li$^+$ from the lattice site to the interstitial site will change the nearest neighbor numbers of O atom from 4 to 8. In order to reduce energy, the reorientation of SO$_4^{2-}$ must exist accompany with the diffusion of Li$^+$ so the nearest neighbor number of O will keep about 5 in the superionic state. Our work not only presents an example for discovering materials from literatures based on prior knowledge but also reveals the micromechanism of cation-anion coupled dynamics for superionic state.Comment: 18pages 5figure

FOXQ1 promotes proliferation and metastasis of epithelial ovarian cancer via activation of SIRT1/NRF2 signaling pathway

Purpose: To investigate the role of FOXQ1 in the progression of epithelial ovarian cancer and the underlying mechanism. Methods: Forkhead Box Q1 overexpression was evaluated by quantitative reverse-transcription (qRTPCR) in clinical epithelial ovarian cancer samples and cell lines. Proliferation, migration, and invasion of cancer cells were determined using CCK8, wound healing and transwell assay. Results: FOXQ1 depletion inhibited the proliferation, migration, and invasion of `epithelial ovarian cancer cells. Moreover, FOXQ1 overexpression increased the amount of cells in S phase of the cell cycle, and FOXQ1 knockdown arrested cells inG1 phase. Results from ChIP and luciferase reporter assays showed that FOXQ1 was able to bind SIRT1 promoters. In addition, it was involved in sustaining the stability of nuclear factor erythroid derived 2-like 2 (NRF2) by decreasing its acetylation (p < 0.01), which was mediated by SIRT1. The data also demonstrated that NRF2 promotes proliferation, migration, and invasion of cancer cells upon FOXQ1 overexpression. Conclusion: Forkhead Box Q1 contributes to the progression of epithelial ovarian cancer partly via SIRT1/NRF2 signaling pathway, this highlighting a novel strategy for treating epithelial ovarian cancer

A Prospective Study of the Incidence of Retinopathy of Prematurity in China: Evaluation of Different Screening Criteria

To investigate the incidence of Retinopathy of Prematurity (ROP) in Beijing, North China, and to evaluate the effectiveness of different ROP screening criteria, we conducted a prospective cohort study in a single-neonatal intensive care unit (NICU). A total of 2997 premature infants with birth weight (BW) ≤ 2000 g and/or gestational age (GA) ≤ 34 weeks had completed ROP screening. ROP was diagnosed in 356 (11.9%) infants. The mean GA was 30.46 ± 1.98 weeks and the mean BW was 1477.35 ± 371.29 g. Of the 59 (2.0%) infants receiving treatment, the mean GA was 29.37 ± 2.10 weeks, and the mean BW was 1240.80 ± 330.71 g. The incidence of ROP declined from 14.7% in 2009 and 11.1% in 2010 to 9.5% in 2011. The United Kingdom (UK) criteria could reduce the screening number by 40.8%, and 3 infants with type I ROP needing treatment were missed, but none in 2011. The United States (US) criteria could reduce the screening number by 66.5%, and 10 infants with type I ROP needing treatment were missed, including one in 2011. So the UK criteria may be appropriate for screening of ROP in our NICU in 2011. Future multisite epidemiologic studies are required to establish suitable ROP screening criteria in China

Effects of Inter-Stimulus Interval on Speech-Evoked Frequency-Following Response in Elderly Adults

Background: The speech-evoked frequency following response (FFR) has shown to be useful in assessing complex auditory processing abilities and in different age groups. While many aspects of FFR have been studied extensively, the effect of timing, as measured by inter-stimulus-interval (ISI), especially in the older adult population, has yet to be thoroughly investigated. Objective: The purpose of this study was to examine the effects of different ISIs on speech evoked FFR in older and younger adults who speak a tonal language, and to investigate whether the older adults’ FFR were more susceptible to the change in ISI. Materials and Methods: Twenty-two normal hearing participants were recruited in our study, including 11 young adult participants and 11 elderly participants. An Intelligent Hearing Systems Smart EP evoke potential system was used to record the FFR in four ISI conditions (40, 80, 120 and 160 ms). A recorded natural speech token with a falling tone /yi/ was used as the stimulus. Two indices, stimulus-to-response correlation coefficient and pitch strength, were used to quantify the FFR responses. Two-way analysis of variance (ANOVA) was used to analyze the differences in different age groups and different ISI conditions. Results: There was no significant difference in stimulus-to-response correlation coefficient and pitch strength among the different ISI conditions, in either age groups. Older adults appeared to have weaker FFR for all ISI conditions when compared to their younger adult counterparts. Conclusion: Shorter ISIs did not result in worse FFRs from older adults or younger adults. For speech-evoked FFR using a recorded natural speech token that is 250 ms in length, an ISI of as short as 40 ms appeared to be sufficient and effective to record FFR for elderly adults

Induction of CCL8/MCP-2 by mycobacteria through the activation of TLR2/PI3K/Akt signaling pathway.

Pleural tuberculosis (TB), together with lymphatic TB, constitutes more than half of all extrapulmonary cases. Pleural effusions (PEs) in TB are representative of lymphocytic PEs which are dominated by T cells. However, the mechanism underlying T lymphocytes homing and accumulation in PEs is still incompletely understood. Here we performed a comparative analysis of cytokine abundance in PEs from TB patients and non-TB patients by protein array analysis and observed that MCP-2/CCL8 is highly expressed in the TB-PEs as compared to peripheral blood. Meanwhile, we observed that CCR5, the primary receptor used by MCP-2/CCL8, is mostly expressed on pleural CD4(+) T lymphocytes. Furthermore, we found that infection with either Mycobacterium bovis Bacillus Calmette-Guérin (BCG) or Mycobacterium tuberculosis H37Rv induced production of MCP-2/CCL8 at both transcriptional and protein level in Raw264.7 and THP-1 macrophage cells, mouse peritoneal macrophages as well as human PBMC monocyte-derived macrophages (MDMs). The induction of MCP-2/CCL8 by mycobacteria is dependent on the activation of TLR2/PI3K/Akt and p38 signaling pathway. We conclude that accumulation of MCP-2/CCL8 in TB-PEs may function as a biomarker for TB diagnosis

Voice Pitch Elicited Frequency Following Response in Chinese Elderlies

Background: Perceptual and electrophysiological studies have found reduced speech discrimination in quiet and noisy environment, delayed neural timing, decreased neural synchrony, and decreased temporal processing ability in elderlies, even those with normal hearing. However, recent studies have also demonstrated that language experience and auditory training enhance the temporal dynamics of sound encoding in the auditory brainstem response. The purpose of this study was to explore the pitch processing ability at the brainstem level in an aging population that has a tonal language background.Method: Mandarin speaking younger (n=12) and older (n=12) adults were recruited for this study. All participants had normal audiometric test results and normal suprathreshold click-evoked auditory brainstem responses (ABR). To record Frequency Following Responses (FFR) elicited by Mandarin lexical tones, two Mandarin Chinese syllables with different fundamental frequency pitch contours (Flat Tone and Falling Tone) were presented at 70 dB SPL. Fundamental frequencies (f0) of both the stimulus and the responses were extracted and compared to individual brainstem responses. Two indices were used to examine different aspects of pitch processing ability at the brainstem level: Pitch Strength and Pitch Correlation. Results: Lexical tone elicited FFR were overall weaker in the older adult group compared to their younger adult counterpart. Measured by Pitch Strength and Pitch Correlation, statistically significant group differences were only found when the tone with a falling f0 (Falling Tone) were used as the stimulus.Conclusion: Results of this study demonstrated that in a tonal language speaking population, pitch processing ability at the brainstem level of older adults are not as strong and robust as their younger counterparts. Findings of this study are consistent with previous reports on brainstem responses of older adults whose native language is English. On the other hand, lexical tone elicited FFRs have been shown to correlate with the length of language exposure. Older adults’ degraded responses in our study may also be due to that, the Mandarin speaking older adults’ long term exposure somewhat counteracted the negative impact on aging and helped maintain, or at least reduced, the degradation rate in their temporal processing capacity at the brainstem level

Voice pitch elicited frequency following response in Chinese elderlies

Background: Perceptual and electrophysiological studies have found reduced speech discrimination in quiet and noisy environment, delayed neural timing, decreased neural synchrony, and decreased temporal processing ability in elderlies, even those with normal hearing. However, recent studies have also demonstrated that language experience and auditory training enhance the temporal dynamics of sound encoding in the auditory brainstem response (ABR). The purpose of this study was to explore the pitch processing ability at the brainstem level in an aging population that has a tonal language background. Method: Mandarin speaking younger (n = 12) and older (n = 12) adults were recruited for this study. All participants had normal audiometric test results and normal suprathreshold click-evoked ABR. To record frequency following responses (FFRs) elicited by Mandarin lexical tones, two Mandarin Chinese syllables with different fundamental frequency pitch contours (Flat Tone and Falling Tone) were presented at 70 dB SPL. Fundamental frequencies (f0) of both the stimulus and the responses were extracted and compared to individual brainstem responses. Two indices were used to examine different aspects of pitch processing ability at the brainstem level: Pitch Strength and Pitch Correlation. Results: Lexical tone elicited FFR were overall weaker in the older adult group compared to their younger adult counterpart. Measured by Pitch Strength and Pitch Correlation, statistically significant group differences were only found when the tone with a falling f0 (Falling Tone) were used as the stimulus. Conclusion: Results of this study demonstrated that in a tonal language speaking population, pitch processing ability at the brainstem level of older adults are not as strong and robust as their younger counterparts. Findings of this study are consistent with previous reports on brainstem responses of older adults whose native language is English. On the other hand, lexical tone elicited FFRs have been shown to correlate with the length of language exposure. Older adults\u27 degraded responses in our study may also be due to that, the Mandarin speaking older adults\u27 long term exposure somewhat counteracted the negative impact on aging and helped maintain, or at least reduced, the degradation rate in their temporal processing capacity at the brainstem level