Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, ...obtained using different microarray platforms to analyze identical RNA samples, has raised concerns about the reliability of this technology. The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and data analysis issues. Expression data on four titration pools from two distinct reference RNA samples were generated at multiple test sites using a variety of microarray-based and alternative technology platforms. Here we describe the experimental design and probe mapping efforts behind the MAQC project. We show intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed. This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings.
We have developed an intelligent multi sensor-based security robot system that can detect abnormal and hazardous situation and notify us. The security robot is constructed using an aluminum frame. ...The contour of the robot is cylindrical. The diameter is about 50 cm, and height is 150 cm. The function of the security robot contains six parts, including software development system; obstacle avoidance and motion planning system, image system, sensor system, remote supervisory system and other systems. In the sensor system, we use multisensor integration algorithm. Then we also present the remote mobile security system (RMS) for the security robot. We use touch panel to display system state, and design a general user interface (GUI) on the security robot. We demonstrate the remote supervisory system to control the security robot using direct control mode and behavior control mode. We design a new recharging station for the security robot. It moves by X axis and rotates by Z axis, and guards the security robot easily to connect using sensor based method. Finally, we implement security function using the security robot to detect fire event and intruder. The security robot can transmit the message of the detection result to the cellular phone using GSM modem, and transmits the detection result to the client computer through Internet.
The ENCODE Consortium's efforts to annotate noncoding cis-regulatory elements (CREs) have advanced our understanding of gene regulatory landscapes. Pooled, noncoding CRISPR screens offer a systematic ...approach to investigate cis-regulatory mechanisms. The ENCODE4 Functional Characterization Centers conducted 108 screens in human cell lines, comprising >540,000 perturbations across 24.85 megabases of the genome. Using 332 functionally confirmed CRE-gene links in K562 cells, we established guidelines for screening endogenous noncoding elements with CRISPR interference (CRISPRi), including accurate detection of CREs that exhibit variable, often low, transcriptional effects. Benchmarking five screen analysis tools, we find that CASA produces the most conservative CRE calls and is robust to artifacts of low-specificity single guide RNAs. We uncover a subtle DNA strand bias for CRISPRi in transcribed regions with implications for screen design and analysis. Together, we provide an accessible data resource, predesigned single guide RNAs for targeting 3,275,697 ENCODE SCREEN candidate CREs with CRISPRi and screening guidelines to accelerate functional characterization of the noncoding genome.
Aluminum nitride (AlN) thin films with
c
-axis preferred orientation have been prepared by reactive direct-current (DC) magnetron sputtering. The degree of preferred crystal orientation, the ...cross-sectional structure, and the surface morphology of AlN thin films grown on Si (100) substrates at various substrate temperatures from 60°C to 520°C have been investigated by x-ray diffraction, scanning electron microscopy, and atomic force microscopy. Results show that the substrate temperature has a significant effect on the structural properties, such as the degree of
c
-axis preferred orientation, the full-width at half-maximum (FWHM) of the rocking curve, the surface morphology, and the cross-sectional structure as well as the deposition rate of the AlN thin films. The optimal substrate temperature is 430°C, with corresponding root-mean-square surface roughness (
R
rms
) of 1.97 nm, FWHM of AlN (002) diffraction of 2.259°, and deposition rate of 20.86 nm/min. The mechanisms behind these phenomena are discussed. Finally, film bulk acoustic resonators based on AlN films were fabricated; the corresponding typical electromechanical coupling coefficient (
k
t
2
) is 5.1% with series and parallel frequencies of 2.37 GHz and 2.42 GHz, respectively.
The respiratory tract is the portal of entry for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although a variety of respiratory pathogens other than SARS-CoV-2 have been ...associated with severe cases of COVID-19 disease, the dynamics of the upper respiratory microbiota during disease the course of disease, and how they impact disease manifestation, remain uncertain.
We collected 349 longitudinal upper respiratory samples from a cohort of 65 COVID-19 patients (cohort 1), 28 samples from 28 recovered COVID-19 patients (cohort 2), and 59 samples from 59 healthy controls (cohort 3). All COVID-19 patients originated from the earliest stage of the epidemic in Wuhan. Based on a modified clinical scale, the disease course was divided into five clinical disease phases (pseudotimes): “Healthy” (pseudotime 0), “Incremental” (pseudotime 1), “Critical” (pseudotime 2), “Complicated” (pseudotime 3), “Convalescent” (pseudotime 4), and “Long-term follow-up” (pseudotime 5). Using meta-transcriptomics, we investigated the features and dynamics of transcriptionally active microbes in the upper respiratory tract (URT) over the course of COVID-19 disease, as well as its association with disease progression and clinical outcomes.
Our results revealed that the URT microbiome exhibits substantial heterogeneity during disease course. Two clusters of microbial communities characterized by low alpha diversity and enrichment for multiple pathogens or potential pathobionts (including Acinetobacter and Candida) were associated with disease progression and a worse clinical outcome. We also identified a series of microbial indicators that classified disease progression into more severe stages. Longitudinal analysis revealed that although the microbiome exhibited complex and changing patterns during COVID-19, a restoration of URT microbiomes from early dysbiosis toward more diverse status in later disease stages was observed in most patients. In addition, a group of potential pathobionts were strongly associated with the concentration of inflammatory indicators and mortality.
This study revealed strong links between URT microbiome dynamics and disease progression and clinical outcomes in COVID-19, implying that the treatment of severe disease should consider the full spectrum of microbial pathogens present.
•The URT microbiome exhibits complex and changing patterns during COVID-19.•A series of microbes are identified to be associated with more severe disease stages.•There are strong links between URT microbiome dynamics and disease progression.
With the depletion of China’s coal resources and the increase in mining depth, high ground stress and high confined water cause frequent accidents. Taking the 12123 working face of Pan’er coal mine ...in Huainan Coalfield as the background, this study discussed the water disaster caused by the connection of water channels induced by mining disturbance with the collapse column. The catastrophic process of water inrush induced by the collapse column was studied through the numerical simulation of stress field and failure evolution of acoustic emission (AE) interpretation. The grouting method of plugging and reinforcement was introduced, and the effect was evaluated and analyzed. Results showed that the inrush formation of fracture channels was related to the coupling of the physical and mechanical properties of the collapse column and the surrounding rock, mining stress disturbance, and other complex factors. Obvious spatiotemporal effects were observed during structure activation, fracture initiation, fracture expansion, and channel formation of water disaster. The surrounding rock of the collapse column was deformed and split under stress and high water pressure. When the mining face was near the collapse column, the number of AE signals increased sharply from its adjacent top region. After passing through the threatening area, the water channels evolved from the structural bottom to top and produced water gushing. After optimized grouting reinforcement was carried out in the surrounding rock area, microseismic monitoring revealed that the failure depth of the floor in the adjacent area was generally large. The events showed obvious deflection and detour in the collapse column. Few microseismic events occurred on top of the collapse column and its boundary rock, and the spatial distribution of microseismic signals was significantly different from that before grouting, which proved the effectiveness of the grouting method. This study will be conducive to the prevention and control of mine water disasters and promote the wide application of effective grouting technology in mining engineering.
The donor–acceptor interface within molecular charge transfer (CT) solids plays a vital role in the hybridization of molecular orbitals to determine their carrier transport and electronic ...delocalization. In this study, we demonstrate molecular assembly-driven bilayer and crystalline solids, consisting of electron donor dibenzotetrathiafulvalene (DBTTF) and acceptor C60, in which interfacial engineering-induced CT degree control is a key parameter for tuning its optical, electronic, and magnetic performance. Compared to the DBTTF/C60 bilayer structure, the DBTTFC60 cocrystalline solids show a stronger degree of charge transfer for broad CT absorption and a large dielectric constant. In addition, the DBTTFC60 cocrystals exhibit distinct CT arrangement-driven anisotropic electron mobility and spin characteristics, which further enables the development of high-penetration and high-energy γ-ray photodetectors. The results presented in this paper provide a basis for the design and control of molecular charge transfer solids, which facilitates the integration of such materials into molecular electronics.
The double-inlet valve and inertance tube are the two main phase shifters of pulse tube refrigerators. They are crucial for the pulse tube refrigerators to obtain an appropriate phase relationship ...between pressure and mass flow. In the past decades, much attention has been given to understand the separate functions of the two phase shifters, and the present work will try to investigate their coupling functions. In this paper, the influence of the double-inlet valve on the cooling performance and characteristics of inertance tubes are numerically studied at first. Then an experimental setup is built to prove the numerical results. Based on the numerical and experimental study, it is concluded that the inertance tube cannot provide the optimum impedance for those pulse tube refrigerators with small cooling power because of turbulent flow. In such case, the double-inlet valve can help to provide a better impedance and further improve the cooling performance. On the other hand, the inertance tube can provide the optimum impedance for those pulse tube refrigerators with large cooling power and the double-inlet is not necessary in such a case.
Background Integrins are the major adhesive molecules in mammalian cells. Each integrin subtype plays a unique role in cell differentiation and embryo development. However, integrin involvement in ...carcinogenesis has not been well defined. Methods We identified mutations in integrin α7 by sequencing genomic DNAs and cDNAs from 122 specimens, including 62 primary human tumor samples, four cell lines, and 56 matched normal tissues. We evaluated the tumor suppressor activity of integrin α7 with colony formation, soft agar colony growth, and cell migration assays by forcing its expression in PC-3 and Du145 prostate cancer cells and SK-UT-1 leiomyosarcoma cells. PC-3 and Du145 xenograft tumors with increased levels of integrin α7 in severe combined immune deficient mice were used to assess the effect of integrin α7 on tumor growth and metastasis. Immunostaining was used to localize and to measure the level of integrin α7 in 701 and 141 specimens of prostate and smooth muscle, respectively. A meta-analysis of integrin α7 mRNA microarray data from four studies was performed. Kaplan–Meier analyses were used to assess survival. All statistical tests were two-sided. Results Integrin α7 mutations that generate truncations were found in specimens of 16 of 28 prostate cancers (57%, 95% confidence interval CI = 37% to 76%), five of 24 hepatocellular carcinomas (21%, 95% CI = 7% to 42%), five of six glioblastomas multiforme (83%, 95% CI = 36% to 99%), and one of four leiomyosarcomas (25%, 95% CI = 0.6% to 81%). Integrin α7 mutations were associated with increased recurrence of human prostate cancer (nine recurrences among 13 patients with integrin α7 mutations versus one among eight without such mutations; odds ratio OR = 14, 95% CI = 1.15 to 782, P = .024) and hepatocellular carcinoma (five recurrences among eight patients with integrin α7 mutations versus one among 16 without such mutations, OR = 21, 95% CI = 1.6 to 1245; P = .007). Forced expression of normal integrin α7 in prostate cancer and leiomyosarcoma cell lines suppressed tumor growth and metastasis both in vitro and in vivo. Focal or no integrin α7 expression in human prostate cancer and soft tissue leiomyosarcoma was associated with a reduction of metastasis-free survival (for example, for prostate cancer with focal or no expression, 5-year metastasis-free survival was 32%, 95% CI = 24.4% to 40.3%, and for prostate cancer with at least weak expression, it was 85%, 95% CI = 79% to 91%; P<.001). Microarray analysis indicated that cyclin D kinase inhibitor 3 and GTPase-activating protein may be possible targets for integrin α7–mediated tumor suppressor activity and inhibition of cell motility. Conclusion Integrin α7 appears to be a tumor suppressor that operates by suppressing tumor growth and retarding migration.
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