Search

The ultrafast monitoring of deoxyribonucleic acid (DNA) dynamic structural changes is an emerging and rapidly growing research topic in biotechnology. The existing optical spectroscopy used to identify different dynamical DNA structures lacks quick response while requiring large consumption of samples and bulky instrumental facilities. It is highly demanded to develop an ultrafast technique that monitors DNA structural changes with the external stimulus or cancer‐related disease scenarios. Here, we demonstrate a novel photonic integrated graphene‐optofluidic device to monitor DNA structural changes with the ultrafast response time. Our approach is featured with an effective and straightforward design of decoding the electronic structure change of graphene induced by its interactions with DNAs in different conformations using ultrafast nanosecond pulse laser and achieving refractive index sensitivity of ~3 × 10−5 RIU. This innovative technique for the first time allows us to perform ultrafast monitoring of the conformational changes of special DNA molecules structures, including G‐quadruplex formation by K+ ions and i‐motif formation by the low pH stimulus. The graphene‐optofluidic device as presented here provides a new class of label‐free, ultrafast, ultrasensitive, compact, and cost‐effective optical biosensors for medical and healthcare applications.

AST3-2 (the second Antarctic Survey Telescope) is located in Antarctic Dome A, the loftiest ice dome on the Antarctic Plateau. It produces a huge amount of observational data which require a more efficient data reduction program to be developed. Also the data transmission in Antarctica is much difficult, thus it is necessary to perform data reduction and detect variable and transient sources remotely and automatically in Antarctica, but this attempt is restricted by the unsatisfactory performance of the low power consumption computer in Antarctica. For realizing this purpose, to develop a new method based on the existing image subtraction method and random forest algorithm, taking the AST3-2 2016 dataset as the test sample, becomes an alternative choice. This method performs image subtraction on the dataset, then applies the principle component analysis to extract the features of residual images. Random forest is used as a machine learning classifier, and in the test a recall rate of 97% is resulted for the positive sample. Our work has verified the feasibility and accuracy of this method, and finally found out a batch of candidates for variable stars in the AST3-2 2016 dataset.

Background: The MSI/MSS status does not fully explain cancer immunotherapy response in colorectal cancer. Thus, we developed a colorectal cancer-specific method that predicts cancer immunotherapy response.Methods: We used gene expression data of 454 samples (MSI = 131, MSI-L = 23, MSS = 284, and Unknown = 16) and developed a TMEPRE method that models signatures of CD8+ T-cell infiltration and CD8+ T-cell exhaustion states in the tumor microenvironment of colorectal cancer. TMEPRE model was validated on three RNAseq datasets of melanoma patients who received pembrolizumab or nivolumab and one RNAseq dataset of purified CD8+ T cells in different exhaustion states.Results: TMEPRE showed predictive power in three datasets of anti-PD1-treated patients (p = 0.056, 0.115, 0.003). CD8+ T-cell exhaustion component of TMEPRE model correlates with anti-PD1 responding progenitor exhausted CD8+ T cells in both tumor and viral infection (p = 0.048, 0.001). The global pattern of TMEPRE on 454 colorectal cancer samples indicated that 10.6% of MSS patients and 67.2% of MSI patients show biological characteristics that can potentially benefit from anti-PD1 treatment. Within MSI nonresponders, approximately 50% showed insufficient tumor-infiltrating CD8+ T cells and 50% showed terminal exhaustion of CD8+ T cells. These terminally exhausted CD8+ T cells coexisted with signatures of myeloid-derived suppressor cells in colorectal cancer.Conclusion: TMEPRE is a colorectal cancer-specific method. It captures characteristics of CD8+ T-cell infiltration and CD8+ T-cell exhaustion state and predicts cancer immunotherapy response. A subset of MSS patients could potentially benefit from anti-PD1 treatment. Anti-PD1 resistance MSI patients with insufficient infiltration of CD8+ T cells or terminal exhaustion of CD8+ T cells need different treatment strategies.

BackgroundFOLFOX is a combination of drugs that is widely used to treat colorectal cancer. The response rate of FOLFOX in colorectal cancer(CRC) is 30-50%. We develop a method that analyzes mechanisms of FOLFOX resistance and predicts whether a patient will benefit from FOLFOX.MethodsGene expression data of 83 stage IV CRC tumor samples (FOLFOX responder n=42, non-responder n=41) were used to develop a supervised learning method IML and analyze subgroups of FOLFOX resistance mechanism. Datasets of 32 FOLFOX treated stage IV CRC patients and 55 FOLFOX treated stage III CRC patients were used as independent validations.ResultsAn iterative supervised learning (IML) method identified two distinct subgroups of CRC patients who resist FOLFOX. Each subgroup relies on different types of DNA damage repair proteins and they are mutually exclusive. Protein-protein networks showed the main mechanism might be the synergistic effect of resisting apoptosis and an altered cell cycle. IML method was validated in two independent validation sets, one FOLFOX treated stage IV CRC patients(HR=2.6, p-value=0.02, 3-years survival rate of the predicted responder group 61.9%, predicted nonresponder group 18.8%) and one FOLFOX treated stage III CRC patients (estimated HR=2.36, p-value=0.02). A subgroup of mesenchymal subtype patients shows the pattern as FOLFOX responders.ConclusionsIML method reflects the underlying biology of FOLFOX resistance and predicts FOLFOX response.

The integrated navigation system is used to estimate the position, velocity, and attitude of a vehicle with the output of inertial sensors. This paper concentrates on the problem of the INS/GPS integrated navigation system design and simulation. The structure of the INS/GPS integrated navigation system is made up of four parts: 1) GPS receiver, 2) Inertial Navigation System, 3) Extended Kalman filter, and 4) Integrated navigation scheme. Afterwards, we illustrate how to simulate the integrated navigation system with the extended Kalman filter by measuring position, velocity and attitude. Particularly, the extended Kalman filter can estimate states of the nonlinear system in the noisy environment. In extended Kalman filter, the estimation of the state vector and the error covariance matrix are computed by steps: 1) time update and 2) measurement update. Finally, the simulation process is implemented by Matlab, and simulation results prove that the error rate of statement measuring is lower when applying the extended Kalman filter in the INS/GPS integrated navigation system.

Atmospheric ducts are horizontal layers that occur under certain weather conditions in the lower atmosphere. Radio signals guided in atmospheric ducts tend to experience less attenuation and spread much farther, i.e, hundreds of kilometers. In a large-scale deployed TD-LTE (Time Division Long Term Evolution) network, atmospheric ducts cause faraway downlink wireless signals to propagate beyond the designed protection distance and interfere with local uplink signals, thus resulting in a large outage probability. In this paper, we analyze the characteristics of ADI atmospheric duct interference (Atmospheric Duct Interference) by the use of real network-side big data from the current operated TD-LTE network owned by China Mobile. The analysis results yield the time varying and directional characteristics of ADI. In addition, we proposed an SVM (Support Vector Machine)-classifier based spacial prediction method of ADI by machine learning over combination of real network-side big data and real meteorological data. Furthermore, an implementation of ADMM (Alternating Direction Methods of Multipliers) framework is proposed to implement a distributed SVM prediction scheme, which reduces data exchange among different regions/cities, maintains similar prediction accuracy and is thus of a more practical use to operators.

To effectively and precisely drive industrial cameras to photograph and then sort long bamboo battens, a surface-defect and color detection device and a sorting device are designed. Further, a sectionalized photography program and sorting program design is proposed. The overall machine employs STM32 as the core master controller, which is connected to the relay drive plate, the photoelectric switch, the industrial camera, etc., for control, to photograph bamboo battens of different lengths in sections, and to sort six types of bamboo batten according to the bamboo-batten category signal sent by the upper computer. Devices for improving bamboo-product processing system efficiency and enhancing the level of automation of modern agricultural products, such as the proposed design, are of considerable importance.

To optimize the architecture of weighted average multiresolution image fusion algorithm,an extended weighted average multiresolution image fusion model to control the decision map only with the match measure is presented based on the Piella pixel-level multiresolution image fusion framework.The extended model changes the fusion pattern that the decision factor must be decided by both activity measure and match measure in the conventional weighted average multiresolution image fusion model.Since the activity measure is removed in the extended model,the corresponding algorithm architecture is rather simpler.By taking the correlated signal intensity ratio as the match measure,a weighted average multiresolution image fusion method based on the extended model is proposed.The experiment on fusing infrared and visible images shows that the proposed method is able to produce better fusion results than the conventional ones and its Edge Fusion Quality Index(EFQI) and Weight Fusion Quality Index(WFQI)has increased by 2.9% and 1.8%,respectively.Moreover,it achieves much lower computational complexity for the decision factor with decreased multiplication and addition times of 66.7% and 33.3%,respectively.

Background Classification of breast cancers into molecular subtypes may be important for the proper selection of therapy for patients as tumors with seemingly similar biology can have strikingly different clinical outcomes. We analyzed response to neo-adjuvant chemotherapy as a function of molecular sub-types and show patient survival from the multi-center neo adjuvant trial, I-SPY I (CALGB 150007/150012; ACRIN 6657). Previous analyses had shown that breast cancer subtypes as identified by immunohistochemistry or molecular analyses, have distinct clinical outcome (Esserman, ASCO 2009). Here, we analyze how the 70-gene signature (MammaPrint) together with an 80-gene molecular subtyping profile (BluePrint=Basal-type, Luminal-type, ERBB2-type; de Snoo, ASCO, 2010 and manuscript under review) can sub-classify patients. Materials: This study was carried out on genomics data of core needle biopsies from 149 out of 221 patients enrolled in the I-SPY I trial, a multi-center trial designed to identify predictive markers of pathological complete response (pCR) and disease-free survival (DFS) in women with locally advanced breast cancer (3 cm or greater). All women received neoadjuvant Doxorubicin & Cytoxan followed by paclitaxel chemotherapy. The 70-gene and the subtyping signatures, Basal, Luminal and ERBB2-type were determined on 44K Agilent arrays available through the I-SPY 1 data portal (Esserman, ASCO, 2009 and manuscript under review). Results: The 70-gene signature classified 9% of patients (13/149) as Low Risk, of whom one patient was ERBB2-type, and the other 12 were Luminal-type. None of these patients experienced a pCR. The remaining 136 were classified as 70-gene High Risk (91%), of whom 47% were classified as Luminal-type with a pCR rate of 13%, 41% were Basal-type with a pCR rate of 34%, and 12% were ERBB2-type with a pCR rate of 56%. Patients with BluePrint Basal-type tumors had a 5-year DFS of 61%; ERBB2-type had a 5-year DFS of 78%; 70-gene High Risk/Luminal-type had a 5-year DFS of 73% and 70-gene Low Risk/Luminal-type showed 5-year DFS of 100%. The molecular subtype classification shows significant association to clinically assessed receptor status. However, clinically assessed HER2+ patients were distributed across all molecular subtypes, where ER+HER+ are predominantly classified as Luminal-type. Conclusion: This study was performed with the I-SPY I dataset, which provides a platform to compare, contrast & combine marker signatures to tailor therapy. We show how combining BluePrint, with MammaPrint risk-classification can detect specific groups of patients who are at high risk of recurrence and who would have a higher likelihood to benefit from chemotherapy. Furthermore, MammaPrint Low Risk patients do not benefit from neo-adjuvant therapy, though have excellent survival rates, suggesting that the Low Risk Luminal-type patients could be managed conservatively. Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-06-20.

When the highly-intensive and highly-directional white light from pulsed fiber laser is focused into water, many directional and colorful rings, coherent rainbows, are observed. The laser generates bubbles with similar sizes in the water, which serve as scatters. The intensive light leads to spatial self-phase modulation and thus generates the coherent rainbows. Such a phenomenon has been observed in many kinds of liquids.

Focusing white laser into samples, many colorful rings (coherent rainbows) come out. Such phenomena have been observed in many materials like water, acetone, absolute ethyl alcohol, soft drink and other liquids, and ice, colored glass, plastics, wax and other solids. From the center of the coherent rainbows to the outer side, the distance between neighboring rings becomes larger and larger. The coherent rainbow is an interference effect, whose optical path difference is induced by locally heating the material with the laser beam. Especially, the coherent rainbows from colored glass in reflection mode can be described with a simple formula, with which simulated results fit the observed interference pattern very well. Several possible mechanisms like nonlinear optical effect, thermal lens effect and self-phase modulation effect are excluded.

Based on a detailed ray-tracing code for capillary optics, a MATLAB program for the simulation of X-ray transmission in a cylindrical polycapillary is described. The simulated and experimental results for the spatial distributions and power density gain of the X-rays in the beam guided through a cylindrical polycapillary are in good agreement, and the results show that the spatial distribution of the X-rays in the beam guided through a cylindrical polycapillary is uneven.

Colorectal cancer patients with the BRAF(p.V600E) mutation have poor prognosis in metastatic setting. Personalized treatment options and companion diagnostics are needed to better treat these patients. Previously, we developed a 58-gene signature to characterize the distinct gene expression pattern of BRAF-mutation-like subtype (accuracy 91.1%). Further experiments repurposed drug Vinorelbine as specifically lethal to this BRAF-mutation-like subtype. The aim of this study is to translate this 58-gene signature from a research setting to a robust companion diagnostic that can use formalin-fixed, paraffin-embedded (FFPE) samples to select patients with the BRAF-mutation-like subtype. BRAF mutation and gene expression data of 302 FFPE samples were measured (mutants = 57, wild-type = 245). The performance of the 58-gene signature in FFPE samples showed a high sensitivity of 89.5%. In the identified BRAF-mutation-like subtype group, 50% of tumours were known BRAF mutants, and 50% were BRAF wild-type. The stability of the 58-gene signature in FFPE samples was evaluated by two control samples over 40 independent experiments. The standard deviations (SD) were within the predefined criteria (control 1: SD = 0.091, SD/Range = 3.0%; control 2: SD = 0.169, SD/Range = 5.5%). The fresh frozen version and translated FFPE version of this 58-gene signature were compared using 170 paired fresh frozen and FFPE samples and the result showed high consistency (agreement = 99.3%). In conclusion, we translated this 58-gene signature to a robust companion diagnostic that can use FFPE samples.

Study design: Cadaveric and clinical studies. Objectives: To investigate the safety and efficiency of modified decancellation posterior closing-wedge osteotomy for traumatic fixed kyphotic deformity of thoracolumbar spine. Methods: Single-level vertebral osteotomy was performed on two groups of fresh-frozen human cadaveric lumbar spines. Group I underwent conventional decancellation posterior closing-wedge osteotomy, and Group II underwent our modified cancellation posterior closing-wedge osteotomy. Sagittal plane angulation as well as anterior height and distance between the most cephalad and caudal endplate were measured before and after osteotomy. Twenty six cases of old thoracolumbar fractures with spinal cord injury were recruited in this study. The mean age was 35.6 years. The mean time from injury to operation was 25 months ranging from 3 months to 11 years. Prior to the index surgery, 9 patients received conservative treatment, and 17 patients underwent surgical treatment. There was complete paraplegia in 10 cases and incomplete paraplegia in 14 (Frankel B in 2 cases, C 10 and D 2). Two patients had no neurological deficit. All patients suffered from low back pain, the average score of Visual Analog Scale (VAS) was 4.5 (range 2.5-6.0). The patients were found to have a mean remaining kyphotic deformity of 35° (range 20°-75°). According to the deformity angles conventional or modified decancellation posterior closing-wedge osteotomy was performed. Results: The mean correction was 36° ± 3.6° for Group I and 49° ± 2.0° for Group II. The mean change in anterior height was only 2–4 mm for Group I and II. All cases were followed up for 10 months to 6 years with a mean of 12.5 months. Successful decompression and satisfied correction of kyphosis was noticed. The post-operatively mean angle of kyphosis deformity was 10.8°, ranging from 0° to 40°. Neurological function recovery was noted in 50% of cases. For complete spinal cord injury, 30% of cases had partial recovery (sensation) whereas recovery was observed in 64.3% of cases with incomplete spinal cord injury. The statistical difference between the groups was p

A new tabletop confocal micro x-ray fluorescence setup with an MCBM 50-0.6B x-ray tube is assembled. The confocal micro x-ray fluorescence setup includes two lenses, a polycapillary full lens in the excitation channel and a polycapillary half lens in the detection channel. A Ni-Cr wire in diameter 25 μm is used to investigate the FWHM of three-dimensional confocal volume. A basso-relievo capital letter of a 1-jiao RMB coin of 2005 version is studied with this confocal micro x-ray fluorescence setup.

Abstr act. 2D to 3D conversion is an important task in 3DTV due to the lack of 3D contents. In this paper, we propose a novel framework of the 2D to 3D video conversion. The proposed framework consists of two main stages: depth map generation and virtual view synthesis. In the depth map generation, motion and relative-height cues are effectively used to generate depth maps. In the virtual view synthesis, depth-image-based-rendering (DIBR) is adopted to generate the left and right virtual views from the depth maps. Experimental results demonstrate that the proposed 2D to 3D conversion is very effective in generating depth maps and providing realistic 3D effects.

Classification of breast cancer into molecular subtypes maybe important for the proper selection of therapy, as tumors with seemingly similar histopathological features can have strikingly different clinical outcomes. Herein, we report the development of a molecular subtyping profile (BluePrint), that enables rationalization in patient selection for either chemotherapy or endocrine therapy prescription. An 80-Gene Molecular Subtyping Profile (BluePrint) was developed using 200 breast cancer patient specimens and confirmed on four independent validation cohorts (n = 784). Additionally, the profile was tested as a predictor of chemotherapy response in 133 breast cancer patients, treated with T/FAC neoadjuvant chemotherapy. BluePrint classification of a patient cohort that was treated with neoadjuvant chemotherapy (n = 133) shows improved distribution of pathological Complete Response (pCR), among molecular subgroups compared with local pathology: 56% of the patients had a pCR in the Basal-type subgroup, 3% in the MammaPrint Low-risk, Luminal-type subgroup, 11% in the MammaPrint High-risk, Luminal-type subgroup, and 50% in the HER2-type subgroup. The group of genes identifying Luminal-type breast cancer is highly enriched for genes having an Estrogen Receptor binding site proximal to the promoter-region, suggesting that these genes are direct targets of the Estrogen Receptor. Implementation of this profile may improve the clinical management of breast cancer patients, by enabling the selection of patients who are most likely to benefit from either chemotherapy or from endocrine therapy.

Both size and distribution of oil mist droplet diameter are important factors for weighing atomized quality of oil mist in lubrication. However, because of the peculiarity of oil mist droplet, it is difficult to obtain its exact dimension. This article selects Laser Particle Sizer which is based on the scattering theory of light to measure size and its distribution of oil mist droplet diameter. At the end of the article, the conclusion about how the working parameters influence atomized droplet size of oil mist is gained through measuring the size and distribution of the oil mist droplet diameter by changing the related parameters within a certain range.

Introduction Adjuvant therapy for stage II patients is recommended for patients with high risk features, especially with T4 tumors, and recommended for all stage III patients. Adjuvant therapy is not indicated for patients with MSI-H status who are considered of being at low risk of disease relapse. However, this leaves the majority of stage II patients with an undetermined risk. ColoPrint is an 18-gene expression classifier that identifies patients at higher risk of disease relapse. Together with a genomic classifier to determine MSI-status, ColoPrint can help making treatment decisions for early stage colon cancer patients. Methods ColoPrint was developed using whole genome expression data and was validated in public datasets (n = 322) and independent patient cohorts from 5 European hospitals (n = 341). Tissue specimen, clinical parameters, MSI-status and follow-up data (median follow-up 70 months) for patients were available and the ColoPrint index was determined using validated diagnostic arrays. The 64-gene MSI-signature (MSI-Print) was developed using full genome expression data of 276 primary stage II and III colorectal tumors with known MSI-status (n = 29 MSI-H, n = 247 MSS). Uni-and multivariate analysis was performed on the pooled stage II and stage IIIA patient set and in the subsets of patients who were stage IIIA or stage II T3/ MSS. Results In the analysis of all stage II and IIIA patients, ColoPrint classified two-third of stage II patients as being at lower risk. The 3-year Relapse-Free-Survival (RFS) was 91% for Low Risk and 74% for patients at higher risk with a HR of 2.9 (p = 0.001). Clinicopathological parameters from the 2012 NCCN guidelines (T4, perforation, Conclusion The diagnostic MSI signature identifies patients with MSI-H status with high accuracy. Combined with ColoPrint, the prognostic accuracy in stage II and stage IIIA patients can be significantly improved, thereby facilitating the identification of patients at higher risk who might be considered for additional treatment.

According to intensity distribution of the synchrotron radiation source focused by a toroidal mirror at the Beijing synchrotron radiation biological macromolecule station, theoretical modeling of the Beijing synchrotron radiation source is developed for capillary optics. Using this theoretical modeling, the influences of the configuration curve of the polycapillary X-ray lens on transmission efficiency and working distance are analyzed. The experimental results of the transmission efficiency and working distance at the biological macromolecule station are in good agreement with the theoretical results.

Introduction Previous analysis of the gene expression data of mutational subgroups in the PETACC3 trial, revealed a very homogenous gene expression pattern in BRAF mutant CRC patients; while KRAS mutant CRC contain at least three different patient groups in terms of gene expression. One of these KRAS mutant groups together with 10% of KRAS/BRAF WT (WT2) patients, resembled the gene expression found in the BRAF mutants. This BRAF-like subgroup is characterized by poor prognosis. In this article we investigate, if heterogeneity in CRC patients can be partly explained by diverse signaling downstream of KRAS, to which the DUSPs take part. Material and methods The expression of DUSP1, DUSP4 and DUSP6, DUSPs previously shown to be induced by mutations in genes of the MAPK pathway, was analyzed in 4 different CRC patient microarray datasets (PETACC3, cetuximab, TCGA and Agendia dataset). We investigated, if patients with low and high DUSP expression behave differently in terms of response, OS, PFS and differ in clinical characteristics both in PETACC3 and TCGA dataset. Findings Unlike DUSP1, DUSP4 and DUSP6 were differentially overexpressed between BRAF mutants and KRAS mutants on one side and between BRAF mutants and WT2 patients on the other side. When we subdivided the patients into low and high DUSP expression within KRAS mutant and WT2 patients, we found a significant difference in OS in both mutational subgroups with high DUSP4 expression in KRAS mutants associated with a better OS and in WT2 associated with a worse OS. Multivariate analysis in the BRAF WT patients in both PETACC3 and cetuximab dataset showed that high DUSP4 expression was still associated with a worse OS (HR = 1.23; p Conclusions DUSP4 is predictive for OS in CRC patients with KRAS mutations. Interestingly, within KRAS mutant and WT2 patients high DUSP4 expression correlates with clinical characteristics that are typical for BRAF mutant CRC patients. If DUSP4 may represent a novel biomarker for a subset of CRC patients needs further research. Download : Download full-size image Fig. 1 . Box plots with DUSP4 expression according to different mutational groups in PETACC3 dataset. Download : Download full-size image Fig. 2 . Kaplan-Meier curve for overall survival according to DUSP4 expression (low and high) in KRAS WT patients.

537 Background: Classification of breast cancer into molecular subtypes may be important for the proper selection of therapy, as tumors with seemingly similar biology can have strikingly different clinical outcomes. We have previously developed an 80-gene molecular subtyping profile (BluePrint) for the classification of breast cancer into three molecular subtypes: triple-negative (“Basal-type”); hormone receptor-positive (“Luminal-type”) and ERBB2-positive (“ERBB2-type”). In this study, we sought to determine if Luminal-type tumors are characterized by active ER signaling. Methods: ERα ChIP-seq data from proliferating MCF-7 breast cancer cells was used from a publically available dataset [Ross-Innes, 2010]. The transcription start sites of the 58 genes in the gene set that identifies the Luminal-type subgroup were determined after which the presence of Estrogen Receptor binding sites was analyzed within a window of −/+ 20 kb from the transcription start site. The sequence track was visualized using the UC...

We present the dispersion relation of guided-mode resonances in planar periodic waveguides, both for s-polarized (TE mode) and p-polarized (TM mode) incident waves. For a fixed homogeneous planar waveguide, dispersion curves of the TE eigenmode cannot cross that of the TM eigenmode at all. That is to say, at a certain wavelength, TE and TM modes cannot be excited with the same propagation constant. Due to Bragg reflection in the planar periodic waveguide, dispersion curves of the TE leaky mode may intersect with that of the TM leaky mode in the first Brillouin zone. We employ these intersections to achieve polarization-independent guided-mode resonance filters.

A ray-tracing theory for the X-ray transmission in a capillary is described based on which a calculation model is built. The transmission efficiency and intensity distribution curve through a capillary are numerically calculated. The simulation results are in good agreement with the experimental results and previous simulations.