Multilevel omic data integration in cancer cell lines: advanced annotation and emergent properties

BACKGROUND: High-throughput (omic) data have become more widespread in both quantity and frequency of use, thanks to technological advances, lower costs and higher precision. Consequently, computational scientists are confronted by two parallel challenges: on one side, the design of efficient methods to interpret each of these data in their own right (gene expression signatures, protein markers, etc.) and, on the other side, realization of a novel, pressing request from the biological field to design methodologies that allow for these data to be interpreted as a whole, i.e. not only as the union of relevant molecules in each of these layers, but as a complex molecular signature containing proteins, mRNAs and miRNAs, all of which must be directly associated in the results of analyses that are able to capture inter-layers connections and complexity. RESULTS: We address the latter of these two challenges by testing an integrated approach on a known cancer benchmark: the NCI-60 cell panel. Here, high-throughput screens for mRNA, miRNA and proteins are jointly analyzed using factor analysis, combined with linear discriminant analysis, to identify the molecular characteristics of cancer. Comparisons with separate (non-joint) analyses show that the proposed integrated approach can uncover deeper and more precise biological information. In particular, the integrated approach gives a more complete picture of the set of miRNAs identified and the Wnt pathway, which represents an important surrogate marker of melanoma progression. We further test the approach on a more challenging patient-dataset, for which we are able to identify clinically relevant markers. CONCLUSIONS: The integration of multiple layers of omics can bring more information than analysis of single layers alone. Using and expanding the proposed integrated framework to integrate omic data from other molecular levels will allow researchers to uncover further systemic information. The application of this approach to a clinically challenging dataset shows its promising potential

Transportation Mode Detection Based on Permutation Entropy and Extreme Learning Machine

With the increasing prevalence of GPS devices and mobile phones, transportation mode detection based on GPS data has been a hot topic in GPS trajectory data analysis. Transportation modes such as walking, driving, bus, and taxi denote an important characteristic of the mobile user. Longitude, latitude, speed, acceleration, and direction are usually used as features in transportation mode detection. In this paper, first, we explore the possibility of using Permutation Entropy (PE) of speed, a measure of complexity and uncertainty of GPS trajectory segment, as a feature for transportation mode detection. Second, we employ Extreme Learning Machine (ELM) to distinguish GPS trajectory segments of different transportation. Finally, to evaluate the performance of the proposed method, we make experiments on GeoLife dataset. Experiments results show that we can get more than 50% accuracy when only using PE as a feature to characterize trajectory sequence. PE can indeed be effectively used to detect transportation mode from GPS trajectory. The proposed method has much better accuracy and faster running time than the methods based on the other features and SVM classifier

Boundary-semantic collaborative guidance network with dual-stream feedback mechanism for salient object detection in optical remote sensing imagery

With the increasing application of deep learning in various domains, salient object detection in optical remote sensing images (ORSI-SOD) has attracted significant attention. However, most existing ORSI-SOD methods predominantly rely on local information from low-level features to infer salient boundary cues and supervise them using boundary ground truth, but fail to sufficiently optimize and protect the local information, and almost all approaches ignore the potential advantages offered by the last layer of the decoder to maintain the integrity of saliency maps. To address these issues, we propose a novel method named boundary-semantic collaborative guidance network (BSCGNet) with dual-stream feedback mechanism. First, we propose a boundary protection calibration (BPC) module, which effectively reduces the loss of edge position information during forward propagation and suppresses noise in low-level features without relying on boundary ground truth. Second, based on the BPC module, a dual feature feedback complementary (DFFC) module is proposed, which aggregates boundary-semantic dual features and provides effective feedback to coordinate features across different layers, thereby enhancing cross-scale knowledge communication. Finally, to obtain more complete saliency maps, we consider the uniqueness of the last layer of the decoder for the first time and propose the adaptive feedback refinement (AFR) module, which further refines feature representation and eliminates differences between features through a unique feedback mechanism. Extensive experiments on three benchmark datasets demonstrate that BSCGNet exhibits distinct advantages in challenging scenarios and outperforms the 17 state-of-the-art (SOTA) approaches proposed in recent years. Codes and results have been released on GitHub: https://github.com/YUHsss/BSCGNet.Comment: Accepted by TGR

Threshold Recognition Based on Non-stationarity of Extreme Rainfall in the Middle and Lower Reaches of the Yangtze River Basin

Analyzing the hydrological sequence from the non-stationary characteristics can better understand the responses of changes in extreme rainfall to climate change. Taking the plain area in the middle and lower reaches of the Yangtze River basin (MLRYRB) as the study area, this study adopted a set of extreme rainfall indices and used the Bernaola-Galvan Segmentation Algorithm (BGSA) method to test the non-stationarity of extreme rainfall events. The General Pareto Distribution (GPD) was used to fit extreme rainfall and was calculated to select the optimal threshold of extreme rainfall. In addition, the cross-wavelet technique was used to explore the correlations of extreme rainfall with El Niño-Southern Oscillation (ENSO) and Western Pacific Subtropical High (WPSH) events. The results showed that: (1) extreme rainfall under different thresholds had different non-stationary characteristics; (2) the GPD distribution could well fit the extreme rainfall in the MLRYRB, and 40–60 mm was considered as the suitable optimal threshold by comparing the uncertainty of the return period; and (3) ENSO and WPSH had significant periodic effects on extreme rainfall in the MLRYRB. These findings highlighted the significance of non-stationary assumptions in hydrological frequency analysis, which were of great importance for hydrological forecasting and water conservancy project management

Antagonistic Actions of Juvenile Hormone and 20-Hydroxyecdysone Within the Ring Gland Determine Developmental Transitions in \u3cem\u3eDrosophila\u3c/em\u3e

In both vertebrates and insects, developmental transition from the juvenile stage to adulthood is regulated by steroid hormones. In insects, the steroid hormone, 20-hydroxyecdysone (20E), elicits metamorphosis, thus promoting this transition, while the sesquiterpenoid juvenile hormone (JH) antagonizes 20E signaling to prevent precocious metamorphosis during the larval stages. However, not much is known about the mechanisms involved in cross-talk between these two hormones. In this study, we discovered that in the ring gland (RG) of Drosophila larvae, JH and 20E control each other’s biosynthesis. JH induces expression of a Krüppel-like transcription factor gene Kr-h1 in the prothoracic gland (PG), a portion of the RG that produces the 20E precursor ecdysone. By reducing both steroidogenesis autoregulation and PG size, high levels of Kr-h1 in the PG inhibit ecdysteriod biosynthesis, thus maintaining juvenile status. JH biosynthesis is prevented by 20E in the corpus allatum, the other portion of the RG that produces JH, to ensure the occurrence of metamorphosis. Hence, antagonistic actions of JH and 20E within the RG determine developmental transitions in Drosophila. Our study proposes a mechanism of cross-talk between the two major hormones in the regulation of insect metamorphosis

Waterfront Analysis and Design:

Waterfront Analysis and Design Comparative Report of Beijing, Suzhou and Yinchuan systematically summarizes the research and planning cases. Conventional concepts and strategies concerning urban planning implemented in Beijing, Suzhou and Yinchuan have long been established, and the construction of many areas in these cities have been widely finished. Under such circumstances, based on analyses of the three cities and several typical cases of waterfront planning, this book breaks through the established conceptual constraints and delves into the commonalities and differences among the cases through systematic scientific approaches. On top of conducting the intensive research into urban waterfronts planning at levels of both basic theory and methodology, this book also presents specific practices of urban waterfront planning and design customized to the urban water system, as well as the layout and space of waterfront areas. By displaying how research findings can be applied into urban design, this book is of unique significance on value transmission. The book is broken down into four chapters, namely Comparison, Beijing, Suzhou and Yinchuan. Comparing and researching the water-city relations of the three cities. Chapter Comparison makes clear of the development characteristics of urban spatial structure based on changes of water systems in these cities with different geographical environments, and researches the patterns of urban spatial organization. Finally, the chapter summarizes the creating mode and focus of urban waterfronts under the effects of different natural environments, water networks and city landscapes. Chapter Beijing is compiled jointly by Harbin Institute of Technology and China Architecture Design and Research Group. Led by Professor Suning Xu, the study is structured as the combination of “research”, “judgment” and “design”. Studying the historical changes of water-city relation in Beijing and comparing the water-city relation of world typical capitals with that of prominent Chinese ancient capitals. This chapter sets the overall goal for Beijing’s waterfront development; The value system of the waterfront area is evaluated in 6 dimensions, including ecology, space, demand, history, economy and aesthetics, based on which the urban design strategy is crafted and verified with the design of typical nodes. Chapter Suzhou is put together by Swiss Federal Institute of Technology in Lausanne, Iuav University of Venice, Tianjin University, Xi’an Jiaotong-Liverpool University in Suzhou and China Architecture Design and Research Group. At the macro level, the joint research team analyzed the spatial structure of Suzhou urban area, selected important urban waterfronts based on the comprehensive considerations of urban functions, different water network structures, ecological protection and urban landscapes, and proposed practical urban design strategy and guidance at various grades and of different types; At the micro level, dedicated to the objectives of “properly clustered water networks, water conservation, living along the water, open and sharing, and reflection of historical culture”, the team offered key points for different urban waterfront designs. Chapter Yinchuan is collectively compiled by Delft University of Technology, Xi’an University of Architecture and Technology, Ningxia University and China Architecture Design and Research Group. Adopting the RTD (research through design) method, in other words, further defining research questions through designing and exploring various possibilities and solutions, the joint research team attempted to identify comprehensive solutions at multiple levels: Yinchuan city as a whole, the urban areas where the waterfronts are located, and the waterfronts themselves; Jointly led by landscape architects and urban designers, the research of waterfront design in Yinchuan highlights the ecology-based analysis method and design strategy

Probing thermally-induced structural evolution during the synthesis of layered Li-, Na-, or K-containing 3d transition-metal oxides

Layered alkali-containing 3d transition-metal oxides are of the utmost importance in the use of electrode materials for advanced energy storage applications such as Li-, Na-, or K-ion batteries. A significant challenge in the field of materials chemistry is understanding the dynamics of the chemical reactions between alkali-free precursors and alkali species during the synthesis of these compounds. In this study, in situ high-resolution synchrotron-based X-ray diffraction was applied to reveal the Li/Na/K-ion insertion-induced structural transformation mechanism during high-temperature solid-state reaction. The in situ diffraction results demonstrate that the chemical reaction pathway strongly depends on the alkali-free precursor type, which is a structural matrix enabling phase transitions. Quantitative phase analysis identifies for the first time the decomposition of lithium sources as the most critical factor for the formation of metastable intermediates or impurities during the entire process of Li-rich layered Li[Li0.2Ni0.2Mn0.6]O2 formation. Since the alkali ions have different ionic radii, Na/K ions tend to be located on prismatic sites in the defective layered structure (Na2/3-x[Ni0.25Mn0.75]O2 or K2/3-x[Ni0.25Mn0.75]O2) during calcination, whereas the Li ions prefer to be localized on the tetrahedral and/or octahedral sites, forming O-type structures

Long‐Range Cationic Disordering Induces two Distinct Degradation Pathways in Co‐Free Ni‐Rich Layered Cathodes

Ni-rich layered oxides are one of the most attractive cathode materials in high-energy-density lithium-ion batteries, their degradation mechanisms are still not completely elucidated. Herein, we report a strong dependence of degradation pathways on the long-range cationic disordering of Co-free Ni-rich Li1−m(Ni0.94Al0.06)1+mO2 (NA). Interestingly, a disordered layered phase with lattice mismatch can be easily formed in the near-surface region of NA particles with very low cation disorder (NA-LCD, m≤0.06) over electrochemical cycling, while the layered structure is basically maintained in the core of particles forming a “core–shell” structure. Such surface reconstruction triggers a rapid capacity decay during the first 100 cycles between 2.7 and 4.3 V at 1 C or 3 C. On the contrary, the local lattice distortions are gradually accumulated throughout the whole NA particles with higher degrees of cation disorder (NA-HCD, 0.06≤m≤0.15) that lead to a slow capacity decay upon cycling

De-escalated radiotherapy for HER2-overexpressing breast cancer patients with 1-3 positive lymph nodes undergoing anti-HER2 targeted therapy

BackgroundIn the era of anti-HER2 targeted therapy, the potential clinical feasibility of considering HER2-overexpressing breast cancer cases presenting with 1-3 positive axillary lymph nodes as low-risk, and thereby contemplating postoperative radiotherapy reduction, remains an important subject for in-depth examination. The aim of this retrospective study was to evaluate the effectiveness of de-escalated radiotherapy in T1-2N1M0 HER2-overexpressing breast cancer patients receiving anti-HER2 targeted therapy. Specifically, omitting regional lymph node irradiation (RNI) after breast-conserving surgery and only performing whole-breast irradiation or omitting postmastectomy radiation therapy.MethodsA retrospective analysis was conducted on 429 patients with stage T1-2N1M0 primary invasive HER2-overexpressing breast cancer from our center between 2004 and 2018. Patients who received anti-HER2 targeted therapy were divided into an RNI group and a no RNI group to assess the role of RNI. The prognostic role of RNI was investigated via the Kaplan-Meier method and Cox proportional hazards modeling.ResultsThe median follow-up time was 46.8 months (range 7.1–225.8 months). In the anti-HER2 targeted therapy group RNI yielded no significant improvements in invasive disease-free survival (IDFS) (p = 0.940), local-regional recurrence-free survival (p = 0.380), distant metastases-free survival (p = 0.698), or overall survival (p = 0.403). Estrogen receptor (ER) status (hazard ratio [HR] 0.105, 95% confidence interval [CI] 0.023–0.749, p = 0.004) and lymph vascular invasion status (LVI) (HR 5.721, 95% CI 1.586–20.633, p = 0.008) were identified as independent prognostic factors for IDFS, and ER-positive and LVI-negative patients exhibited better prognoses.ConclusionOmitting RNI may be a safe option in T1-2N1 HER2-overexpressing breast cancer patients receiving standardized anti-HER2 targeted therapy; particularly in ER-positive or LVI-negative subgroups

Reduced expression of N-Myc downstream-regulated gene 2 in human thyroid cancer

<p>Abstract</p> <p>Background</p> <p><it>NDRG</it>2 (N-Myc downstream-regulated gene 2) was initially cloned in our laboratory. Previous results have shown that <it>NDRG</it>2 expressed differentially in normal and cancer tissues. Specifically, <it>NDRG</it>2 mRNA was down-regulated or undetectable in several human cancers, and over-expression of <it>NDRG</it>2 inhibited the proliferation of cancer cells. <it>NDRG</it>2 also exerts important functions in cell differentiation and tumor suppression. However, it remains unclear whether <it>NDRG</it>2 participates in carcinogenesis of the thyroid.</p> <p>Methods</p> <p>In this study, we investigated the expression profile of human <it>NDRG</it>2 in thyroid adenomas and carcinomas, by examining tissues from individuals with thyroid adenomas (n = 40) and carcinomas (n = 35), along with corresponding normal tissues. Immunohistochemistry, quantitative RT-PCR and western blot methods were utilized to determine both the protein and mRNA expression status of Ndrg2 and c-Myc.</p> <p>Results</p> <p>The immunostaining analysis revealed a decrease of Ndrg2 expression in thyroid carcinomas. When comparing adenomas or carcinomas with adjacent normal tissue from the same individual, the mRNA expression level of <it>NDRG</it>2 was significantly decreased in thyroid carcinoma tissues, while there was little difference in adenoma tissues. This differential expression was confirmed at the protein level by western blotting. However, there were no significant correlations of <it>NDRG</it>2 expression with gender, age, different histotypes of thyroid cancers or distant metastases.</p> <p>Conclusion</p> <p>Our data indicates that <it>NDRG</it>2 may participate in thyroid carcinogenesis. This finding provides novel insight into the important role of <it>NDRG2 </it>in the development of thyroid carcinomas. Future studies are needed to address whether the down-regulation of <it>NDRG</it>2 is a cause or a consequence of the progression from a normal thyroid to a carcinoma.</p