Using multitask classification methods to investigate the kinase-specific phosphorylation sites

<p>Abstract</p> <p>Background</p> <p>Identification of phosphorylation sites by computational methods is becoming increasingly important because it reduces labor-intensive and costly experiments and can improve our understanding of the common properties and underlying mechanisms of protein phosphorylation.</p> <p>Methods</p> <p>A multitask learning framework for learning four kinase families simultaneously, instead of studying each kinase family of phosphorylation sites separately, is presented in the study. The framework includes two multitask classification methods: the Multi-Task Least Squares Support Vector Machines (MTLS-SVMs) and the Multi-Task Feature Selection (MT-Feat3).</p> <p>Results</p> <p>Using the multitask learning framework, we successfully identify 18 common features shared by four kinase families of phosphorylation sites. The reliability of selected features is demonstrated by the consistent performance in two multi-task learning methods.</p> <p>Conclusions</p> <p>The selected features can be used to build efficient multitask classifiers with good performance, suggesting they are important to protein phosphorylation across 4 kinase families.</p

Deep CFHT Y-band imaging of VVDS-F22 field: I. data products and photometric redshifts

We present our deep $Y$-band imaging data of a two square degree field within the F22 region of the VIMOS VLT Deep Survey. The observations were conducted using the WIRCam instrument mounted at the Canada--France--Hawaii Telescope (CFHT). The total on-sky time was 9 hours, distributed uniformly over 18 tiles. The scientific goals of the project are to select faint quasar candidates at redshift $z>2.2$, and constrain the photometric redshifts for quasars and galaxies. In this paper, we present the observation and the image reduction, as well as the photometric redshifts that we derived by combining our $Y$-band data with the CFHTLenS $u^*g'r'i'z'$ optical data and UKIDSS DXS $JHK$ near-infrared data. With $J$-band image as reference total $\sim$80,000 galaxies are detected in the final mosaic down to $Y$-band $5\sigma$ point source limiting depth of 22.86 mag. Compared with the $\sim$3500 spectroscopic redshifts, our photometric redshifts for galaxies with $z<1.5$ and $i'\lesssim24.0$ mag have a small systematic offset of $|\Delta{z}|\lesssim0.2$, 1$\sigma$ scatter $0.03<\sigma_{\Delta z} < 0.06$, and less than 4.0% of catastrophic failures. We also compare to the CFHTLenS photometric redshifts, and find that ours are more reliable at $z\gtrsim0.6$ because of the inclusion of the near-infrared bands. In particular, including the $Y$-band data can improve the accuracy at $z\sim 1.0-2.0$ because the location of the 4000\AA-break is better constrained. The $Y$-band images, the multi-band photometry catalog and the photometric redshifts are released at \url{http://astro.pku.edu.cn/astro/data/DYI.html}.Comment: 16 pages, 12 figures, 4 tables. AJ accepted. Updated access to the data: https://zenodo.org/record/140003

Investigation of Durability and Performance of High Friction Surface Treatment

The Indiana Department of Transportation (INDOT) completed a total of 25 high friction surface treatment (HFST) projects across the state in 2018. This research study attempted to investigate the durability and performance of HFST in terms of its HFST-pavement system integrity and surface friction performance. Laboratory tests were conducted to determine the physical and mechanical properties of epoxy-bauxite mortar. Field inspections were carried out to identify site conditions and common early HFST distresses. Cyclic loading test and finite element method (FEM) analysis were performed to evaluate the bonding strength between HFST and existing pavement, in particular chip seal with different pretreatments such as vacuum sweeping, shotblasting, and scarification milling. Both surface friction and texture tests were undertaken periodically (generally once every 6 months) to evaluate the surface friction performance of HFST. Crash records over a 5-year period, i.e., 3 years before installation and 2 years after installation, were examined to determine the safety performance of HFST, crash modification factor (CMF) in particular. It was found that HFST epoxy-bauxite mortar has a coefficient of thermal expansion (CTE) significantly higher than those of hot mix asphalt (HMA) mixtures and Portland cement concrete (PCC), and good cracking resistance. The most common early HFST distresses in Indiana are reflective cracking, surface wrinkling, aggregate loss, and delamination. Vacuum sweeping is the optimal method for pretreating existing pavements, chip seal in particular. Chip seal in good condition is structurally capable of providing a sound base for HFST. On two-lane highway curves, HFST is capable of reducing the total vehicle crash by 30%, injury crash by 50%, and wet weather crash by 44%, and providing a CMF of 0.584 in Indiana. Great variability may arise in the results of friction tests on horizontal curves by the use of locked wheel skid tester (LWST) due both to the nature of vehicle dynamics and to the operation of test vehicle. Texture testing, however, is capable of providing continuous texture measurements that can be used to calculate a texture height parameter, i.e., mean profile depth (MPD), not only for evaluating friction performance but also implementing quality control (QC) and quality assurance (QA) plans for HFST

Aspirations and environmental performance feedback: a behavioral perspective for green supply chain management

Purpose – This study investigates the relationships between environmental performance feedback and green supply chain management (GSCM). It explores how environmental performance above or below aspirations affects the implementation of GSCM practices (specifically sustainable production [SP] and sustainable sourcing [SS]) through the lens of the behavioral theory of the firm (BTOF), which has received scant attention in the operations management literature. Design/methodology/approach – The study used data from the sixth round of the International Manufacturing Strategy Survey (IMSS). It employed hierarchical linear regression to test the proposed hypotheses. Moreover, the study tested an alternate model to rule out the possible role of financial performance aspirations in explaining the implementation of SP and SS. Findings – The results indicate that organizations determine their efforts put into the two GSCM practices according to environmental performance feedback: the greater the aspiration–environmental performance discrepancy, the stronger the efforts put into implementing GSCM practices. Originality/value – This study contributes to the GSCM literature by revealing the impact of environmental performance aspirations on the implementation of GSCM practices through the lens of the BTOF. It also extends the BTOF by applying it in the GSCM context and indicating that performance feedback is based on environmental performance instead of financial performance in this specific context

Low-carbon developments in Northeast China: Evidence from cities

Cities are a major source of energy use and greenhouse gases emissions, as well as being at the core of the climate change mitigation. With the Revitalizing Old Industrial Base of Northeast China strategy, Northeast China has been a typical developing region with rapid industrialization and urbanization accompanied by substantial energy consumption and carbon emissions. Therefore, northeastern Chinese cities should play an important role in regional low-carbon developments. This study presents several improvements to previous method to improve the accuracy of the results. Using the modified method, for the first time, we compile carbon emission inventories for 30 cities in Northeast China based on fossil fuel combustion and industrial processes. The results indicate that Anshan emitted the most carbon emissions annually, followed by Benxi and the vice-provincial cities (including Changchun, Shenyang, Dalian and Harbin). In 2012, the total carbon emissions of the 30 cities amounted to 973.95 million tonnes, accounting for 9.71% and 2.75% of national and global carbon emissions, respectively. Most of the CO2 emissions of these cities were from the ‘nonmetal and metal industry’ and ‘energy production and supply’. Raw coal was the primary source of carbon emissions in Northeast China, and industrial processes also played a significant role in determining the carbon emissions. Additionally, both the average per capita carbon emissions and carbon emission intensity in the 30 cities were higher than the national levels. According to the differences in carbon emissions characteristics, we present several policy recommendations for carbon mitigation for northeastern Chinese cities. This study provides consistent and comparable spatial-temporal city-level emission database for further research on relationships between economic development and environmental protection in Northeast China. Simultaneously, this study provides practical reference values for other developing regions throughout the world to create low-carbon road maps

Metachronous pulmonary and adrenal metastases after liver transplantation for hepatocarcinoma

<p>Abstract</p> <p>Background</p> <p>The worldwide experience of surgical resection for isolated metastasis following liver transplantation (LT) for hepatocellular carcinoma (HCC) is limited.</p> <p>Methods</p> <p>The case of a 60-year-old patient performed successful surgical management for metachronous pulmonary and adrenal metastases from HCC after LT.</p> <p>Results</p> <p>Eighty months after LT, he was presently alive and disease-free with a normal AFP value.</p> <p>Conclusion</p> <p>The case is an interesting report on a somehow indolent metastatic spread of HCC after LT. It should be considered that metachronous metastatic resectable disease, with no data of recurrence at the primary site in an operable patient, is an indication to perform a surgical resection.</p

Resample-based Ensemble Framework for Drifting Imbalanced Data Streams

Machine learning in real-world scenarios is often challenged by concept drift and class imbalance. This paper proposes a Resample-based Ensemble Framework for Drifting Imbalanced Stream (RE-DI). The ensemble framework consists of a long-term static classifier to handle gradual and multiple dynamic classifiers to handle sudden concept drift. The weights of the ensemble classifier are adjusted from two aspects. First, a time-decayed strategy decreases the weights of the dynamic classifiers to make the ensemble classifier focus more on the new concept of the data stream. Second, a novel reinforcement mechanism is proposed to increase the weights of the base classifiers that perform better on the minority class and decrease the weights of the classifiers that perform worse. A resampling buffer is used for storing instances of the minority class to balance the imbalanced distribution over time. In our experiment, we compare the proposed method with other state-of-the-art algorithms on both real-world and synthetic data streams. The results show that the proposed method achieves the best performance in terms of both the Prequential AUC and accuracy