bluuebunny/crossref_metadata_2025 huggingface dataset:
Extracellular Matrix Rigidity-dependent Sphingosine-1-phosphate Secretion Regulates Metastatic Cancer Cell Invasion and Adhesion
Authors: Ko Panseon , Kim Daehwan , You Eunae , Jung Jangho , Oh Somi , Kim Jaehyun , Lee Kwang-Ho , Rhee Sangmyung
Published: February 2016

Dynamic interaction between cancer cells and the surrounding microenvironment is critical for cancer progression via changes in cellular behavior including alteration of secreted molecules. However, the molecular mechanisms underlying the influence exerted by the cancer microenvironment on secretion of molecules during cancer progression remain largely unknown. In this study, we report that secretion of spingsine-1-phosphate (S1P) and its regulator, SphK1 expression is dependent of the substrate rigidity, which is critical for the balance between cancer cell invasion and adhesion. Conditioned media (CM) of MDA-MB-231, an aggressive breast cancer cell obtained from soft substrate (~0.5 kPa) induced chemo-attractive invasion, while CM obtained from stiff substrate (~2.5 kPa) increased cell adhesion instead. We found that the expression of SphK1 is upregulated in the stiff substrate, resulting in an increase in S1P levels in the CM. We also found that upregulation of SphK1 expression in the stiff substrate is dominant in metastatic cancer cells but not in primary cancer cells. These results suggest that alterations in the mechanical environment of the ECM surrounding the tumor cells actively regulate cellular properties such as secretion, which in turn, may contribute to cancer progression.
Superconductivity in Ta3Pd3Te14 with quasi-one-dimensional PdTe2 chains
Authors: Jiao Wen-He , He Lan-Po , Liu Yi , Xu Xiao-Feng , Li Yu-Ke , Zhang Chu-Hang , Zhou Nan , Xu Zhu-An , Li Shi-Yan , Cao Guang-Han
Published: February 2016

We report bulk superconductivity at 1.0 K in a low-dimensional ternary telluride Ta3Pd3Te14 containing edge-sharing PdTe2 chains along crystallographic b axis, similar to the recently discovered superconductor Ta4Pd3Te16. The electronic heat capacity data show an obvious anomaly at the transition temperature, which indicates bulk superconductivity. The specific-heat jump is ΔC/(γnTc) ≈ 1.35, suggesting a weak coupling scenario. By measuring the low-temperature thermal conductivity, we conclude that Ta3Pd3Te14 is very likely a dirty s-wave superconductor. The emergence of superconductivity in Ta3Pd3Te14 with a lower Tc, compared to that of Ta4Pd3Te16, may be attributed to the lower density of states.
Influence of light exposure at nighttime on sleep development and body growth of preterm infants
Authors: Kaneshi Yosuke , Ohta Hidenobu , Morioka Keita , Hayasaka Itaru , Uzuki Yutaka , Akimoto Takuma , Moriichi Akinori , Nakagawa Machiko , Oishi Yoshihisa , Wakamatsu Hisanori , Honma Naoki , Suma Hiroki , Sakashita Ryuichi , Tsujimura Sei-ichi , Higuchi Shigekazu , Shimokawara Miyuki , Cho Kazutoshi , Minakami Hisanori
Published: February 2016

Previous studies have demonstrated that a light-dark cycle has promoted better sleep development and weight gain in preterm infants than constant light or constant darkness. However, it was unknown whether brief light exposure at night for medical treatment and nursing care would compromise the benefits brought about by such a light-dark cycle. To examine such possibility, we developed a special red LED light with a wavelength of >675 nm which preterm infants cannot perceive. Preterm infants born at <36 weeks’ gestational age were randomly assigned for periodic exposure to either white or red LED light at night in a light-dark cycle after transfer from the Neonatal Intensive Care Unit to the Growing Care Unit, used for supporting infants as they mature. Activity, nighttime crying and body weight were continuously monitored from enrolment until discharge. No significant difference in rest-activity patterns, nighttime crying, or weight gain was observed between control and experimental groups. The data indicate that nursing care conducted at 3 to 4-hour intervals exposing infants to light for <15 minutes does not prevent the infants from developing circadian rest-activity patterns, or proper body growth as long as the infants are exposed to regular light-dark cycles.
A self-sacrifice template route to iodine modified BiOIO3: band gap engineering and highly boosted visible-light active photoreactivity
Authors: Feng Jingwen , Huang Hongwei , Yu Shixin , Dong Fan , Zhang Yihe
Published: February 2016

In this work we demonstrate the continuously adjustable band gap and visible-light photocatalysis activation of WBG BiOIO3via iodine surface modification.
Enhanced catalytic activity of cobalt catalysts for Fischer–Tropsch synthesis via carburization and hydrogenation and its application to regeneration
Authors: Kwak Geunjae , Kim Du-Eil , Kim Yong Tae , Park Hae-Gu , Kang Seok Chang , Ha Kyoung-Su , Jun Ki-Won , Lee Yun-Jo
Published: February 2016

In Fischer–Tropsch synthesis (FTS), cobalt carbide (Co2C) is not a catalytically active material, but rather an undesired cobalt phase associated with low catalytic performance.
Impacts of nanomaterials on bacterial quorum sensing: differential effects on different signals
Authors: Mohanty Anee , Tan Chuan Hao , Cao Bin
Published: February 2016

We report for the first time that different QS signals may respond differently to nanomaterials, which may result in a complex influence of nanomaterials on the overall structure and function of the whole community.
Genetically modified bacteriophages
Authors: Sagona Antonia P. , Grigonyte Aurelija M. , MacDonald Paul R. , Jaramillo Alfonso
Published: February 2016

Applications of genetically modified bacteriophages.
Preparation of a nano-MnO2 surface-modified reduced graphene oxide/PVDF flat sheet membrane for adsorptive removal of aqueous Ni(ii)
Authors: Li Renjie , Liu Lifen , Zhang Yuehua , Yang Fenglin
Published: February 2016

In this paper, nanoscale MnO2 particles, formed from KMnO4 through microwave assisted oxidation of HI reduced graphene oxide, dispersed in PVDF membrane, adsorb and remove Ni2+ ions.
Following nanoparticles in complex turbid media
Authors: Mikhailovskaya A. , Crassous J. , Salonen A. , Langevin D.
Published: February 2016

Diffusing wave spectroscopy (DWS) was used to determine the size and volume fraction of nanoparticles within a foam taken as an example of a turbid media.
1-Dimensional fiber-based field-effect transistors made by low-temperature photochemically activated sol–gel metal-oxide materials for electronic textiles
Authors: Park Chang Jun , Heo Jae Sang , Kim Kyung-Tae , Yi Gyengmin , Kang Jingu , Park Jong S. , Kim Yong-Hoon , Park Sung Kyu
Published: February 2016

We report the high performance metal-oxide fiber field-effect transistors (F-FETs) for electronic textiles (e-textiles).
Improved electrochemical performances of layered lithium rich oxide 0.6Li[Li1/3Mn2/3]O2·0.4LiMn5/12Ni5/12Co1/6O2 by Zr doping
Authors: Ma Zheng , Huang Jichun , Quan Jingbin , Mei Lin , Guo Jun , Li Decheng
Published: February 2016

HRTEM patterns of undoped and Zr4% doped samples, (0a) x = 0 before cycle, (0a1) x = 0 after 101 cycles, (4a) x = 4% before cycle, (4a1) x = 4% after 101 cycles.
Complex toxicological interaction between ionic liquids and pesticides to Vibrio qinghaiensis sp.-Q67
Authors: Qu Rui , Liu Shu-Shen , Chen Fu , Li Kai
Published: February 2016

Ionic liquids (ILs) and pesticides may coexist in ecosystems, because more and more people try to extract pesticides from various samples using ILs.
Performance of mesoporous silicas (MCM-41 and SBA-15) and carbon (CMK-3) in the removal of gas-phase naphthalene: adsorption capacity, rate and regenerability
Authors: Liu Yingshu , Li Ziyi , Yang Xiong , Xing Yi , Tsai Chuenjinn , Yang Quan , Wang Zhanying , Yang Ralph T.
Published: February 2016

The adsorption isotherms of gas-phase naphthalene on mesosilicas MCM-41 and SBA-15, and mesocarbon CMK-3 were determined by column tests at 125 °C, with feed concentrations ranging from 7.63 × 10−5 to 4.64 × 10−2 mol m−3 (1.88 to 1140 ppm).
Talking through the problems: a study of discourse in peer-led small groups
Authors: Repice Michelle D. , Keith Sawyer R. , Hogrebe Mark C. , Brown Patrick L. , Luesse Sarah B. , Gealy Daniel J. , Frey Regina F.
Published: February 2016

Increasingly, studies are investigating the factors that influence student discourse in science courses, and specifically the mechanisms and discourse processes within small groups, to better understand the learning that takes place as students work together. This paper contributes to a growing body of research by analyzing how students engage in conversation and work together to solve problems in a peer-led small-group setting. This qualitative study evaluates video of Peer-Led Team Learning (PLTL) sessions in general chemistry, with attention to both the activity structures and the function of discourse as students undertook different types of problems across one semester. Our findings suggest that students talk their way through the problems; practicing a combination of regulative and instructional language to manage the group dynamics of their community of peer learners while developing and using specific disciplinary vocabulary. Additionally, student discourse patterns revealed a focus on the process of complex problem-solving, where students engage in joint decision-making by taking turns, questioning and explaining, and building on one another's ideas. While students in our study engaged in less of the deeper, meaning-making discourse than expected, these observations about the function of language in small-group learning deepens an understanding of how PLTL and other types of small-group learning based on the tenets of social constructivism may lead to improvements in science education, with implications for the structure of small-group learning environments, problem design, and training of peer group leaders to encourage students to engage in more of the most effective discourse in these learning contexts.
Evaluating the effectiveness of POGIL-PCL workshops
Authors: Stegall Stacy L. , Grushow Alexander , Whitnell Robert , Hunnicutt Sally S.
Published: February 2016

The POGIL-PCL (Process-Oriented Guided Inquiry Learning in the Physical Chemistry Laboratory) project has developed a series of workshops to introduce faculty to POGIL-PCL and to facilitate the development of new experiments. More than 60 faculty members from various institutions have attended these workshops. Workshop participants were surveyed in order to evaluate the effectiveness of the workshop and better understand why faculty choose to adopt POGIL-PCL. Of the participants who completed the survey, 77% had used POGIL-PCL experiments. The results of the survey show that personal influence is a major factor in all stages of the adoption process.
Robust hybrid hydrogels with good rectification properties and their application as active materials for dye-sensitized solar cells: insights from AC impedance spectroscopy
Authors: Das Sujoy , Chakraborty Priyadarshi , Shit Arnab , Mondal Sanjoy , Nandi Arun K.
Published: February 2016

A robust tri-hybrid hydrogel containing GO exhibits excellent rectification properties and acts as an active material for DSSCs showing an efficiency of 4.5%.
The design of a bipodal bis(pentafluorophenoxy)aluminate supported on silica as an activator for ethylene polymerization using surface organometallic chemistry
Authors: Sauter Dominique W. , Popoff Nicolas , Bashir Muhammad Ahsan , Szeto Kai C. , Gauvin Régis M. , Delevoye Laurent , Taoufik Mostafa , Boisson Christophe
Published: February 2016

A well-defined solid activator for supported metallocene polymerization catalysts.
Well-defined silica-supported zirconium–imido complexes mediated heterogeneous imine metathesis
Authors: Hamzaoui Bilel , Pelletier Jérémie D. A. , Abou-Hamad Edy , Basset Jean-Marie
Published: February 2016

Well-defined silica-supported zirconium–imido complexes effectively catalyze imine/imine cross-metathesis and are thus considered as the first heterogeneous catalysts active for imine metathesis.
The construction of functional protein nanotubes by small molecule-induced self-assembly of cricoid proteins
Authors: Miao Lu , Fan Qiusheng , Zhao Linlu , Qiao Qinglong , Zhang Xiyu , Hou Chunxi , Xu Jiayun , Luo Quan , Liu Junqiu
Published: February 2016

Induced by small molecular ethylenediamine and “zero-length” covalent crosslinking, covalently crosslinked SeSP1 protein nanotubes with great GPx activity was fabricated.
Ceratonia siliqua L. hydroethanolic extract obtained by ultrasonication: antioxidant activity, phenolic compounds profile and effects in yogurts functionalized with their free and microencapsulated forms
Authors: Rached Irada , Barros Lillian , Fernandes Isabel P. , Santos-Buelga Celestino , Rodrigues Alírio E. , Ferchichi Ali , Barreiro Maria Filomena , Ferreira Isabel C. F. R.
Published: February 2016

Microencapsulated polyphenols extracted from carob pulp are a viable functional ingredient for the food industry.
Comparison of boron-assisted oxime and hydrazone formations leads to the discovery of a fluorogenic variant
Authors: Stress Cedric J. , Schmidt Pascal J. , Gillingham Dennis. G.
Published: February 2016

We use kinetic data, photophysical properties, and mechanistic analyses to compare recently developed high-rate constant oxime and hydrazone formations.
Catalytic selective deuteration of halo(hetero)arenes
Authors: Janni Manojkumar , Peruncheralathan S.
Published: February 2016

A library of deuterated compounds was synthesized and the mechanism of D-incorporation explored.
Primary alkyl bis-catecholato silicates in dual photoredox/nickel catalysis: aryl- and heteroaryl-alkyl cross coupling reactions
Authors: Lévêque Christophe , Chenneberg Ludwig , Corcé Vincent , Goddard Jean-Philippe , Ollivier Cyril , Fensterbank Louis
Published: February 2016

Primary alkyl bis-catecholato silicates have been successfully engaged with aryl and heteroaryl bromide substrates in photoredox/nickel dual catalysis to provide cross coupling products.
Novel wearable polyacrylonitrile/phase-change material sheath/core nano-fibers fabricated by coaxial electro-spinning
Authors: Wan Yafan , Zhou Pucha , Liu Yaodong , Chen Hongxiang
Published: February 2016

This study focused on the preparation of wearable polyacrylonitrile (PAN)/phase-change material (PCM) sheath/core nano-fibers by coaxial electro-spinning technology.
Stable stereocomplex micelles from Y-shaped amphiphilic copolymers MPEG–(scPLA)2: preparation and characteristics
Authors: Zhang Weiwei , Zhang Delong , Fan Xiaoshan , Bai Guangyue , Yuming guo Yuming guo , Hu Zhiguo
Published: February 2016

Four new Y-shaped amphiphilic copolymers based on MPEG and PLA were synthesized by ROP and click chemistry. The aggregation behaviors in aqueous solution, biocompatibility and drug release profile of the corresponding stereocomplex were studied.
Anti-allergic prenylated hydroquinones and alkaloids from the fruiting body of Ganoderma calidophilum
Authors: Huang Sheng Zhuo , Cheng Bao Hui , Ma Qing Yun , Wang Qi , Kong Fan Dong , Dai Hao Fu , Qiu Shu Qi , Zheng Peng Yuan , Liu Zhi Qiang , Zhao You-Xing
Published: February 2016

Six new prenylated hydroquinones of ganocalidin A–F (1–6) and two new compounds of ganocalicine A (7) and B (8), together with sixteen known compounds (9–24) were isolated from an extract of the fruiting body of Ganoderma calidophilum.
Mild, efficient, and environmentally friendly synthesis of symmetrical N,N′-alkylidenebisamides under solvent-free conditions catalyzed by H7[(P2W17O61)FeIII(H2O)]
Authors: Tayebee R. , Maleki B. , Zonoz F. M. , Kakhki R. M. , Kunani T.
Published: February 2016

H7[(P2W17O61)FeIII(H2O)] is introduced as an effective catalyst for the one-pot synthesis ofN,N′-alkylidenebisamides. The catalyst could be easily separated without noticeable reduction in activity.
Water turbidity sensing using a smartphone
Authors: Hussain I. , Ahamad K. , Nath P.
Published: February 2016

Smartphone based platform turbidimeter measuring turbidity in drinking and different environmental water bodies.
Analysis of transition state mimicry by tight binding aminothiazoline inhibitors provides insight into catalysis by human O-GlcNAcase
Authors: Cekic N. , Heinonen J. E. , Stubbs K. A. , Roth C. , He Y. , Bennet A. J. , McEachern E. J. , Davies G. J. , Vocadlo D. J.
Published: February 2016

2′-Aminothiazoline inhibitors of human OGA are tight binding transition state mimics for which binding depends on inhibitor pKa.
Insight into the effect of functional groups on visible-fluorescence emissions of graphene quantum dots
Authors: Du Jianglin , Wang Haiyu , Wang Lei , Zhu Shoujun , Song Yubin , Yang Bai , Sun Hongbo
Published: February 2016

Various functional groups in graphene quantum dots may play critical roles in their fluorescent emissions, and different groups contribute to different light-emitting wavelengths.
Correction: Radiative and non-radiative decay rate of K2SiF6:Mn4+ phosphors
Authors: Kim Minseuk , Park Woon Bae , Bang Bokeuk , Kim Chang Hae , Sohn Kee-Sun
Published: February 2016

Correction for ‘Radiative and non-radiative decay rate of K2SiF6:Mn4+ phosphors’ by Minseuk Kim et al., J. Mater. Chem. C, 2015, 3, 5484–5489.
Distributed state observer design for networked dynamic systems
Authors: Liu Huabo , Zhou Tong
Published: February 2016

Two linear matrix inequality (LMI)‐based sufficient conditions are derived for stability analysis of networked systems with linear time invariant dynamics, which depend only on the parameters of each subsystem and the subsystem connection matrix. Relations among the new sufficient conditions and the previous one are discussed. Then, a distributed state observer is constructed for networked systems. Several LMI‐based conditions are further established to design a completely distributed state observer that can be stabilised by a block diagonal gain matrix. Numerical simulations show that these methods are attractive in the analysis and synthesis of large‐scale networked systems.
Video analytics revisited
Authors: Choudhary Ayesha , Chaudhury Santanu
Published: February 2016

Video, rich in visual real‐time content, is however, difficult to interpret and analyse. Video collections necessarily have large data volume. Video analytics strives to automatically discover patterns and correlations present in the large volume of video data, which can help the end‐user to take informed and intelligent decisions as well as predict the future based on the patterns discovered across space and time. In this study, the authors discuss various issues and problems in video analytics, proposed solutions and present some of the important current applications of video analytics.
Analysis, design, and implementation of soft‐switching cells applied to the single‐phase full‐bridge inverter
Authors: Tofoli Fernando Lessa , Gallo Carlos Alberto
Published: February 2016

This study presents an auxiliary cell that can be applied to the single‐phase full‐bridge inverter. The cell employs two auxiliary switches, two auxiliary diodes, one resonant capacitor, and one resonant inductor, as it can be used in both inverter legs so that switching losses are minimised, thus implying increased efficiency and low electromagnetic interference levels. Three possible configurations are investigated and theoretical analyses are carried out. Besides, the control strategy provides nearly sinusoidal output voltage with reduced harmonic distortion. Experimental results are presented and discussed to validate the proposal.
Redundant data minimisation using hexagonal scalar premier neighbourhood for optimum camera actuation scheme
Authors: Priyadarshini Sushree Bibhuprada B. , Panigrahi Suvasini
Published: February 2016

This study reports an efficient scheme inspired by scalar premier (SP) selection for actuation of optimum number of cameras so as to minimise the amount of redundant data transmission. The proposed algorithm passes through three major steps. Initially, all the sensors are randomly deployed and messages are exchanged among themselves to know the location information of each other. In the second step, the entire monitored region is divided into number of virtual sub‐regions, in which the scalars present at each sub‐region select six SPs in a hexagonal manner in such a way that the cameras to be activated due to them cover distinct portions of geographic regions. Finally, when event takes place, these SPs communicate their respective cameras regarding its occurrence. Consequently, the cameras exchange messages among each other for deciding which among them are to be actuated. The less camera actuation, improved coverage ratio, reduced event‐loss ratio, least redundancy ratio along with minimised energy and power consumption obtained from the experimental evaluation reveal the effectiveness of the proposed algorithm as compared with two other recently devised approaches in the literature.
Forty years afterLau
Authors: Arias M. Beatriz , Wiley Terrence G.
Published: February 2016

This article addresses the right to an education (including the right of access), and the right to an education in one’s native language, within the broader context of educational human rights, and language minority educational policy in the United States. Included in this discussion is an overview of educational and linguistic human rights as recognized in the US, followed by a review of the legal and historical background prior to the passage of theLau v Nicholsdecision in 1974. The implications of demographic changes coupled with federal policy for language minority students forty years after Lau are discussed.
Centralising rents and dispersing power while pursuing development? Exploring the strategic uses of military firms in Rwanda
Authors: Behuria Pritish
Published: February 2016

The Rwandan Patriotic Front has achieved significant economic progress while also maintaining political stability. However, frictions among ruling elites have threatened progress. This paper explores the use of military firms in Rwanda. Such firms are used to invest in strategic industries, but the use of such firms reflects the vulnerability faced by ruling elites. Military firms serve two related purposes. First, ruling elites use such firms to centralise rents and invest in strategic sectors. Second, the proliferation of such enterprises and the separation of party- and military-owned firms contribute to dispersing power within a centralised hierarchy.
MultiGeMS: detection of SNVs from multiple samples using model selection on high-throughput sequencing data
Authors: Murillo Gabriel H. , You Na , Su Xiaoquan , Cui Wei , Reilly Muredach P. , Li Mingyao , Ning Kang , Cui Xinping
Published: February 2016

Motivation: Single nucleotide variant (SNV) detection procedures are being utilized as never before to analyze the recent abundance of high-throughput DNA sequencing data, both on single and multiple sample datasets. Building on previously published work with the single sample SNV caller genotype model selection (GeMS), a multiple sample version of GeMS (MultiGeMS) is introduced. Unlike other popular multiple sample SNV callers, the MultiGeMS statistical model accounts for enzymatic substitution sequencing errors. It also addresses the multiple testing problem endemic to multiple sample SNV calling and utilizes high performance computing (HPC) techniques.

Results: A simulation study demonstrates that MultiGeMS ranks highest in precision among a selection of popular multiple sample SNV callers, while showing exceptional recall in calling common SNVs. Further, both simulation studies and real data analyses indicate that MultiGeMS is robust to low-quality data. We also demonstrate that accounting for enzymatic substitution sequencing errors not only improves SNV call precision at low mapping quality regions, but also improves recall at reference allele-dominated sites with high mapping quality.

Availability and implementation: The MultiGeMS package can be downloaded from https://github.com/cui-lab/multigems.

Contact:  xinping.cui@ucr.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Improving microRNA target prediction by modeling with unambiguously identified microRNA-target pairs from CLIP-ligation studies
Authors: Wang Xiaowei
Published: February 2016

Motivation: MicroRNAs (miRNAs) are small non-coding RNAs that are extensively involved in many physiological and disease processes. One major challenge in miRNA studies is the identification of genes targeted by miRNAs. Currently, most researchers rely on computational programs to initially identify target candidates for subsequent validation. Although considerable progress has been made in recent years for computational target prediction, there is still significant room for algorithmic improvement.

Results: Here, we present an improved target prediction algorithm, which was developed by modeling high-throughput profiling data from recent CLIPL (crosslinking and immunoprecipitation followed by RNA ligation) sequencing studies. In these CLIPL-seq studies, the RNA sequences in each miRNA-target pair were covalently linked and unambiguously determined experimentally. By analyzing the CLIPL data, many known and novel features relevant to target recognition were identified and then used to build a computational model for target prediction. Comparative analysis showed that the new algorithm had improved performance over existing algorithms when applied to independent experimental data.

Availability and implementation: All the target prediction data as well as the prediction tool can be accessed at miRDB (http://mirdb.org).

Contact:  xwang@radonc.wustl.edu
Realizing privacy preserving genome-wide association studies
Authors: Simmons Sean , Berger Bonnie
Published: February 2016

Motivation: As genomics moves into the clinic, there has been much interest in using this medical data for research. At the same time the use of such data raises many privacy concerns. These circumstances have led to the development of various methods to perform genome-wide association studies (GWAS) on patient records while ensuring privacy. In particular, there has been growing interest in applying differentially private techniques to this challenge. Unfortunately, up until now all methods for finding high scoring SNPs in a differentially private manner have had major drawbacks in terms of either accuracy or computational efficiency.

Results: Here we overcome these limitations with a substantially modified version of the neighbor distance method for performing differentially private GWAS, and thus are able to produce a more viable mechanism. Specifically, we use input perturbation and an adaptive boundary method to overcome accuracy issues. We also design and implement a convex analysis based algorithm to calculate the neighbor distance for each SNP in constant time, overcoming the major computational bottleneck in the neighbor distance method. It is our hope that methods such as ours will pave the way for more widespread use of patient data in biomedical research.

Availability and implementation: A python implementation is available at http://groups.csail.mit.edu/cb/DiffPriv/.

Contact:  bab@csail.mit.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Collaborative analysis of multi-gigapixel imaging data using Cytomine
Authors: Marée Raphaël , Rollus Loïc , Stévens Benjamin , Hoyoux Renaud , Louppe Gilles , Vandaele Rémy , Begon Jean-Michel , Kainz Philipp , Geurts Pierre , Wehenkel Louis
Published: February 2016

Motivation: Collaborative analysis of massive imaging datasets is essential to enable scientific discoveries.

Results: We developed Cytomine to foster active and distributed collaboration of multidisciplinary teams for large-scale image-based studies. It uses web development methodologies and machine learning in order to readily organize, explore, share and analyze (semantically and quantitatively) multi-gigapixel imaging data over the internet. We illustrate how it has been used in several biomedical applications.

Availability and implementation: Cytomine (http://www.cytomine.be/) is freely available under an open-source license from http://github.com/cytomine/. A documentation wiki (http://doc.cytomine.be) and a demo server (http://demo.cytomine.be) are also available.

Contact:  info@cytomine.be

Supplementary information:  Supplementary data are available at Bioinformatics online.
FINEMAP: efficient variable selection using summary data from genome-wide association studies
Authors: Benner Christian , Spencer Chris C.A. , Havulinna Aki S. , Salomaa Veikko , Ripatti Samuli , Pirinen Matti
Published: February 2016

Motivation: The goal of fine-mapping in genomic regions associated with complex diseases and traits is to identify causal variants that point to molecular mechanisms behind the associations. Recent fine-mapping methods using summary data from genome-wide association studies rely on exhaustive search through all possible causal configurations, which is computationally expensive.

Results: We introduce FINEMAP, a software package to efficiently explore a set of the most important causal configurations of the region via a shotgun stochastic search algorithm. We show that FINEMAP produces accurate results in a fraction of processing time of existing approaches and is therefore a promising tool for analyzing growing amounts of data produced in genome-wide association studies and emerging sequencing projects.

Availability and implementation: FINEMAP v1.0 is freely available for Mac OS X and Linux at http://www.christianbenner.com.

Contact: christian.benner@helsinki.fi or matti.pirinen@helsinki.fi
lodGWAS: a software package for genome-wide association analysis of biomarkers with a limit of detection
Authors: Vaez Ahmad , van der Most Peter J. , Prins Bram P. , Snieder Harold , van den Heuvel Edwin , Alizadeh Behrooz Z. , Nolte Ilja M.
Published: February 2016

Summary: Genome-wide association study (GWAS) of a biomarker is complicated when the assay procedure of the biomarker is restricted by a Limit of Detection (LOD). Those observations falling outside the LOD cannot be simply discarded, but should be included into the analysis by applying an appropriate statistical method. However, the problem of LOD in GWAS analysis of such biomarkers is usually overlooked. ‘lodGWAS’ is a flexible, easy-to-use R package that provides a simple and elegant way for GWAS analysis of such biomarkers while simultaneously accommodating the problem of LOD by applying a parametric survival analysis method.

Availability and implementation:  http://cran.r-project.org/web/packages/lodGWAS

Contacts:  a.vaez@umcg.nl or i.m.nolte@umcg.nl

Supplementary information:  Supplementary data are available at Bioinformatics online.
MS-REDUCE: an ultrafast technique for reduction of big mass spectrometry data for high-throughput processing
Authors: Awan Muaaz Gul , Saeed Fahad
Published: February 2016

Motivation: Modern proteomics studies utilize high-throughput mass spectrometers which can produce data at an astonishing rate. These big mass spectrometry (MS) datasets can easily reach peta-scale level creating storage and analytic problems for large-scale systems biology studies. Each spectrum consists of thousands of peaks which have to be processed to deduce the peptide. However, only a small percentage of peaks in a spectrum are useful for peptide deduction as most of the peaks are either noise or not useful for a given spectrum. This redundant processing of non-useful peaks is a bottleneck for streaming high-throughput processing of big MS data. One way to reduce the amount of computation required in a high-throughput environment is to eliminate non-useful peaks. Existing noise removing algorithms are limited in their data-reduction capability and are compute intensive making them unsuitable for big data and high-throughput environments. In this paper we introduce a novel low-complexity technique based on classification, quantization and sampling of MS peaks.

Results: We present a novel data-reductive strategy for analysis of Big MS data. Our algorithm, called MS-REDUCE, is capable of eliminating noisy peaks as well as peaks that do not contribute to peptide deduction before any peptide deduction is attempted. Our experiments have shown up to 100× speed up over existing state of the art noise elimination algorithms while maintaining comparable high quality matches. Using our approach we were able to process a million spectra in just under an hour on a moderate server.

Availability and implementation: The developed tool and strategy has been made available to wider proteomics and parallel computing community and the code can be found at https://github.com/pcdslab/MSREDUCE

Contact: fahad.saeed@wmich.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
TFBSTools: an R/bioconductor package for transcription factor binding site analysis
Authors: Tan Ge , Lenhard Boris
Published: February 2016

Summary: The ability to efficiently investigate transcription factor binding sites (TFBSs) genome-wide is central to computational studies of gene regulation. TFBSTools is an R/Bioconductor package for the analysis and manipulation of TFBSs and their associated transcription factor profile matrices. TFBStools provides a toolkit for handling TFBS profile matrices, scanning sequences and alignments including whole genomes, and querying the JASPAR database. The functionality of the package can be easily extended to include advanced statistical analysis, data visualization and data integration.

Availability and implementation: The package is implemented in R and available under GPL-2 license from the Bioconductor website (http://bioconductor.org/packages/TFBSTools/).

Contact:  ge.tan09@imperial.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Differential methylation analysis for BS-seq data under general experimental design
Authors: Park Yongseok , Wu Hao
Published: February 2016

Motivation: DNA methylation is an epigenetic modification with important roles in many biological processes and diseases. Bisulfite sequencing (BS-seq) has emerged recently as the technology of choice to profile DNA methylation because of its accuracy, genome coverage and higher resolution. Current statistical methods to identify differential methylation mainly focus on comparing two treatment groups. With an increasing number of experiments performed under a general and multiple-factor design, particularly in reduced representation bisulfite sequencing, there is a need to develop more flexible, powerful and computationally efficient methods.

Results: We present a novel statistical model to detect differentially methylated loci from BS-seq data under general experimental design, based on a beta-binomial regression model with ‘arcsine’ link function. Parameter estimation is based on transformed data with generalized least square approach without relying on iterative algorithm. Simulation and real data analyses demonstrate that our method is accurate, powerful, robust and computationally efficient.

Availability and implementation: It is available as Bioconductor package DSS.

Contact:  yongpark@pitt.edu or hao.wu@emory.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Selecting a classification function for class prediction with gene expression data
Authors: Jong Victor L. , Novianti Putri W. , Roes Kit C.B. , Eijkemans Marinus J.C.
Published: February 2016

Motivation: Class predicting with gene expression is widely used to generate diagnostic and/or prognostic models. The literature reveals that classification functions perform differently across gene expression datasets. The question, which classification function should be used for a given dataset remains to be answered. In this study, a predictive model for choosing an optimal function for class prediction on a given dataset was devised.

Results: To achieve this, gene expression data were simulated for different values of gene-pairs correlations, sample size, genes' variances, deferentially expressed genes and fold changes. For each simulated dataset, ten classifiers were built and evaluated using ten classification functions. The resulting accuracies from 1152 different simulation scenarios by ten classification functions were then modeled using a linear mixed effects regression on the studied data characteristics, yielding a model that predicts the accuracy of the functions on a given data. An application of our model on eight real-life datasets showed positive correlations (0.33–0.82) between the predicted and expected accuracies.

Conclusion: The here presented predictive model might serve as a guide to choose an optimal classification function among the 10 studied functions, for any given gene expression data.

Availability and implementation: The R source code for the analysis and an R-package ‘SPreFuGED’ are available at Bioinformatics online.

Contact:  v.l.jong@umcutecht.nl

Supplementary information:  Supplementary data are available at Bioinformatics online.
Unipept web services for metaproteomics analysis
Authors: Mesuere Bart , Willems Toon , Van der Jeugt Felix , Devreese Bart , Vandamme Peter , Dawyndt Peter
Published: February 2016

Summary Unipept is an open source web application that is designed for metaproteomics analysis with a focus on interactive datavisualization. It is underpinned by a fast index built from UniProtKB and the NCBI taxonomy that enables quick retrieval of all UniProt entries in which a given tryptic peptide occurs. Unipept version 2.4 introduced web services that provide programmatic access to the metaproteomics analysis features. This enables integration of Unipept functionality in custom applications and data processing pipelines.

Availability and implementation: The web services are freely available at http://api.unipept.ugent.be and are open sourced under the MIT license.

Contact:  Unipept@ugent.be

Supplementary information:  Supplementary data are available at Bioinformatics online.
Galaxy Portal: interacting with the galaxy platform through mobile devices
Authors: Børnich Claus , Grytten Ivar , Hovig Eivind , Paulsen Jonas , Čech Martin , Sandve Geir Kjetil
Published: February 2016

Summary: We present Galaxy Portal app, an open source interface to the Galaxy system through smart phones and tablets. The Galaxy Portal provides convenient and efficient monitoring of job completion, as well as opportunities for inspection of results and execution history. In addition to being useful to the Galaxy community, we believe that the app also exemplifies a useful way of exploiting mobile interfaces for research/high-performance computing resources in general.

Availability and implementation: The source is freely available under a GPL license on GitHub, along with user documentation and pre-compiled binaries and instructions for several platforms: https://github.com/Tarostar/QMLGalaxyPortal. It is available for iOS version 7 (and newer) through the Apple App Store, and for Android through Google Play for version 4.1 (API 16) or newer.

Contact: geirksa@ifi.uio.no
FILTUS: a desktop GUI for fast and efficient detection of disease-causing variants, including a novel autozygosity detector
Authors: Vigeland Magnus D. , Gjøtterud Kristina S. , Selmer Kaja K.
Published: February 2016

Summary: FILTUS is a stand-alone tool for working with annotated variant files, e.g. when searching for variants causing Mendelian disease. Very flexible in terms of input file formats, FILTUS offers efficient filtering and a range of downstream utilities, including statistical analysis of gene sharing patterns, detection of de novo mutations in trios, quality control plots and autozygosity mapping. The autozygosity mapping is based on a hidden Markov model and enables accurate detection of autozygous regions directly from exome-scale variant files.

Availability and implementation: FILTUS is written in Python and runs on Windows, Mac and Linux. Binaries and source code are freely available at http://folk.uio.no/magnusv/filtus.html and on GitHub: https://github.com/magnusdv/filtus. Automatic installation is available via PyPI (e.g. pip install filtus).

Contact:  magnusdv@medisin.uio.no

Supplementary information:  Supplementary data are available at Bioinformatics online.
Sprites: detection of deletions from sequencing data by re-aligning split reads
Authors: Zhang Zhen , Wang Jianxin , Luo Junwei , Ding Xiaojun , Zhong Jiancheng , Wang Jun , Wu Fang-Xiang , Pan Yi
Published: February 2016

Motivation: Advances of next generation sequencing technologies and availability of short read data enable the detection of structural variations (SVs). Deletions, an important type of SVs, have been suggested in association with genetic diseases. There are three types of deletions: blunt deletions, deletions with microhomologies and deletions with microsinsertions. The last two types are very common in the human genome, but they pose difficulty for the detection. Furthermore, finding deletions from sequencing data remains challenging. It is highly appealing to develop sensitive and accurate methods to detect deletions from sequencing data, especially deletions with microhomology and deletions with microinsertion.

Results: We present a novel method called Sprites (SPlit Read re-alIgnment To dEtect Structural variants) which finds deletions from sequencing data. It aligns a whole soft-clipping read rather than its clipped part to the target sequence, a segment of the reference which is determined by spanning reads, in order to find the longest prefix or suffix of the read that has a match in the target sequence. This alignment aims to solve the problem of deletions with microhomologies and deletions with microinsertions. Using both simulated and real data we show that Sprites performs better on detecting deletions compared with other current methods in terms of F-score.

Availability and implementation: Sprites is open source software and freely available at https://github.com/zhangzhen/sprites.

Contact:  jxwang@mail.csu.edu.cn

Supplementary data:  Supplementary data are available at Bioinformatics online.
The geospatial data quality REST API for primary biodiversity data
Authors: Otegui Javier , Guralnick Robert P.
Published: February 2016

Summary: We present a REST web service to assess the geospatial quality of primary biodiversity data. It enables access to basic and advanced functions to detect completeness and consistency issues as well as general errors in the provided record or set of records. The API uses JSON for data interchange and efficient parallelization techniques for fast assessments of large datasets.

Availability and implementation: The Geospatial Data Quality API is part of the VertNet set of APIs. It can be accessed at http://api-geospatial.vertnet-portal.appspot.com/geospatial and is already implemented in the VertNet data portal for quality reporting. Source code is freely available under GPL license from http://www.github.com/vertnet/api-geospatial.

Contact:  javier.otegui@gmail.com or rguralnick@flmnh.ufl.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Model-based media selection to minimize the cost of metabolic cooperation in microbial ecosystems
Authors: Zampieri Mattia , Sauer Uwe
Published: February 2016

Motivation: Simple forms of mutualism between microorganisms are widespread in nature. Nevertheless, the role played by the environmental nutrient composition in mediating cross-feeding in microbial ecosystems is still poorly understood.

Results: Here, we use mixed-integer bilevel linear programming to investigate the cost of sharing metabolic resources in microbial communities. The algorithm infers an optimal combination of nutrients that can selectively sustain synergistic growth for a pair of species and guarantees minimum cost of cross-fed metabolites. To test model-based predictions, we selected a pair of Escherichia coli single gene knockouts auxotrophic, respectively, for arginine and leucine: ΔargB and ΔleuB and we experimentally verified that model-predicted medium composition significantly favors mutualism. Moreover, mass spectrometry profiling of exchanged metabolites confirmed the predicted cross-fed metabolites, supporting our constraint based modeling approach as a promising tool for engineering microbial consortia.

Availability and implementation: The software is freely available as a matlab script in the Supplementary materials.

Contact:  zampieri@imsb.biol.ethz.ch.

Supplementary information:  Supplementary data are available at Bioinformatics online.
Privacy-preserving microbiome analysis using secure computation
Authors: Wagner Justin , Paulson Joseph N. , Wang Xiao , Bhattacharjee Bobby , Corrada Bravo Héctor
Published: February 2016

Motivation: Developing targeted therapeutics and identifying biomarkers relies on large amounts of research participant data. Beyond human DNA, scientists now investigate the DNA of micro-organisms inhabiting the human body. Recent work shows that an individual’s collection of microbial DNA consistently identifies that person and could be used to link a real-world identity to a sensitive attribute in a research dataset. Unfortunately, the current suite of DNA-specific privacy-preserving analysis tools does not meet the requirements for microbiome sequencing studies.

Results: To address privacy concerns around microbiome sequencing, we implement metagenomic analyses using secure computation. Our implementation allows comparative analysis over combined data without revealing the feature counts for any individual sample. We focus on three analyses and perform an evaluation on datasets currently used by the microbiome research community. We use our implementation to simulate sharing data between four policy-domains. Additionally, we describe an application of our implementation for patients to combine data that allows drug developers to query against and compensate patients for the analysis.

Availability and implementation: The software is freely available for download at: http://cbcb.umd.edu/∼hcorrada/projects/secureseq.html

Supplementary information:  Supplementary data are available at Bioinformatics online.

Contact:  hcorrada@umiacs.umd.edu
Trinculo: Bayesian and frequentist multinomial logistic regression for genome-wide association studies of multi-category phenotypes
Authors: Jostins Luke , McVean Gilean
Published: February 2016

Motivation: For many classes of disease the same genetic risk variants underly many related phenotypes or disease subtypes. Multinomial logistic regression provides an attractive framework to analyze multi-category phenotypes, and explore the genetic relationships between these phenotype categories. We introduce Trinculo, a program that implements a wide range of multinomial analyses in a single fast package that is designed to be easy to use by users of standard genome-wide association study software.

Availability and implementation: An open source C implementation, with code and binaries for Linux and Mac OSX, is available for download at http://sourceforge.net/projects/trinculo

Supplementary information:  Supplementary data are available at Bioinformatics online.

Contact: lj4@well.ox.ac.uk