bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nano‐ampere PTAT current source with temperature inaccuracy <±1°C
Authors: Chouhan S.S. , Halonen K. 
Published: December 2014

The architecture for generating a nano‐ampere proportional to absolute temperature (PTAT) current source is proposed. The circuit has been designed and fabricated in a standard 180 nm CMOS technology. Measurements were performed on 10 prototypes in the temperature range of −40 to +85°C. The operating supply voltage of the proposed circuit is 850 mV ± 10%. The measured averaged temperature inaccuracy and the linearity of the proposed architecture is between +0.86/− 0.93°C and +0.69/−0.75%, respectively.
6.2 GHz 0.5 mW two‐dimensional oscillator array‐based injection‐locked frequency divider in 0.18 μm CMOS
Authors: Yu Xiaopeng , Song Xiong , Lim Wei Meng , Yeo Kiat‐Seng 
Published: December 2014

A new two‐dimensional oscillator array‐based injection‐locked frequency divider is proposed. Instead of using the conventional analogue tuning technique or the one‐dimensional delay chain, a two‐dimensional array is implemented to digitally and precisely control the total delay in the oscillator core. This makes it possible to achieve a programmable delay, hence attaining potential programmable division ratios for the injection‐locked divider. Fabricated in a standard 0.18 μm CMOS technology, a prototype chip, namely a divide‐by‐4/5 prescaler using this technique, is able to work up to 6.2 GHz with 0.5 mW power consumption from a 1.8 V supply voltage.
Compact lowpass filter with wide stopband using stepped impedance hairpin units
Authors: Liu Shuai , Xu Jun , Xu Zhitao 
Published: December 2014

A novel microstrip lowpass filter (LPF) with a wide stopband is presented. The basic resonator is composed of two stepped impedance hairpin units with one embedded in another, which can obtain two more transmission zeros and extend a wide stopband. Based on the proposed resonator, a demonstration LPF of compact size, sharp transition and wide stopband has been designed, fabricated and measured. The proposed filter exhibits a small size of 0.081λg × 0.113λg, where λg is the waveguide length at the cutoff frequency of 1.6 GHz. Results show good agreement with simulations and the 20 dB rejection stopband can be extended to more than 15 GHz.
Life cycle air quality impacts of conventional and alternative light-duty transportation in the United States
Authors: Tessum Christopher W. , Hill Jason D. , Marshall Julian D. 
Published: December 2014

Significance
Our assessment of the life cycle air quality impacts on human health of 10 alternatives to conventional gasoline vehicles finds that electric vehicles (EVs) powered by electricity from natural gas or wind, water, or solar power are best for improving air quality, whereas vehicles powered by corn ethanol and EVs powered by coal are the worst. This work advances the current debate over the environmental impacts of conventional versus alternative transportation options by combining detailed spatially and temporally explicit emissions inventories with state-of-the-science air quality impact analysis using advanced chemical transport modeling. Our results reinforce previous findings that air quality-related health damages from transportation are generally comparable to or larger than climate change-related damages.
Myosin binding protein-C activates thin filaments and inhibits thick filaments in heart muscle cells
Authors: Kampourakis Thomas , Yan Ziqian , Gautel Mathias , Sun Yin-Biao , Irving Malcolm 
Published: December 2014

Significance
Myosin binding protein-C (MyBP-C) is a regulatory protein of heart muscle. Mutations in MyBP-C are frequently associated with heart disease, but the mechanism of action of MyBP-C is poorly understood. By characterizing the effects of its N-terminal domains on the structures of the thin and thick filaments in contracting heart muscle cells, we showed that MyBP-C stabilizes the ON state of thin filaments and the OFF state of thick filaments. The results lead to a model for the control of heart muscle contraction in which the regulatory functions of the thin and thick filaments are coordinated by MyBP-C, providing an integrated framework for the design and development of therapeutic interventions in heart disease.
Complementary genomic approaches highlight the PI3K/mTOR pathway as a common vulnerability in osteosarcoma
Authors: Perry Jennifer A. , Kiezun Adam , Tonzi Peter , Van Allen Eliezer M. , Carter Scott L. , Baca Sylvan C. , Cowley Glenn S. , Bhatt Ami S. , Rheinbay Esther , Pedamallu Chandra Sekhar , Helman Elena , Taylor-Weiner Amaro , McKenna Aaron , DeLuca David S. , Lawrence Michael S. , Ambrogio Lauren , Sougnez Carrie , Sivachenko Andrey , Walensky Loren D. , Wagle Nikhil , Mora Jaume , de Torres Carmen , Lavarino Cinzia , Dos Santos Aguiar Simone , Yunes Jose Andres , Brandalise Silvia Regina , Mercado-Celis Gabriela Elisa , Melendez-Zajgla Jorge , Cárdenas-Cardós Rocío , Velasco-Hidalgo Liliana , Roberts Charles W. M. , Garraway Levi A. , Rodriguez-Galindo Carlos , Gabriel Stacey B. , Lander Eric S. , Golub Todd R. , Orkin Stuart H. , Getz Gad , Janeway Katherine A. 
Published: December 2014

SignificanceWe present, to our knowledge, the first comprehensive next-generation sequencing of osteosarcoma in combination with a functional genomic screen in a genetically defined mouse model of osteosarcoma. Our data provide a strong rationale for targeting the phosphatidylinositol 3-kinase/mammalian target of rapamycin pathway in osteosarcoma and a foundation for rational clinical trial design. These findings present an immediate clinical opportunity because multiple inhibitors of this pathway are currently in clinical trials.
Auxin depletion from leaf primordia contributes to organ patterning
Authors: Qi Jiyan , Wang Ying , Yu Ting , Cunha Alexandre , Wu Binbin , Vernoux Teva , Meyerowitz Elliot , Jiao Yuling 
Published: December 2014

Significance
Stem cells not only initiate organs, but may also contribute to organ patterning, at least in the shoot apex of flowering plants: classical microsurgical experiments imply that the shoot apical meristem promotes development of the leaf adaxial side, i.e., the upper side. In this study, we show the existence of a transient low auxin zone in the adaxial side that contributes to adaxial development. We further find that this adaxial low auxin zone results from auxin transport from leaves to the shoot apex. Thus, it is not a positive signal from stem cells, but departure of a signaling molecule from primordia to stem cells, that delivers polarity information—opposite to what is generally assumed.
Structural dynamics inside a functionalized metal–organic framework probed by ultrafast 2D IR spectroscopy
Authors: Nishida Jun , Tamimi Amr , Fei Honghan , Pullen Sonja , Ott Sascha , Cohen Seth M. , Fayer Michael D. 
Published: December 2014

Significance
A unique aspect of metal–organic frameworks (MOFs) is their structural flexibility coexisting with a degree of regularity. Adsorbed guest molecules can cause MOF pore shapes to deform. Pore shape changes may be related to the high capacity and selectivity of the MOFs for gas adsorption and other processes. MOF flexibility and other properties are influenced by fast dynamics of the framework. Direct measurements to characterize fast motions of the MOFs have not been applied previously. We show that 2D IR spectroscopy can be performed on functionalized MOFs. We use 2D IR and other ultrafast IR methods to elucidate the timescales for ultrafast structural fluctuations and how they are influenced by a solvent filling the pores.
Estrogen-related receptor α is required for efficient human cytomegalovirus replication
Authors: Hwang Jesse , Purdy John G. , Wu Kai , Rabinowitz Joshua D. , Shenk Thomas 
Published: December 2014

Significance
Viruses use the host cell’s resources, including numerous cellular metabolites, to successfully replicate and produce progeny. Here, we report that estrogen-related receptor α (ERRα), an orphan nuclear receptor and transcriptional regulator, supports the expression of multiple metabolic enzymes that contribute to the metabolic program induced by human cytomegalovirus in cultured primary fibroblasts. Loss or inhibition of ERRα impedes the viral replication cycle at multiple levels, leading to a reduction in progeny virus. Our findings identify ERRα as a host factor that is manipulated by the virus for its replicative needs and establish its potential as a pharmacological target for treatment of cytomegalovirus infection.
Ramalin inhibits VCAM-1 expression and adhesion of monocyte to vascular smooth muscle cells through MAPK and PADI4-dependent NF-kB and AP-1 pathways
Authors: Park Bongkyun , Yim Joung-Han , Lee Hong-Kum , Kim Byung-Oh , Pyo Suhkneung 
Published: December 2014

Abstract
Cell adhesion molecules play a critical role in inflammatory processes and atherosclerosis. In this study, we investigated the effect of ramalin, a chemical compound from the Antarctic lichen Ramalina terebrata, on vascular cell adhesion molecule-1 (VCAM-1) expression induced by TNF-α in vascular smooth muscular cells (VSMCs). Pretreatment of VSMCs with ramalin (0.1–10 μg/mL) concentration-dependently inhibited TNF-α-induced VCAM-1 expression. Additionally, ramalin inhibited THP-1 (human acute monocytic leukemia cell line) cell adhesion to TNF-α-stimulated VSMCs. Ramalin suppressed TNF-α-induced production of reactive oxygen species (ROS), PADI4 expression, and phosphorylation of p38, ERK, and JNK. Moreover, ramalin inhibited TNF-α-induced translocation of NF-κB and AP-1. Inhibition of PADI4 expression by small interfering RNA or the PADI4-specific inhibitor markedly attenuated TNF-α-induced activation of NF-κB and AP-1 and VCAM-1 expression in VSMCs. Our study provides insight into the mechanisms underlying ramalin activity and suggests that ramalin may be a potential therapeutic agent to modulate inflammation within atherosclerosis.
High-level expression of tamavidin 2 in human cells by codon-usage optimization
Authors: Takakura Yoshimitsu , Katayama Sakurako , Nagata Yuki 
Published: December 2014

AbstractTamavidin 2 is a fungal protein that binds to biotin with an extremely high affinity. Tamavidin 2 is superior to avidin or streptavidin in terms of its low-level non-specific binding and high-level thermal stability. However, the gene for tamavidin 2 is highly expressed in Escherichia coli but not in mammalian cells, restricting its application as an affinity tag in mammalian cells. Here, we optimized the codon usage of tamavidin 2 for human cells and found that the resultant mutant expressed tamavidin 2 at approximately 30-fold higher level compared with the native gene. The protein thus produced in human cells could be purified by iminobiotin affinity chromatography, bound tightly to biotin, and was stable at high temperature (82 °C). This powerful technology for high-level expression of tamavidin 2 in mammalian cells will be of value in evaluating various fusion proteins produced in mammalian cells for numerous applications.
THE CONTINUED OPTICAL TO MID-INFRARED EVOLUTION OF V838 MONOCEROTIS*
Authors: Loebman S. R. , Wisniewski J. P. , Schmidt S. J. , Kowalski A. F. , Barry R. K. , Bjorkman K. S. , Hammel H. B. , Hawley S. L. , Hebb L. , Kasliwal M. M. , Lynch D. K. , Russell R. W. , Sitko M. L. , Szkody P. 
Published: December 2014

ABSTRACT
The eruptive variable V838 Monocerotis (V838 Mon) gained notoriety in 2002 when it brightened nine magnitudes in a series of three outbursts and then rapidly evolved into an extremely cool supergiant. We present optical, near-infrared (near-IR), and mid-IR spectroscopic and photometric observations of V838 Mon obtained between 2008 and 2012 at the Apache Point Observatory 3.5 m, NASA IRTF 3 m, and Gemini South 8 m telescopes. We contemporaneously analyze the optical and IR spectroscopic properties of V838 Mon to arrive at a revised spectral type L3 supergiant and effective temperature

–2200 K. Because there are no existing optical observational data for L supergiants, we speculate that V838 Mon may represent the prototype for L supergiants in this wavelength regime. We find a low level of Hα emission present in the system, consistent with interaction between V838 Mon and its B3V binary; however, we cannot rule out a stellar collision as the genesis event, which could result in the observed Hα activity. Based upon a two-component blackbody fit to all wavelengths of our data, we conclude that, as of 2009, a shell of ejecta surrounded V838 Mon at a radius of

AU with a temperature of

K. This result is consistent with IR interferometric observations from the same era and predictions from the Lynch et al. model of the expanding system, which provides a simple framework for understanding this complicated system.
A FRAMEWORK FOR COLLABORATIVE REVIEW OF CANDIDATE EVENTS IN HIGH DATA RATE STREAMS: THE V-FASTR EXPERIMENT AS A CASE STUDY
Authors: Hart Andrew F. , Cinquini Luca , Khudikyan Shakeh E. , Thompson David R. , Mattmann Chris A. , Wagstaff Kiri , Lazio Joseph , Jones Dayton 
Published: December 2014

ABSTRACT
“Fast radio transients” are defined here as bright millisecond pulses of radio-frequency energy. These short-duration pulses can be produced by known objects such as pulsars or potentially by more exotic objects such as evaporating black holes. The identification and verification of such an event would be of great scientific value. This is one major goal of the Very Long Baseline Array (VLBA) Fast Transient Experiment (V-FASTR), a software-based detection system installed at the VLBA. V-FASTR uses a “commensal” (piggy-back) approach, analyzing all array data continually during routine VLBA observations and identifying candidate fast transient events. Raw data can be stored from a buffer memory, which enables a comprehensive off-line analysis. This is invaluable for validating the astrophysical origin of any detection. Candidates discovered by the automatic system must be reviewed each day by analysts to identify any promising signals that warrant a more in-depth investigation. To support the timely analysis of fast transient detection candidates by V-FASTR scientists, we have developed a metadata-driven, collaborative candidate review framework. The framework consists of a software pipeline for metadata processing composed of both open source software components and project-specific code written expressly to extract and catalog metadata from the incoming V-FASTR data products, and a web-based data portal that facilitates browsing and inspection of the available metadata for candidate events extracted from the VLBA radio data.
Prevalence, Determinants, and Clinical Significance of Masked Hypertension in a Population-Based Sample of African Americans: The Jackson Heart Study
Authors: Diaz Keith M. , Veerabhadrappa Praveen , Brown Michael D. , Whited Matthew C. , Dubbert Patricia M. , Hickson DeMarc A. 
Published: December 2014

BACKGROUND
The disproportionate rates of cardiovascular disease in African Americans may, in part, be due to suboptimal assessment of blood pressure (BP) with clinic BP measurements alone. To date, however, the prevalence of masked hypertension in African Americans has not been fully delineated. The purpose of this study was to evaluate masked hypertension prevalence in a large population-based sample of African Americans and examine its determinants and association with indices of target organ damage (TOD).

METHODS
Clinic and 24-hour ambulatory BP monitoring were conducted in 972 African Americans enrolled in the Jackson Heart Study. Common carotid artery intima-media thickness, left ventricular mass index, and the urinary albumin:creatinine excretion ratio were evaluated as indices of TOD.

RESULTS
Masked hypertension prevalence was 25.9% in the overall sample and 34.4% in participants with normal clinic BP. All indices of TOD were significantly higher in masked hypertensives compared to sustained normotensives and were similar between masked hypertensives and sustained hypertensives. Male gender, smoking, diabetes, and antihypertensive medication use were independent determinants of masked hypertension in multivariate analyses.

CONCLUSIONS
In this population-based cohort of African Americans, approximately one-third of participants with presumably normal clinic BP had masked hypertension when BP was assessed in their daily environment. Masked hypertension was accompanied by a greater degree of TOD in this cohort.
Identifying cancer-related microRNAs based on gene expression data
Authors: Zhao Xing-Ming , Liu Ke-Qin , Zhu Guanghui , He Feng , Duval Béatrice , Richer Jean-Michel , Huang De-Shuang , Jiang Chang-Jun , Hao Jin-Kao , Chen Luonan 
Published: December 2014

Abstract
Motivation: MicroRNAs (miRNAs) are short non-coding RNAs that play important roles in post-transcriptional regulations as well as other important biological processes. Recently, accumulating evidences indicate that miRNAs are extensively involved in cancer. However, it is a big challenge to identify which miRNAs are related to which cancer considering the complex processes involved in tumors, where one miRNA may target hundreds or even thousands of genes and one gene may regulate multiple miRNAs. Despite integrative analysis of matched gene and miRNA expression data can help identify cancer-associated miRNAs, such kind of data is not commonly available. On the other hand, there are huge amount of gene expression data that are publicly accessible. It will significantly improve the efficiency of characterizing miRNA’s function in cancer if we can identify cancer miRNAs directly from gene expression data.
Results: We present a novel computational framework to identify the cancer-related miRNAs based solely on gene expression profiles without requiring either miRNA expression data or the matched gene and miRNA expression data. The results on multiple cancer datasets show that our proposed method can effectively identify cancer-related miRNAs with higher precision compared with other popular approaches. Furthermore, some of our novel predictions are validated by both differentially expressed miRNAs and evidences from literature, implying the predictive power of our proposed method. In addition, we construct a cancer-miRNA-pathway network, which can help explain how miRNAs are involved in cancer.
Availability and implementation: The R code and data files for the proposed method are available at http://comp-sysbio.org/miR_Path/
Contact: liukeq@gmail.com
Supplementary information: supplementary data are available at Bioinformatics online.
JEPEG: a summary statistics based tool for gene-level joint testing of functional variants
Authors: Lee Donghyung , Williamson Vernell S. , Bigdeli T. Bernard , Riley Brien P. , Fanous Ayman H. , Vladimirov Vladimir I. , Bacanu Silviu-Alin 
Published: December 2014

Abstract
Motivation: Gene expression is influenced by variants commonly known as expression quantitative trait loci (eQTL). On the basis of this fact, researchers proposed to use eQTL/functional information univariately for prioritizing single nucleotide polymorphisms (SNPs) signals from genome-wide association studies (GWAS). However, most genes are influenced by multiple eQTLs which, thus, jointly affect any downstream phenotype. Therefore, when compared with the univariate prioritization approach, a joint modeling of eQTL action on phenotypes has the potential to substantially increase signal detection power. Nonetheless, a joint eQTL analysis is impeded by (i) not measuring all eQTLs in a gene and/or (ii) lack of access to individual genotypes.
Results: We propose joint effect on phenotype of eQTL/functional SNPs associated with a gene (JEPEG), a novel software tool which uses only GWAS summary statistics to (i) impute the summary statistics at unmeasured eQTLs and (ii) test for the joint effect of all measured and imputed eQTLs in a gene. We illustrate the behavior/performance of the developed tool by analysing the GWAS meta-analysis summary statistics from the Psychiatric Genomics Consortium Stage 1 and the Genetic Consortium for Anorexia Nervosa.
Conclusions: Applied analyses results suggest that JEPEG complements commonly used univariate GWAS tools by: (i) increasing signal detection power via uncovering (a) novel genes or (b) known associated genes in smaller cohorts and (ii) assisting in fine-mapping of challenging regions, e.g. major histocompatibility complex for schizophrenia.
Availability and implementation: JEPEG, its associated database of eQTL SNPs and usage examples are publicly available at http://code.google.com/p/jepeg/.
Contact: dlee4@vcu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Sputnik: ad hoc distributed computation
Authors: Völkel Gunnar , Lausser Ludwig , Schmid Florian , Kraus Johann M. , Kestler Hans A. 
Published: December 2014

Abstract
Motivation: In bioinformatic applications, computationally demanding algorithms are often parallelized to speed up computation. Nevertheless, setting up computational environments for distributed computation is often tedious. Aim of this project were the lightweight ad hoc set up and fault-tolerant computation requiring only a Java runtime, no administrator rights, while utilizing all CPU cores most effectively.
Results: The Sputnik framework provides ad hoc distributed computation on the Java Virtual Machine which uses all supplied CPU cores fully. It provides a graphical user interface for deployment setup and a web user interface displaying the current status of current computation jobs. Neither a permanent setup nor administrator privileges are required. We demonstrate the utility of our approach on feature selection of microarray data.
Availability and implementation: The Sputnik framework is available on Github http://github.com/sysbio-bioinf/sputnik under the Eclipse Public License.
Contact: hkestler@fli-leibniz.de or hans.kestler@uni-ulm.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Epock: rapid analysis of protein pocket dynamics
Authors: Laurent Benoist , Chavent Matthieu , Cragnolini Tristan , Dahl Anna Caroline E. , Pasquali Samuela , Derreumaux Philippe , Sansom Mark S.P. , Baaden Marc 
Published: December 2014

Abstract
Summary: The volume of an internal protein pocket is fundamental to ligand accessibility. Few programs that compute such volumes manage dynamic data from molecular dynamics (MD) simulations. Limited performance often prohibits analysis of large datasets. We present Epock, an efficient command-line tool that calculates pocket volumes from MD trajectories. A plugin for the VMD program provides a graphical user interface to facilitate input creation, run Epock and analyse the results.
Availability and implementation: Epock C++ source code, Python analysis scripts, VMD Tcl plugin, documentation and installation instructions are freely available at http://epock.bitbucket.org.
Contact: benoist.laurent@gmail.com or baaden@smplinux.de
Supplementary information: Supplementary data are available at Bioinformatics online.