bluuebunny/crossref_metadata_2025 huggingface dataset:
Local false discovery rate estimation using feature reliability in LC/MS metabolomics data
Authors: Chong Elizabeth Y. , Huang Yijian , Wu Hao , Ghasemzadeh Nima , Uppal Karan , Quyyumi Arshed A. , Jones Dean P. , Yu Tianwei
Published: November 2015

False discovery rate (FDR) control is an important tool of statistical inference in feature selection. In mass spectrometry-based metabolomics data, features can be measured at different levels of reliability and false features are often detected in untargeted metabolite profiling as chemical and/or bioinformatics noise. The traditional false discovery rate methods treat all features equally, which can cause substantial loss of statistical power to detect differentially expressed features. We propose a reliability index for mass spectrometry-based metabolomics data with repeated measurements, which is quantified using a composite measure. We then present a new method to estimate the local false discovery rate (lfdr) that incorporates feature reliability. In simulations, our proposed method achieved better balance between sensitivity and controlling false discovery, as compared to traditional lfdr estimation. We applied our method to a real metabolomics dataset and were able to detect more differentially expressed metabolites that were biologically meaningful.
Production of liquid hydrocarbon fuels with acetoin and platform molecules derived from lignocellulose
Authors: Zhu Chenjie , Shen Tao , Liu Dong , Wu Jinglan , Chen Yong , Wang Linfeng , Guo Kai , Ying Hanjie , Ouyang Pingkai
Published: November 2015

Acetoin, a novel C4 platform molecule derived from a new ABE fermentation system was used as a bio-based building block for the production of liquid hydrocarbon fuels.
A novel protocol for the one-pot borylation/Suzuki reaction provides easy access to hinge-binding groups for kinase inhibitors
Authors: Hooper A. , Zambon A. , Springer C. J.
Published: November 2015

This new microwave-assisted method provides a quick one-pot borylation/Suzuki protocol that does not require additional ligands nor double loading of catalyst.
Biomedical potential of natural products derived through metagenomic approaches
Authors: Sanka Loganathachetti Dinesh , Muthuraman Sundararaman
Published: November 2015

Microbes are ubiquitous, irrespective of the environment they thrive in. Only 1% of these are culturable in laboratory. Metagenomics is useful in exploring biomedically important small molecules using culture independent approaches.
Space charge-induced unusually-high mobility of a solution-processed indium oxide thin film transistor with an ethylene glycol incorporated aluminum oxide gate dielectric
Authors: Park Hyungjin , Nam Yunyong , Jin Jungho , Bae Byeong-Soo
Published: November 2015

Undecomposed ethylene glycol residuals in solution processed aluminum oxide gate dielectric result in the frequency-dependent capacitance.
Luminescence properties of Na3LuSi3O9:Ce3+ as a potential scintillator material
Authors: Zhou Jianbang , Pan Fengjuan , Zhong Jiuping , Liang Hongbin , Su Qiang , Moretti Federico , Lebbou Kheirreddine , Dujardin Christophe
Published: November 2015

Comparison between the X-ray excited luminescence spectra of the Bi4Ge3O12 (BGO) and Na3Lu0.99Ce0.01Si3O9 powders.
Elucidating the fundamental forces in protein crystal formation: the case of crambin
Authors: Delle Piane Massimo , Corno Marta , Orlando Roberto , Dovesi Roberto , Ugliengo Piero
Published: November 2015

This study demonstrates the feasibility of periodic all-electron hybrid density functional theory calculations in the description of protein crystals, using crambin as a test case.
Enhanced high temperature thermoelectric response of sulphuric acid treated conducting polymer thin films
Authors: Kumar S. R. Sarath , Kurra Narendra , Alshareef H. N.
Published: November 2015

Enhanced thermoelectric response of acid treated conducting polymer thin films.
Mitochondrial dysfunction in fatty acid oxidation disorders: insights from human and animal studies
Authors: Wajner Moacir , Amaral Alexandre Umpierrez
Published: November 2015

Mitochondrial fatty acid oxidation (FAO) plays a pivotal role in maintaining body energy homoeostasis mainly during catabolic states. Oxidation of fatty acids requires approximately 25 proteins. Inherited defects of FAO have been identified in the majority of these proteins and constitute an important group of inborn errors of metabolism. Affected patients usually present with severe hepatopathy, cardiomyopathy and skeletal myopathy, whereas some patients may suffer acute and/or progressive encephalopathy whose pathogenesis is poorly known. In recent years growing evidence has emerged indicating that energy deficiency/disruption of mitochondrial homoeostasis is involved in the pathophysiology of some fatty acid oxidation defects (FAOD), although the exact underlying mechanisms are not yet established. Characteristic fatty acids and carnitine derivatives are found at high concentrations in these patients and more markedly during episodes of metabolic decompensation that are associated with worsening of clinical symptoms. Therefore, it is conceivable that these compounds may be toxic. We will briefly summarize the current knowledge obtained from patients and genetic mouse models with these disorders indicating that disruption of mitochondrial energy, redox and calcium homoeostasis is involved in the pathophysiology of the tissue damage in the more common FAOD, including medium-chain acyl-CoA dehydrogenase (MCAD), long-chain 3-hydroxyacyl-CoA dehydrogenase (LCHAD) and very long-chain acyl-CoA dehydrogenase (VLCAD) deficiencies. We will also provide evidence that the fatty acids and derivatives that accumulate in these diseases disrupt mitochondrial homoeostasis. The elucidation of the toxic mechanisms of these compounds may offer new perspectives for potential novel adjuvant therapeutic strategies in selected disorders of this group.
Three macroscopic indices for describing the quality of AC/DC power grid structures
Authors: Xu Zheng , Song Pengcheng , Huang Hongyang
Published: November 2015

This study proposes three macroscopic indices to evaluate the quality of AC/DC hybrid power grid structures, which are the corridor strength index, the voltage support strength index and the frequency support strength index. The corridor strength index includes the ratio of the AC corridor strength to the DC corridor strength and the strength of the AC corridor to resist the sudden power transferred from the DC corridor. The multi‐infeed effective short‐circuit ratio is used as the voltage support strength index to evaluate the voltage support ability for the DC converter stations. The frequency bias factor is adopted as the frequency support strength index to measure the frequency support ability of the power grids. These three macroscopic indices can reflect some important qualities of the AC/DC hybrid power grid structures and provide an effective tool for quantitative assessments of the AC/DC hybrid power grid structures. Application of the three indices in China Southern Power Grid is presented, which proves the validity of the three indices.
Impulsive noise reduction for transient Earth voltage‐based partial discharge using Wavelet‐entropy
Authors: Luo Guomin , Zhang Daming , Tseng King Jet , He Jinghan
Published: November 2015

Partial discharge (PD) is caused by the localised electrical field intensification in insulating materials. Early detection and accurate measurement of PD are very important for preventing premature failure of the insulating material. Detection of PDs in metal‐clad apparatus through the transient Earth voltage method is a promising approach in non‐intrusive on‐line tests. However, the electrical interference from background environment remains the major barrier to improving its measurement accuracy. In this study, a wavelet‐entropy‐based PD de‐noising method has been proposed. The unique features of PD are characterised by combining wavelet analysis that reveals the local features and entropy that measures the disorder. With such features, a feed‐forward back‐propagation artificial neural network is adopted to recognise the actual PDs from noisy background. Comparing with other methods such as the energy‐based method and the similarity‐comparing method, the proposed wavelet‐entropy‐based method is more effective in PD signal de‐noising.
Physiological trade-offs of stomatal closure under high evaporative gradients in field grown soybean
Authors: Medina Viviana , Gilbert Matthew E.
Published: November 2015

Limited rainfall is the main constraint to agriculture, making agricultural research to understand plant behaviour that leads to avoidance of soil water deficit a matter of priority. One focus has screened for crop varieties that decrease stomatal conductance under high vapour pressure deficit (VPD), a proxy for the leaf evaporative gradient. However, the link between stomatal closure and physiological consequences in field environments is not yet clear. A field experiment on soybeans demonstrated that considerable variation in leaf temperature relative to air temperature occurred, leading to evaporative gradients differing substantially from VPD. Thus, transpiration is decreased by stomatal closure at high VPD, but to compensate, transpiration is somewhat increased due to higher leaf temperatures. Soil water deficit led to lower stomatal conductance, particularly under low evaporative conditions, not just under hot conditions. Non-stomatal photosynthetic limitations were observed due to combined occurrence of stomatal closure and high temperature under high VPD. Although leaves reached temperatures higher than the threshold for a decrease in maximum photochemical efficiency, and displayed non-stomatal photosynthetic limitations, no photoinhibition or damage was observed by night-time. The results demonstrate that more understanding of physiological strategies for achieving altered water use is needed to avoid trade-offs and heat stress.
iPQF: a new peptide-to-protein summarization method using peptide spectra characteristics to improve protein quantification
Authors: Fischer Martina , Renard Bernhard Y.
Published: November 2015

Motivation: Isobaric labelling techniques such as iTRAQ and TMT are popular methods for relative protein abundance estimation in proteomic studies. However, measurements are assessed at the peptide spectrum level and exhibit substantial heterogeneity per protein. Hence, clever summarization strategies are required to infer protein ratios. So far, current methods rely exclusively on quantitative values, while additional information on peptides is available, yet it is not considered in these methods.

Methods: We present iPQF (isobaric Protein Quantification based on Features) as a novel peptide-to-protein summarization method, which integrates peptide spectra characteristics as well as quantitative values for protein ratio estimation. We investigate diverse features characterizing spectra reliability and reveal significant correlations to ratio accuracy in spectra. As a result, we developed a feature-based weighting of peptide spectra.

Results: A performance evaluation of iPQF in comparison to nine different protein ratio inference methods is conducted on five published MS2 and MS3 datasets with predefined ground truth. We demonstrate the benefit of using peptide feature information to improve protein ratio estimation. Compared to purely quantitative approaches, our proposed strategy achieves increased accuracy by addressing peptide spectra reliability.

Availability and implementation: The iPQF algorithm is available within the established R/Bioconductor package MSnbase (version ≥ 1.17.8).

Contact:  renardB@rki.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
CDSfold: an algorithm for designing a protein-coding sequence with the most stable secondary structure
Authors: Terai Goro , Kamegai Satoshi , Asai Kiyoshi
Published: November 2015

Motivation: An important problem in synthetic biology is to design a nucleotide sequence of an mRNA that confers a desirable expression level of a target protein. The secondary structure of protein-coding sequences (CDSs) is one potential factor that could have both positive and negative effects on protein production. To elucidate the role of secondary structure in CDSs, algorithms for manipulating secondary structure should be developed.

Results: We developed an algorithm for designing a CDS with the most stable secondary structure among all possible ones translated into the same protein, and implemented it as the program CDSfold. The algorithm runs the Zuker algorithm under the constraint of a given amino acid sequence. The time and space complexity is O(L3) and O(L2), respectively, where L is the length of the CDS to be designed. Although our algorithm is slower than the original Zuker algorithm, it could design a relatively long (2.7-kb) CDS in approximately 1 h.

Availability and implementation: The CDSfold program is freely available for non-commercial users as stand-alone and web-based software from http://cdsfold.trahed.jp/cdsfold/.

Contacts:  terai-goro@aist.go.jp or asai@k.u-tokyo.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
AccessFold: predicting RNA–RNA interactions with consideration for competing self-structure
Authors: DiChiacchio Laura , Sloma Michael F. , Mathews David H.
Published: November 2015

Motivation: There are numerous examples of RNA–RNA complexes, including microRNA–mRNA and small RNA–mRNA duplexes for regulation of translation, guide RNA interactions with target RNA for post-transcriptional modification and small nuclear RNA duplexes for splicing. Predicting the base pairs formed between two interacting sequences remains difficult, at least in part because of the competition between unimolecular and bimolecular structure.

Results: Two algorithms were developed for improved prediction of bimolecular RNA structure that consider the competition between self-structure and bimolecular structure. These algorithms utilize two novel approaches to evaluate accessibility: free energy density minimization and pseudo-energy minimization. Free energy density minimization minimizes the folding free energy change per nucleotide involved in an intermolecular secondary structure. Pseudo-energy minimization (called AccessFold) minimizes the sum of free energy change and a pseudo-free energy penalty for bimolecular pairing of nucleotides that are unlikely to be accessible for bimolecular structure. The pseudo-free energy, derived from unimolecular pairing probabilities, is applied per nucleotide in bimolecular pairs, and this approach is able to predict binding sites that are split by unimolecular structures. A benchmark set of 17 bimolecular RNA structures was assembled to assess structure prediction. Pseudo-energy minimization provides a statistically significant improvement in sensitivity over the method that was found in a benchmark to be the most accurate previously available method, with an improvement from 36.8% to 57.8% in mean sensitivity for base pair prediction.

Availability and implementation: Pseudo-energy minimization is available for download as AccessFold, under an open-source license and as part of the RNAstructure package, at: http://rna.urmc.rochester.edu/RNAstructure.html.

Contact:  david_mathews@urmc.rochester.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Large-scale machine learning for metagenomics sequence classification
Authors: Vervier Kévin , Mahé Pierre , Tournoud Maud , Veyrieras Jean-Baptiste , Vert Jean-Philippe
Published: November 2015

Motivation: Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is assigned to a taxonomic clade. Because of the large volume of metagenomics datasets, binning methods need fast and accurate algorithms that can operate with reasonable computing requirements. While standard alignment-based methods provide state-of-the-art performance, compositional approaches that assign a taxonomic class to a DNA read based on the k-mers it contains have the potential to provide faster solutions.

Results: We propose a new rank-flexible machine learning-based compositional approach for taxonomic assignment of metagenomics reads and show that it benefits from increasing the number of fragments sampled from reference genome to tune its parameters, up to a coverage of about 10, and from increasing the k-mer size to about 12. Tuning the method involves training machine learning models on about 108 samples in 107 dimensions, which is out of reach of standard softwares but can be done efficiently with modern implementations for large-scale machine learning. The resulting method is competitive in terms of accuracy with well-established alignment and composition-based tools for problems involving a small to moderate number of candidate species and for reasonable amounts of sequencing errors. We show, however, that machine learning-based compositional approaches are still limited in their ability to deal with problems involving a greater number of species and more sensitive to sequencing errors. We finally show that the new method outperforms the state-of-the-art in its ability to classify reads from species of lineage absent from the reference database and confirm that compositional approaches achieve faster prediction times, with a gain of 2–17 times with respect to the BWA-MEM short read mapper, depending on the number of candidate species and the level of sequencing noise.

Availability and implementation: Data and codes are available at http://cbio.ensmp.fr/largescalemetagenomics.

Contact:  pierre.mahe@biomerieux.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
SomVarIUS: somatic variant identification from unpaired tissue samples
Authors: Smith Kyle S. , Yadav Vinod K. , Pei Shanshan , Pollyea Daniel A. , Jordan Craig T. , De Subhajyoti
Published: November 2015

Motivation: Somatic variant calling typically requires paired tumor-normal tissue samples. Yet, paired normal tissues are not always available in clinical settings or for archival samples.

Results: We present SomVarIUS, a computational method for detecting somatic variants using high throughput sequencing data from unpaired tissue samples. We evaluate the performance of the method using genomic data from synthetic and real tumor samples. SomVarIUS identifies somatic variants in exome-seq data of  ∼150 ×  coverage with at least 67.7% precision and 64.6% recall rates, when compared with paired-tissue somatic variant calls in real tumor samples. We demonstrate the utility of SomVarIUS by identifying somatic mutations in formalin-fixed samples, and tracking clonal dynamics of oncogenic mutations in targeted deep sequencing data from pre- and post-treatment leukemia samples.

Availability and implementation: SomVarIUS is written in Python 2.7 and available at http://www.sjdlab.org/resources/

Contact:  subhajyoti.de@ucdenver.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
CellTracker (not only) for dummies
Authors: Piccinini Filippo , Kiss Alexa , Horvath Peter
Published: November 2015

Motivation: Time-lapse experiments play a key role in studying the dynamic behavior of cells. Single-cell tracking is one of the fundamental tools for such analyses. The vast majority of the recently introduced cell tracking methods are limited to fluorescently labeled cells. An equally important limitation is that most software cannot be effectively used by biologists without reasonable expertise in image processing. Here we present CellTracker, a user-friendly open-source software tool for tracking cells imaged with various imaging modalities, including fluorescent, phase contrast and differential interference contrast (DIC) techniques.

Availability and implementation: CellTracker is written in MATLAB (The MathWorks, Inc., USA). It works with Windows, Macintosh and UNIX-based systems. Source code and graphical user interface (GUI) are freely available at: http://celltracker.website/.

Contact:  horvath.peter@brc.mta.hu

Supplementary information:  Supplementary data are available at Bioinformatics online.
FoCuS-point: software for STED fluorescence correlation and time-gated single photon counting
Authors: Waithe Dominic , Clausen Mathias P. , Sezgin Erdinc , Eggeling Christian
Published: November 2015

Motivation: Fluorescence Correlation Spectroscopy (FCS) is a popular tool for measuring molecular mobility and how mobility relates to molecular interaction dynamics and bioactivity in living cells. The FCS technique has been significantly advanced by its combination with super-resolution STED microscopy (STED-FCS). Specifically, the use of gated detection has shown great potential for enhancing STED-FCS, but has also created a demand for software which is efficient and also implements the latest algorithms. Prior to this study, no open software has been available which would allow practical time-gating and correlation of point data derived from STED-FCS experiments.

Results: The product of this study is a piece of stand-alone software called FoCuS-point. FoCuS-point utilizes advanced time-correlated single-photon counting (TCSPC) correlation algorithms along with time-gated filtering and innovative data visualization. The software has been designed to be highly user-friendly and is tailored to handle batches of data with tools designed to process files in bulk. FoCuS-point also includes advanced fitting algorithms which allow the parameters of the correlation curves and thus the kinetics of diffusion to be established quickly and efficiently.

Availability and implementation: FoCuS-point is written in python and is available through the github repository: https://github.com/dwaithe/FCS_point_correlator. Furthermore, compiled versions of the code are available as executables which can be run directly in Linux, Windows and Mac OSX operating systems.

Contact:  dominic.waithe@imm.ox.ac.uk
LocusExplorer: a user-friendly tool for integrated visualization of human genetic association data and biological annotations
Authors: Dadaev Tokhir , Leongamornlert Daniel A. , Saunders Edward J. , Eeles Rosalind , Kote-Jarai Zsofia
Published: November 2015

Summary: In this article, we present LocusExplorer, a data visualization and exploration tool for genetic association data. LocusExplorer is written in R using the Shiny library, providing access to powerful R-based functions through a simple user interface. LocusExplorer allows users to simultaneously display genetic, statistical and biological data for humans in a single image and allows dynamic zooming and customization of the plot features. Publication quality plots may then be produced in a variety of file formats.

Availability and implementation: LocusExplorer is open source and runs through R and a web browser. It is available at www.oncogenetics.icr.ac.uk/LocusExplorer/ or can be installed locally and the source code accessed from https://github.com/oncogenetics/LocusExplorer.

Contact:  tokhir.dadaev@icr.ac.uk
The Northern
récit paysan
: Regional Variations of the Modern Peasant Novel in Haiti
Authors: Stieber Chelsea
Published: November 2015

In a revisionist reading of the Haitian peasant novel, this article addresses the short shrift given to Haiti's regionalism in scholarship, a lacuna that social geographer Georges Anglade attributes to ‘les effets d'occultation propre à la structure dominante centralisée’. Contrary to Port-au-Prince-centric renderings of Haitian literary history, which locate the elaboration of the modern peasant novel in the elite (read: Port-au-Princean) intelligentsia's quest for a more authentic national identity, I show that the modern peasant novel emerged in the pages of the northern literary magazine
Stella
(Cap-Haïtien, 1926–30) out of a primarily regional context. Through a close reading of several short and virtually unstudied
récits paysans
published in
Stella
, I argue that northern writers deployed the peasant novel genre as a regional response to the process of centralization and regional ‘occultation’ by the centralized nation-state apparatus. In particular, I examine how the lived experience of dramatic demographic and economic decline in the north informed the specific contours of this new literary expression.
Mountain lion (
Puma concolor
) feeding behavior in the Little Missouri Badlands of North Dakota
Authors: Wilckens David T. , Smith Joshua B. , Tucker Stephanie A. , Thompson Daniel J. , Jenks Jonathan A.
Published: November 2015

Recent recolonization of mountain lions ( Puma concolor ) into the Little Missouri Badlands of North Dakota has led to questions regarding the potential impacts of predation on prey populations in the region. From 2012 to 2013, we deployed 9 real-time GPS collars to investigate mountain lion feeding habits. We monitored mountain lions for 1,845 telemetry-days, investigated 506 GPS clusters, and identified 292 feeding events. Deer ( Odocoileus spp.) were the most prevalent item in mountain lion diets (76.9%). We used logistic regression to predict feeding events and size of prey consumed at an additional 535 clusters. Our top model for predicting presence of prey items produced a receiver operating characteristic score of 0.90 and an overall accuracy of 81.4%. Application of our models to all GPS clusters resulted in an estimated ungulate kill rate of 1.09 ungulates/week (95% confidence interval [ CI ] = 0.83–1.36) in summer (15 May‒15 November) and 0.90 ungulates/week (95% CI = 0.69–1.12) in winter (16 November‒14 May). Estimates of total biomass consumed were 5.8kg/day (95% CI = 4.7–6.9) in summer and 7.2kg/day (95% CI = 5.3–9.2) in winter. Overall scavenge rates were 3.7% in summer and 11.9% in winter. Prey composition included higher proportions of nonungulates in summer (female = 21.5%; male = 24.8%) than in winter (female = 4.8%; male = 7.5%). Proportion of juvenile ungulates in mountain lion diets increased during the fawning season (June‒August) following the ungulate birth pulse in June (June–August = 60.7%, 95% CI = 43.0–78.3; September–May = 37.2%, 95% CI = 30.8–43.7), resulting in an ungulate kill rate 1.61 times higher (1.41 ungulates/week, 95% CI = 1.12–1.71) than during the remainder of the year (0.88 ungulates/week, 95% CI = 0.62–1.13). Quantifying these feeding characteristics is essential to assessing the potential impacts of mountain lions on prey populations in the North Dakota Badlands, where deer dominate the available prey base and mountain lions represent the lone apex predator.
Tuberculosis Incidence and Risk Factors Among Human Immunodeficiency Virus (HIV)-Infected Adults Receiving Antiretroviral Therapy in a Large HIV Program in Nigeria
Authors: Chang Charlotte A. , Meloni Seema Thakore , Eisen Geoffrey , Chaplin Beth , Akande Patrick , Okonkwo Prosper , Rawizza Holly E. , Tchetgen Tchetgen Eric , Kanki Phyllis J.
Published: November 2015

Background.  Despite the benefits of antiretroviral therapy (ART), tuberculosis (TB) is the leading cause of mortality among human immunodeficiency virus (HIV)-infected persons in Africa. Nigeria bears the highest TB burden in Africa and second highest HIV burden globally. This long-term multicenter study aimed to determine the incidence rate and predictors of TB in adults in the Harvard/AIDS Prevention Initiative in Nigeria (APIN) and President's Emergency Plan for AIDS Relief (PEPFAR) Nigeria ART program.

Methods.  This retrospective evaluation used data collected from 2004 to 2012 through the Harvard/APIN PEPFAR program. Risk factors for incident TB were determined using multivariate Cox proportional hazards regression with time-dependent covariates.

Results.  Of 50 320 adults enrolled from 2005 to 2010, 11 092 (22%) had laboratory-confirmed active TB disease at ART initiation, and 2021 (4%) developed active TB after commencing ART. During 78 228 total person-years (PY) of follow-up, the TB incidence rate was 25.8 cases per 1000 PY (95% confidence interval [CI], 24.7–27.0) overall, and it decreased significantly both with duration on ART and calendar year. Risk factors at ART initiation for incident TB included the following: earlier ART enrollment year, tenofovir-containing initial ART regimen, and World Health Organization clinical stage above 1. Time-updated risk factors included the following: low body mass index, low CD4+ cell count, unsuppressed viral load, anemia, and ART adherence below 80%.

Conclusions.  The rate of incident TB decreased with longer duration on ART and over the program years. The strongest TB risk factors were time-updated clinical markers, reinforcing the importance of consistent clinical and laboratory monitoring of ART patients in prompt diagnosis and treatment of TB and other coinfections.
The Excess Burden of Cytomegalovirus in African American Communities: A Geospatial Analysis
Authors: Lantos Paul M. , Permar Sallie R. , Hoffman Kate , Swamy Geeta K.
Published: November 2015

Background.  Cytomegalovirus (CMV) is a common cause of birth defects and hearing loss in infants and opportunistic infections in the immunocompromised. Previous studies have found higher CMV seroprevalence rates among minorities and among persons with lower socioeconomic status. No studies have investigated the geographic distribution of CMV and its relationship to age, race, and poverty in the community.

Methods.  We identified patients from 6 North Carolina counties who were tested in the Duke University Health System for CMV immunoglobulin G. We performed spatial statistical analyses to analyze the distributions of seropositive and seronegative individuals.

Results.  Of 1884 subjects, 90% were either white or African American. Cytomegalovirus seropositivity was significantly more common among African Americans (73% vs 42%; odds ratio, 3.31; 95% confidence interval, 2.7–4.1), and this disparity persisted across the life span. We identified clusters of high and low CMV odds, both of which were largely explained by race. Clusters of high CMV odds were found in communities with high proportions of African Americans.

Conclusions.  Cytomegalovirus seropositivity is geographically clustered, and its distribution is strongly determined by a community's racial composition. African American communities have high prevalence rates of CMV infection, and there may be a disparate burden of CMV-associated morbidity in these communities.
Signals at ground level of relativistic solar particles associated with a radiation storm on 2014 April 18
Authors: Augusto Carlos , Navia Carlos , de Oliveira Marcel N. , Fauth Anderson , Nepomuceno André
Published: November 2015

Active region NOAA AR2036, located at S20W34 at the Sun disk, produced a moderately strong (GOES class M7.3) flare on 2014 April 18. The flare itself was long in duration, and a halo coronal mass ejection (CME) was emitted. In addition, a radiation storm, that is, solar energetic particles (SEP), began to reach the Earth at 13:30 UT in the aftermath of the solar blast, meeting the condition of an S1 (minor) radiation storm level. In temporal coincidence with the onset of the S1 radiation storm, the Tupi telescopes located within the South Atlantic Anomaly (SAA) detected a fast rise in the muon counting rate, caused by relativistic protons from this solar blast, with a confidence of up to 3.5% at peak. At the time of the solar blast, of all ground-based detectors, the Tupi telescopes had the best geoeffective location. Indeed, in association with the radiation storm, a gradual increase in the particle intensity was found in some neutron monitors (NMs), all of them in the west region relative to the Sun–Earth line, yet within the geoeffective region. However, their confidence levels are smaller: up to 3%. The fast rising observed at Tupi suggests possible detection of solar particles emitted during the impulsive phase, following by a gradual phase observed also at NMs. Details of these observations, including the expected energy spectrum, are reported.
Failed eruptions of two intertwining small-scale filaments
Authors: Xue Zhike , Yan Xiaoli , Zhao Li , Xiang Yongyuan , Yang Liheng , Guo Yang
Published: November 2015

Using multi-wavelength observations of the New Vacuum Solar Telescope (NVST), the Atmospheric Imaging Assembly (AIA) and Helioseismic and Magnetic Imager (HMI) on board the Solar Dynamics Observatory (SDO), we study the topology and evolutions of two filaments observed in NOAA active region (AR) 12031 on 2014 April 7. Before their eruptions, the two filaments (F1 and F2) were sinistral filaments, and the left part of F1 (LP) was located above F2, the right part of F1 (RP) under F2. They show an overall intertwining structure. LP erupted first and rotated clockwise. The total rotation angle was about 470° (≈2.61π). With its rotation, most of the plasma fell back, and thus it was a failed eruption. Meanwhile, when LP erupted to a higher altitude, the overlying magnetic loops were partially pushed from the northeast to the southwest with projected speeds from 36 to 105 km s−1. Next, F2 began to erupt and, when reaching a certain height, the plasma of F2 started to fall down to their footpoints. Using the potential-field source-surface (PFSS) model, the decay indexes at five positions along the polarity inversion line of AR 12031 were calculated to be from 1.03 to 1.25 with an average value of 1.20 that was lower than the critical value for torus instability. These results imply that the kink instability was the main triggering mechanism for the eruption of F1, and the eruption of F2 was due to the decreasing of overlying magnetic loops caused by the eruption of F1. The eruptions of two filaments were confined by the large-scale overlying magnetic loops.
Differential Opioid Tolerance and Opioid-induced Hyperalgesia
Authors: Hayhurst Christina J. , Durieux Marcel E.
Published: November 2015

Differential opioid tolerance (different degrees and speed of tolerance to various opioid side effects) and opioid-induced hyperalgesia (increased pain with escalating doses of opioids) potentially complicate the postoperative management.
Serial Mehta Cast Utilization in Infantile Idiopathic Scoliosis: Evaluation of Radiographic Predictors
Authors: Hassanzadeh Hamid , Nandyala Sreeharsha V. , Puvanesarajah Varun , Manning Blaine T. , Jain Amit , Hammerberg Kim W.
Published: November 2015

Background:

Mehta cast utilization has gained a considerable momentum as a nonoperative treatment modality for the initial management of infantile idiopathic scoliosis (IIS). Despite its acceptance, there is paucity of data that characterize the radiographic parameters associated with Mehta casting and the factors correlated with a sustained curve correction.

Methods:

A retrospective review of IIS patients who underwent Mehta casting was performed with a mean 2-year follow-up. X-rays were evaluated at each visit for the Cobb angle, focal deformity, rib-vertebral angle difference, and height of concavity and convexity of the apical 3 vertebrae. Concave-to-convex height ratios were calculated and tracked for each patient. Radiographic parameters were compared from precasting to after final casting, and from final casting to most recent follow-up.

Results:

A total of 45 patients were identified, of whom 18 (40%) were male and 27 (60%) were female, with a mean age of 18.8±9.5 months at first casting and a mean follow-up of 37.7±19.7 months. Following final casting, the mean Cobb angle (25.6 vs. 52.7 degrees), focal deformity (17.4 vs. 30.5 degrees), rib-vertebral angle difference (18 vs. 32.3 degrees), and the concave-to-convex height ratios improved relative to precast parameters, respectively (P<0.001). At final follow-up, mean Cobb angle (16.2 vs. 25.6 degrees) and concave-to-convex height ratios progressively improved when compared with final cast measurements, respectively (P<0.001). Five (11%) patients did not demonstrate sustained curve correction at final follow-up, whereas 4 (9%) required growing-rod placement. Lastly, the regression analysis demonstrated improvements in the focal deformity (17.4 vs. 30.5) and the concave-to-convex height ratios of the +1 and −1 apical vertebrae from the precast to last cast periods (P<0.001). These findings were correlated with sustained Cobb angle correction from cast removal to the most recent follow-up.

Conclusions:

Radiographic parameters associated with control of progressive deformity for IIS include improvements in focal deformity and concave-to-convex height ratios for +1 and −1 apical vertebrae after final casting. Mehta casting is an effective treatment for symptomatic IIS and continues to provide IIS patients with significant curve correction.

Level of Evidence:

Level IV.
Effects of Antifungal Soaked Silicone Hydrogel Contact Lenses on Candida albicans in an Agar Eye Model
Authors: Phan Chau-Minh , Bajgrowicz Magdalena , McCanna David J. , Subbaraman Lakshman N. , Jones Lyndon
Published: November 2015

Purpose:

To evaluate the effects of two commercial silicone hydrogel contact lenses (CLs) soaked with natamycin (NA) or fluconazole (FL) on the growth of Candida albicans in an in vitro eye model.

Methods:

Three-D printed molds were used as a cast for making eye-shaped models comprising potato dextrose agar. Senofilcon A (SA) and lotrafilcon B (LB) CLs were incubated with either 2 mL of NA or FL at a concentration of 1 mg/mL for 24 hr. To simulate a fungal infection, the eye models were coated with C. albicans. The drug-soaked lenses were placed on top of the eye models. Seven experimental conditions were examined: (1) NA-SA, (2) NA-LB, (3) FL-SA, (4) FL-LB, (5) SA, (6) LB, and (7) control—no lens. At specified time points (t=1, 8, 16, 24, 48 hr), the agar eyes from each experimental condition were removed from the incubator and photographed. The yeast cells from the 24 and 48 hr time point were also analyzed using light microscopy.

Results:

At 24 and 48 hr, there was considerable growth observed for all conditions except for the NA-SA and NA-LB conditions. When observed under the microscope at 24 and 48 hr, the morphology of the yeast cells in the FL-SA and SA condition were similar to that of the control (oval shaped). There was limited hyphae growth observed for LB and significant visible hyphae growth for the NA-LB group. For NA-SA, NA-LB, and FL-LB groups, the cells were significantly smaller compared with the control.

Conclusions:

For NA-SA and NA-LB, there was limited growth of C. albicans observed on the eye models even after 48 hr. Under the microscope, the cell morphology differ noticeably between each testing condition, and is dependent on drug-lens combinations.
Effect of Ambient Temperature on the Human Tear Film
Authors: Abusharha Ali A. , Pearce E. Ian , Fagehi Raied
Published: November 2015

Purpose:

During everyday life, the tear film is exposed to a wide range of ambient temperatures. This study aims to investigate the effect of ambient temperature on tear film physiology.

Method:

A controlled environment chamber was used to create different ambient temperatures (5, 10, 15, 20, and 25°C) at a constant relative humidity of 40%. Subjects attended for two separate visits and were exposed to 25, 20, and 15°C at one visit and to 10 and 5°C at the other visit. The subjects were exposed to each room temperature for 10 min before investigating tear film parameters. The order of the visits was random. Tear physiology parameters assessed were tear evaporation rate, noninvasive tear break-up time (NITBUT), lipid layer thickness (LLT), and ocular surface temperature (OST). Each parameter was assessed under each condition.

Result:

A threefold increase in tear evaporation rate was observed as ambient temperature increased to 25°C (P=0.00). The mean evaporation rate increased from 0.056 μL/min at 5°C to 0.17 μL/min at 25°C. The mean NITBUT increased from 7.31 sec at 5°C to 12.35 sec at 25°C (P=0.01). A significant change in LLT was also observed (P=0.00), LLT median ranged between 20 and 40 nm at 5 and 10°C and increased to 40 and 90 nm at 15, 20, and 25°C. Mean reduction of 4°C OST was observed as ambient temperature decreased from 25 to 5°C.

Conclusion:

Ambient temperature has a considerable effect on human tear film characteristics. Tear evaporation rate, tear LLT, tear stability, and OST were considerably affected by ambient temperature. Chronic exposure to low ambient temperature would likely result in symptoms of dry eye and ultimately ocular surface disorders.
A Study of Interpersonal Intimacy and Meaning of Life Among Elderly Institutionalized Veterans
Authors: Niu Chen-Chun , Huang Hui-Man , Hung Yun-Ying , Lee Hsiu-Li
Published: November 2015

Background:

Most senior veterans who live in veterans’ homes in Taiwan are single and have few intimate, interpersonal relationships. Aging is often accompanied by solitude and illness, which causes senior veterans to doubt the meaning of life and to lose confidence in the value of life.

Purpose:

This study investigated the personal characteristics that influence interpersonal intimacy and the meaning of life as well as the relationship between interpersonal intimacy and the meaning of life among senior veterans living in veterans’ homes.

Methods:

A cross-sectional design was used, and 120 senior male veterans were convenience sampled from three veterans’ homes in southern Taiwan. Three structured questionnaires were used in this study: personal characteristics questionnaire, interpersonal intimacy scale, and purpose in life test.

Results:

(a) Interpersonal intimacy was influenced by source of income or funds, type of residence institution, religious affiliation, and the quality of the participant’s relationships with family, friends, and fellow residents. Educational level and self-perceived health status correlated positively with interpersonal intimacy, and period of residence correlated negatively with interpersonal intimacy. (b) Meaning of life was influenced by the quality of relationships with family and friends. Educational level and self-perceived health status correlated significantly and positively with meaning of life, and period of residence correlated negatively with meaning of life. (c) Significant, positive correlations were found among interpersonal intimacy, the four domains of interpersonal intimacy, and meaning of life.

Conclusions/Implications for Practice:

Health professionals involved in the care of senior veterans in institutions may use the results of this study to develop and implement interventions that promote a higher degree of interpersonal intimacy and a higher appreciation of the meaning of life, thus enabling senior veterans to confront old age in a more positive manner.
Uterine Tumor Resembling Ovarian Sex Cord Tumor (UTROSCT) Commonly Exhibits Positivity With Sex Cord Markers FOXL2 and SF-1 but Lacks FOXL2 and DICER1 Mutations
Authors: Croce Sabrina , de Kock Leanne , Boshari Talia , Hostein Isabelle , Velasco Valerie , Foulkes William D. , McCluggage W. Glenn
Published: November 2015

Uterine tumor resembling ovarian sex cord tumor (UTROSCT) is a rare neoplasm which morphologically and immunohistochemically exhibits overlap with an ovarian sex cord tumor. Although many of these neoplasms are positive with markers of ovarian sex cord-stromal tumors, staining is often limited and the pathogenesis of UTROSCT is unknown. To further explore the sex cord lineage of UTROSCT, we studied 19 of these neoplasms and examined the expression of 2 recently described markers of ovarian sex cord-stromal tumors, FOXL2, and steroidogenic factor-1. We also undertook FOXL2 and DICER1 mutation analysis in these cases; a somatic missense mutation in codon C134W (402C→G) of FOXL2 gene has been demonstrated in the vast majority (>95%) of ovarian adult granulosa cell tumors and somatic DICER1 mutations are found in approximately 60% of ovarian Sertoli-Leydig cell tumors. Ten of 19 cases (53%) exhibited nuclear immunoreactivity with FOXL2 and 11 of 19 (58%) exhibited nuclear staining with steroidogenic factor-1. Neither FOXL2 nor DICER1 mutations were identified in any case where there was sufficient tumor tissue for analysis (18 and 9 cases, respectively). Despite exhibiting an immunophenotype characteristic of a sex cord-stromal tumor, mutations in FOXL2 and DICER1, the 2 most common mutations hitherto reported in ovarian sex cord-stromal tumors, are not a feature of UTROSCT.
Pulse Pressure Is Associated With Early Brain Atrophy and Cognitive Decline
Authors: Nation Daniel A. , Preis Sarah R. , Beiser Alexa , Bangen Katherine J. , Delano-Wood Lisa , Lamar Melissa , Libon David J. , Seshadri Sudha , Wolf Philip A. , Au Rhoda
Published: November 2015

We investigated whether midlife pulse pressure is associated with brain atrophy and cognitive decline, and whether the association was modified by apolipoprotein-E ε4 (APOE-ε4) and hypertension. Participants (549 stroke-free and dementia-free Framingham Offspring Cohort Study participants, age range=55.0 to 64.9 y) underwent baseline neuropsychological and magnetic resonance imaging (subset, n=454) evaluations with 5- to 7-year follow-up. Regression analyses investigated associations between baseline pulse pressure (systolic−diastolic pressure) and cognition, total cerebral volume and temporal horn ventricular volume (as an index of smaller hippocampal volume) at follow-up, and longitudinal change in these measures. Interactions with APOE-ε4 and hypertension were assessed. Covariates included age, sex, education, assessment interval, and interim stroke. In the total sample, baseline pulse pressure was associated with worse executive ability, lower total cerebral volume, and greater temporal horn ventricular volume 5 to 7 years later, and longitudinal decline in executive ability and increase in temporal horn ventricular volume. Among APOE-ε4 carriers only, baseline pulse pressure was associated with longitudinal decline in visuospatial organization. Findings indicate arterial stiffening, indexed by pulse pressure, may play a role in early cognitive decline and brain atrophy in mid to late life, particularly among APOE-ε4 carriers.
The larval nervous system of the penis wormPriapulus caudatus(Ecdysozoa)
Authors: Martín-Durán José M. , Wolff Gabriella H. , Strausfeld Nicholas J. , Hejnol Andreas
Published: November 2015

The origin and extreme diversification of the animal nervous system is a central question in biology. While most of the attention has traditionally been paid to those lineages with highly elaborated nervous systems (e.g. arthropods, vertebrates, annelids), only the study of the vast animal diversity can deliver a comprehensive view of the evolutionary history of this organ system. In this regard, the phylogenetic position and apparently conservative molecular, morphological and embryological features of priapulid worms (Priapulida) place this animal lineage as a key to understanding the evolution of the Ecdysozoa (i.e. arthropods and nematodes). In this study, we characterize the nervous system of the hatching larva and first lorica larva of the priapulid wormPriapulus caudatusby immunolabelling against acetylated and tyrosinated tubulin, pCaMKII, serotonin and FMRFamide. Our results show that a circumoral brain and an unpaired ventral nerve with a caudal ganglion characterize the central nervous system of hatching embryos. After the first moult, the larva attains some adult features: a neck ganglion, an introvert plexus, and conspicuous secondary longitudinal neurites. Our study delivers a neuroanatomical framework for future embryological studies in priapulid worms, and helps illuminate the course of nervous system evolution in the Ecdysozoa.