bluuebunny/crossref_metadata_2025 huggingface dataset:
Design of lifestyle intervention trials to prevent excessive gestational weight gain in women with overweight or obesity
Authors: Clifton Rebecca G. , Evans Mary , Cahill Alison G. , Franks Paul W. , Gallagher Dympna , Phelan Suzanne , Pomeroy Jeremy , Redman Leanne M. , Van Horn Linda ,   The LIFE‐Moms Research Group
Published: December 2015

Objective

The Lifestyle Interventions for Expectant Moms (LIFE‐Moms) Consortium is designed to determine, in pregnant women with overweight or obesity, whether various behavioral and lifestyle interventions reduce excessive gestational weight gain (GWG) and subsequent adverse maternal and neonatal outcomes and obesity in offspring. The design and planning process of the LIFE‐Moms Consortium is described.

Methods

The LIFE‐Moms Consortium is a collaboration among seven clinical centers, a Research Coordinating Unit, and the NIH designed to support each clinical center's conduct of a separate trial of a unique intervention. Specific common measures, procedures, and eligibility criteria are consistent across the seven trials allowing data to be combined in exploratory analyses and/or compared readily.

Results

Numerous committees and working groups were created to define common measures and outcomes during pregnancy and through 1 year postpartum, develop Consortium policies, and oversee progress of the trials. The primary outcome for the Consortium is excessive GWG. Secondary outcomes include maternal, neonatal, and infant anthropometric measures, physical activity, sleep, and complications of pregnancy and delivery.

Conclusions

A multi‐center consortium of independent, lifestyle interventions with common measures and outcomes may enhance the ability to identify promising interventions for improving outcomes in pregnant women and their offspring.
Adipose tissue R2* signal is increased in subjects with obesity: A preliminary MRI study
Authors: Manuel Fernández‐Real José , Blasco Gerard , Puig Josep , Moreno Maria , Xifra Gemma , Sánchez‐Gonzalez Javier , Maria Alustiza Jose , Pedraza Salvador , Ricart Wifredo , María Moreno‐Navarrete José
Published: December 2015

Objective: Circulating and adipose tissue markers of iron overload are increased in subjects with obesity. The aim is to study iron signals in adipose tissue.

Methods: Adipose tissue R2* values and hepatic iron concentration (HIC) were evaluated using magnetic resonance imaging (MRI) in 23 middle‐aged subjects with obesity and 20 subjects without obesity.

Results: Subcutaneous (SAT) and visceral adipose tissue (VAT) R2* were increased in subjects with obesity (P = 0.004 and P = 0.008) and correlated significantly and positively with HIC in all subjects. Strikingly, most of the associations of liver iron with metabolic parameters were replicated with SAT and VAT R2*. BMI, waist circumference, fat mass, HOMA value, and C‐reactive protein positively correlated with HIC and SAT and VAT R2*. BMI or percent fat mass (but not insulin resistance) contributed independently to 26.8‐34.8% of the variance in sex‐ and age‐adjusted SAT or VAT R2* (β > 0.40, P < 0.005). Within subjects with obesity, total cholesterol independently contributed to 14.8% of sex‐ and age‐adjusted VAT iron variance (β = 0.50, P = 0.025).

Conclusions: Increased R2* in adipose tissue, which might indicate iron content, runs in parallel to liver iron stores of subjects with obesity. VAT iron seems also associated with serum cholesterol within subjects with obesity.
Inactivation of adipose angiotensinogen reduces adipose tissue macrophages and increases metabolic activity
Authors: LeMieux Monique J. , Ramalingam Latha , Mynatt Randall L. , Kalupahana Nishan S. , Kim Jung Han , Moustaïd‐Moussa Naïma
Published: December 2015

Objective

The adipose renin‐angiotensin system (RAS) has been linked to obesity‐induced inflammation, though mechanisms are not completely understood. In this study, adipose‐specific angiotensinogen knockout mice (Agt‐KO) were generated to determine whether Agt inactivation reduces inflammation and alters the metabolic profile of the Agt‐KO mice compared to wild‐type (WT) littermates.

Methods

Adipose tissue‐specific Agt‐KO mice were created using the Cre‐LoxP system with both Agt‐KO and WT littermates fed either a low‐fat or high‐fat diet to assess metabolic changes. White adipose tissue was used for gene/protein expression analyses and WAT stromal vascular cells for metabolic extracellular flux assays.

Results

No significant differences were observed in body weight or fat mass between both genotypes on either diet. However, improved glucose clearance was observed in Agt‐KO compared to WT littermates, consistent with higher expression of genes involved in insulin signaling, glucose transport, and fatty acid metabolism. Furthermore, Agt inactivation reduced total macrophage infiltration in Agt‐KO mice fed both diets. Lastly, stroma vascular cells from Agt‐KO mice revealed higher metabolic activity compared to WT mice.

Conclusions

These findings indicate that adipose‐specific Agt inactivation leads to reduced adipose inflammation and increased glucose tolerance mediated in part via increased metabolic activity of adipose cells.
Effect of a weight reduction program on baseline and stress‐induced heart rate variability in children with obesity
Authors: Mazurak Nazar , Sauer Helene , Weimer Katja , Dammann Dirk , Zipfel Stephan , Horing Björn , Muth Eric R. , Teufel Martin , Enck Paul , Mack Isabelle
Published: December 2015

Objective

Autonomic dysregulation is a well‐established feature in adults with obesity but not in children. Since this dysregulation could contribute to weight dynamics, this study aimed to compare autonomic regulation in children with obesity and normal‐weight peers and to track autonomic status during weight reduction.

Methods

Sixty children with obesity and 27 age‐ and sex‐matched normal‐weight healthy participants were included. Heart rate variability (HRV) was assessed at baseline and during a mental stress test and a subsequent recovery period. Children with obesity were investigated both upon admission and discharge.

Results

Upon admission, no significant differences in HRV parameters were found for normal‐weight participants and those with obesity. Inpatient treatment led to significant changes in HRV with increase in general variability (standard deviation of the normal‐to‐normal interval (SDNN), P < 0.001) as well as of parasympathetic regulation (root mean square successive difference (RMSSD) and high frequency power (logHF), P < 0.01). Children with obesity had sympathetic activation similar to normal‐weight controls during mental stress with subsequent return to baseline values, and weight loss did not affect this profile.

Conclusions

A weight reduction program induced a change in autonomic activity in children with obesity toward parasympathetic dominance but had no influence on autonomic nervous system reactivity during stress conditions.
Tumor suppressor RIZ1 in obesity and the PI3K/AKT/mTOR pathway
Authors: Xie Xiaolei , Man Xian , Zhu Zuobin , Yuan Dejian , Huang Shi
Published: December 2015

Objective

The aim of this study was to investigate the shared molecular pathways of obesity and cancer by exploring the role of RIZ1 in obesity and the phospatidylinositol 3‐kinase (PI3K)/V‐Akt murine thymoma viral oncogene homolog (PKB) (AKT)/mechanistic target of rapamycin (mTOR) pathway.

Methods

Male wild type (WT) and Riz1−/− mice (KO) were fed a standard diet (STD) or a high‐fat (HF) diet for up to 8 months. These mice were studied for phenotypic and molecular changes.

Results

Riz1−/− mice gained more weight on a HF diet compared to WT mice, with higher free fatty acid and increased visceral fat. Metabolic cage analysis of Riz1−/− mice showed lower oxygen consumption but no changes in food intake and ambulatory activity. Riz1−/− mice showed impaired glucose regulation but no change in insulin sensitivity. RNA‐seq and quantitative RT‐PCR analysis found altered expression in certain glycolysis and ATP production genes such as Ubiad1, Atp5g2, and Cyp4a12. The PI3K/AKT/mTOR pathway was activated in the Riz1−/− mice fed a HF diet with higher Akt3 mRNA levels and increased phosphorylation of AKT (Ser473), mTOR, and S6.

Conclusions

The results identify RIZ1 as an important regulator of both Akt3 transcription and AKT phosphorylation and suggest a role for RIZ1 in HF‐induced obesity and the AKT pathway.
Adiposity trajectory and its associations with plasma adipokine levels in children and adolescents—A prospective cohort study
Authors: Li Shenghui , Liu Rong , Arguelles Lester , Wang Guoying , Zhang Jun , Shen Xiaoming , Wang Xiaobin
Published: December 2015

Objective

This study aimed to examine the associations of longitudinal adiposity measures with two adipokines, leptin and adiponectin, and their ratio in children and adolescents.

Methods

A total of 953 children and adolescents participated in a 6‐year longitudinal study. Body mass index (BMI), percentage body fat (%BF), and fat mass index (FMI) were used to assess adiposity status.

Results

After adjusting for possible confounders, our regression models revealed that BMI, %BF, and FMI, in both the baseline and follow‐up surveys were independently associated with a higher level of leptin and the leptin/adiponectin ratio at the follow‐up survey, whereas the significant association with adiponectin only partly existed in adiposity measures at the follow‐up visit. Moreover, the longitudinal change in adiposity measures was found to be a significant predictor for follow‐up plasma adipokine levels. Compared with the low→low group, the medium→medium group, up‐trend group, and high→high group all showed a significantly increased level of leptin and leptin/adiponectin ratio. The up‐trend group and high→high group also had significantly decreased adiponectin levels.

Conclusions

These findings highlight the importance of adiposity surveillance and the utility of adipokines as biomarkers for adverse metabolic consequences of childhood adiposity.
Reader interactome of epigenetic histone marks in birds
Authors: Bluhm Alina , Casas‐Vila Nuria , Scheibe Marion , Butter Falk
Published: December 2015

Lysine methylation is part of the posttranscriptional histone code employed to recruit modification specific readers to chromatin. Unbiased, quantitative mass spectrometry approaches combined with peptide pull‐downs have been used to study histone methylation‐dependent binders in mammalian cells. Here, we extend the study to birds by investigating the interaction partners for H3K4me3, H3K9me3, H3K27me3 and H3K36me3 in chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) using label‐free quantitative proteomics. In general, we find very strong overlap in interaction partners for the trimethyl marks in birds compared to mammals, underscoring the known conserved function of these modifications. In agreement with their epigenetic role, we find binding of PHF2 and members of the TFIID, SAGA, SET1 and NURF complex to the activation mark H3K4me3. Our data furthermore supports the existence of a LID complex in vertebrates recruited to the H3K4me3 mark. The repressive marks are bound by the HP1 proteins and the EED subunit of the PRC2 complex as well as by WIZ. Like reported in the previous mammalian screens, we found ZNF462, ZNF828 and POGZ enriched at H3K9me3. However, we noted some unexpected differences. N‐PAC (also known as GLYR1), an H3K36me3 interactor in mammals, is reproducible not enriched at this modification in our screen in birds. This initial finding suggests that despite strong conservation of the histone tail sequence, a few species‐specific differences in epigenetic readers may have evolved between birds and mammals. All MS data have been deposited in the ProteomeXchange with identifier PXD002282 (http://proteomecentral.proteomexchange.org/dataset/PXD002282).
Design and synthesis of magnetic binary metal oxides nanocomposites through dopamine chemistry for highly selective enrichment of phosphopeptides
Authors: Wang Mengyi , Sun Xueni , Li Yan , Deng Chunhui
Published: December 2015

In this work, for the first time, magnetic binary metal oxides nanocomposites which integrated Zr and Ti into one entity on an atomic scale on polydopamine coated magnetic graphene (magG/PD/(Zr‐Ti)O4) was designed and synthesized, and applied to the enrichment of phosphopeptides. The newly prepared magG/PD/(Zr‐Ti)O4 composites gathered the advantages of large surface area, superparamagnetism, biocompatibility and the enhanced affinity properties to phosphopeptides. MagG/PD/ZrO2, magG/PD/TiO2, as well as the simple physical mixture of them were introduced to compare with magG/PD/(Zr‐Ti)O4 composites. High sensitivity (1 pg/μL or 4.0 × 10–11 M) and selectivity (weight ratio of β‐casein and BSA reached up to 1:8000) toward phosphopeptides were also presented for magG/PD/(Zr‐Ti)O4 composites. Additionally, mouse brain tissue was chose as the real samples to further investigate the phosphopeptides enrichment ability of this new material.
Biomarker discovery in mass spectrometry‐based urinary proteomics
Authors: Thomas Samuel , Hao Ling , Ricke William A. , Li Lingjun
Published: December 2015

Urinary proteomics has become one of the most attractive topics in disease biomarker discovery. MS‐based proteomic analysis has advanced continuously and emerged as a prominent tool in the field of clinical bioanalysis. However, only few protein biomarkers have made their way to validation and clinical practice. Biomarker discovery is challenged by many clinical and analytical factors including, but not limited to, the complexity of urine and the wide dynamic range of endogenous proteins in the sample. This article highlights promising technologies and strategies in the MS‐based biomarker discovery process, including study design, sample preparation, protein quantification, instrumental platforms, and bioinformatics. Different proteomics approaches are discussed, and progresses in maximizing urinary proteome coverage and standardization are emphasized in this review. MS‐based urinary proteomics has great potential in the development of noninvasive diagnostic assays in the future, which will require collaborative efforts between analytical scientists, systems biologists, and clinicians.
Several stories from theoretical chemistry with some Russian flavor and implications for theorems of chemistry, vagueness of its concepts, fuzziness of its definitions, iconicity of its language, and peculiarities of its nomenclature
Authors: Tchougréeff Andrei L.
Published: December 2015

We present an informal discussion of the problems related to emergence and development of theoretical chemistry concepts and their relation to those of quantum mechanics and general mathematical thinking. This also brings us to a discussion of axiomatization of chemical knowledge, relation between iconic language of (organic) chemistry and symbolic language of physics, relations between molecular orbital and valence bond pictures of molecular electronic structure and other similar problems. Because of the thematic orientation of the present issue of the Int. J. Quantum Chem. Russian contributions to setting and solving the above problems are highlighted. © 2015 Wiley Periodicals, Inc.
Cover Image, Volume 8, Issue 1
Authors: Mitra Rajendra Narayan , Zheng Min , Han Zongchao
Published: December 2015

The cover image, by Zongchao Han et al. is based on the Advanced Review “Nanoparticle motivated gene delivery for ophthalmic application”, DOI 10.1002/wnan.1356.

image
Efficient extracellular expression of Bacillus deramificans pullulanase in Brevibacillus choshinensis
Authors: Zou Chun , Duan Xuguo , Wu Jing
Published: December 2015

In this study, the pullulanase gene from Bacillus deramificans was efficiently expressed in Brevibacillus choshinensis. The optimal medium for protein expression was determined through a combination of single-factor experiments and response surface methodology. The initial pH of the medium and the culture temperature were optimized. The pullulanase yield increased 10.8-fold through medium and condition optimization at the shake-flask level. From the results of these experiments, the dissolved oxygen level was optimized in a 3-L fermentor. Under these optimized conditions, the pullulanase activity and the specific pullulanase productivity reached 1005.8 U/mL and 110.5 × 103 U/g dry cell weight, respectively, with negligible intracellular expression. The Brevibacillus choshinensis expression system has proven to be valuable for the extracellular production of pullulanase.
On the stoichiometry and stability of americium(III) complexes with a hydrophilic SO3–Ph–BTP ligand, studied by liquid–liquid extraction
Authors: Steczek Łukasz , Rejnis Magdalena , Narbutt Jerzy , Charbonnel Marie-Christine , Moisy Philippe
Published: December 2015

1:1 and 1:2 complexes of americium(III) with a hydrophilic anionic SO3–Ph–BTP4− ligand were detected in acidic aqueous nitrate solutions by a solvent extraction method. The determined conditional stability constants of these complexes, logβ
1 = 4.35 ± 0.07 and logβ
2 = 7.67 ± 0.06, related to 1 M aqueous solutions, are much lower than the literature values for the analogous curium species, determined by TRLFS in very dilute aqueous solutions. There is also no evidence for the existence of the 1:3 Am3+ complex similar to the reported curium(III) complex. A hypothesis has been formulated to explain these discrepancies. It suggests the necessity to carefully check the equilibria in each phase of solvent extraction systems containing two competing ligands—lipophilic and hydrophilic.
A Review of Gemini Surfactants: Potential Application in Enhanced Oil Recovery
Authors: Kamal Muhammad Shahzad
Published: December 2015

Gemini surfactants are a group of novel surfactants with more than one hydrophilic head group and hydrophobic tail group linked by a spacer at or near the head groups. Unique properties of gemini surfactants, such as low critical micelle concentration, good water solubility, unusual micelle structures and aggregation behavior, high efficiency in reducing oil/water interfacial tension, and interesting rheological properties have attracted the attention of academic researchers and field experts. Rheological characterization and determination of the interfacial tension are two of the most important screening techniques for the evaluation and selection of chemicals for enhanced oil recovery (EOR). This review deals with rheology, wettability alteration, adsorption and interfacial properties of gemini surfactants and various factors affecting their performance. The review highlights the current research activities on the application of gemini surfactants in EOR.
Challenges in circulating tumor cell detection by the CellSearch system
Authors: Andree Kiki C. , van Dalum Guus , Terstappen Leon W.M.M.
Published: December 2015

Enumeration and characterization of circulating tumor cells (CTC) hold the promise of a real time liquid biopsy. They are however present in a large background of hematopoietic cells making their isolation technically challenging. In 2004, the CellSearch system was introduced as the first and only FDA cleared method designed for the enumeration of circulating tumor cells in 7.5 mL of blood. Presence of CTC detected by CellSearch is associated with poor prognosis in metastatic carcinomas. CTC remaining in patients after the first cycles of therapy indicates a futile therapy. Here we review challenges faced during the development of the CellSearch system and the difficulties in assigning objects as CTC. The large heterogeneity of CTC and the different approaches introduced in recent years to isolate, enumerate and characterize CTC results in a large variation of the number of CTC reported urging the need for uniform definitions and at least a clear definition of what the criteria are for assigning an object as a CTC.
Can the North Brazil Current Help Us Understand Atlantic Water Flow?
Authors: Shultz David
Published: December 2015

Currents off the coast of northern Brazil can be used to study changes in the larger oceanic circulation pattern in the Atlantic, when variable winds in the regions are properly accounted for.
World's Smallest Glaciers Risk Vanishing in Warm Climate
Authors: Wendel JoAnna
Published: December 2015

Scientists studying tiny glaciers in Switzerland created models to determine how the world's diminutive glaciers would fare under rising temperatures.
Monodispersed calcium carbonate nanoparticles modulate local pH and inhibit tumor growth in vivo
Authors: Som Avik , Raliya Ramesh , Tian Limei , Akers Walter , Ippolito Joseph E. , Singamaneni Srikanth , Biswas Pratim , Achilefu Samuel
Published: December 2015

Intravenously administered CaCO3 nanoparticles can induce tumor growth inhibition via local increases in tumor extracellular pH in vivo.
CNTs threaded (001) exposed TiO2 with high activity in photocatalytic NO oxidation
Authors: Xiao Shuning , Zhu Wei , Liu Peijue , Liu Fanfan , Dai Wenrui , Zhang Dieqing , Chen Wei , Li Hexing
Published: December 2015

CNTs-threaded (001) exposed TiO2 provides a high percentage of active facets and direct electron highway to largely enhance solar NO oxidation.
Analysis of the N-terminal region of human MLKL, as well as two distinct MLKL isoforms, reveals new insights into necroptotic cell death
Authors: Arnež Katja Hrovat , Kindlova Michaela , Bokil Nilesh J. , Murphy James M. , Sweet Matthew J. , Gunčar Gregor
Published: December 2015

The pseudokinase mixed lineage kinase domain-like (MLKL) is an essential effector of necroptotic cell death. Two distinct human MLKL isoforms have previously been reported, but their capacities to trigger cell death have not been compared directly. Herein, we examine these two MLKL isoforms, and further probe the features of the human MLKL N-terminal domain that are required for cell death. Expression in HEK293T cells of the N-terminal 201 amino acids (aa) of human MLKL is sufficient to cause cell death, whereas expression of the first 154 aa is not. Given that aa 1–125 are able to initiate necroptosis, our findings indicate that the helix that follows this region restrains necroptotic activity, which is again restored in longer constructs. Furthermore, MLKL isoform 2 (MLKL2), which lacks much of the regulatory pseudokinase domain, is a much more potent inducer of cell death than MLKL isoform 1 (MLKL1) in ectopic expression studies in HEK293T cells. Modelling predicts that a C-terminal helix constrains the activity of MLKL1, but not MLKL2. Although both isoforms are expressed by human monocyte-derived macrophages at the mRNA level, MLKL2 is expressed at much lower levels. We propose that it may have a regulatory role in controlling macrophage survival, either in the steady state or in response to specific stimuli.
Identification of Escherichia coli ygaQ and rpmG as novel mitomycin C resistance factors implicated in DNA repair
Authors: Bolt Edward L. , Jenkins Tabitha , Russo Valeria Moreira , Ahmed Sharlene , Cavey James , Cass Simon D.
Published: December 2015

Using the ASKA (A Complete Set of Escherichia coliK-12 ORF Archive) library for genome-wide screening of E. coli proteins we identified that expression of ygaQ and rpmG promotes mitomycin C resistance (MMCR). YgaQ mediated MMCR was independent of homologous recombination involving RecA or RuvABC, but required UvrD. YgaQ is an uncharacterized protein homologous with α-amylases that we identified to have nuclease activity directed to ssDNA of 5′ flaps. Nuclease activity was inactivated by mutation of two amino acid motifs, which also abolished MMCR. RpmG is frequently annotated as a bacterial ribosomal protein, although forms an operon with MutM glycosylase and a putative deubiquitinating (DUB) enzyme, YicR. RpmG associated MMCR was dependent on MutM. MMCR from RpmG resembles DNA repair phenotypes reported for ‘idiosyncratic ribosomal proteins’ in eukaryotes.
Interrupted E2F1-miR-34c-SCF negative feedback loop by hyper-methylation promotes colorectal cancer cell proliferation
Authors: Yang Shu , Wu Bo , Sun Haimei , Ji Fengqing , Sun Tingyi , Zhao Yan , Zhou Deshan
Published: December 2015

Tumour suppressor miR-34c deficiency resulted from hyper-methylation in its promoter is believed to be one of the main causes of colorectal cancer (CRC). Till date, miR-34c has been validated as a direct target of p53; but previous evidence suggested other transcription factor(s) must be involved in miR-34c transcription. In the present study, we in the first place identified a core promoter region (−1118 to −883 bp) of pre-miR-34c which was embedded within a hyper-methylated CpG island. Secondly, E2F1 promoted miR-34c transcription by physical interaction with the miR-34c promoter at site −897 to −889 bp. The transcriptional activating effect of E2F1 on miR-34c was in a p53 independent manner but profoundly promoted in the presence of p53 with exposure to 5-aza-2′-deoxycytidine (DAC). Thirdly, stem cell factor (SCF), a miR-34c target, was specifically reduced upon an introduction of E2F1 which lead to suppression of CRC cell proliferation. The E2F1-suppressed cell proliferation was partially abrogated by additional miR-34c inhibitor, indicating that the anti-proliferation effect of E2F1 was probably through activating miR-34c-SCF axis. Finally, SCF/KIT signalling increased E2F1 production by reducing its proteosomal degradation dependent on PI3K/Akt-GSK3β pathway. In conclusion, our results suggested the existence of E2F1-miR-34c-SCF negative feedback loop which was interrupted by the hyper-methylation of miR-34c promoter in CRC cells and increased cell proliferation.
OfftargetFinder: a web tool for species-specific RNAi design
Authors: Good R.T. , Varghese T. , Golz J.F. , Russell D.A. , Papanicolaou A. , Edwards O. , Robin C.
Published: December 2015

Motivation: RNA interference (RNAi) technology is being developed as a weapon for pest insect control. To maximize the specificity that such an approach affords we have developed a bioinformatic web tool that searches the ever-growing arthropod transcriptome databases so that pest-specific RNAi sequences can be identified. This will help technology developers finesse the design of RNAi sequences and suggests which non-target species should be assessed in the risk assessment process.

Availability and implementation:  http://rnai.specifly.org.

Contact:  crobin@unimelb.edu.au
Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment
Authors: Sundfeld Daniel , Havgaard Jakob H. , de Melo Alba C. M. A. , Gorodkin Jan
Published: December 2015

Motivation: Structured RNAs can be hard to search for as they often are not well conserved in their primary structure and are local in their genomic or transcriptomic context. Thus, the need for tools which in particular can make local structural alignments of RNAs is only increasing.

Results: To meet the demand for both large-scale screens and hands on analysis through web servers, we present a new multithreaded version of Foldalign. We substantially improve execution time while maintaining all previous functionalities, including carrying out local structural alignments of sequences with low similarity. Furthermore, the improvements allow for comparing longer RNAs and increasing the sequence length. For example, lengths in the range 2000–6000 nucleotides improve execution up to a factor of five.

Availability and implementation: The Foldalign software and the web server are available at http://rth.dk/resources/foldalign

Contact:  gorodkin@rth.dk

Supplementary information:  Supplementary data are available at Bioinformatics online.
MCAST: scanning for cis-regulatory motif clusters
Authors: Grant Charles E. , Johnson James , Bailey Timothy L. , Noble William Stafford
Published: December 2015

Summary: Precise regulatory control of genes, particularly in eukaryotes, frequently requires the joint action of multiple sequence-specific transcription factors. A cis-regulatory module (CRM) is a genomic locus that is responsible for gene regulation and that contains multiple transcription factor binding sites in close proximity. Given a collection of known transcription factor binding motifs, many bioinformatics methods have been proposed over the past 15 years for identifying within a genomic sequence candidate CRMs consisting of clusters of those motifs.

Results: The MCAST algorithm uses a hidden Markov model with a P-value-based scoring scheme to identify candidate CRMs. Here, we introduce a new version of MCAST that offers improved graphical output, a dynamic background model, statistical confidence estimates based on false discovery rate estimation and, most significantly, the ability to predict CRMs while taking into account epigenomic data such as DNase I sensitivity or histone modification data. We demonstrate the validity of MCAST’s statistical confidence estimates and the utility of epigenomic priors in identifying CRMs.

Availability and implementation: MCAST is part of the MEME Suite software toolkit. A web server and source code are available at http://meme-suite.org and http://alternate.meme-suite.org.

Contact:  t.bailey@imb.uq.edu.au or william-noble@uw.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Feeding strategy of mackerel in the Norwegian Sea relative to currents, temperature, and prey
Authors: Nøttestad Leif , Diaz Justine , Penã Hector , Søiland Henrik , Huse Geir , Fernö Anders
Published: December 2015

High abundance of Northeast Atlantic mackerel (Scomber scombrus L.), combined with limited food resources, may now force mackerel to enter new and productive regions in the northern Norwegian Sea. However, it is not known how mackerel exploit the spatially varying feeding resources, and their vertical distribution and swimming behaviour are also largely unknown. During an ecosystem survey in the Norwegian Sea during the summer feeding season, swimming direction, and speed of mackerel schools were recorded with high-frequency omnidirectional sonar in four different regions relative to currents, ambient temperature, and zooplankton. A total of 251 schools were tracked, and fish and zooplankton were sampled with pelagic trawl and WP-2 plankton net. Except for the southwest region, swimming direction of the tracked schools coincided with the prevailing northerly Atlantic current direction in the Norwegian Sea. Swimming with the current saves energy, and the current also provides a directional cue towards the most productive areas in the northern Norwegian Sea. Average mean swimming speed in all regions combined was ∼3.8 body lengths s−1. However, fish did not swim in a straight course, but often changed direction, suggesting active feeding in the near field. Fish were largest and swimming speed lowest in the northwest region which had the highest plankton concentrations and lowest temperature. Mackerel swam close to the surface at a depth of 8–39 m, with all schools staying above the thermocline in waters of at least 6°C. In surface waters, mackerel encounter improved foraging rate and swimming performance. Going with the flow until temperature is too low, based on an expectation of increasing foraging rate towards the north while utilizing available prey under way, could be a simple and robust feeding strategy for mackerel in the Norwegian Sea.
Microplastic interactions with North Atlantic mesopelagic fish
Authors: Lusher Amy L. , O'Donnell Ciaran , Officer Rick , O'Connor Ian
Published: December 2015

Microplastics in the marine environment are well documented, and interactions with marine biota have been described worldwide. However, interactions with vertically migrating fish are poorly understood. The diel vertical migration of mesopelagic fish represents one, if not the largest, vertical migration of biomass on the planet, and is thus an important link between the euphotic zone, transporting carbon and other nutrients to global deep sea communities. Knowledge of how mesopelagic fish interact and distribute plastic as a marine contaminant is required as these populations have been identified as a potential global industrial fishery for fishmeal production. Ingestion of microplastic by mesopelagic fish in the Northeast Atlantic was studied. Approximately 11% of the 761 fish examined had microplastics present in their digestive tracts. No clear difference in ingestion frequency was identified between species, location, migration behaviour, or time of capture. While ingesting microplastic may not negatively impact individual mesopelagic fish, the movement of mesopelagic fish from the euphotic zone to deeper waters could mediate transfer of microplastics to otherwise unexposed species and regions of the world's oceans.
Observations of vertical movements and depth distribution of migrating female lumpfish (Cyclopterus lumpus) in Iceland from data storage tags and trawl surveys
Authors: Kennedy James , Jónsson Sigurður Þ. , Ólafsson Halldór G. , Kasper Jacob M.
Published: December 2015

Lumpfish (Cyclopterus lumpus) is a high latitude species most abundant in Arctic and sub-Arctic waters of the North Atlantic. Vertical behaviour of this fish is unclear as it is often caught by both pelagic and demersal trawls. To gain greater insight into its behaviour, 41 female lumpfish caught during the Icelandic Groundfish Survey (IGFS) in March were tagged with data storage tags (DSTs); the IGFS finishes ∼1 week before the beginning of the lumpfish fishing season (20 March). Data retrieved from returned tags were compared with information on depth and distribution of catches of lumpfish from the IGFS. Thirteen tags were returned with days at liberty ranging from 20 to 61 d. Maximum depth recorded was 308 m (maximum depth of the tag) but based upon interpolation of temperature recordings, one fish may have descended to ∼418 m. Lumpfish displayed a range of vertical behaviours termed demersal, surface, and pelagic. During March, most exhibited either demersal or pelagic behaviour but the time spent in surface behaviour increased from March to April. During demersal behaviour, depth was rarely constant indicating the fish were not stationary. Both DST and catch data from the IGFS indicate that lumpfish exhibit diel patterns in vertical behaviour. As lumpfish frequently exhibit demersal behaviour, the use of the IGFS to monitor changes in abundance is justified. As lumpfish spend a significant amount of time in both the pelagic and demersal zone, they should be considered as a semi-pelagic (or semi-demersal) fish during this life stage/time of year.
Slave to the rhythm: seasonal signals in otolith microchemistry reveal age of eastern Baltic cod (Gadus morhua)
Authors: Hüssy K. , Gröger J. , Heidemann F. , Hinrichsen H.-H. , Marohn L.
Published: December 2015

Annual growth zones in cod otoliths from the eastern Baltic stock are less discrete than in other cod stocks leading to biased age reading, which recently led to a failure of age-based assessment in the eastern Baltic cod stock. In this study, we explored the applicability of minor and trace element patterns in cod otoliths for age determination. By first identifying elements of interest in a stock without ageing problems, western Baltic cod, we then tested their applicability on another stock without ageing problems, North Sea cod, and finally applied this knowledge to estimate age of eastern Baltic cod. In western Baltic cod, matching patterns with respect to occurrence of minima and maxima in both otolith opacity and element concentrations were found for Cu, Zn, and Rb, and inverse patterns with Mg and Mn. No match was found for Pb, Ba, and Sr. In the test stock, the North Sea cod, the same patterns in Cu, Zn, Rb, Mg, and Mn signals occurred. All eastern Baltic cod with low visual contrast between growth zones exhibited clearly defined synchronous cycles in Cu, Zn, Rb and Pb. Using a combined finite differencing method and structural break models approach, the statistical significance of the local profile minima were identified, based on which their age could be estimated. Despite extensive environmental differences between the three areas examined, the element concentrations of Cu, Zn, and Rb were strongly correlated in all individuals with similar correlations in all three areas, suggesting that the incorporation mechanisms are the same for these elements and independent of environmental concentrations.
Low genetic diversity, restricted dispersal, and elevation-specific patterns of population decline in American pikas in an atypical environment
Authors: Robson Kelsey M. , Lamb Clayton T. , Russello Michael A.
Published: December 2015

In the face of climate change, there is a growing need for research into the ability of organisms to persist at the limits of their bioclimatic envelope. American pikas ( Ochotona princeps ) have emerged as a focal mammalian species for investigating extinction risk related to climate change; however, most studies have occurred in characteristic alpine talus habitat within the range core. In the Columbia River Gorge (CRG), Oregon, American pikas inhabit low-elevation talus slopes previously considered outside the species’ bioclimatic range. We used microsatellite genotypic data to reconstruct levels of genetic variation, population connectivity, and demographic history at 11 CRG sites spanning an elevational gradient (104–1,292 m). Sampled sites separated into 2 genetic clusters largely explained by elevation, topography, and geographic proximity, with pairwise estimates of differentiation and migration rates suggesting little gene flow may be occurring. Sites were characterized by levels of allelic richness and heterozygosity substantially lower than values reported at characteristic alpine sites from the range core. Evidence of recent demographic contraction was found almost exclusively at high-elevation sites despite these areas being considered refuges from climate warming in more typical habitat. Given their unique genetic characteristics and persistence in an atypical environment, the CRG pika populations likely constitute a significant component of intraspecific biodiversity with high conservation value.
Pelvic sexual dimorphism among species monomorphic in body size: relationship to relative newborn body mass
Authors: Tague Robert G.
Published: December 2015

Females have larger pelves than males among eutherians to mitigate obstetrical difficulty. This study addresses 3 issues concerning pelvic sexual dimorphism using 8 species that are sexually monomorphic in nonpelvic size: Aotus azarae , Castor canadensis , Dasypus novemcinctus , Hylobates lar , Saguinus geoffroyi , Sciurus carolinensis , Sylvilagus floridanus , and Urocyon cinereoargenteus . Using published data to compute the index of relative newborn body mass (RNBM = [newborn body mass/adult female body mass]100%) for 266 eutherian species, A. azarae , H. lar , and S. geoffroyi are characterized as giving birth to relatively large newborns and the other 5 species as giving birth to relatively small newborns. The 3 issues are, compared to species giving birth to relatively small newborns, whether species that give birth to relatively large newborns have 1) higher magnitude of pelvic sexual size dimorphism (SSD), 2) lower prevalence of pelvic joint fusion, and 3) dissociation between pelvic and nonpelvic sizes. Nine measures of the pelvis were taken, and fusion of interpubic and sacroiliac joints was observed. Species grouped by high and low RNBM do not differ significantly in magnitude of SSD of pelvic inlet circumference. Species with high RNBM have significantly lower prevalence of interpubic joint fusion than those with low RNBM. Sexes do not differ in their multiple correlation coefficients between inlet circumference and nonpelvic body size in 7 of 8 species. Results suggest that 1) there are multiple anatomical pathways for pelvic obstetrical sufficiency, 2) an unfused interpubic joint is obstetrically advantageous, and 3) relative newborn size does not change the association between pelvic and nonpelvic size in females and males.
Feral cats and the fitoaty : first population assessment of the black forest cat in Madagascar’s rainforests
Authors: Farris Zach J. , Boone Hailey M. , Karpanty Sarah , Murphy Asia , Ratelolahy Felix , Andrianjakarivelo Vonjy , Kelly Marcella J.
Published: December 2015

Despite exceptionally high levels of biodiversity and endemism found in Madagascar, much of its wildlife remains little studied, particularly the carnivore community. The recently described, little-known black forest cat (locally known as “ fitoaty ”) is believed to be restricted to NE Madagascar and has been investigated only through village surveys and anecdotal accounts. From 2008 to 2012, we photographically sampled 7 forest sites with varying degrees of degradation and fragmentation across Makira Natural Park with the goals of: 1) estimating landscape occupancy for fitoaty ( Felis spp.), 2) identifying variables influencing fitoaty occupancy, and 3) comparing fitoaty and feral cat ( Felis spp.) occupancy across the landscape. We observed higher occupancy for fitoaty , minimal co-occurrence between fitoaty and feral cats ( n = 2 sites), and strong divergence in habitat use. We provide the 1st assessment of fitoaty morphology, including comparisons with anecdotal reports, and the 1st population assessment of Madagascar’s exotic cat community with insights into factors associated with carnivore population trends in Madagascar. We suggest the described fitoaty is a phenotypically different form of the feral cat, but additional research is needed. Targeted management plans are needed to diminish the spread and potential negative effects of invasive cats across this important biologically diverse ecoregion.
Phylogenetic relationships of
Chacodelphys
(Marsupialia: Didelphidae: Didelphinae) based on “ancient” DNA sequences
Authors: Díaz-Nieto Juan F. , Jansa Sharon A. , Voss Robert S.
Published: December 2015

Morphological character data are inadequate to resolve the evolutionary relationships of the didelphid genus Chacodelphys , which previous phylogenetic analyses have alternatively suggested might be the sister taxon of Lestodelphys and Thylamys (tribe Thylamyini) or of Monodelphis (tribe Marmosini) in the subfamily Didelphinae. Because fresh material of Chacodelphys is unavailable, we extracted DNA from microscopic fragments of soft tissue adhering to the 95-year-old holotype skull of C. formosa. Phylogenetic analyses of the resulting sequence data convincingly resolve Chacodelphys as the sister taxon of Cryptonanus , a genus with which it had not previously been thought to be closely related. This novel clade ( Chacodelphys + Cryptonanus ) belongs to an unnamed thylamyine lineage with Gracilinanus and Lestodelphys + Thylamys , but relationships among these taxa remain to be convincingly resolved.

Los análisis basados en caracteres morfológicos han sido inadecuados para resolver las relaciones evolutivas del género marsupial didélfido Chacodelphys . Previos análisis filogenéticos han sugerido como hipótesis alternativas que Chacodelphys sea el grupo hermano de Lestodelphys y Thylamys (tribu Thylamyini) o de Monodelphis (tribu Marmosini), todos estos géneros pertenecientes a la subfamilia Didelphinae. Debido a la ausencia de material fresco de Chacodelphys , extrajimos ADN de fragmentos microscópicos de tejido adherido al cráneo de 95 años del holotipo de C. formosa . Análisis filogenéticos de las secuencias obtenidas resuelven convincentemente la posición filogenética de Chacodelphys como el taxón hermano de Cryptonanus , un género con el cual nunca antes se había pensado que estuviera cercanamente relacionado. Aunque reconocemos a este nuevo clado ( Chacodelphys + Cryptonanus ) junto con Gracilinanus y Lestodelphys + Thylamys pertenecientes a un linaje sin nombre, las relaciones entre estas taxa siguen sin estar convincentemente resueltas.
General polytropic magnetohydrodynamic cylinder under self-gravity
Authors: Lou Yu-Qing , Xing Heng-Rui
Published: December 2015

Based on general polytropic (GP) magnetohydrodynamics (MHD), we offer a self-similar dynamic formalism for a magnetized, infinitely long, axially uniform cylinder of axisymmetry under self-gravity with radial and axial flows and with helical magnetic field. We identify two major classes of solution domains and obtain a few valuable MHD integrals in general. We focus on one class that has the freedom of prescribing a GP dynamic equation of state including the isothermal limit and derive analytic asymptotic solutions for illustration. In particular, we re-visit the isothermal MHD problem of Tilley & Pudritz (TP) and find that TP's main conclusion regarding the MHD solution behaviour for a strong ring magnetic field of constant toroidal flux-to-mass ratio Γφ to be incorrect. As this is important for conceptual scenarios, MHD cylinder models, testing numerical codes and potential observational diagnostics of magnetized filaments in various astrophysical contexts, we show comprehensive theoretical analysis and reasons as well as extensive numerical results to clarify pertinent points in this Letter. In short, for any given Γφ value be it small or large, the asymptotic radial scaling of the reduced mass density α(x) at sufficiently large x should always be ∼x−4 instead of ∼x−2 contrary to the major claim of TP.
The mass discrepancy acceleration relation in a ΛCDM context
Authors: Di Cintio Arianna , Lelli Federico
Published: December 2015

The mass discrepancy acceleration relation (MDAR) describes the coupling between baryons and dark matter (DM) in galaxies: the ratio of total-to-baryonic mass at a given radius anticorrelates with the acceleration due to baryons. The MDAR has been seen as a challenge to the Λ cold dark matter (ΛCDM) galaxy formation model, while it can be explained by Modified Newtonian Dynamics. In this Letter, we show that the MDAR arises in a ΛCDM cosmology once observed galaxy scaling relations are taken into account. We build semi-empirical models based on ΛCDM haloes, with and without the inclusion of baryonic effects, coupled to empirically motivated structural relations. Our models can reproduce the MDAR: specifically, a mass-dependent density profile for DM haloes can fully account for the observed MDAR shape, while a universal profile shows a discrepancy with the MDAR of dwarf galaxies with M⋆ < 109.5 M⊙, a further indication suggesting the existence of DM cores. Additionally, we reproduce slope and normalization of the baryonic Tully–Fisher relation (BTFR) with 0.17 dex scatter. These results imply that in ΛCDM (i) the MDAR is driven by structural scaling relations of galaxies and DM density profile shapes, and (ii) the baryonic fractions determined by the BTFR are consistent with those inferred from abundance-matching studies.
Parameter inference with estimated covariance matrices
Authors: Sellentin Elena , Heavens Alan F.
Published: December 2015

When inferring parameters from a Gaussian-distributed data set by computing a likelihood, a covariance matrix is needed that describes the data errors and their correlations. If the covariance matrix is not known a priori, it may be estimated and thereby becomes a random object with some intrinsic uncertainty itself. We show how to infer parameters in the presence of such an estimated covariance matrix, by marginalizing over the true covariance matrix, conditioned on its estimated value. This leads to a likelihood function that is no longer Gaussian, but rather an adapted version of a multivariate t-distribution, which has the same numerical complexity as the multivariate Gaussian. As expected, marginalization over the true covariance matrix improves inference when compared with Hartlap et al.'s method, which uses an unbiased estimate of the inverse covariance matrix but still assumes that the likelihood is Gaussian.