bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

Abstract
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

Abstract
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

AbstractHigh 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

AbstractMicroplastics 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

Abstract
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

Abstract
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

AbstractIn 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

AbstractFemales 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

AbstractDespite 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

Abstract
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

Abstract
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

Abstract
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⋆ &lt; 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

Abstract
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.