bluuebunny/crossref_metadata_2025 huggingface dataset:
PyWATER: a PyMOL plug-in to find conserved water molecules in proteins by clustering
Authors: Patel Hitesh , Grüning Björn A. , Günther Stefan , Merfort Irmgard
Published: July 2014

Summary : Conserved water molecules play a crucial role in protein structure, stabilization of secondary structure, protein activity, flexibility and ligand binding. Clustering of water molecules in superimposed protein structures, obtained by X-ray crystallography at high resolution, is an established method to identify consensus water molecules in all known protein structures of the same family. PyWATER is an easy-to-use PyMOL plug-in and identifies conserved water molecules in the protein structure of interest. PyWATER can be installed via the user interface of PyMOL. No programming or command-line knowledge is required for its use.

Availability and Implementation : PyWATER and a tutorial are available at https://github.com/hiteshpatel379/PyWATER . PyMOL is available at http://www.pymol.org/ or http://sourceforge.net/projects/pymol/ .

Contact : stefan.guenther@pharmazie.uni-freiburg.de
Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA)
Authors: Güell Marc , Yang Luhan , Church George M.
Published: July 2014

Summary: Clustered regularly interspaced short palindromic repeats (CRISPR)-based technologies have revolutionized human genome engineering and opened countless possibilities to basic science, synthetic biology and gene therapy. Albeit the enormous potential of these tools, their performance is far from perfect. It is essential to perform a posterior careful analysis of the gene editing experiment. However, there are no computational tools for genome editing assessment yet, and current experimental tools lack sensitivity and flexibility.

We present a platform to assess the quality of a genome editing experiment only with three mouse clicks. The method evaluates next-generation data to quantify and characterize insertions, deletions and homologous recombination. CRISPR Genome Analyzer provides a report for the locus selected, which includes a quantification of the edited site and the analysis of the different alterations detected. The platform maps the reads, estimates and locates insertions and deletions, computes the allele replacement efficiency and provides a report integrating all the information.

Availability and implementation: CRISPR-GA Web is available at http://crispr-ga.net . Documentation on CRISPR-GA instructions can be found at http://crispr-ga.net/documentation.html

Contact:  mguell@genetics.med.harvard.edu
Distribution of benthic megafauna in the Barents Sea: baseline for an ecosystem approach to management
Authors: Jørgensen Lis Lindal , Ljubin Pavel , Skjoldal Hein Rune , Ingvaldsen Randi B. , Anisimova Natalia , Manushin Igor
Published: July 2014

Benthos plays a significant role as substrate, refuge from predation and food for a wide variety of fish and invertebrates of all life stages and should therefore be considered in the ecosystem approach (EA) to management. Epibenthos from trawl catches, used in annual assessments of commercial fish stocks, was identified and measured on-board. The 2011 dataset present the baseline mapping for monitoring and included 354 taxa (218 to species level) analysed with multivariate statistical methods. This revealed four main megafaunal regions: southwestern (SW), banks/slopes in southeast and west (SEW), northwestern (NW), and northeastern (NE) which were significantly related to depth, temperature, salinity, and number of ice-days. The SW region was dominated by filter-feeders (sponges) in the inflow area of warm Atlantic water while the deeper trenches had a detritivorous fauna (echinoderms). In the SEW region, predators (sea stars, anemones and snow crabs) prevailed together with filtrating species (sea cucumber and bivalves) within a mosaic of banks and slopes. Plankton-feeding brittlestars were common in the NW and NE region, but with increasing snow crab population in NE. Climate change, potentially expanding trawling activity, and increasing snow and king crab populations might all have impacts on the benthos. Benthos should therefore be a part of an integrated assessment of a changing sea, and national agencies might consider adding benthic taxonomic expertise on-board scientific research vessels to identify the invertebrate “by-catch” as part of routine trawl surveys.
Lyman edges in supermassive black hole binaries
Authors: Generozov Aleksey , Haiman Zoltán
Published: July 2014

We propose a new spectral signature for supermassive black hole binaries (SMBHBs) with circumbinary gas discs: a sharp drop in flux bluewards of the Lyman limit. A prominent edge is produced if the gas dominating the emission in the Lyman continuum region of the spectrum is sufficiently cold (T ≲ 20 000 K) to contain significant neutral hydrogen. Circumbinary discs may be in this regime if the binary torques open a central cavity in the disc and clear most of the hot gas from the inner region, and if any residual UV emission from the individual BHs is either dim or intermittent. We model the vertical structure and spectra of circumbinary discs using the radiative transfer code tlusty, and identify the range of BH masses and binary separations producing a Lyman edge. We find that compact supermassive (M ≳ 108 M⊙) binaries with orbital periods of ∼0.1–10 yr, whose gravitational waves are expected to be detectable by pulsar timing arrays, could have prominent Lyman edges. Such strong spectral edge features are not typically present in AGN spectra and could serve as corroborating evidence for the presence of an SMBHB.
Variations in the initial mass function in early-type galaxies: a critical comparison between dynamical and spectroscopic results
Authors: Smith Russell J.
Published: July 2014

I present a comparison between published dynamical (ATLAS3D) and spectroscopic (Conroy & van Dokkum) constraints on the stellar initial mass function (IMF) in early-type galaxies, using the 34 galaxies in common between the two works. Both studies infer an average IMF mass factor α (the stellar mass relative to a Kroupa-IMF population of similar age and metallicity) greater than unity, i.e. both methods favour an IMF which is heavier than that of the Milky Way, on average over the sample. However, on a galaxy-by-galaxy basis, there is no correlation between α inferred from the two approaches. I investigate how the two estimates of α are correlated systematically with the galaxy velocity dispersion, σ, and with the Mg/Fe abundance ratio. The spectroscopic method, based on the strengths of metal absorption lines, yields a correlation only with metal abundance ratios: at fixed Mg/Fe, there is no residual correlation with σ. The dynamical method, applied to exactly the same galaxy sample, yields the opposite result: the IMF variation correlates only with dynamics, with no residual correlation with Mg/Fe after controlling for σ. Hence, although both methods indicate a heavy IMF on average in ellipticals, they lead to incompatible results for the systematic trends, when applied to the same set of galaxies. The sense of the disagreement could suggest that one (or both) of the methods has not accounted fully for the main confounding factors, i.e. element abundance ratios or dark matter contributions. Alternatively, the poor agreement might indicate additional variation in the detailed shape of the IMF, beyond what can currently be inferred from the spectroscopic features.
Robustness of H0 determination at intermediate redshifts
Authors: Holanda R. F. L. , Busti V. C. , Pordeus da Silva G.
Published: July 2014

The most recent Hubble constant (H0) estimates from local methods (z ≪ 1), H0 = 73.8 ± 2.4 km s−1 Mpc−1, and the one from high redshifts, H0 = 67.3 ± 1.2 km s−1 Mpc−1, are discrepant at 2.4σ confidence level. Within this context, Lima & Cunha (LC) derived a new determination of H0 using four cosmic probes at intermediate redshifts (0.1 < z < 1.8) based on the so-called flat ΛCDM model. They obtained H0 = 74.1 ± 2.2 km s−1 Mpc−1, in full agreement with local measurements. In this Letter, we explore the robustness of the LC result searching for systematic errors and its dependence from the cosmological model used. We find that the H0 value from this joint analysis is very weakly dependent on the underlying cosmological model, but the morphology adopted to infer the distance to galaxy clusters changes the result sizeably, being the main source of systematic errors. Therefore, a better understanding of the cluster morphology is paramount to transform this method into a powerful cross-check for H0.
Kinematical fingerprints of star cluster early dynamical evolution
Authors: Vesperini Enrico , Varri Anna Lisa , McMillan Stephen L. W. , Zepf Stephen E.
Published: July 2014

We study the effects of the external tidal field on the violent relaxation phase of star clusters dynamical evolution, with particular attention to the kinematical properties of the equilibrium configurations emerging at the end of this phase. We show that star clusters undergoing the process of violent relaxation in the tidal field of their host galaxy can acquire significant internal differential rotation and are characterized by a distinctive radial variation of the velocity anisotropy. These kinematical properties are the result of the symmetry breaking introduced by the external tidal field in the collapse phase and of the action of the Coriolis force on the orbit of the stars. The resulting equilibrium configurations are characterized by differential rotation, with a peak located between one and two half-mass radii. As for the anisotropy, similar to clusters evolving in isolation, the systems explored in this Letter are characterized by an inner isotropic core, followed by a region of increasing radial anisotropy. However, for systems evolving in an external tidal field, the degree of radial anisotropy reaches a maximum in the cluster intermediate regions and then progressively decreases, with the cluster outermost regions being characterized by isotropy or a mild tangential anisotropy. Young or old but less-relaxed dynamically young star clusters may keep memory of these kinematical fingerprints of their early dynamical evolution.
Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm
Authors: Lomsadze Alexandre , Burns Paul D. , Borodovsky Mark
Published: July 2014

We present a new approach to automatic training of a eukaryotic ab initio gene finding algorithm. With the advent of Next-Generation Sequencing, automatic training has become paramount, allowing genome annotation pipelines to keep pace with the speed of genome sequencing. Earlier we developed GeneMark-ES, currently the only gene finding algorithm for eukaryotic genomes that performs automatic training in unsupervised ab initio mode. The new algorithm, GeneMark-ET augments GeneMark-ES with a novel method that integrates RNA-Seq read alignments into the self-training procedure. Use of ‘assembled’ RNA-Seq transcripts is far from trivial; significant error rate of assembly was revealed in recent assessments. We demonstrated in computational experiments that the proposed method of incorporation of ‘unassembled’ RNA-Seq reads improves the accuracy of gene prediction; particularly, for the 1.3 GB genome of Aedes aegypti the mean value of prediction Sensitivity and Specificity at the gene level increased over GeneMark-ES by 24.5%. In the current surge of genomic data when the need for accurate sequence annotation is higher than ever, GeneMark-ET will be a valuable addition to the narrow arsenal of automatic gene prediction tools.
Objective and Subjective Burden of Informal Caregivers 4 Years After a Severe Traumatic Brain Injury: Results From the PariS-TBI Study
Authors: Bayen Eléonore , Jourdan Claire , Ghout Idir , Darnoux Emmanuelle , Azerad Sylvie , Vallat-Azouvi Claire , Weiss Jean-Jacques , Aegerter Philippe , Pradat-Diehl Pascale , Joël Marie-Eve , Azouvi Philippe
Published: July 2014

Objective:

Prospective assessment of informal caregiver (IC) burden 4 years after the traumatic brain injury of a relative.

Setting:

Longitudinal cohort study (metropolitan Paris, France).

Participants:

Home dwelling adults (N = 98) with initially severe traumatic brain injury and their primary ICs.

Main Outcome Measures:

Informal caregiver objective burden (Resource Utilization in Dementia measuring Informal Care Time [ICT]), subjective burden (Zarit Burden Inventory), monetary self-valuation of ICT (Willingness-to-pay, Willingness-to-accept).

Results:

Informal caregivers were women (81%) assisting men (80%) of mean age of 37 years. Fifty-five ICs reported no objective burden (ICT = 0) and no/low subjective burden (average Zarit Burden Inventory = 12.1). Forty-three ICs reported a major objective burden (average ICT = 5.6 h/d) and a moderate/severe subjective burden (average Zarit Burden Inventory = 30.3). In multivariate analyses, higher objective burden was associated with poorer Glasgow Outcome Scale-Extended scores, with more severe cognitive disorders (Neurobehavioral Rating Scale-revised) and with no coresidency status; higher subjective burden was associated with poorer Glasgow Outcome Scale-Extended scores, more Neurobehavioral Rating Scale-revised disorders, drug-alcohol abuse, and involvement in litigation. Economic valuation showed that on average, ICs did not value their ICT as free and preferred to pay a mean Willingness-to-pay = €17 per hour to be replaced instead of being paid for providing care themselves (Willingness-to-accept = €12).

Conclusion:

Four years after a severe traumatic brain injury, 44% of ICs experienced a heavy multidimensional burden.
Optimization of the analogue-sensitive Cdc2/Cdk1 mutant byin vivoselection eliminates physiological limitations to its use in cell cycle analysis
Authors: Aoi Yuki , Kawashima Shigehiro A. , Simanis Viesturs , Yamamoto Masayuki , Sato Masamitsu
Published: July 2014

Analogue-sensitive (as) mutants of kinases are widely used to selectively inhibit a single kinase with few off-target effects. The analogue-sensitive mutantcdc2-asof fission yeast (Schizosaccharomyces pombe) is a powerful tool to study the cell cycle, but the strain displays meiotic defects, and is sensitive to high and low temperature even in the absence of ATP-analogue inhibitors. This has limited the use of the strain for use in these settings. Here, we usedin vivoselection for intragenic suppressor mutations ofcdc2-asthat restore full function in the absence of ATP-analogues. Thecdc2-asM17underwent meiosis and produced viable spores to a similar degree to the wild-type strain. The suppressor mutation also rescued the sensitivity of thecdc2-asstrain to high and low temperature, genotoxins and an anti-microtubule drug. We have usedcdc2-asM17to show that Cdc2 activity is required to maintain the activity of the spindle assembly checkpoint. Furthermore, we also demonstrate that maintenance of the Shugoshin Sgo1 at meiotic centromeres does not require Cdc2 activity, whereas localization of the kinase aurora does. The modifiedcdc2-asM17allele can be thus used to analyse many aspects of cell-cycle-related events in fission yeast.
Consensus proposals for classification of the family Hepeviridae
Authors: Smith Donald B. , Simmonds Peter ,   members of the International Committee on the Taxonomy of Viruses  Study Group, Jameel Shahid , Emerson Suzanne U. , Harrison Tim J. , Meng Xiang-Jin , Okamoto Hiroaki , Van der Poel Wim H. M. , Purdy Michael A.
Published: July 2014

The family Hepeviridae consists of positive-stranded RNA viruses that infect a wide range of mammalian species, as well as chickens and trout. A subset of these viruses infects humans and can cause a self-limiting acute hepatitis that may become chronic in immunosuppressed individuals. Current published descriptions of the taxonomical divisions within the family Hepeviridae are contradictory in relation to the assignment of species and genotypes. Through analysis of existing sequence information, we propose a taxonomic scheme in which the family is divided into the genera Orthohepevirus (all mammalian and avian hepatitis E virus (HEV) isolates) and Piscihepevirus (cutthroat trout virus). Species within the genus Orthohepevirus are designated Orthohepevirus A (isolates from human, pig, wild boar, deer, mongoose, rabbit and camel), Orthohepevirus B (isolates from chicken), Orthohepevirus C (isolates from rat, greater bandicoot, Asian musk shrew, ferret and mink) and Orthohepevirus D (isolates from bat). Proposals are also made for the designation of genotypes within the human and rat HEVs. This hierarchical system is congruent with hepevirus phylogeny, and the three classification levels (genus, species and genotype) are consistent with, and reflect discontinuities in the ranges of pairwise distances between amino acid sequences. Adoption of this system would include the avoidance of host names in taxonomic identifiers and provide a logical framework for the assignment of novel variants.
Nuclear stability and transcriptional directionality separate functionally distinct RNA species
Authors: Andersson Robin , Andersen Peter Refsing , Valen Eivind , Core Leighton J. , Bornholdt Jette , Boyd Mette , Jensen Torben Heick , Sandelin Albin
Published: July 2014

Mammalian genomes are pervasively transcribed, yielding a complex transcriptome with high variability in composition and cellular abundance. While recent efforts have identified thousands of new long non-coding (lnc) RNAs and demonstrated a complex transcriptional repertoire produced by protein-coding (pc) genes, limited progress has been made in distinguishing functional RNA from spurious transcription events. This is partly due to present RNA classification, which is typically based on technical rather than biochemical criteria. Here we devise a strategy to systematically categorize human RNAs by their sensitivity to the ribonucleolytic RNA exosome complex and by the nature of their transcription initiation. These measures are surprisingly effective at correctly classifying annotated transcripts, including lncRNAs of known function. The approach also identifies uncharacterized stable lncRNAs, hidden among a vast majority of unstable transcripts. The predictive power of the approach promises to streamline the functional analysis of known and novel RNAs.
A New LxxxA Motif in the Transmembrane Helix3 of Maize Aquaporins Belonging to the Plasma Membrane Intrinsic Protein PIP2 Group Is Required for Their Trafficking to the Plasma Membrane
Authors: Chevalier Adrien S. , Bienert Gerd Patrick , Chaumont François
Published: July 2014

Aquaporins play important roles in maintaining plant water status under challenging environments. The regulation of aquaporin density in cell membranes is essential to control transcellular water flows. This work focuses on the maize (Zea mays) plasma membrane intrinsic protein (ZmPIP) aquaporin subfamily, which is divided into two sequence-related groups (ZmPIP1s and ZmPIP2s). When expressed alone in mesophyll protoplasts, ZmPIP2s are efficiently targeted to the plasma membrane, whereas ZmPIP1s are retained in the endoplasmic reticulum (ER). A protein domain-swapping approach was utilized to demonstrate that the transmembrane domain3 (TM3), together with the previously identified N-terminal ER export diacidic motif, account for the differential localization of these proteins. In addition to protoplasts, leaf epidermal cells transiently transformed by biolistic particle delivery were used to confirm and refine these results. By generating artificial proteins consisting of a single transmembrane domain, we demonstrated that the TM3 of ZmPIP1;2 or ZmPIP2;5 discriminates between ER and plasma membrane localization, respectively. More specifically, a new LxxxA motif in the TM3 of ZmPIP2;5, which is highly conserved in plant PIP2s, was shown to regulate its anterograde routing along the secretory pathway, particularly its export from the ER.
Water Balance, Hormone Homeostasis, and Sugar Signaling Are All Involved in Tomato Resistance toTomato Yellow Leaf Curl Virus
Authors: Sade Dagan , Sade Nir , Shriki Oz , Lerner Stephen , Gebremedhin Alem , Karavani Asaf , Brotman Yariv , Osorio Sonia , Fernie Alisdair R. , Willmitzer Lothar , Czosnek Henryk , Moshelion Menachem
Published: July 2014

Vacuolar water movement is largely controlled by membrane channels called tonoplast-intrinsic aquaporins (TIP-AQPs). Some TIP-AQP genes, such as TIP2;2 and TIP1;1, are up-regulated upon exposure to biotic stress. Moreover, TIP1;1 transcript levels are higher in leaves of a tomato (Solanum lycopersicum) line resistant to Tomato yellow leaf curl virus (TYLCV) than in those of a susceptible line with a similar genetic background. Virus-induced silencing of TIP1;1 in the tomato resistant line and the use of an Arabidopsis (Arabidopsis thaliana) tip1;1 null mutant showed that resistance to TYLCV is severely compromised in the absence of TIP1:1. Constitutive expression of tomato TIP2;2 in transgenic TYLCV-susceptible tomato and Arabidopsis plants was correlated with increased TYLCV resistance, increased transpiration, decreased abscisic acid levels, and increased salicylic acid levels at the early stages of infection. We propose that TIP-AQPs affect the induction of leaf abscisic acid, which leads to increased levels of transpiration and gas exchange, as well as better salicylic acid signaling.
Bis(pyrene)metal complexes of vanadium, niobium and titanium: isolable homoleptic pyrene complexes of transition metals
Authors: Kucera Benjamin E. , Jilek Robert E. , Brennessel William W. , Ellis John E.
Published: July 2014

Reduction of VCl3(THF)3(THF is tetrahydrofuran) and NbCl4(THF)2by alkali metal pyrene radical anion salts in THF affords the paramagnetic sandwich complexes bis[(1,2,3,3a,10a,10b-η)-pyrene]vanadium(0), [V(C16H10)2], and bis[(1,2,3,3a,10a,10b-η)-pyrene]niobium(0), [Nb(C16H10)2]. Treatment of tris(naphthalene)titanate(2−) with pyrene provides the isoelectronic titanium species, isolated as an (18-crown-6)potassium salt, namelycatena-poly[[(18-crown-6)potassium]-μ-[(1,2-η:1,2,3,3a,10a,10b-η)-pyrene]-titanate(−I)-μ-[(1,2,3,3a,10a,10b-η:6,7-η)-pyrene]], {[K(C12H24O6)][Ti(C16H10)2]}n. The first two compounds have very similar packing, with neighboring molecules arranged orthogonally to one another, such that aromatic donor–acceptor interactions are likely responsible for the specific arrangement. The asymmetric unit contains a half-occupancy metal center η6-coordinated to one pyrene ligand, with the fullM(pyrene)2molecule generated by a crystallographic inversion center. In the titanium compound, the cations and anions are in alternating contact throughout the crystal structure, in one-dimensional chains along the [101] direction. As in the other two compounds, the asymmetric unit contains a half-occupancy Ti atom η6-coordinated to one pyrene ligand. Additionally, the asymmetric unit contains one half of an (18-crown-6)potassium cation, located on a crystallographic inversion center coincident with the K atom. The full formula units are generated by those inversion centers. In all three structures, the pyrene ligands are eclipsed and sandwich the metals in one of two inversion-related sites. These species are of interest as the first isolable homoleptic pyrene transition metal complexes to be described in the scientific literature.
Gender ‘Hostility’, Rape, and the Hate Crime Paradigm
Authors: Walters Mark Austin , Tumath Jessica
Published: July 2014

This article examines whether crimes motivated by, or which demonstrate, gender ‘hostility’ should be included within the current framework of hate crime legislation in England and Wales. The article uses the example of rape to explore the parallels (both conceptual and evidential) between gender‐motivated violence and other ‘archetypal’ forms of hate crime. It is asserted that where there is clear evidence of gender hostility during the commission of an offence, a defendant should be pursued in lawadditionallyas a hate crime offender. In particular it is argued that by focusing on the hate‐motivation of many sexual violence offenders, the criminal justice system can begin to move away from its current focus on the ‘sexual’ motivations of offenders and begin to more effectively challenge the gendered prejudices that are frequently causal to such crimes.
Inferring model‐based probability of occurrence from preferentially sampled data with uncertain absences using expert knowledge
Authors: Manceur Ameur M. , Kühn Ingolf
Published: July 2014

For several data bases in species distribution modelling (SDM), presences are known but absences are uncertain and can be non‐detections. The environment influences both the non‐detections and the species occurrences (preferential sampling), affecting model predictions.

The objective is to estimate model‐based probability of occurrence when absences are uncertain and sampling is preferential. Our Bayesian image restoration (BIR) model has an environmental, spatial and non‐detection component. The latter is based on the number of ‘control species’ (selected by expert knowledge to have wide geographic range and occupy several habitats) observed. Control species are assumed present in all grid cells so an observed absence of the control species is a non‐detection.

The observed absence of a focal species is likely a non‐detection when the environment is conducive, the focal species was observed in the neighbourhood, and the number of control species is small.

Simulating an artificial species (true prevalence 0·31) and preferential sampling (observed prevalence 0·18), the BIR modelled prevalence was 0·32 (0·30–0·34). The estimation was robust to failure of assumptions with a mis‐specified environmental model. The restored map was close to the true map, and the true realized niche of the species was inferred (with uncertainty). The link between the non‐detection and control species is crucial, and a sensitivity analysis is recommended.

BIR restored the simulated atlas map more accurately than a covariate adjustment method. When applied to the vascular plant Asarum europaeum L., BIR changed the interpretation. The uncertainty maps assisted decision‐making. A BIR implementation new to the SDM field is presented.

BIR using control species is most fruitfully applied at coarse scale and intermediate extent, with limited environmental extremes and sufficient expert knowledge (e.g. many Central European countries).

BIR is a framework, and we studied one implementation. Any proxy (road density, distance to city, direct expert knowledge, detectability traits, etc.) associated with non‐detection can be used so BIR can be applied in diverse settings. Including non‐detections reduces model indeterminacy but often requires expert knowledge. However, the benefits of using a priori knowledge and Bayesian estimation are expected to outweigh the risks of model‐based inference.
Deleted in Breast Cancer 1 regulates cellular senescence during obesity
Authors: Escande Carlos , Nin Veronica , Pirtskhalava Tamar , Chini Claudia C. , Thereza Barbosa Maria , Mathison Angela , Urrutia Raul , Tchkonia Tamar , Kirkland James L. , Chini Eduardo N.
Published: July 2014

Chronic obesity leads to inflammation, tissue dysfunction, and cellular senescence. It was proposed that cellular senescence during obesity and aging drives inflammation and dysfunction. Consistent with this, clearance of senescent cells increases healthspan in progeroid mice. Here, we show that the protein Deleted in Breast Cancer‐1 (DBC1) regulates cellular senescence during obesity. Deletion of DBC1 protects preadipocytes against cellular senescence and senescence‐driven inflammation. Furthermore, we show protection against cellular senescence in DBC1 KO mice during obesity. Finally, we found that DBC1 participates in the onset of cellular senescence in response to cell damage by mechanism that involves binding and inhibition of HDAC3. We propose that by regulating HDAC3 activity during cellular damage, DBC1 participates in the fate decision that leads to the establishment of cellular senescence and consequently to inflammation and tissue dysfunction during obesity.
Roaming characteristics and feeding practices of village dogs scavenging sea‐turtle nests
Authors: Ruiz‐Izaguirre E. , van Woersem A. , Eilers K. (C.) H. A. M. , van Wieren S. E. , Bosch G. , van der Zijpp A. J. , de Boer I. J. M.
Published: July 2014

Village dogs are reported to prey on sea‐turtle nests at various beaches worldwide. Sea‐turtle species present in Mexico include six species, which are listed under the International Union for Conservation of Nature Red List. It is however not clear why dogs scavenge and how they enter nesting areas; this hinders effective management of dogs at sea‐turtle nesting beaches. Hunger, for example, could be a driving factor for village dogs to scavenge sea‐turtle nests. The aim of this study was to gain insight into roaming characteristics and feeding practices of dogs scavenging sea‐turtle nests. Movements of 19 village dogs (9 nest scavengers and 10 non‐nest scavengers) at Colola village and beach (an important nesting ground for the eastern Pacific green turtle: Chelonia mydas) were monitored through radio‐tracking and direct observations. A prerequisite for nest scavenging is traveling to the beach. We computed ‘distance from home to beach’ and ‘the activity range’ of nest scavengers and non‐nest scavengers. Furthermore, the dogs' owners were interviewed regarding feeding practices. Nest scavengers had a lower metabolic energy intake of their daily food corn tortillas (296 kJ kg−1 BW0.75) than non‐nest scavengers (464 kJ kg−1 BW0.75) (two‐sample t‐test = 2.67, P = 0.017). Moreover, 39% of owners reported that they provided turtle eggs or egg shells to their dogs at least once. The activity range of nest scavengers was significantly larger than that of non‐nest scavengers (F = 11.64, P = 0.007). Dogs were generally found at the beach at night (42%) and dawn (34%). Our findings have implications for the management of dogs at sea‐turtle nesting beaches. We recommend that dogs' movements should be restricted between night (09:00 pm) and dawn (06:00 am) and that sufficient and adequate feeding of dogs should be promoted among dog owners.
Functional groups of woody species in semi‐arid regions at low latitudes
Authors: de Oliveira Clemir Candeia , Zandavalli Roberta Boscaini , de Lima André Luiz Alves , Rodal Maria Jesus Nogueira
Published: July 2014

In seasonally dry environments, woody species have different survival strategies. However, little is known about how environmental variables affect the phenology and water dynamics of these species. We aim to understand which variables initiate the vegetative phenophases of species in a tropical semiarid climate at 3°S latitude, where variation in photoperiod is minimal and rainfall is seasonal. We hypothesize that groups of species with similar vegetative phenologies, under similar conditions, are functionally similar in terms of water storage and use. We analyse the relationship between functional characteristics related to the acquisition and utilization of water, such as wood density, water storage capacity, water potential and vegetative phenology. The attributes were ordered by multidimensional scaling, and a multiple response permutation procedure was used to test consistency of the groups. Canonical correspondence analysis and Mantel tests were used to evaluate the phenophase response to environmental variables. We found four functional groups: (i) deciduous low wood density, which lose 75% of their leaves one month before the end of the rains; (ii) evergreen high wood density; (iii) early deciduous high wood density, which lose 75% of their leaves one month after the end of the rains; and (iv) late deciduous high wood density, which lose 75% of their leaves two months after the end of the rains. As expected, the vegetative phenodynamics of the deciduous high wood density group were mainly influenced by water availability. The evergreens did not show a correlation with rainfall. Only leaf shedding of the late deciduous, and the vegetative phenophases of the evergreens, responded to an increase in temperature and photoperiod. Bud‐break responded to increased photoperiod and soil humidity in the deciduous low wood density group. The foliar periodicity groups can be explained by the presence of species that differ mainly in their mechanisms of water acquisition and use.
The genetics of brown coat color and white spotting in domestic yaks (Bos grunniens)
Authors: Zhang M.‐Q. , Xu X. , Luo S.‐J.
Published: July 2014

Domestic yaks (Bos grunniens) exhibit two major coat color variations: a brown vs. wild‐type black pigmentation and a white spotting vs. wild‐type solid color pattern. The genetic basis for these variations in color and distribution remains largely unknown and may be complicated by a breeding history involving hybridization between yaks and cattle. Here, we investigated 92 domestic yaks from China using a candidate gene approach. Sequence variations in MC1R, PMEL and TYRP1 were surveyed in brown yaks; TYRP1 was unassociated with the coloration and excluded. Recessive mutations from MC1R, or p.Gln34*, p.Met73Leu and possibly p.Arg142Pro, are reported in bovids for the first time and accounted for approximately 40% of the brown yaks in this study. The remaining 60% of brown individuals correlated with a cattle‐derived deletion mutation from PMEL (p.Leu18del) in a dominant manner. Degrees of white spotting found in yaks vary from color sidedness and white face, to completely white. After examining the candidate gene KIT, we suggest that color‐sided and all‐white yaks are caused by the serial translations of KIT (Cs6 or Cs29) as reported for cattle. The white‐faced phenotype in yaks is associated with the KIT haplotype Swf. All KIT mutations underlying the serial phenotypes of white spotting in yaks are identical to those in cattle, indicating that cattle are the likely source of white spotting in yaks. Our results reveal the complex genetic origins of domestic yak coat color as either native in yaks through evolution and domestication or as introduced from cattle through interspecific hybridization.
Riches, Real Estate, and Resistance: How Land Speculation, Debt, and Trade Monopolies Led to theAmerican Revolution
Authors: Curtis Thomas D.
Published: July 2014

Why did the colonies ofNorthAmerica rebel againstEngland in 1775? More than ideas of political freedom were at stake. It is unlikely that the colonists would have demanded independence if powerful land speculators, merchants, and urban artisans had not joined forces to protect their economic interests.England had levied taxes on the colonies, and the colonists had successfully overturned those measures. Taxation was a superficial problem. But in 1773, when England imposed a commercial monopoly on tea sales, and in 1774, when it cut off settlement in western lands, the colonists saw no choice but to rebel and create their own nation.GeorgeWashington,ThomasJefferson,PatrickHenry,GeorgeMason,RichardHenryLee, and other wealthyVirginians who led theAmericanRevolution stood to lose their huge investment in potential land sales ifEngland maintained control of the colonies.
Comparison of postoperative pain between single‐incision and conventional laparoscopic appendectomy in children
Authors: Miyauchi Yuya , Sato Masahito , Hattori Kengo
Published: July 2014

Introduction

The aim of this study was to evaluate differences in postoperative pain between single‐incision laparoscopic appendectomy (SLA) and conventional laparoscopic appendectomy (CLA) for uncomplicated appendicitis in children.

Methods

In total, 30 patients underwent CLA, and 12 patients underwent SLA. Patients with perforated appendicitis or an abscess were excluded. We evaluated the length of hospital stay, the frequency of postoperative analgesic requirement, and the duration of postoperative pain.

Results

The mean length of hospital stay was 3.67 ± 0.75 days for the CLA group and 4.0 ± 0.70 days for the SLA group. The mean frequency of postoperative analgesic requirement was 1.93 ± 1.63 times for the CLA group and 2.00 ± 1.00 times for the SLA group. The mean duration of postoperative pain was 52.63 ± 20.82 hours for the CLA group and 55.91 ± 18.45 hours for the SLA group. These postoperative outcomes were similar between the two groups.

Conclusion

Our study suggests that SLA, which results in similar postoperative pain as CLA, is a feasible technique for uncomplicated appendicitis in children.
Hepatocellular carcinoma in thalassaemia: an update of the Italian Registry
Authors: Borgna‐Pignatti Caterina , Garani Maria Chiara , Forni Gian Luca , Cappellini Maria Domenica , Cassinerio Elena , Fidone Carmelo , Spadola Vincenzo , Maggio Aurelio , Restivo Pantalone Gaetano , Piga Antonio , Longo Filomena , Gamberini Maria Rita , Ricchi Paolo , Costantini Silvia , D'Ascola Domenico , Cianciulli Paolo , Lai Maria Eliana , Carta Maria Paola , Ciancio Angela , Cavalli Paola , Putti Maria Caterina , Barella Susanna , Amendola Giovanni , Campisi Saveria , Capra Marcello , Caruso Vincenzo , Colletta Grazia , Volpato Stefano
Published: July 2014

The risk of developing hepatocellular carcinoma (HCC) in patients with thalassaemia is increased by transfusion‐transmitted infections and haemosiderosis. All Italian Thalassaemia Centres use an ad hoc form to report all diagnoses of HCC to the Italian Registry. Since our last report, in 2002, up to December 2012, 62 new cases were identified, 52% of whom were affected by thalassaemia major (TM) and 45% by thalassaemia intermedia (TI). Two had sickle‐thalassaemia (ST). The incidence of the tumour is increasing, possibly because of the longer survival of patients and consequent longer exposure to the noxious effects of the hepatotropic viruses and iron. Three patients were hepatitis B surface antigen‐positive, 36 patients showed evidence of past infection with hepatitis B virus (HBV). Fifty‐four patients had antibodies against hepatitis C virus (HCV), 43 of whom were HCV RNA positive. Only 4 had no evidence of exposure either to HCV or HBV. The mean liver iron concentration was 8 mg/g dry weight. Therapy included chemoembolization, thermoablation with radiofrequency and surgical excision. Three patients underwent liver transplant, 21 received palliative therapy. As of December 2012, 41 patients had died. The average survival time from HCC detection to death was 11·5 months (1·4–107·2 months). Ultrasonography is recommended every 6 months to enable early diagnosis of HCC, which is crucial to decrease mortality.
Interleukin 6 augments lung cancer chemotherapeutic resistance via ataxia‐telangiectasia mutated/NF‐kappaB pathway activation
Authors: Yan Hong Qiong , Huang Xiao Bo , Ke Shi Zhong , Jiang Yi Na , Zhang Yue Hua , Wang Yi Nan , Li Juan , Gao Feng Guang
Published: July 2014

Although it is known that ataxia‐telangiectasia mutated (ATM) and interleukin 6 (IL‐6) contribute to multiple drug resistance (MDR) in tumor chemotherapy, the exact role of ATM activation in MDR resulting from increased IL‐6 expression is still unclear. In the present study, we demonstrate that the activation of the ATM‐NF‐kappaB pathway, resulting from increased IL‐6 expression, plays a central role in augmented chemoresistance in lung cancer cell lines. This result was supported by the increased expressions of Bcl‐2, Mcl‐1, Bcl‐xl, and the upregulation of MDR‐associated protein ABCG2. The higher level of IL‐6 reveals not only higher ATM/NF‐kappaB activity but also increased expressions of ABCG2, Bcl‐2, Mcl‐1 and Bcl‐xl. Most importantly, lung cancer cells themselves upregulated IL‐6 secretion by activating the p38/NF‐kappaB pathway through treatment with cisplatin and camptothecin. Taken together, these findings demonstrate that chemotherapeutic agents increase IL‐6 expression, hence activating the ATM/NF‐kappaB pathway, augmenting anti‐apoptotic protein expression and contributing to MDR. This indicates that both IL‐6 and ATM are potential targets for the treatment of chemotherapeutic resistance in lung cancer.
The Goldilocks Effect in Infant Auditory Attention
Authors: Kidd Celeste , Piantadosi Steven T. , Aslin Richard N.
Published: July 2014

Infants must learn about many cognitive domains (e.g., language, music) from auditory statistics, yet capacity limits on their cognitive resources restrict the quantity that they can encode. Previous research has established that infants can attend to only a subset of available acoustic input. Yet few previous studies have directly examined infant auditory attention, and none have directly tested theorized mechanisms of attentional selection based on stimulus complexity. This work utilizes model‐based behavioral methods that were recently developed to examine visual attention in infants (e.g., Kidd, Piantadosi, & Aslin, 2012). The present results demonstrate that 7‐ to 8‐month‐old infants selectively attend to nonsocial auditory stimuli that are intermediately predictable/complex with respect to their current implicit beliefs and expectations. These findings provide evidence of a broad principle of infant attention across modalities and suggest that sound‐to‐sound transitional statistics heavily influence the allocation of auditory attention in human infants.
Maxillary Sinus Augmentation without Grafting Material with Simultaneous Implant Installation: A Three‐Dimensional Finite Element Analysis
Authors: Yan Xu , Zhang Xinwen , Gao Jie , Matsushita Yasuyuki , Koyano Kiyoshi , Jiang Xi , Ai Hongjun
Published: July 2014

Purpose

The study aims to provide a theoretical guidance of postmaxillary implant in the augmented sinus without grafting materials by establishing a three‐dimensional model of this new implant restorative technique, evaluating failure risk of sinus augmentation without grafting materials of different alveolar ridge heights, and analyzing stress distribution of different healing stage.

Materials and Methods

Seventeen three‐dimensional finite element models of a posterior maxillary region with sinus mucosa and different elevation heights were constructed according to anatomical data of sinus area, and the standard implant model based on Nobel Biocare implant system were created via computer‐aided design software. All materials were assumed to be isotropic and linearly elastic. Axial force of 150 N was applied. The von Mises stress, stress distribution, and implant displacement were calculated with software.

Results

With the height of the alveolar ridge reducing, the maximum von Mises stress of tissues and the displacement of the implant are on the rise, especially when the height of the bone is less than 7 mm. When the height decreased to 4 mm, the data may be doubled. After the stiff callus stage, the stress and displacement were close to the control model.

Conclusion

For maxillary sinus augmentation without grafting material implant technique, the stress of different tissues and the displacement of the implant were not increased much when the height of alveolar ridge is more than 7 mm. But if the alveolar bone height is less than 4 mm, this implant technique is not suggested. Immediately loading is not suggested and the loading opportunity should be after the stiff callus stage at least to improve the success rate.
A 7‐year prospective radiographic evaluation of marginal bone level around two different implant systems: a randomized clinical trial
Authors: Burtscher Doris , Norer Burkhard , Dalla Torre Daniel , Beier Ulrike , Schubert Katharina , Grunert Ingrid
Published: July 2014

Objective

The aim of this study was to evaluate the change in marginal bone level radiographically around two different implant systems after 7 years of use.

Material and methods

Twenty fully edentulous patients were included in the study and randomly assigned to two treatment groups of machined surface implants (Brånemark, n = 40) and rough‐surface implants (Xive, n = 40). The implants were early loaded with individual bar‐retained overdentures. All patients were treated by the same surgeon and the same prosthodontist. Clinical and radiographic examinations were conducted at the time of implant loading (baseline) and annually for up to 7 years of use. Measurements to the nearest 0.1 mm were taken at the mesial and distal site, and the average values were calculated for each implant. A three‐level mixed‐effect analysis of covariance (ANOVA) was used to test the significance of the mean marginal bone change in the two implant groups.

Results

The study population consisted of 15 women (75%) and five men (25%) with an average age of 61.6 years. A total of 79 of 80 implants integrated successfully. n = 1 Brånemark implant failed after 3 weeks. There was a significant difference (P < 0.001) between the two implant systems at the baseline measurements (0.14 mm Brånemark vs. 0.39 mm Xive) and a highly significant difference for the annual bone loss (0.07 mm [Brånemark] vs. 0.18 mm [Xive], P < 0.001).

Conclusion

Both the implant systems are clinically satisfying. Nevertheless, the Brånemark group showed a better radiological performance than the Xive group.
High Frequency and Intensity of Drinking may Attenuate Increased Inflammatory Cytokine Levels of Major Depression in Alcohol‐use Disorders
Authors: Neupane Sudan P. , Lien Lars , Martinez Priscilla , Aukrust Pål , Ueland Thor , Mollnes Tom E. , Hestad Knut , Bramness Jørgen G.
Published: July 2014

Aims

As major depression (MD) is often comorbid with alcohol‐use disorders (AUD) and alcohol itself modulates the immune system, we examined serum levels of interleukin (IL)‐6, IL‐10, tumor necrosis factor (TNF), and interferon (IFN)‐γ in AUD patients with and without MD. Putative interactions between alcohol variables and MD on cytokine levels were also assessed.

Methods

A consecutive sample of inpatients with AUD (N = 176) from eight alcohol treatment centers in Kathmandu, Nepal, was assessed for alcohol use and depression by administering fully structured psychiatric interviews. Serum cytokine levels were determined using multiplex technology.

Results

Alcohol‐use disorders patients with a positive history of MD had higher levels of the inflammatory cytokines IL‐6 (P = 0.019), TNF (P = 0.020), and IFN‐γ (P = 0.001), but not of IL‐10 (P = 0.853). AUD patients with MD had higher concentrations of cytokines compared with those without, regardless of the severity of the alcohol problem, but the difference was greater among those drinking in lower frequency and intensity.

Conclusion

These findings provide evidence for altered functioning of the immune system in AUD patients with comorbid MD. However, frequent and intense drinking may attenuate the difference in the cytokine profiles between AUD patients with and without MD.