bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elephant poaching in Niassa Reserve, Mozambique: population impact revealed by combined survey trends for live elephants and carcasses
Authors: Booth Vernon R. , Dunham Kevin M. 
Published: October 2014

AbstractTrends in the populations of large herbivores in Niassa Reserve, Mozambique, have been monitored through biennial aerial surveys since 1998. The elephant Loxodonta africana population has been subjected to intensive illegal hunting since 2006. We used a simple population model to mimic the observed trends in the numbers of live and dead elephants to demonstrate the impact of poaching. The number of fresh or recent carcasses recorded was used in the model as an index of the annual mortality rate. A maximum likelihood analysis to compare population models revealed that the best fit to the survey estimates of both live elephants and old or very old carcasses was a model that started with 6,635 elephants in 1987. This number increased through births by 4.6% annually and decreased through deaths from natural and anthropogenic causes. In the best-fit model, the mean mortality rate in any year was 3.2 times the observed 1 + 2 carcass ratio (ratio for carcasses in age categories 1 and 2), and carcasses remained visible for a mean of 6 years. The model suggested that c. 900 elephants were poached during 2007–2010 and another c. 1,000 during 2011. Population estimates for live elephants and carcasses are now routine outcomes of aerial surveys conducted as part of the CITES programme for Monitoring the Illegal Killing of Elephants, and our method can be applied to any population with a time series of estimates for live and dead elephants.
Relational FastSLAM: an improved Rao-Blackwellized particle filtering framework using particle swarm characteristics
Authors: Lee Seung-Hwan , Eoh Gyuho , Lee Beom H. 
Published: October 2014

SUMMARYThis paper presents an improved Rao-Blackwellized particle filtering framework with consideration of the particle swarm characteristics in FastSLAM, called Relational FastSLAM or R-FastSLAM. The R-FastSLAM seeks to cope with the inherent problems of FastSLAM, i.e., a particle depletion problem and an error accumulation problem in large environments. The R-FastSLAM uses the particle swarm characteristics in calculating the importance weight and maintaining a particle formation. We assign more accurate weights to particles by clustering them using the Expectation-Maximization (EM) algorithm according to an adaptive weight compensation scheme. In addition, particles constitute an adaptive triangular mesh formation to maintain multiple data association hypotheses without any resampling step. Its outstanding accomplishments are verified on simulations and a test using the Victoria Park dataset by comparing the standard FastSLAM 2.0 with the particle swarm optimization based FastSLAM.
Calcite V: a hundred-year-old mystery has been solved
Authors: Ishizawa Nobuo 
Published: October 2014

Since Boeke's finding of a reversible phase transition of calcite (calcium carbonate, CaCO3) at elevated temperatures [Boeke, H. E. (1912). Neues Jahrb. Mineral. 1, 91–121], and following W. L. Bragg's determination of the structure of the room-temperature Phase I [Bragg, W. L. (1914). Proc. R. Soc. Lond. A 89, 468–489.], the high-temperature Phase V of calcite has been an enduring mystery. Here, we summarize a paper on the structure of Phase V [Ishizawa, N., Setoguchi, H. and Yanagisawa, K. (2013). Sci. Rep. 3, 2832], as well as the intermediate Phase IV which exists between Phases I and V, and add new aspects. An in situ single-crystal X-ray diffraction study revealed that the I–IV and IV–V transitions occurred reversibly at approximately 985 and 1240 K, respectively, in a carbon dioxide atmosphere. Phase V was stable only over a narrow temperature range between 1240 and 1275 K. The crystal decomposed immediately at temperatures above 1275 K, leaving a nanoporous calcium oxide reaction product which retained the shape of the parent calcite crystal. The I–IV transition can be described as an orientational order/disorder transition of the carbonate group, occurring within the same space group $R\bar 3c$. In Phase V, the oxygen sublattice is melted. The joint-probability density function obtained from the anharmonic atomic displacement parameters of the oxygen atoms revealed that the oxygen triangles of the carbonate group in Phase V do not sit still at specified Wyckoff positions in the space group $R\bar 3m$, but are instead distributed with equal probability along the undulated circular orbital about the central carbon. The carbonate group in Phase V is no longer flat on the basal plane when the oxygen triangle comes to troughs or peaks in the undulated orbital, but is instead deformed like an umbrella. Assuming that the oxygen triangle migrates about carbon, the carbonate group should repeat the umbrella inversion in Phase V as a function of time. Finally, possible thermal decomposition mechanisms of calcite are briefly discussed.
Antibody response and risk factors for seropositivity in backyard poultry following mass vaccination against highly pathogenic avian influenza and Newcastle disease in Indonesia
Authors: McLAWS M. , PRIYONO W. , BETT B. , AL-QAMAR S. , CLAASSEN I. , WIDIASTUTI T. , POOLE J. , SCHOONMAN L. , JOST C. , MARINER J. 
Published: October 2014

SUMMARYA large-scale mass vaccination campaign was carried out in Java, Indonesia in an attempt to control outbreaks of highly pathogenic avian influenza (HPAI) in backyard flocks and commercial smallholder poultry. Sero-monitoring was conducted in mass vaccination and control areas to assess the proportion of the target population with antibodies against HPAI and Newcastle disease (ND). There were four rounds of vaccination, and samples were collected after each round resulting in a total of 27 293 samples. Sampling was performed irrespective of vaccination status. In the mass vaccination areas, 20–45% of poultry sampled had a positive titre to H5 after each round of vaccination, compared to 2–3% in the control group. In the HPAI + ND vaccination group, 12–25% of the population had positive ND titres, compared to 5–13% in the areas without ND vaccination. The level of seropositivity varied by district, age of the bird, and species (ducks vs. chickens).
Lineage shift of dengue virus in Eastern India: an increased implication for DHF/DSS
Authors: SHRIVASTAVA A. , SONI M. , SHRIVASTAVA S. , SHARMA S. , DASH P. K. , GOPALAN N. , BEHERA P. K. , PARIDA M. M. 
Published: October 2014

SUMMARYDengue fever, a mosquito-borne viral disease, has become a major public health problem with marked expansion in recent decades. Dengue has now become hyperendemic in India with co-circulation of all the four serotypes. Herein, we report an unprecedented outbreak which occurred during August to October 2011 in Odisha, eastern India. This is the first report of a large epidemic in Odisha. Detailed serological and molecular investigation was carried out to identify the aetiology. Almost half of the samples were found to be dengue antigen (NS1) positive. Further molecular assays revealed circulation of mixed dengue serotypes (DENV-2 and DENV-3). Cosmopolitan genotype of DENV-2 and -3 were identified as the aetiology by phylogenetic analysis. Interestingly, a new lineage of DENV-3 within cosmopolitan genotype was incriminated in this outbreak. The emergence of the unprecedented magnitude of the dengue outbreak with the involvement of a novel lineage of DENV in a newer state of India is a major cause for concern. There is an urgent need to monitor phylodynamics of dengue viruses in other endemic areas.
Trust and the willingness to contribute to environmental goods in selected African countries
Authors: Yogo Urbain Thierry 
Published: October 2014

AbstractUsing data from the World Value Survey for the period 1981–2007, this paper shows that the level of trust is positively linked to the willingness to contribute to environmental goods in selected African countries. The results are robust to possible errors in measuring trust, to the presence of various controls, and the potential endogeneity bias. These findings complement and extend the existing literature in the sense that they provide evidence on the importance of trust in improving the collective management of natural resources in Africa.
Parkin regulates kainate receptors by interacting with the GluK2 subunit
Authors: Maraschi AnnaMaria , Ciammola Andrea , Folci Alessandra , Sassone Francesca , Ronzitti Giuseppe , Cappelletti Graziella , Silani Vincenzo , Sato Shigeto , Hattori Nobutaka , Mazzanti Michele , Chieregatti Evelina , Mulle Christophe , Passafaro Maria , Sassone Jenny 
Published: October 2014

AbstractAlthough loss-of-function mutations in thePARK2gene, the gene that encodes the protein parkin, cause autosomal recessive juvenile parkinsonism, the responsible molecular mechanisms remain unclear. Evidence suggests that a loss of parkin dysregulates excitatory synapses. Here we show that parkin interacts with the kainate receptor (KAR) GluK2 subunit and regulates KAR function. Loss of parkin function in primary cultured neurons causes GluK2 protein to accumulate in the plasma membrane, potentiates KAR currents and increases KAR-dependent excitotoxicity. Expression in the mouse brain of a parkin mutant causing autosomal recessive juvenile parkinsonism results in GluK2 protein accumulation and excitotoxicity. These findings show that parkin regulates KAR functionin vitroandin vivo, and suggest that KAR upregulation may have a pathogenetic role in parkin-related autosomal recessive juvenile parkinsonism.
Lateral opening of the bacterial translocon on ribosome binding and signal peptide insertion
Authors: Ge Yan , Draycheva Albena , Bornemann Thomas , Rodnina Marina V. , Wintermeyer Wolfgang 
Published: October 2014

AbstractProteins are co-translationally inserted into the bacterial plasma membrane via the SecYEG translocon by lateral release of hydrophobic transmembrane segments into the phospholipid bilayer. The trigger for lateral opening of the translocon is not known. Here we monitor lateral opening by photo-induced electron transfer (PET) between two fluorophores attached to the two SecY helices at the rim of the gate. In the resting translocon, the fluorescence is quenched, consistent with a closed conformation. Ribosome binding to the translocon diminishes PET quenching, indicating opening of the gate. The effect is larger with ribosomes exposing hydrophobic transmembrane segments and vanishes at low temperature. We propose a temperature-dependent dynamic equilibrium between closed and open conformations of the translocon that is shifted towards partially and fully open by ribosome binding and insertion of a hydrophobic peptide, respectively. The combined effects of ribosome and peptide binding allow for co-translational membrane insertion of successive transmembrane segments.
Identifying Determinants of EGFR‐Targeted Therapeutic Biochemical Efficacy Using Computational Modeling
Authors: Monast C S , Lazzara M J 
Published: October 2014

We modeled cellular epidermal growth factor receptor (EGFR) tyrosine phosphorylation dynamics in the presence of receptor‐targeting kinase inhibitors (e.g., gefitinib) or antibodies (e.g., cetuximab) to identify systematically the factors that contribute most to the ability of the therapeutics to antagonize EGFR phosphorylation, an effect we define here as biochemical efficacy. Our model identifies distinct processes as controlling gefitinib or cetuximab biochemical efficacy, suggests biochemical efficacy is favored in the presence of certain EGFR ligands, and suggests new drug design principles. For example, the model predicts that gefitinib biochemical efficacy is preferentially sensitive to perturbations in the activity of tyrosine phosphatases regulating EGFR, but that cetuximab biochemical efficacy is preferentially sensitive to perturbations in ligand binding. Our results highlight numerous other considerations that determine biochemical efficacy beyond those reflected by equilibrium affinities. By integrating these considerations, our model also predicts minimum therapeutic combination concentrations to maximally reduce receptor phosphorylation.CPT Pharmacometrics Syst. Pharmacol. (2014) 3, e141; doi:10.1038/psp.2014.39; published online 15 October 2014
Nanoparticle role on the repeatability of stimuli-responsive nanocomposites
Authors: Ahn Sungsook , Lee Sang Joon 
Published: October 2014

AbstractRepeatability of the responsiveness with time is one important concern for effective durable functions of stimuli-responsive materials. Although the increase in the yield and tensile strength of the hybrid composite materials by nanoparticle (NP) incorporation has been reported, exact NP effect on stimuli-responsiveness is rarely reported. In this study, a set of nanoscale actuating system is demonstrated by a thermo-sensitive process operated by polyethylene glycol (PEG) linked by gold nanoparticle (AuNP). This designed nanocomposite exclusively provides an artificial on/off gate function for selective passages of permeate molecules. The results demonstrate high repetition efficiency with sharp responding in a timely manner. In terms of the morphology changes induced by repeated swelling-deswelling mechanics, the nanocomposite exhibits phase separation between AuNP clusters and PEG domains. This leads to a delay in responsiveness in a cumulative way with time. Acting as stable junction points in the nanocomposite network structures, the incorporated AuNPs contribute to maintain repeatability in responsiveness. This study contributes to new-concept smart material design and fundamental understanding on the hybrid nanomaterials for various applications in terms of a dynamic mechanical behavior.
Aggregation propensities of superoxide dismutase G93 hotspot mutants mirror ALS clinical phenotypes
Authors: Pratt Ashley J. , Shin David S. , Merz Gregory E. , Rambo Robert P. , Lancaster W. Andrew , Dyer Kevin N. , Borbat Peter P. , Poole Farris L. , Adams Michael W. W. , Freed Jack H. , Crane Brian R. , Tainer John A. , Getzoff Elizabeth D. 
Published: October 2014

Significance
Mutations in human Cu, Zn superoxide dismutase (SOD) cause the motor neuron disease ALS. To better understand why, we compared the aggregation, metal binding, and conformational dynamics of normal and mutant SOD proteins by using the biophysical techniques of X-ray scattering, inductively coupled plasma MS, and ESR spectroscopy. For SOD proteins with defects at a mutational hotspot, we found that copper deficiency, flexibility, and aggregation paralleled clinical severity in ALS patients. These data support a unifying protein framework destabilization mechanism for SOD-linked ALS and thereby point to potential therapies for this lethal condition with few treatment options.
Functional improvements in β-lactoglobulin by conjugating with soybean soluble polysaccharide
Authors: Inada Naoki , Hayashi Mai , Yoshida Tadashi , Hattori Makoto 
Published: October 2014

Abstract
Soybean soluble polysaccharide (SSPS) was hydrolyzed by autoclaving for 6 and 12 h to obtain SSPS (6 h) and SSPS (12 h). Bovine β-lactoglobulin (BLG) was conjugated with each SSPS by the Maillard reaction to improve its function. Conjugation between BLG and each SSPS was confirmed by Sodium dodecyl sulfate polyacrylamide gel electrophoresis and isoelectric focusing. BLG-SSPS (6 h) and BLG-SSPS (12 h), respectively, retained approximately 56 and 43% of the retinol-binding activity of BLG. Structural analyses by intrinsic fluorescence and enzyme-linked immunosorbent assay with monoclonal antibodies indicated that the native structure of BLG had almost been maintained in each conjugate and that the surface structure was covered by conjugated SSPS. The emulsifying properties of BLG were improved in each conjugate at pH 3, 5, and 7 in the presence of 0.2 M NaCl. The antibody responses to BLG-SSPS (6 h) and BLG-SSPS (12 h) were considerably reduced in BALB/c mice. We conclude that conjugation with SSPS was very effective for improving the function of BLG and this study would contribute to greater utilization of SSPS.
Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in
Escherichia coli
Authors: Vlasblom James , Zuberi Khalid , Rodriguez Harold , Arnold Roland , Gagarinova Alla , Deineko Viktor , Kumar Ashwani , Leung Elisa , Rizzolo Kamran , Samanfar Bahram , Chang Luke , Phanse Sadhna , Golshani Ashkan , Greenblatt Jack F. , Houry Walid A. , Emili Andrew , Morris Quaid , Bader Gary , Babu Mohan 
Published: October 2014

Abstract
Motivation: The model bacterium Escherichia coli is among the best studied prokaryotes, yet nearly half of its proteins are still of unknown biological function. This is despite a wealth of available large-scale physical and genetic interaction data. To address this, we extended the GeneMANIA function prediction web application developed for model eukaryotes to support E.coli .
Results: We integrated 48 distinct E.coli functional interaction datasets and used the GeneMANIA algorithm to produce thousands of novel functional predictions and prioritize genes for further functional assays. Our analysis achieved cross-validation performance comparable to that reported for eukaryotic model organisms, and revealed new functions for previously uncharacterized genes in specific bioprocesses, including components required for cell adhesion, iron–sulphur complex assembly and ribosome biogenesis. The GeneMANIA approach for network-based function prediction provides an innovative new tool for probing mechanisms underlying bacterial bioprocesses.
Contact: gary.bader@utoronto.ca ; mohan.babu@uregina.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
Formation of an embryonic supermassive star in the first galaxy
Authors: Inayoshi Kohei , Omukai Kazuyuki , Tasker Elizabeth 
Published: October 2014

Abstract
We studied the gravitational collapse of a warm (∼8000 K) primordial-gas cloud as a candidate progenitor for a supermassive star (SMS; ≳ 105 M⊙) using a three-dimensional hydrodynamical simulation including all the relevant cooling processes of both H2 and H, which can potentially induce cloud fragmentation. This is the first simulation of this kind to resolve protostar formation. We find that from a weakly turbulent initial condition, the cloud undergoes runaway collapse without a major episode of fragmentation. Although the H2 fraction jumps by a large factor via the three-body reaction at ∼10−13 g cm−3, its cooling remains inefficient due to the optical thickness, and the temperature remains ≳ 3000 K. When the central core of the cloud becomes opaque to continuum radiation at ∼10−8 g cm−3, a hydrostatic protostar with ≃0.2 M⊙ is formed. The protostar grows to the mass ≃1 M⊙ and the radius ≃2 au within ∼1 yr via rapid accretion of dense filamentary flows. With high accretion rate, ∼2 M⊙ yr−1, the protostar is expected to turn into an SMS within its lifetime, eventually collapsing to a seed for the supermassive black hole observed in the early Universe at z ∼ 7.
FinisherSC : A repeat-aware tool for upgrading de-novo assembly using long reads
Authors: Lam Ka-Kit , LaButti Kurt , Khalak Asif , Tse David 
Published: October 2014

ABSTRACTWe introduce FinisherSC, a repeat-aware and scalable tool for upgrading de-novo assembly using long reads. Experiments with real data suggest that FinisherSC can provide longer and higher quality contigs than existing tools while maintaining high concordance.AvailabilityThe tool and data are available and will be maintained athttp://kakitone.github.io/finishingTool/Contactdntse@stanford.edu
Recent evolution of the mutation rate and spectrum in Europeans
Authors: Harris Kelley 
Published: October 2014

AbstractAs humans dispersed out of Africa, they adapted to new environmental challenges including changes in exposure to mutagenic solar radiation. Humans in temperate latitudes have acquired light skin that is relatively transparent to ultraviolet light, and some evidence suggests that their DNA damage response pathways have also experienced local adaptation. This raises the possibility that different populations have experienced different selective pressures affecting genome integrity. Here, I present evidence that the rate of a particular mutation type has recently increased in the European population, rising in frequency by 50% during the 40,000–80,000 years since Europeans began diverging from Asians. A comparison of single nucleotide polymorphisms (SNPs) private to Africa, Asia, and Europe in the 1000 Genomes data reveals that private European variation is enriched for the transition 5’-TCC-3’→5’-TTC-3’. Although it is not clear whether UV played a causal role in the changing the European mutational spectrum, 5’-TCC-3’→5’-TTC-3’ is known to be the most common somatic mutation present in melanoma skin cancers, as well as the mutation most frequently inducedin vitroby UV. Regardless of its causality, this change indicates that DNA replication fidelity has not remained stable even since the origin of modern humans and might have changed numerous times during our recent evolutionary history.
Similar efficacies of selection shape mitochondrial and nuclear genes inDrosophila melanogasterandHomo sapiens
Authors: Cooper Brandon S. , Burrus Chad R. , Ji Chao , Hahn Matthew W. , Montooth Kristi L. 
Published: October 2014

ABSTRACTDeleterious mutations contribute to polymorphism even when selection effectively prevents their fixation. The efficacy of selection in removing deleterious mitochondrial mutations from populations depends on the effective population size (Ne) of the mtDNA, and the degree to which a lack of recombination magnifies the effects of linked selection. Using complete mitochondrial genomes fromDrosophila melanogasterand nuclear data available from the same samples, we re-examine the hypothesis that non-recombining animal mtDNA harbor an excess of deleterious polymorphisms relative to the nuclear genome. We find no evidence of recombination in the mitochondrial genome, and the much-reduced level of mitochondrial synonymous polymorphism relative to nuclear genes is consistent with a reduction inNe. Nevertheless, we find that the neutrality index (NI), a measure of the excess of nonsynonymous polymorphism relative to the neutral expectation, is not significantly different between mitochondrial and nuclear loci. Reanalysis of published data fromHomo sapiensreveals the same lack of a difference between the two genomes, though small samples in previous studies had suggested a strong difference in both species. Thus, despite a smallerNe, mitochondrial loci of both flies and humans appear to experience similar efficacies of selection as do loci in the recombining nuclear genome.