bluuebunny/crossref_metadata_2025_split huggingface dataset:
R47H TREM2 variant increases risk of typical early‐onset Alzheimer's disease but not of prion or frontotemporal dementia
Authors: Slattery Catherine F. , Beck Jonathan A. , Harper Lorna , Adamson Gary , Abdi Zeinab , Uphill James , Campbell Tracy , Druyeh Ron , Mahoney Colin J. , Rohrer Jonathan D. , Kenny Janna , Lowe Jessica , Leung Kelvin K. , Barnes Josephine , Clegg Shona L. , Blair Melanie , Nicholas Jennifer M. , Guerreiro Rita J. , Rowe James B. , Ponto Claudia , Zerr Inga , Kretzschmar Hans , Gambetti Pierluigi , Crutch Sebastian J. , Warren Jason D. , Rossor Martin N. , Fox Nick C. , Collinge John , Schott Jonathan M. , Mead Simon 
Published: August 2014

AbstractBackgroundRare TREM2 variants are significant risk factors for Alzheimer's disease (AD).MethodsWe used next generation sequencing of the whole gene (n = 700), exon 2 Sanger sequencing (n = 2634), p.R47H genotyping (n = 3518), and genome wide association study imputation (n = 13,048) to determine whether TREM2 variants are risk factors or phenotypic modifiers in patients with AD (n = 1002), frontotemporal dementia (n = 358), sporadic (n = 2500), and variant (n = 115) Creutzfeldt‐Jakob disease (CJD).ResultsWe confirm only p.R47H as a risk factor for AD (odds ratio or OR = 2.19; 95% confidence interval or CI = 1.04‐4.51; P = .03). p.R47H does not significantly alter risk for frontotemporal dementia (OR = 0.81), variant or sporadic CJD (OR = 1.06 95%CI = 0.66‐1.69) in our cohorts. Individuals with p.R47H associated AD (n = 12) had significantly earlier symptom onset than individuals with no TREM2 variants (n = 551) (55.2 years vs. 61.7 years, P = .02). We note that heterozygous p.R47H AD is memory led and otherwise indistinguishable from “typical” sporadic AD.ConclusionWe find p.R47H is a risk factor for AD, but not frontotemporal dementia or prion disease.
Reduced cerebrovascular reactivity in young adults carrying the APOE ε4 allele
Authors: Suri Sana , Mackay Clare E. , Kelly Michael E. , Germuska Michael , Tunbridge Elizabeth M. , Frisoni Giovanni B. , Matthews Paul M. , Ebmeier Klaus P. , Bulte Daniel P. , Filippini Nicola 
Published: August 2014

AbstractBackgroundFunctional magnetic resonance imaging (MRI) studies have shown that APOE ε2‐ and ε4‐carriers have similar patterns of blood‐oxygenation‐level‐dependent (BOLD) activation suggesting that we need to look beyond the BOLD signal to link APOE's effect on the brain to Alzheimer's disease (AD)‐risk.MethodsWe evaluated APOE‐related differences in BOLD activation in response to a memory task, cerebrovascular reactivity using a CO2‐inhalation challenge (CO2‐CVR), and the potential contribution of CO2‐CVR to the BOLD signal.ResultsAPOE ε4‐carriers had the highest task‐related hippocampal BOLD signal relative to non‐carriers. The largest differences in CO2‐CVR were between ε2‐ and ε4‐carriers, with the latter having the lowest values. Genotype differences in CO2‐CVR accounted for ∼70% of hippocampal BOLD differences between groups.ConclusionBecause CO2‐CVR gauges vascular health, the differential effect of APOE in young adults may reflect a vascular contribution to the vulnerability of ε4‐carriers to late‐life pathology. Studies confirming our findings are warranted.
Natural coal fires in the Kuznetsk Coal Basin: geologic causes, climate, and age
Authors: Sokol E.V. , Novikova S.A. , Alekseev D.V. , Travin A.V. 
Published: August 2014

Abstract
The paper summarizes data on the Pleistocene combustion metamorphic complexes of the Kuznetsk Coal Basin. Paralava and clinker samples are dated by 40Ar/39Ar incremental heating. The 40Ar/39Ar ages of the combustion metamorphic rocks permit reconstructions of the succession of renewed activity of ancient faults in the Salair zone and age estimates for the evolution of the present-day drainage network. Cross sections of burned rocks from the western margin and center of the Kuznetsk Basin are compared. The geologic factors of coal ignition risks are analyzed. On the western margin of the Kuznetsk Basin, paleofires occurred in steeply dipping thick seams with predominant crushed vitrain–clarain coal, which has a high oxygen and methane adsorption capacity. Highly denuded high-temperature combustion metamorphic complexes are most often localized in the arches of slightly broken anticlines. Oxygen was supplied to the coals during the Late Cenozoic renewed fault activity and the subsequent erosion of the sediments. The natural fires in the area were a result of external rather than spontaneous ignition. The depths of the paleofires (up to 200 m) indicate that they occurred in a warm and dry climate. In the center of the Kuznetsk Basin, dispersed fire foci appeared in seams of self-igniting coals with the erosion propagation of the current drainage network. The combustion metamorphic complexes here are partly eroded and consist mostly of clinkers with a low degree of alteration. The 40Ar/39Ar ages and geological data indicate that the earliest large-scale combustion events on the western periphery of the basin occurred in the Eopleistocene (1.3–0.9 Ma). The oldest 40Ar/39Ar age of a coal fire episode (1.7 ± 0.3 Ma) might be the upper age boundary of the altitude differentiation of topography, which corresponds to the renewed activity of the Tyrgan and Afonino–Kiselevsk faults. The later synchronous combustion events on the western margin (0.2 ± 0.1 Ma) and in the center of the basin (0.13–0.02 Ma), most probably, occurred during the Kazantsevian interglacial, which gave rise to the present-day drainage network.
A-type granites and related rocks: petrogenesis and classification
Authors: Grebennikov A.V. 
Published: August 2014

Abstract
The problems of identification of A-type granitoids are analyzed. These rocks occur in different geodynamic settings. Owing to their mantle nature, they show distinct REE specialization. These are acid intrusive rocks, whose volcanic products are of crucial scientific and practical significance. However, neither the great number of proposed classification schemes and diagrams, including those based on expensive analytical data, nor hot scientific discussions of their identification and the ambiguity of the term A-granitoids helped to determine their classification features in full measure. A principally new discriminant diagram is proposed for the classification of igneous A-type rocks, based on the analysis of earlier obtained results and the petrochemical composition of these rocks. A comparative analysis of subdivision of granites and related felsic volcanic rocks (SiO2 &gt; 67 wt.%), based on the ternary (Na2O + K2O)–Fe2O3*×5–(CaO + MgO)×5 and other widely applied diagrams, has shown the advantage of the proposed discriminant diagram for the classification of A-type granitoids from different geodynamic settings.
Mineral inclusions in sapphire from the basalt-related deposit in Bo Phloi, Kanchanaburi, western Thailand: indication of their genesis
Authors: Khamloet P. , Pisutha-Arnond V. , Sutthirat C. 
Published: August 2014

Abstract
The Bo Phloi gem field in Kanchanaburi Province, Western Thailand, is closely associated with Cenozoic basalts. Blue and yellow sapphire, black spinel, and minor zircon have been mined for over three decades. The mineral inclusions observed in sapphire samples are alkali feldspar, nepheline, hercynitic spinel, zircon, manganiferous ilmenite, silica-rich enstatite, almandine–pyrope garnet, monazite, calcite, sapphirine, biotite–phlogopite mica, and staurolite. Based on their geochemical affinity, these mineral inclusions can be categorized into two main groups: felsic alkaline and contact-metamorphic, which appear to have originated from different processes. These inclusions provide new evidence for proposing a bimodal genetic model. Felsic alkaline origin is evidenced by the occurrence of a felsic alkaline inclusion suite and the REE geochemistry of sapphire-associated zircon, which indicates that most of the sapphires crystallized from a high-alkali felsic melt (probably, in the lower crust). Contact-metamorphic origin is evidenced by the presence of a contact-metamorphic inclusion suite, suggesting that some of these sapphires might also have originated from metasomatized crustal rocks and a contaminated melt along the contact zone of a basaltic intrusion (probably, in the upper mantle or lower crust).
Evaluation of radiation dose due to naturally occurring radionuclides in rock samples of different origins collected from Azad Kashmir
Authors: Rafique M. , Khan A.R. , Jabbar A. , Rahman S.U. , Kazmi S.J.A. , Nasir T. , Arshed W. , Matiullah  
Published: August 2014

Abstract
The state of Azad Kashmir is rich in three types of rocks, namely, sedimentary, metamorphic, and igneous rocks. These rocks contain extensive deposits of graphite, marble, limestone, quartzite, granite, dolerite, and sandstone, which are widely used for the construction of dwellings in Azad Kashmir and Pakistan. Therefore, knowledge about the presence of natural radioactivity in these materials is desirable to assess the radiological hazards associated with it. In this context, 30 rock samples were collected from different geologic formations of the Muzaffarabad Division, Azad Kashmir. After processing the samples, the specific activities of 226Ra, 232Th, and 40K in them were measured using a P-type coaxial high-purity germanium detector. The observed highest dose rate values for sedimentary, metamorphic, and igneous rocks have been found to be 83.16 ± 1.08, 135.87 ± 1.18, and 115.98 ± 1 nGy ⋅ h–1, respectively. The radium equivalent activity (Raeq) varied from 23.76 ± 1.15 for dolerite sample (igneous rock) to 293.69 ± 2.60 Bq ⋅ kg–1 for marble (metamorphic rock). The Raeq values of all rock samples are lower than the limit mentioned in the Organization for Economic Cooperation and Development (OECD, 1979) report (370 Bq ⋅ kg–1, equivalent to γ-dose of 1.5 mSv ⋅ y–1). The values of external (Hex) and internal hazard indices (Hin) are less than unity. The mean outdoor and indoor annual effective dose equivalents are 0.073 mSv ⋅ y–1 and 0.29 mSv ⋅ y–1, respectively. The mean (over all types of rock samples) annual effective dose equivalent is reported as 0.36 mSv ⋅ y–1.
The experience of mapping of Baikal subsurface gas hydrates and gas recovery
Authors: Khlystov O.M. , Nishio Sh. , Manakov A.Yu. , Sugiyama H. , Khabuev A.V. , Belousov O.V. , Grachev M.A. 
Published: August 2014

Abstract
Lake Baikal is the only fresh-water lake where natural gas hydrate accumulations were found in sediments. For the recent decade, Baikal has become a natural laboratory for investigation of the properties of gas hydrates, their indicators, and recovery of gas from subsurface (subbottom) gas hydrates. We present the main results of subsurface gas hydrate mapping and gas recovery test near the delta of the Goloustnaya River.
Method for deep temperature estimation with regard to the paleoclimate influence on heat flow
Authors: Golovanova I.V. , Sal’manova R.Yu. , Tagirova Ch.D. 
Published: August 2014

Abstract
New results of the study of the distorting effect of paleoclimate on the formation of the thermal field of the Earth’s uppermost crust in the South Urals are presented. We discuss some consequences of taking into account the paleoclimate influence on estimates of deep heat flow and possible applications of these data. The dependence of the heat flow density on the studied depth of boreholes is considered, and deep heat loss and deep temperatures are estimated. A new method for deep temperature estimation is proposed, which takes into account the paleoclimate influence on the heat flow. The method is tested on the available high-quality temperature data for deep boreholes. Deep temperatures to a depth of –10,000 m are estimated for the platform part of the Republic of Bashkortostan using the proposed method. Isotherm schemes are constructed for elevations of –5000 and –10,000 m below sea level.
The necessity of using heat flow values corrected for the paleoclimate influence to estimate the Earth’s thermal state is justified. Some examples illustrate that underestimation of heat flow values measured in shallow boreholes might lead to underestimation of deep temperatures and global heat losses.
Instability of layered media under gravity stress
Authors: Rebetsky Yu.L. 
Published: August 2014

Abstract
It is proposed to consider data both on the deep density distribution (gravity instability) and the bulk modulus of elasticity on estimation of the stability of layered mountain ranges. It is shown that an increase in bulk elastic rigidity with depth is the stable state of layered media in terms of energy in the field of gravity stress. In the tectonosphere, in which the moduli of elasticity are inverted (decrease) with depth, excess energy of elastic strain of volume change is generated by body forces, and it will determine the instability of the geologic medium.
Optimized two-color super resolution imaging of Drp1 during mitochondrial fission with a slow-switching Dronpa variant
Authors: Rosenbloom Alyssa B. , Lee Sang-Hyuk , To Milton , Lee Antony , Shin Jae Yen , Bustamante Carlos 
Published: August 2014

Significance
Optimal performance of super resolution fluorescence localization microscopy relies on a clear understanding of the photo-physical properties of photoactivatable (photo-switchable) fluorescent proteins [PA(PS)-FPs] at the single-molecule level. Our comparative study of Dronpa and a novel variant, rsKame, demonstrates the crucial role of photo-switching kinetics in super resolution imaging. rsKame, with its superior properties, significantly broadens the green PA(PS)-FP palette. We demonstrate the efficacy of rsKame and our two-color super resolution imaging method (paired with PAmCherry1) by visualizing the inner and outer mitochondrial membranes and in situ structural parameters of dynamin related protein 1 helical rings during mitochondrial fission. Our two-color super resolution imaging method presented here is a reliable and user-friendly technique without complicated sample preparation.
ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments
Authors: Khan Imtiaz A. , Fraser Adam , Bray Mark-Anthony , Smith Paul J. , White Nick S. , Carpenter Anne E. , Errington Rachel J. 
Published: August 2014

Abstract
Motivation: Experimental reproducibility is fundamental to the progress of science. Irreproducible research decreases the efficiency of basic biological research and drug discovery and impedes experimental data reuse. A major contributing factor to irreproducibility is difficulty in interpreting complex experimental methodologies and designs from written text and in assessing variations among different experiments. Current bioinformatics initiatives either are focused on computational research reproducibility (i.e. data analysis) or laboratory information management systems. Here, we present a software tool, ProtocolNavigator, which addresses the largely overlooked challenges of interpretation and assessment. It provides a biologist-friendly open-source emulation-based tool for designing, documenting and reproducing biological experiments.
Availability and implementation: ProtocolNavigator was implemented in Python 2.7, using the wx module to build the graphical user interface. It is a platform-independent software and freely available from http://protocolnavigator.org/index.html under the GPL v2 license.
Contact: wpciak@cf.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Cosi2: an efficient simulator of exact and approximate coalescent with selection
Authors: Shlyakhter Ilya , Sabeti Pardis C. , Schaffner Stephen F. 
Published: August 2014

Abstract
Motivation: Efficient simulation of population genetic samples under a given demographic model is a prerequisite for many analyses. Coalescent theory provides an efficient framework for such simulations, but simulating longer regions and higher recombination rates remains challenging. Simulators based on a Markovian approximation to the coalescent scale well, but do not support simulation of selection. Gene conversion is not supported by any published coalescent simulators that support selection.
Results: We describe cosi2, an efficient simulator that supports both exact and approximate coalescent simulation with positive selection. cosi2 improves on the speed of existing exact simulators, and permits further speedup in approximate mode while retaining support for selection. cosi2 supports a wide range of demographic scenarios, including recombination hot spots, gene conversion, population size changes, population structure and migration.
cosi2 implements coalescent machinery efficiently by tracking only a small subset of the Ancestral Recombination Graph, sampling only relevant recombination events, and using augmented skip lists to represent tracked genetic segments. To preserve support for selection in approximate mode, the Markov approximation is implemented not by moving along the chromosome but by performing a standard backwards-in-time coalescent simulation while restricting coalescence to node pairs with overlapping or near-overlapping genetic material. We describe the algorithms used by cosi2 and present comparisons with existing selection simulators.
Availability and implementation: A free C++ implementation of cosi2 is available at http://broadinstitute.org/mpg/cosi2.
Contact: ilya@broadinstitute.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Inter-species pathway perturbation prediction via data-driven detection of functional homology
Authors: Hafemeister Christoph , Romero Roberto , Bilal Erhan , Meyer Pablo , Norel Raquel , Rhrissorrakrai Kahn , Bonneau Richard , Tarca Adi L. 
Published: August 2014

Motivation: Experiments in animal models are often conducted to infer how humans will respond to stimuli by assuming that the same biological pathways will be affected in both organisms. The limitations of this assumption were tested in the IMPROVER Species Translation Challenge, where 52 stimuli were applied to both human and rat cells and perturbed pathways were identified. In the Inter-species Pathway Perturbation Prediction sub-challenge, multiple teams proposed methods to use rat transcription data from 26 stimuli to predict human gene set and pathway activity under the same perturbations. Submissions were evaluated using three performance metrics on data from the remaining 26 stimuli.Results: We present two approaches, ranked second in this challenge, that do not rely on sequence-based orthology between rat and human genes to translate pathway perturbation state but instead identify transcriptional response orthologs across a set of training conditions. The translation from rat to human accomplished by these so-called direct methods is not dependent on the particular analysis method used to identify perturbed gene sets. In contrast, machine learning-based methods require performing a pathway analysis initially and then mapping the pathway activity between organisms. Unlike most machine learning approaches, direct methods can be used to predict the activation of a human pathway for a new (test) stimuli, even when that pathway was never activated by a training stimuli.Availability: Gene expression data are available from ArrayExpress (accession E-MTAB-2091), while software implementations are available from http://bioinformaticsprb.med.wayne.edu?p=50 and http://goo.gl/hJny3h.Contact: christoph.hafemeister@nyu.edu or atarca@med.wayne.edu.Supplementary information: Supplementary Data are available at Bioinformatics online.
Elevated Carbon Monoxide to Carbon Dioxide Ratio in the Exhaled Breath of Mice Treated With a Single Dose of Lipopolysaccharide
Authors: Langeroudi Arash Ghalyanchi , Hirsch Charlotte M. , Estabragh Azadeh Shojaee , Meinardi Simone , Blake Donald R. , Barbour Alan G. 
Published: August 2014

Background.  Analysis of volatile organic chemicals in breath holds promise for noninvasive diagnosis and monitoring of patients, but investigation of this in experimental mouse models has been limited. Of particular interest is endogenous production of carbon monoxide as a biomarker of inflammation and, more particularly, during sepsis.
Methods.  Using a nose-only collection procedure for unanesthetized individual adult mice and sensitive gas chromatography of carbon monoxide (CO) and carbon dioxide (CO2) of sampled breath, we investigated the responses of mice to one-time injections with different doses of purified Escherichia coli lipopolysaccharide. Two strains of mice were examined: BALB/c and C3H, including an endotoxin-resistant mutant (HeJ) as well as the wild type (HOuJ).
Results.  The CO to CO2 ratio increased in a dose-responsive manner within hours in treated BALC/c mice but not control mice. The CO/CO2 values declined to the range of control mice within 48–72 h after the injection of lipopolysaccharide. Breath CO/CO2 values correlated with systemic inflammation biomarkers in serum and heme oxygenase-1 gene expression in blood. C3H/HOuJ mice, but not the HeJ mice, had similar increases of the CO/CO2 ratio in response to the endotoxin.
Conclusions.  Carbon monoxide concentrations in exhaled breath of at least 2 strains of mice increase in response to single injections of endotoxin. The magnitude of increase was similar to what was observed with a bacteremia model. These findings with an experimental model provide a rationale for further studies of normalized CO concentrations in human breath as an informative biomarker for staging and monitoring of sepsis.
Tree diversity and the role of non‐host neighbour tree species in reducing fungal pathogen infestation
Authors: Hantsch Lydia , Bien Steffen , Radatz Stine , Braun Uwe , Auge Harald , Bruelheide Helge 
Published: August 2014

Summary

The degree to which plant pathogen infestation occurs in a host plant is expected to be strongly influenced by the level of species diversity among neighbouring host and non‐host plant species. Since pathogen infestation can negatively affect host plant performance, it can mediate the effects of local biodiversity on ecosystem functioning.

We tested the effects of tree diversity and the proportion of neighbouring host and non‐host species with respect to the foliar fungal pathogens of Tilia cordata and Quercus petraea in the Kreinitz tree diversity experiment in Germany. We hypothesized that fungal pathogen richness increases while infestation decreases with increasing local tree diversity. In addition, we tested whether fungal pathogen richness and infestation are dependent on the proportion of host plant species present or on the proportion of particular non‐host neighbouring tree species.

Leaves of the two target species were sampled across three consecutive years with visible foliar fungal pathogens on the leaf surface being identified macro‐ and microscopically. Effects of diversity among neighbouring trees were analysed: (i) for total fungal species richness and fungal infestation on host trees and (ii) for infestation by individual fungal species.

We detected four and five fungal species on T. cordata and Q. petraea, respectively. High local tree diversity reduced (i) total fungal species richness and infestation of T. cordata and fungal infestation of Q. petraea and (ii) infestation by three host‐specialized fungal pathogen species. These effects were brought about by local tree diversity and were independent of host species proportion. In general, host species proportion had almost no effect on fungal species richness and infestation. Strong effects associated with the proportion of particular non‐host neighbouring tree species on fungal species richness and infestation were, however, recorded.

Synthesis. For the first time, we experimentally demonstrated that for two common forestry tree species, foliar fungal pathogen richness and infestation depend on local biodiversity. Thus, local tree diversity can have positive impacts on ecosystem functioning in managed forests by decreasing the level of fungal pathogen infestation.