bluuebunny/crossref_metadata_2025_split huggingface dataset:
In Nature, There Is Only Diversity
Authors: McLaren Michael R. , Callahan Benjamin J. 
Published: January 2018

ABSTRACT

Microbial ecology has been transformed by the advent of high-throughput marker gene and metagenomic sequencing methods. These tools provide expansive descriptions of microbial communities, but the descriptions are framed in terms of molecular objects, such as 97% ribosomal operational taxonomic units (OTUs), rather than biological objects, such as species. A recent study by A. B. Chase and colleagues (mBio 8:e01809-17, 2017,
https://doi.org/10.1128/mBio.01809-17
) explores the so-called microdiversity within the
Curtobacterium
OTU, the most abundant OTU in a leaf litter community. Perhaps unsurprisingly, they find that some important ecologic traits, such as drought response, are coherent within the OTU, but that others vary significantly. Here we discuss their findings in relation to the more general issue of how molecular tools can be effectively used to study microbial ecology. We specifically note the need for investigators to choose the right molecular methods for their biological problem, as nature does not respect the limitations and conventions associated with our methods.
Geospatial analysis of Oklahoma (USA) earthquakes (2011–2016): Quantifying the limits of regional-scale earthquake mitigation measures
Authors: Pollyea Ryan M. , Mohammadi Neda , Taylor John E. , Chapman Martin C. 
Published: January 2018

Abstract
The annual earthquake rate in Oklahoma (United States) has increased dramatically in recent years, owing in large part to the rapid proliferation of salt-water disposal (SWD) wells associated with unconventional oil and gas recovery. This study presents a geospatial analysis of earthquake occurrence and SWD volume within a 68,420 km2 area in north-central Oklahoma between 2011 and 2016. Results indicate that (1) the annual geographic centroid of Arbuckle Group SWD well locations predicts the geographic centroid for M3.0+ earthquake occurrence within an ∼1σ radius of gyration when the well centroid is geometrically weighted by SWD volume; (2) between 2014 and 2016 Arbuckle SWD volume and earthquake occurrence are spatially cross-correlated to a length scale of 125 km; and (3) earthquake mitigation strategies implemented in late 2015 and 2016 are preferentially affecting the joint variability of SWD volume and small-magnitude earthquakes. These results suggest that current earthquake mitigation may require further volume reductions and/or greater areal extent to increase effectiveness.
Do less populous countries receive more development assistance for health per capita? Longitudinal evidence for 143 countries, 1990–2014
Authors: Martinsen Lene , Ottersen Trygve , Dieleman Joseph L , Hessel Philipp , Kinge Jonas Minet , Skirbekk Vegard 
Published: January 2018

BackgroundPer capita allocation of overall development assistance has been shown to be biased towards countries with lower population size, meaning funders tend to provide proportionally less development assistance to countries with large populations. Individuals that happen to be part of large populations therefore tend to receive less assistance. However, no study has investigated whether this is also true regarding development assistance for health. We examined whether this so-called ‘small-country bias’ exists in the health aid sector.MethodsWe analysed the effect of a country’s population size on the receipt of development assistance for health per capita (in 2015 US$) among 143 countries over the period 1990–2014. Explanatory variables shown to be associated with receipt of development assistance for health were included: gross domestic product per capita, burden of disease, under-5 mortality rate, maternal mortality ratio, vaccination coverage (diphtheria, tetanus and pertussis) and fertility rate. We used the within-between regression analysis, popularised by Mundluck, as well as a number of robustness tests, including ordinary least squares, random-effects and fixed-effects regressions.ResultsOur results suggest there exists significant negative effect of population size on the amount of development assistance for health per capita countries received. According to the within-between estimator, a 1% larger population size is associated with a 0.4% lower per capita development assistance for health between countries (−0.37, 95% CI −0.45 to –0.28), and 2.3% lower per capita development assistance for health within countries (−2.29, 95% CI −3.86 to –0.72).ConclusionsOur findings support the hypothesis that small-country bias exists within international health aid, as has been previously documented for aid in general. In a rapidly changing landscape of global health and development, the inclusion of population size in allocation decisions should be challenged on the basis of equitable access to healthcare and health aid effectiveness.
Inequalities in access to cardiac rehabilitation after an acute coronary syndrome: the EPiHeart cohort
Authors: Viana Marta , Borges Andreia , Araújo Carla , Rocha Afonso , Ribeiro Ana I , Laszczyńska Olga , Dias Paula , Maciel Maria J , Moreira Ilídio , Lunet Nuno , Azevedo Ana 
Published: January 2018

ObjectivesTo estimate cardiac rehabilitation (CR) referral and participation rates among patients with acute coronary syndrome (ACS) and to identify their determinants, in two Portuguese regions.DesignProspective cohort study.SettingPatients consecutively admitted to the cardiology department of two hospitals, one in the district of Porto and one in the north-east region (NER) of Portugal, were enrolled in the EPIHeart cohort and then followed up for 6 months.ParticipantsBetween August 2013 and December 2014, 939 patients were included in the cohort, and 853 were re-evaluated at 6-month follow-up.Outcome measuresReferral rate was defined as the proportion of eligible patients who were referred to a CR programme, whereas participation rate was defined as the proportion of eligible patients who completed a CR programme, as was recommended by their physicians.ResultsPatients referred were 32.3% and 10.7% of those eligible in Porto and NER, respectively. In both regions, referral to CR decreased with age and with longer travel times to CR centres and increased with education or social class. At follow-up, 128 patients from Porto (26.2% of those eligible and 81.0% of those referred) and 26 from NER (7.1% of those eligible and 66.7% of those referred) reported actually participating in a CR programme. In Porto, the main barriers to participation were the long time until a programme was available and lack of perceived benefit. Patients in NER identified distance to CR and costs as the main barriers.ConclusionsCR remains clearly underused in Portugal, with major inequalities in access between regions. Achieving equitable and greater use of CR requires a multilevel approach addressing barriers related to healthcare system, providers and patients in order to improve provision, referral and participation.
In vitro measurement of the permeability of endovascular coils deployed in cerebral aneurysms
Authors: Sadasivan Chander , Swartwout Erica , Kappel Ari D , Woo Henry H , Fiorella David J , Lieber Barry B 
Published: January 2018

Background and purposeAneurysm recurrence is the primary limitation of endovascular coiling treatment for cerebral aneurysms. Coiling is currently quantified by a volumetric porosity measure called packing density (pd). Blood flow through a coil mass depends on the permeability of the coil mass, and not just its pd. The permeability of coil masses has not yet been quantified. Here we measure coil permeability with a traditional falling-head permeameter modified to incorporate idealized aneurysms.MethodsSilicone replicas of idealized aneurysms were manufactured with three different aneurysm diameters (4, 5, and 8 mm). Four different coil types (Codman Trufill Orbit, Covidien Axium, Microvention Microplex 10, and Penumbra 400) were deployed into the aneurysms with a target pd of 35%. Coiled replicas were installed on a falling-head permeameter setup and the time taken for a column of fluid above the aneurysm to drop a certain height was recorded. Permeability of the samples was calculated based on a simple modification of the traditional permeameter equation to incorporate a spherical aneurysm.ResultsThe targeted 35% pd was achieved for all samples (35%±1%, P=0.91). Coil permeabilities were significantly different from each other (P<0.001) at constant pd. Microplex 10 coils had the lowest permeability of all coil types. Data suggest a trend of increasing permeability with thicker coil wire diameter (not statistically significant).ConclusionsA simple in vitro setup was developed to measure the permeabilities of coil masses based on traditional permeametry. Coil permeability should be considered when evaluating the hemodynamic efficacy of coiling instead of just packing density. Coils made of thicker wires may be more permeable, and thus less effective, than coils made from thinner wires. Whether aneurysm recurrence is affected by coil wire diameter or permeability needs to be confirmed with clinical trials.
Electronic structures and magnetic properties of Fe3Si films epitaxial on Si(001)
Authors: Xie Jing , Xie Quan 
Published: January 2018

The electronic structures and magnetic properties of Fe3Si films epitaxial on Si(001) were systematically investigated by using the first-principle calculations on plane-wave pseudo-potential theory. The calculated results show that Fe3Si films epitaxial on Si(001) have the most stable equilibrium state at the lattice constant c = 5.63 Å. The negative heat of formation and cohesive energy of Fe3Si(001)//Si(001) imply that Fe3Si films epitaxial on Si(001) formed in this manner have high structural stability. The calculated spin polarized energy band structures and density of states indicate that Fe3Si films epitaxial on Si(001) have characteristic of metal, whose bonding modes are covalent bond and metallic bond. The band through Fermi level is mainly due to the Fe 3d states and the Si 3p states. Ferromagnetic properties of Fe3Si(001)//Si(001) are attributed to 3d states of the Fe atoms. The atomic magnetic moments of Fe[A,C] and Fe[B] are different from each other, likewise implying Fe3Si films epitaxial on Si(001) is ferromagnetic.
Kernels for (Connected) Dominating Set on Graphs with Excluded Topological Minors
Authors: Fomin Fedor V. , Lokshtanov Daniel , Saurabh Saket , Thilikos Dimitrios M. 
Published: January 2018

We give the first linear kernels for the D
ominating
S
et
and C
onnected
D
ominating
S
et
problems on graphs excluding a fixed graph
H
as a topological minor. In other words, we prove the existence of polynomial time algorithms that, for a given
H
-topological-minor-free graph
G
and a positive integer
k
, output an
H
-topological-minor-free graph
G
′
on
O
(
k
) vertices such that
G
has a (connected) dominating set of size
k
if and only if
G
′
has one.

Our results extend the known classes of graphs on which the D
ominating
S
et
and C
onnected
D
ominating
S
et
problems admit linear kernels. Prior to our work, it was known that these problems admit linear kernels on graphs excluding a fixed apex graph
H
as a minor. Moreover, for D
ominating
S
et
, a kernel of size
k

c
(
H
)

, where
c
(
H
) is a constant depending on the size of
H
, follows from a more general result on the kernelization of D
ominating
S
et
on graphs of bounded degeneracy. Alon and Gutner explicitly asked whether one can obtain a linear kernel for D
ominating
S
et
on
H
-minor-free graphs. We answer this question in the affirmative and in fact prove a more general result. For C
onnected
D
ominating
S
et
no polynomial kernel even on
H
-minor-free graphs was known prior to our work. On the negative side, it is known that C
onnected
D
ominating
S
et
on 2-degenerated graphs does not admit a polynomial kernel unless coNP ⊆ NP/poly.

Our kernelization algorithm is based on a non-trivial combination of the following ingredients

• The structural theorem of Grohe and Marx [STOC 2012] for graphs excluding a fixed graph
H
as a topological minor;

• A novel notion of protrusions, different than the one defined in [FOCS 2009];

• Our results are based on a generic reduction rule that produces an equivalent instance (in case the input graph is
H
-minor-free) of the problem, with treewidth
O
(√
k
). The application of this rule in a divide-and-conquer fashion, together with the new notion of protrusions, gives us the linear kernels.

A protrusion in a graph [FOCS 2009] is a subgraph of constant treewidth which is separated from the rest of the graph by at most a constant number of vertices. In our variant of protrusions, instead of stipulating that the subgraph be of constant
treewidth
, we ask that it contains a
constant number of vertices from a solution
. We believe that this new take on protrusions would be useful for other graph problems and in different algorithmic settings.
CoCoA-5.2.2 and CoCoALib
Authors: Abbott John , Bigatti Anna M. 
Published: January 2018

CoCoA-5 is an interactive Computer Algebra System for Computations in Commutative Algebra, particularly Gröbner bases. It offers a dedicated, mathematician-friendly programming language, with many built-in functions. Its mathematical core is a user-friendly C++ library, called CoCoALib; being a software library facilitates integration with other software. The software is free and open source (C++, GPL3).
CoCoALib has been designed so that other "external" software libraries can be easily integrated with it, and also made accessible via CoCoA-5.
We give an overview of CoCoA-5 and CoCoALib, highlighting the latest developments.
AltitudeOmics: effect of reduced barometric pressure on detection of intrapulmonary shunt, pulmonary gas exchange efficiency, and total pulmonary resistance
Authors: Petrassi Frank A. , Davis James T. , Beasley Kara M. , Evero Oghenero , Elliott Jonathan E. , Goodman Randall D. , Futral Joel E. , Subudhi Andrew , Solano-Altamirano J. Manuel , Goldman Saul , Roach Robert C. , Lovering Andrew T. 
Published: January 2018

Blood flow through intrapulmonary arteriovenous anastomoses (QIPAVA) occurs in healthy humans at rest and during exercise when breathing hypoxic gas mixtures at sea level and may be a source of right-to-left shunt. However, at high altitudes, QIPAVA is reduced compared with sea level, as detected using transthoracic saline contrast echocardiography (TTSCE). It remains unknown whether the reduction in QIPAVA (i.e., lower bubble scores) at high altitude is due to a reduction in bubble stability resulting from the lower barometric pressure (PB) or represents an actual reduction in QIPAVA. To this end, QIPAVA, pulmonary artery systolic pressure (PASP), cardiac output (QT), and the alveolar-to-arterial oxygen difference (AaDO2) were assessed at rest and during exercise (70–190 W) in the field (5,260 m) and in the laboratory (1,668 m) during four conditions: normobaric normoxia (NN; [Formula: see text] = 121 mmHg, PB = 625 mmHg; n = 8), normobaric hypoxia (NH; [Formula: see text] = 76 mmHg, PB = 625 mmHg; n = 7), hypobaric normoxia (HN; [Formula: see text] = 121 mmHg, PB = 410 mmHg; n = 8), and hypobaric hypoxia (HH; [Formula: see text] = 75 mmHg, PB = 410 mmHg; n = 7). We hypothesized QIPAVA would be reduced during exercise in isooxic hypobaria compared with normobaria and that the AaDO2 would be reduced in isooxic hypobaria compared with normobaria. Bubble scores were greater in normobaric conditions, but the AaDO2 was similar in both isooxic hypobaria and normobaria. Total pulmonary resistance (PASP/QT) was elevated in HN and HH. Using mathematical modeling, we found no effect of hypobaria on bubble dissolution time within the pulmonary transit times under consideration (<5 s). Consequently, our data suggest an effect of hypobaria alone on pulmonary blood flow. NEW & NOTEWORTHY Blood flow through intrapulmonary arteriovenous anastomoses, detected by transthoracic saline contrast echocardiography, was reduced during exercise in acute hypobaria compared with normobaria, independent of oxygen tension, whereas pulmonary gas exchange efficiency was unaffected. Modeling the effect(s) of reduced air density on contrast bubble lifetime did not result in a significantly reduced contrast stability. Interestingly, total pulmonary resistance was increased by hypobaria, independent of oxygen tension, suggesting that pulmonary blood flow may be changed by hypobaria.
The effects of age and sex on mechanical ventilatory constraint and dyspnea during exercise in healthy humans
Authors: Molgat-Seon Yannick , Dominelli Paolo B. , Ramsook Andrew H. , Schaeffer Michele R. , Molgat Sereacki Stéfan , Foster Glen E. , Romer Lee M. , Road Jeremy D. , Guenette Jordan A. , Sheel A. William 
Published: January 2018

We examined the effects of age, sex, and their interaction on mechanical ventilatory constraint and dyspnea during exercise in 22 older (age = 68 ± 1 yr; n = 12 women) and 22 younger (age = 25 ± 1 y, n = 11 women) subjects. During submaximal exercise, older subjects had higher end-inspiratory (EILV) and end-expiratory (EELV) lung volumes than younger subjects (both P < 0.05). During maximal exercise, older subjects had similar EILV ( P > 0.05) but higher EELV than younger subjects ( P < 0.05). No sex differences in EILV or EELV were observed. We noted that women had a higher work of breathing (Wb) for a given minute ventilation (V̇e) ≥65 l/min than men ( P < 0.05) and older subjects had a higher Wb for a given V̇e ≥60 l/min ( P < 0.05). No sex or age differences in Wb were present at any submaximal relative V̇e. At absolute exercise intensities, older women experienced expiratory flow limitation (EFL) more frequently than older men ( P < 0.05), and older subjects were more likely to experience EFL than younger subjects ( P < 0.05). At relative exercise intensities, women and older individuals experienced EFL more frequently than men and younger individuals, respectively (both P < 0.05). There were significant effects of age, sex, and their interaction on dyspnea intensity during exercise at absolute, but not relative, intensities (all P < 0.05). Across subjects, dyspnea at 80 W was significantly correlated with indexes of mechanical ventilatory constraint (all P < 0.05). Collectively, our findings suggest age and sex have significant impacts on Wb, operating lung volumes, EFL, and dyspnea during exercise. Moreover, it appears that mechanical ventilatory constraint may partially explain sex differences in exertional dyspnea in older individuals. NEW & NOTEWORTHY We found that age and sex have a significant effect on mechanical ventilatory constraint and the perception of dyspnea during exercise. We also observed that the perception of exertional dyspnea is associated with indexes of mechanical ventilatory constraint. Collectively, our results suggest that the combined influences of age and biological sex on mechanical ventilatory constraint during exercise contributes, in part, to the increased perception of dyspnea during exercise in older women.
Voluntary exercise slows breast tumor establishment and reduces tumor hypoxia in ApoE−/− mice
Authors: Buss Linda A. , Dachs Gabi U. 
Published: January 2018

Exercise reduces the risk of breast cancer development and improves survival in breast cancer patients. However, the underlying mechanisms of this protective effect remain to be fully elucidated, and it is unclear whether exercise can attenuate the protumor effects of obesity and related hyperlipidemia on breast cancer growth and development. We hypothesized that exercise attenuates the negative effect of hyperlipidemia through normalization of the tumor microenvironment and improved T cell infiltrate. Hyperlipidemic ApoE−/− mice with orthotopic EO771 breast tumors were randomly assigned to one of two voluntary running groups or sedentary controls, and muscular cytochrome c oxidase subunit IV (COX-IV) expression was used as a biomarker for the level of exercise. Tumors from mice with high muscular COX-IV expression took significantly longer to reach 100 mm3 ( P = 0.008), but showed no difference in growth rate once the tumor was established. Wheel running appeared to reduce internal metastases, but did not affect T cell infiltrate or the proportion of regulatory and cytotoxic T cells within the tumor. Serum levels of monocyte chemoattractant protein-1 (MCP-1) were significantly increased by tumor burden ( P = 0.02) and correlated with spleen weight ( P < 0.0001, R = 0.65). Furthermore, tumor hypoxia was significantly decreased in mice with high muscular COX-IV expression ( P = 0.01). Taken together, these results indicate that wheel running can slow the establishment of primary and secondary EO771 breast tumors and induce beneficial changes in the breast tumor microenvironment in ApoE−/− mice. NEW & NOTEWORTHY In this first study to investigate the effect of exercise on tumor behavior in a hyperlipidemic model, we hypothesized that wheel running would counteract the protumorigenic environment generated by hyperlipidemia. Wheel running slowed establishment of primary and secondary tumors and reduced tumor hypoxia but did not affect exponential tumor growth in ApoE−/− mice. Overall, voluntary wheel running induced favorable microenvironmental changes in breast tumors.
Effects of −12° head-down tilt with and without elevated levels of CO2 on cognitive performance: the SPACECOT study
Authors: Basner Mathias , Nasrini Jad , Hermosillo Emanuel , McGuire Sarah , Dinges David F. , Moore Tyler M. , Gur Ruben C. , Rittweger Jörn , Mulder Edwin , Wittkowski Martin , Donoviel Dorit , Stevens Brian , Bershad Eric M. ,   the SPACECOT Investigator Group
Published: January 2018

Microgravity and elevated levels of CO2 are two common environmental stressors in spaceflight that may affect cognitive performance of astronauts. In this randomized, double-blind, crossover trial (SPACECOT), 6 healthy males (mean ± SD age: 41 ± 5 yr) were exposed to 0.04% (ambient air) and 0.5% CO2 concentrations during 26.5-h periods of −12° head-down tilt (HDT) bed rest with a 1-wk washout period between exposures. Subjects performed the 10 tests of the Cognition Test Battery before and on average 0.1, 5.2, and 21.0 h after the initiation of HDT bed rest. HDT in ambient air induced a change in response strategy, with increased response speed (+0.19 SD; P = 0.0254) at the expense of accuracy (−0.19 SD; P = 0.2867), resulting in comparable cognitive efficiency. The observed effects were small and statistically significant for cognitive speed only. However, even small declines in accuracy can potentially cause errors during mission-critical tasks in spaceflight. Unexpectedly, exposure to 0.5% CO2 reversed the response strategy changes observed under HDT in ambient air. This was possibly related to hypercapnia-induced cerebrovascular reactivity that favors cortical regions in general and the frontal cortex in particular, or to the CNS arousing properties of mildly to moderately increased CO2 levels. There were no statistically significant time-in-CO2 effects for any cognitive outcome. The small sample size and the small effect sizes are major limitations of this study and its findings. The results should not be generalized beyond the group of investigated subjects until they are confirmed by adequately powered follow-up studies. NEW & NOTEWORTHY Simulating microgravity with exposure to 21 h of −12° head-down tilt bed rest caused a change in response strategy on a range of cognitive tests, with a statistically significant increase in response speed at the expense of accuracy. Cognitive efficiency was not affected. The observed speed-accuracy tradeoff was small but may nevertheless be important for mission-critical tasks in spaceflight. Importantly, the change in response strategy was reversed by increasing CO2 concentrations to 0.5%.