bluuebunny/crossref_metadata_2025 huggingface dataset:
Internal fatigue crack initiation in drawn Ti–6Al–4V wires
Authors: Everaerts J. , Verlinden B. , Wevers M.
Published: January 2016

Fatigue cracks in titanium alloys are often found to initiate at faceted alpha grains. In the very high cycle fatigue regime, crack initiation tends to shift from the surface towards the interior of the material, and more initiation facets can be found on the fracture surface. In this study, fatigue tests were performed on drawn and heat-treated Ti–6Al–4V wires. Only a few samples fractured due to interior initiation. The facets at the initiation sites of these samples were not flat, but had markings on the nano-scale, and were highly inclined. A possible explanation for these aspects is the crystallographic texture of the wire, and a reflection is made on the suggested mechanisms of facet formation.

This paper is part of a Themed Issue on Euromech 570: Interface-dominated materials.
Role of MgO nanoparticles on zirconia-toughened alumina-5 wt-% CeO2 ceramics mechanical properties
Authors: Rejab N. A. , Ahmad Azhar A. Z. , Ratnam M. M. , Ahmad Z. A.
Published: January 2016

The poor hardness of zirconia-toughened alumina (ZTA) with 5 wt-% CeO2 (ZTA5CeO2) ceramic has limited its applications as a cutting insert. Therefore, in this work, the possibility of MgO nanoparticles (20 nm) as reinforcement to ZTA5CeO2 ceramics was investigated. Mgo nanoparticles with different weight percentages (0-2 wt-%) were added to ZTA5CeO2 ceramics. ZTA5CeO2 with 0.5 wt-%MgO showed the highest fracture toughness of 9.14 MPa.√m. The addition of 0.5 wt-%MgO nanoparticles showed the excellent role of MgAl11CeO19 grains as a crack deflector, which consequently produced a reasonable hardness value of 1591 HV and lowered the wear areas to 0.0528 mm2.
Very high cycle fatigue of bearing steels with artificial defects in vacuum
Authors: Spriestersbach D. , Brodyanski A. , Lösch J. , Kopnarski M. , Kerscher E.
Published: January 2016

At high-strength steels very high cycle fatigue (VHCF) failure always occurs at subsurface inclusions. As a result, the failure shows large scatter and is not observable or predictable prior to failure. In order to understand the mechanisms leading to crack initiation in VHCF, it is necessary to make the failure observable. Within our work, a new testing procedure is introduced that enables the simulation of subsurface conditions at the surface and thereby the localisation of the failure. Therefore, specimens with artificial surface defects were tested in vacuum atmosphere. In our work, we will show the testing procedure and the validation of the results. Further, the transferability of our results on the failure at subsurface inclusions is discussed.

This paper is part of a Themed Issue on Recent developments in bearing steels.
Sliding wear behaviour and microstructure of PEO coatings formed on aluminium alloy
Authors: Zhuang J. J. , Guo Y. Q. , Xiang N. , Lu X. Y. , Hu Q. , Song R. G.
Published: January 2016

In this work, plasma electrolytic oxidation coating was formed on aluminium alloy in a cheap and inexpensive electrolyte to improve its wear resistance. It was found the micro-hardness of coatings increased first and then decreased with increasing the oxidised time. It was showed that the specimen treated under the time of 35 minutes exhibited the highest micro-hardness and lowest wear loss. The surface and cross-sectional morphology indicated that the coatings have a dense structure with low porosity. The presence of wear scars on the worn surface morphology demonstrates that the three-body rolling was the main wear mechanism for coated specimen. X-ray diffraction results showed the coating was formed mainly from α-Al2O3 and γ-Al2O3.
What Speeds up the Internal Clock? Effects of Clicks and Flicker on Duration Judgements and Reaction Time
Authors: Wearden J. H. , Williams Emily A. , Jones Luke A.
Published: January 2016

Four experiments investigated the effect of pre-stimulus events on judgements of the subjective duration of tones that they preceded. Experiments 1 to 4 used click trains, flickering squares, expanding circles, and white noise as pre-stimulus events and showed that (a) periodic clicks appeared to “speed up” the pacemaker of an internal clock but that the effect wore off over a click-free delay, (b) aperiodic click trains, and visual stimuli in the form of flickering squares and expanding circles, also produced similar increases in estimated tone duration, as did white noise, although its effect was weaker. A fifth experiment examined the effects of periodic flicker on reaction time and showed that, as with periodic clicks in a previous experiment, reaction times were shorter when preceded by flicker than without.
Rapid communication: The politics of insight
Authors: Salvi Carola , Cristofori Irene , Grafman Jordan , Beeman Mark
Published: January 2016

Previous studies showed that liberals and conservatives differ in cognitive style. Liberals are more flexible, and tolerant of complexity and novelty, whereas conservatives are more rigid, are more resistant to change, and prefer clear answers. We administered a set of compound remote associate problems, a task extensively used to differentiate problem-solving styles (via insight or analysis). Using this task, several researches have proven that self-reports, which differentiate between insight and analytic problem-solving, are reliable and are associated with two different neural circuits. In our research we found that participants self-identifying with distinct political orientations demonstrated differences in problem-solving strategy. Liberals solved significantly more problems via insight instead of in a step-by-step analytic fashion. Our findings extend previous observations that self-identified political orientations reflect differences in cognitive styles. More specifically, we show that type of political orientation is associated with problem-solving strategy. The data converge with previous neurobehavioural and cognitive studies indicating a link between cognitive style and the psychological mechanisms that mediate political beliefs.
Workfare: conditioning the attitudes of benefit recipients towards social security?
Authors: Humpage Louise , Baillie Simone
Published: January 2016

Have increasing levels of conditionality fundamentally changed the attitudes of the unemployed towards social security, work obligations and welfare dependency? Both neopaternalist and governmentalist theorising suggests that workfare policies should have shifted this group's conceptions of self-interest over time yet previous evidence has been rather mixed. This article makes a fresh contribution to the literature by drawing upon New Zealand Election Study data (1990–2014) and New Zealand qualitative data (2007–2008; 2014) to analyse the attitudes of “undeserving” unemployed benefit recipients who are subject to work obligations over 21 yearsandby comparing their attitudes to those of “deserving” benefit recipients not subject to work obligations (the retired and students) and wage/salary earners. It finds a notable hardening of unemployed people's attitudes towards some welfare dependency propositions over time and evidence of “self-governing rationalities” being adopted by some unemployed individuals but, overall, attitudes amongst this group remain nuanced and ambivalent.
A first integral for 𝐶^{∞}, k-basic Finsler surfaces and applications to rigidity
Authors: Foulon P. , Ruggiero R.
Published: January 2016

We show that a compact

C

∞

C^{\infty }

, k-basic Finsler surface without conjugate points and genus greater than one is Riemannian. This result is a

C

∞

C^{\infty }

version of the fact, proved by G. Paternain, that analytic, compact, k-basic Finsler surfaces with genus greater than one are Riemannian. The proof in the

C

∞

C^{\infty }

case relies mainly on two facts: first of all the existence of a first integral for the geodesic flow of any k-basic Finsler surface, one of the main contributions of this note; and secondly the triviality of every first integral assuming the absence of conjugate points.
Connected cochain DG algebras of Calabi-Yau dimension 0
Authors: He J.-W. , Mao X.-F.
Published: January 2016

Let

A
A

be a connected cochain differential graded (DG, for short) algebra. This note shows that

A
A

is a

0
0

-Calabi-Yau DG algebra if and only if

A
A

is a Koszul DG algebra and

T
o
r

A
0

(

k
A

,

A

k
)

\mathrm {Tor}_A^0(\Bbbk _A,{}_A\Bbbk )

is a symmetric coalgebra. Let

V
V

be a finite dimensional vector space and

w
w

a potential in

T
(
V
)

T(V)

. Then the minimal subcoalgebra of

T
(
V
)

T(V)

containing

w
w

is a symmetric coalgebra, which implies that a locally finite connected cochain DG algebra is

0
0

-CY if and only if it is defined by a potential

w
w

.
Metapopulation viability of swamp rabbits in southern Illinois: potential impacts of habitat change
Authors: Robinson Christopher D. , Crawford Joanne C. , Corcoran Lyann , Schauber Eric M. , Nielsen Clayton K.
Published: January 2016

Swamp rabbits ( Sylvilagus aquaticus ) in southern Illinois exist as a metapopulation due to fragmentation of the bottomland hardwood forests in which they live. This fragmentation makes their persistence in Illinois uncertain. We used population viability analysis (PVA) to estimate the probability of persistence of the swamp rabbit metapopulation in Illinois, using a habitat suitability map we created and life history parameters drawn from the literature. We varied the parameters used in our PVA from 50% to 150% of the initial value to compare their effects on extinction risk and to direct future management and research. We tested the effects of potential habitat loss and fragmentation by 1) removing patches individually and in groups from the analysis and by 2) adding 60, 120, and 180 m to the edge of all patches. We also tested the potential effect of dispersal corridors by increasing dispersal between connected patches. Under baseline conditions, the model suggests a 0% chance of quasi-extinction (90% metapopulation decline) of swamp rabbits within 25 (or even 50) years. Changes in fecundity values and the effects of catastrophic flooding had the greatest effect on extinction risk, and changes in no other parameter yielded any appreciable impact. Removing the largest patches from the population increased the 25-year risk of extinction to 4%, whereas any other modifications to the habitat did not change the extinction risk. We suggest that managers focus on sustaining habitat quality, particularly upland habitats adjacent to occupied bottomland hardwood forests to improve the likelihood of swamp rabbit persistence in Illinois.
The complete mitochondrial genomes of nine white-tailed deer subspecies and their genomic differences
Authors: Ambriz-Morales Pascuala , De La Rosa-Reyna Xochitl F. , Sifuentes-Rincon Ana Maria , Parra-Bracamonte G. Manuel , Villa-Melchor Abraham , Chassin-Noria Omar , Arellano-Vera Williams
Published: January 2016

The white-tailed deer ( Odocoileus virginianus ) is an important, sustainable-use species in Mexico; 14 subspecies are widely distributed throughout the Mexican territory. The criteria for classifying subspecies is based on morphological features throughout their geographical range; however, the complete genetic characterization of Mexican subspecies has not been established. The objective of the present work is to report the mitogenomes of 9 of the 14 white-tailed deer subspecies from Mexico and identify their unique variations. Typical vertebrate mitogenomes structures (i.e., 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes) were observed in the studied subspecies. The greatest numbers of polymorphisms were identified in the D-loop, ND4, ND5, CYTB/COI, ATP6, and COIII genes. Phylogenetic analyses showed that the southern and southeastern subspecies were distinct from the central and northern subspecies; the greatest genetic distances were also observed between these 2 groups. These subspecies-specific variations could be useful for designing a strategy to genetically characterize the studied subspecies.

El venado cola blanca es una de las especies de mayor importancia dentro del aprovechamiento de la fauna silvestre de México, donde se distribuyen de manera natural 14 subespecies. Actualmente, estas subespecies se han clasificado de acuerdo a sus variaciones fenotípicas que presentan a lo largo de su rango de distribución, sin embargo no se ha establecido la caracterización genética completa de las mismas. Es por esto que el objetivo del presente estudio es reportar los mitogenomas de 9 de las 14 subespecies de venado cola blanca, así como identificar las variaciones únicas de cada subespecie. En las 9 subespecies se observó la estructura típica de los mitogenomas de vertebrados (13 genes que codifican para proteínas, 22 ARNt, 2 ARNr). Los genes con mayor polimorfismo fueron D-loop, ND4, ND5, CYTB/COI, ATP6 y COIII. El análisis filogenético mostró la separación de las subespecies del sur y sureste de las subespecies del centro y norte del país, a su vez las distancias genéticas entre estos dos grupos fueron las más altas. Estas variaciones subespecie-específicas podrían ser útiles para diseñar una estrategia para caracterizar genéticamente las subespecies estudiadas.
A Genomic Signature of Influenza Infection Shows Potential for Presymptomatic Detection, Guiding Early Therapy, and Monitoring Clinical Responses
Authors: McClain Micah T. , Nicholson Bradly P. , Park Lawrence P. , Liu Tzu-Yu , Hero Alfred O. , Tsalik Ephraim L. , Zaas Aimee K. , Veldman Timothy , Hudson Lori L. , Lambkin-Williams Robert , Gilbert Anthony , Burke Thomas , Nichols Marshall , Ginsburg Geoffrey S. , Woods Christopher W.
Published: January 2016

Early, presymptomatic intervention with oseltamivir (corresponding to the onset of a published host-based genomic signature of influenza infection) resulted in decreased overall influenza symptoms (aggregate symptom scores of 23.5 vs 46.3), more rapid resolution of clinical disease (20 hours earlier), reduced viral shedding (total median tissue culture infectious dose [TCID50] 7.4 vs 9.7), and significantly reduced expression of several inflammatory cytokines (interferon-γ, tumor necrosis factor-α, interleukin-6, and others). The host genomic response to influenza infection is robust and may provide the means for early detection, more timely therapeutic interventions, a meaningful reduction in clinical disease, and an effective molecular means to track response to therapy.
Reduced expression of CDP-DAG synthase changes lipid composition and leads to male sterility inDrosophila
Authors: Laurinyecz Barbara , Péter Mária , Vedelek Viktor , Kovács Attila L. , Juhász Gábor , Maróy Péter , Vígh László , Balogh Gábor , Sinka Rita
Published: January 2016

Drosophilaspermatogenesis is an ideal system to study the effects of changes in lipid composition, because spermatid elongation and individualization requires extensive membrane biosynthesis and remodelling. The bulk of transcriptional activity is completed with the entry of cysts into meiotic division, which makes post-meiotic stages of spermatogenesis very sensitive to even a small reduction in gene products. In this study, we describe the effect of changes in lipid composition during spermatogenesis using a hypomorphic male sterile allele of theDrosophila CDP-DAG synthase(CdsA) gene. We find that theCdsAmutant shows defects in spermatid individualization and enlargement of mitochondria and the axonemal sheath of the spermatids. Furthermore, we could genetically rescue the male sterile phenotype by overexpressing Phosphatidylinositol synthase (dPIS) in aCdsAmutant background. The results of lipidomic and genetic analyses of theCdsAmutant highlight the importance of correct lipid composition during sperm development and show that phosphatidic acid levels are crucial in late stages of spermatogenesis.
C-Myc regulation by costimulatory signals modulates the generation of CD8
+
memory T cells during viral infection
Authors: Haque Mohammad , Song Jianyong , Fino Kristin , Wang Youfei , Sandhu Praneet , Song Xinmeng , Norbury Christopher , Ni Bing , Fang Deyu , Salek-Ardakani Shahram , Song Jianxun
Published: January 2016

The signalling mechanisms of costimulation in the development of memory T cells remain to be clarified. Here, we show that the transcription factor c-Myc in CD8
+
T cells is controlled by costimulatory molecules, which modulates the development of memory CD8
+
T cells. C-Myc expression was dramatically reduced in
Cd28
−/−
or

Ox40
−/−

memory CD8
+
T cells, and c-Myc over-expression substantially reversed the defects in the development of T-cell memory following viral infection. C-Myc regulated the expression of survivin, an inhibitor of apoptosis, which promoted the generation of virus-specific memory CD8
+
T cells. Moreover, over-expression of survivin with bcl-xL, a downstream molecule of NF-
κ
B and intracellular target of costimulation that controls survival, in
Cd28
−/−
or

Ox40
−/−

CD8
+
T cells, reversed the defects in the generation of memory T cells in response to viral infection. These results identify c-Myc as a key controller of memory CD8
+
T cells from costimulatory signals.
Auxin/AID versus conventional knockouts: distinguishing the roles of CENP-T/W in mitotic kinetochore assembly and stability
Authors: Wood Laura , Booth Daniel G. , Vargiu Giulia , Ohta Shinya , deLima Alves Flavia , Samejima Kumiko , Fukagawa Tatsuo , Rappsilber Juri , Earnshaw William C.
Published: January 2016

Most studies using knockout technologies to examine protein function have relied either on shutting off transcription (conventional conditional knockouts with tetracycline-regulated gene expression or gene disruption) or destroying the mature mRNA (RNAi technology). In both cases, the target protein is lost at a rate determined by its intrinsic half-life. Thus, protein levels typically fall over at least 1–3 days, and cells continue to cycle while exposed to a decreasing concentration of the protein. Here we characterise the kinetochore proteome of mitotic chromosomes isolated from a cell line in which the essential kinetochore protein CENP-T is present as an auxin-inducible degron (AID) fusion protein that is fully functional and able to support the viability of the cells. Stripping of the protein from chromosomes in early mitosis via targeted proteasomal degradation reveals the dependency of other proteins on CENP-T for their maintenance in kinetochores. We compare these results with the kinetochore proteome of conventional CENP-T/W knockouts. As the cell cycle is mostly formed from G1, S and G2 phases a gradual loss of CENP-T/W levels is more likely to reflect dependencies associated with kinetochore assembly pre-mitosis and upon entry into mitosis. Interestingly, a putative super-complex involving Rod-Zw10-zwilch (RZZ complex), Spindly, Mad1/Mad2 and CENP-E requires the function of CENP-T/W during kinetochore assembly for its stable association with the outer kinetochore, but once assembled remains associated with chromosomes after stripping of CENP-T during mitosis. This study highlights the different roles core kinetochore components may play in the assembly of kinetochores (upon entry into mitosis) versus the maintenance of specific components (during mitosis).
Isotopic evidence for residential mobility of farming communities during the transition to agriculture in Britain
Authors: Neil Samantha , Evans Jane , Montgomery Janet , Scarre Chris
Published: January 2016

Development of agriculture is often assumed to be accompanied by a decline in residential mobility, and sedentism is frequently proposed to provide the basis for economic intensification, population growth and increasing social complexity. In Britain, however, the nature of the agricultural transition (ca4000 BC) and its effect on residence patterns has been intensely debated. Some authors attribute the transition to the arrival of populations who practised a system of sedentary intensive mixed farming similar to that of the very earliest agricultural regimes in central Europe,ca5500 BC, with cultivation of crops in fixed plots and livestock keeping close to permanently occupied farmsteads. Others argue that local hunter–gatherers within Britain adopted selected elements of a farming economy and retained a mobile way of life. We use strontium and oxygen isotope analysis of tooth enamel from an Early Neolithic burial population in Gloucestershire, England, to evaluate the residence patterns of early farmers. Our results are consistent with the hypothesis that early farming communities in Britain were residentially mobile and were not fully sedentary. Results highlight the diverse nature of settlement strategies associated with early farming in Europe and are of wider significance to understanding the effect of the transition to agriculture on residence patterns.
To boldly climb: behavioural and cognitive differences in migrating European glass eels
Authors: Podgorniak T. , Blanchet S. , De Oliveira E. , Daverat F. , Pierron F.
Published: January 2016

European eel (
Anguilla anguilla
) is a catadromous fish species that received substantial attention as its population has markedly declined in the last three decades. The possible causes of this decline include habitat fragmentation factors such as dams and weirs. In some cases, these obstacles are equipped with fish friendly passage devices that may select young eels according to their climbing behaviour. We tested how individual climbing tendency was related to the event of fishway passage experienced in the field and classified fish climbing profiles as climbing ‘leaders’, ‘followers’, ‘finishers’ and ‘no climbers’. Moreover, we analysed the brain transcription level of genes related to neurogenesis and synaptic plasticity and compared it to climbing profiles. We found that fish from the upstream segments of an impounded river had a higher climbing propensity. Their behaviour was also more repeatable throughout the whole test than the obstacle-naive fish from the downstream segment. Moreover, we found that boldly climbing ‘leaders’ had lower levels of transcription of synapse-related genes than the climbing ‘followers’. These differences could be related to coping styles of fish, where proactive ‘leaders’ express a routine and risky behaviour, whereas reactive fish need an environmental assessment before exploratory behaviour. Our study showed that differences in climbing propensity exist in glass eels separated by water obstacles. Moreover, eels could adopt climbing different strategies according to the way they deal with environmental stress and to the cognitive abilities they possess.
Neutron reflectometry on highly absorbing films and its application to
10
B
4
C-based neutron detectors
Authors: Piscitelli F. , Khaplanov A. , Devishvili A. , Schmidt S. , Höglund C. , Birch J. , Dennison A. J. C. , Gutfreund P. , Hall-Wilton R. , Van Esch P.
Published: January 2016

Neutron reflectometry is a powerful tool used for studies of surfaces and interfaces. The absorption in the typical studied materials is neglected and this technique is limited only to the reflectivity measurement. For strongly absorbing nuclei, the absorption can be directly measured by using the neutron-induced fluorescence technique which exploits the prompt particle emission of absorbing isotopes. This technique is emerging from soft matter and biology where highly absorbing nuclei, in very small quantities, are used as a label for buried layers. Nowadays, the importance of absorbing layers is rapidly increasing, partially because of their application in neutron detection; a field that has become more active also due to the
3
He
-shortage. We extend the neutron-induced fluorescence technique to the study of layers of highly absorbing materials, in particular
10
B
4
C. The theory of neutron reflectometry is a commonly studied topic; however, when a strong absorption is present the subtle relationship between the reflection and the absorption of neutrons is not widely known. The theory for a general stack of absorbing layers has been developed and compared to measurements. We also report on the requirements that a
10
B
4
C layer must fulfil in order to be employed as a converter in neutron detection.
Joint torques in a freely walking insect reveal distinct functions of leg joints in propulsion and posture control
Authors: Dallmann Chris J. , Dürr Volker , Schmitz Josef
Published: January 2016

Determining the mechanical output of limb joints is critical for understanding the control of complex motor behaviours such as walking. In the case of insect walking, the neural infrastructure for single-joint control is well described. However, a detailed description of the motor output in form of time-varying joint torques is lacking. Here, we determine joint torques in the stick insect to identify leg joint function in the control of body height and propulsion. Torques were determined by measuring whole-body kinematics and ground reaction forces in freely walking animals. We demonstrate that despite strong differences in morphology and posture, stick insects show a functional division of joints similar to other insect model systems. Propulsion was generated by strong depression torques about the coxa–trochanter joint, not by retraction or flexion/extension torques. Torques about the respective thorax–coxa and femur–tibia joints were often directed opposite to fore–aft forces and joint movements. This suggests a posture-dependent mechanism that counteracts collapse of the leg under body load and directs the resultant force vector such that strong depression torques can control both body height and propulsion. Our findings parallel propulsive mechanisms described in other walking, jumping and flying insects, and challenge current control models of insect walking.
Seminal fluid of honeybees contains multiple mechanisms to combat infections of the sexually transmitted pathogen
Nosema apis
Authors: Peng Yan , Grassl Julia , Millar A. Harvey , Baer Boris
Published: January 2016

The societies of ants, bees and wasps are genetically closed systems where queens only mate during a brief mating episode prior to their eusocial life and males therefore provide queens with a lifetime supply of high-quality sperm. These ejaculates also contain a number of defence proteins that have been detected in the seminal fluid but their function and efficiency have never been investigated in great detail. Here, we used the honeybee
Apis mellifera
and quantified whether seminal fluid is able to combat infections of the fungal pathogen
Nosema apis
, a widespread honeybee parasite that is also sexually transmitted. We provide the first empirical evidence that seminal fluid has a remarkable antimicrobial activity against
N. apis
spores and that antimicrobial seminal fluid components kill spores in multiple ways. The protein fraction of seminal fluid induces extracellular spore germination, which disrupts the life cycle of
N. apis
, whereas the non-protein fraction of seminal fluid induces a direct viability loss of intact spores. We conclude that males provide their ejaculates with efficient antimicrobial molecules that are able to kill
N. apis
spores and thereby reduce the risk of disease transmission during mating. Our findings could be of broader significance to master honeybee diseases in managed honeybee stock in the future.
Madagascar's grasses and grasslands: anthropogenic or natural?
Authors: Vorontsova Maria S. , Besnard Guillaume , Forest Félix , Malakasi Panagiota , Moat Justin , Clayton W. Derek , Ficinski Paweł , Savva George M. , Nanjarisoa Olinirina P. , Razanatsoa Jacqueline , Randriatsara Fetra O. , Kimeu John M. , Luke W. R. Quentin , Kayombo Canisius , Linder H. Peter
Published: January 2016

Grasses, by their high productivity even under very low
p
CO
2
, their ability to survive repeated burning and to tolerate long dry seasons, have transformed the terrestrial biomes in the Neogene and Quaternary. The expansion of grasslands at the cost of biodiverse forest biomes in Madagascar is often postulated as a consequence of the Holocene settlement of the island by humans. However, we show that the Malagasy grass flora has many indications of being ancient with a long local evolutionary history, much predating the Holocene arrival of humans. First, the level of endemism in the Madagascar grass flora is well above the global average for large islands. Second, a survey of many of the more diverse areas indicates that there is a very high spatial and ecological turnover in the grass flora, indicating a high degree of niche specialization. We also find some evidence that there are both recently disturbed and natural stable grasslands: phylogenetic community assembly indicates that recently severely disturbed grasslands are phylogenetically clustered, whereas more undisturbed grasslands tend to be phylogenetically more evenly distributed. From this evidence, it is likely that grass communities existed in Madagascar long before human arrival and so were determined by climate, natural grazing and other natural factors. Humans introduced zebu cattle farming and increased fire frequency, and may have triggered an expansion of the grasslands. Grasses probably played the same role in the modification of the Malagasy environments as elsewhere in the tropics.
Ecological and morphological traits predict depth-generalist fishes on coral reefs
Authors: Bridge Tom C. L. , Luiz Osmar J. , Coleman Richard R. , Kane Corinne N. , Kosaki Randall K.
Published: January 2016

Ecological communities that occupy similar habitats may exhibit functional convergence despite significant geographical distances and taxonomic dissimilarity. On coral reefs, steep gradients in key environmental variables (e.g. light and wave energy) restrict some species to shallow depths. We show that depth-generalist reef fishes are correlated with two species-level traits: caudal fin aspect ratio and diet. Fishes with high aspect ratio (lunate) caudal fins produce weaker vortices in the water column while swimming, and we propose that ‘silent swimming’ reduces the likelihood of detection and provides an advantage on deeper reefs with lower light irradiance and water motion. Significant differences in depth preference among trophic guilds reflect variations in the availability of different food sources along a depth gradient. The significance of these two traits across three geographically and taxonomically distinct assemblages suggests that deep-water habitats exert a strong environmental filter on coral reef-fish assemblages.
Convergence of broad-scale migration strategies in terrestrial birds
Authors: La Sorte Frank A. , Fink Daniel , Hochachka Wesley M. , Kelling Steve
Published: January 2016

Migration is a common strategy used by birds that breed in seasonal environments. Selection for greater migration efficiency is likely to be stronger for terrestrial species whose migration strategies require non-stop transoceanic crossings. If multiple species use the same transoceanic flyway, then we expect the migration strategies of these species to converge geographically towards the most optimal solution. We test this by examining population-level migration trajectories within the Western Hemisphere for 118 migratory species using occurrence information from eBird. Geographical convergence of migration strategies was evident within specific terrestrial regions where geomorphological features such as mountains or isthmuses constrained overland migration. Convergence was also evident for transoceanic migrants that crossed the Gulf of Mexico or Atlantic Ocean. Here, annual population-level movements were characterized by clockwise looped trajectories, which resulted in faster but more circuitous journeys in the spring and more direct journeys in the autumn. These findings suggest that the unique constraints and requirements associated with transoceanic migration have promoted the spatial convergence of migration strategies. The combination of seasonal atmospheric and environmental conditions that has facilitated the use of similar broad-scale migration strategies may be especially prone to disruption under climate and land-use change.
Meiotic recombination counteracts male-biased mutation (male-driven evolution)
Authors: Mawaribuchi Shuuji , Ito Michihiko , Ogata Mitsuaki , Oota Hiroki , Katsumura Takafumi , Takamatsu Nobuhiko , Miura Ikuo
Published: January 2016

Meiotic recombination is believed to produce greater genetic variation despite the fact that deoxyribonucleic acid (DNA)-replication errors are a major source of mutations. In some vertebrates, mutation rates are higher in males than in females, which developed the theory of male-driven evolution (male-biased mutation). However, there is little molecular evidence regarding the relationships between meiotic recombination and male-biased mutation. Here we tested the theory using the frog
Rana rugosa,
which has both XX/XY- and ZZ/ZW-type sex-determining systems within the species. The male-to-female mutation-rate ratio (
α
) was calculated from homologous sequences on the X/Y or Z/W sex chromosomes, which supported male-driven evolution. Surprisingly, each
α
value was notably higher in the XX/XY-type group than in the ZZ/ZW-type group, although
α
should have similar values within a species. Interestingly, meiotic recombination between homologous chromosomes did not occur except at terminal regions in males of this species. Then, by subdividing
α
into two new factors, a replication-based male-to-female mutation-rate ratio (
β
) and a meiotic recombination-based XX-to-XY/ZZ-to-ZW mutation-rate ratio (
γ
), we constructed a formula describing the relationship among a nucleotide-substitution rate and the two factors,
β
and
γ
. Intriguingly, the
β
- and
γ
-values were larger and smaller than 1, respectively, indicating that meiotic recombination might reduce male-biased mutations.
Temperature regimes impact coral assemblages along environmental gradients on lagoonal reefs in Belize
Authors: Baumann Justin H. , Townsend Joseph E. , Courtney Travis A. , Aichelman Hannah E. , Davies Sarah W. , Lima Fernando P. , Castillo Karl D.
Published: January 2016

Coral reefs are increasingly threatened by global and local anthropogenic stressors such as rising seawater temperature, nutrient enrichment, sedimentation, and overfishing. Although many studies have investigated the impacts of local and global stressors on coral reefs, we still do not fully understand how these stressors influence coral community structure, particularly across environmental gradients on a reef system. Here, we investigate coral community composition across three different temperature and productivity regimes along a nearshore-offshore gradient on lagoonal reefs of the Belize Mesoamerican Barrier Reef System (MBRS). A novel metric was developed using ultra-high-resolution satellite-derived estimates of sea surface temperatures (SST) to classify reefs as exposed to low (lowTP), moderate (modTP), or high (highTP) temperature parameters over 10 years (2003 to 2012). Coral species richness, abundance, diversity, density, and percent cover were lower at highTPsites relative to lowTPand modTPsites, but these coral community traits did not differ significantly between lowTPand modTPsites. Analysis of coral life history strategies revealed that highTPsites were dominated by hardy stress tolerant and fast-growing weedy coral species, while lowTPand modTPsites consisted of competitive, generalist, weedy, and stress-tolerant coral species. Satellite-derived estimates ofChlorophyll-a (chl-a)were obtained for 13-years (2003-2015) as a proxy for primary production.Chl-aconcentrations were highest at highTPsites, medial at modTPsites, and lowest at lowTPsites. Notably, thermal parameters correlated better with coral community traits between site types than productivity, suggesting that temperature (specifically number of days above the thermal bleaching threshold) played a greater role in defining coral community structure than productivity on the MBRS. Dominance of weedy and stress-tolerant genera at highTPsites suggests that corals utilizing these two life history strategies may be better suited to cope with warmer oceans and thus may warrant protective status under climate change.
Evolution of corticosteroid specificity for human, chicken, alligator and frog glucocorticoid receptors
Authors: Katsu Yoshinao , Kohno Satomi , Oka Kaori , Baker Michael E.
Published: January 2016

We investigated the evolution of the response of human, chicken, alligator and frog glucocorticoid receptors (GRs) to dexamethasone, cortisol, corticosterone, 11-deoxycorticosterone, 11-deoxycortisol and aldosterone. We find significant differences among these vertebrates in the transcriptional activation of their full length GRs by these steroids, indicating that there were changes in the specificity of the GR for steroids during the evolution of terrestrial vertebrates. To begin to study the role of interactions between different domains on the GR in steroid sensitivity and specificity for terrestrial GRs, we investigated transcriptional activation of truncated GRs containing their hinge domain and ligand binding domain (LBD) fused to a GAL4 DNA binding domain (GAL4 DBD). Compared to corresponding full length GRs, transcriptional activation of GAL4 DBD-GR hinge/LBD constructs required higher steroid concentrations and displayed altered steroid specificity, indicating that interactions between the hinge/LBD and other domains are important in glucocorticoid activation of these terrestrial GRs.
Searching more genomic sequence with less memory for fast and accurate metagenomic profiling
Authors: Gardner Shea N. , Ames Sasha K. , Gokhale Maya B. , Slezak Tom R. , Allen Jonathan E.
Published: January 2016

Software for rapid, accurate, and comprehensive microbial profiling of metagenomic sequence data on a desktop will play an important role in large scale clinical use of metagenomic data. Here we describe LMAT-ML (Livermore Metagenomics Analysis Toolkit-Marker Library) which can be run with 24 GB of DRAM memory, an amount available on many clusters, or with 16 GB DRAM plus a 24 GB low cost commodity flash drive (NVRAM), a cost effective alternative for desktop or laptop users. We compared results from LMAT with five other rapid, low-memory tools for metagenome analysis for 131 Human Microbiome Project samples, and assessed discordant calls with BLAST. All the tools except LMAT-ML reported overly specific or incorrect species and strain resolution of reads that were in fact much more widely conserved across species, genera, and even families. Several of the tools misclassified reads from synthetic or vector sequence as microbial or human reads as viral. We attribute the high numbers of false positive and false negative calls to a limited reference database with inadequate representation of known diversity. Our comparisons with real world samples show that LMAT-ML is the only tool tested that classifies the majority of reads, and does so with high accuracy.
Structural variation detection with read pair information — An improved null-hypothesis reduces bias
Authors: Sahlin Kristoffer , Frånberg Mattias , Arvestad Lars
Published: January 2016

Reads from paired-end and mate-pair libraries are often utilized to find structural variation in genomes, and one common approach is to use their fragment length for detection. After aligning read-pairs to the reference, read-pair distances are analyzed for statistically significant deviations. However, previously proposed methods are based on a simplified model of observed fragment lengths that does not agree with data. We show how this model limits statistical analysis of identifying variants and propose a new model, by adapting a model we have previously introduced for contig scaffolding, which agrees with data. From this model we derive an improved improved null hypothesis that, when applied in the variant caller CLEVER, reduces the number of false positives and corrects a bias that contributes to more deletion calls than insertion calls. A reference implementation is freely available athttps://github.com/ksahlin/GetDistr.
Tempo and mode of genome evolution in a 50,000-generation experiment
Authors: Tenaillon Olivier , Barrick Jeffrey E. , Ribeck Noah , Deatherage Daniel E. , Blanchard Jeffrey L. , Dasgupta Aurko , Wu Gabriel C. , Wielgoss Sébastien , Cruveiller Stéphane , Médigue Claudine , Schneider Dominique , Lenski Richard E.
Published: January 2016

Adaptation depends on the rates, effects, and interactions of many mutations. We analyzed 264 genomes from 12Escherichia colipopulations to characterize their dynamics over 50,0 generations. The trajectories for genome evolution in populations that retained the ancestral mutation rate fit a model where most fixed mutations are beneficial, the fraction of beneficial mutations declines as fitness rises, and neutral mutations accumulate at a constant rate. We also compared these populations to lines evolved under a mutation-accumulation regime that minimizes selection. Nonsynonymous mutations, intergenic mutations, insertions, and deletions are overrepresented in the long-term populations, supporting the inference that most fixed mutations are favored by selection. These results illuminate the shifting balance of forces that govern genome evolution in populations adapting to a new environment.
Fast and accurate single-cell RNA-Seq analysis by clustering of transcript-compatibility counts
Authors: Ntranos Vasilis , Kamath Govinda M. , Zhang Jesse , Pachter Lior , Tse David N.
Published: January 2016

Current approaches to single-cell transcriptomic analysis are computationally intensive and require assay-specific modeling which limit their scope and generality. We propose a novel method that departs from standard analysis pipelines, comparing and clustering cells based not on their transcript or gene quantifications but on their transcript-compatibility read counts. In re-analysis of two landmark yet disparate single-cell RNA-Seq datasets, we show that our method is up to two orders of magnitude faster than previous approaches, provides accurate and in some cases improved results, and is directly applicable to data from a wide variety of assays.
Changes in attractor dynamics predict altered perceptual decision making with dorsolateral prefrontal tDCS
Authors: Bonaiuto James J. , de Berker Archy , Bestmann Sven
Published: January 2016

The left dorsolateral prefrontal cortex (dlPFC) has been linked to the accumulation and comparison of perceptual evidence for decision making independent of sensory and response modalities. We investigated the possible neural dynamics underlying the role of dlPFC in perceptual decision making, through a combination of noninvasive neurostimulation in humans and computational modeling. First, we used an established and biophysically realistic model of a decision making network that employs competition between neural populations. Simulation of depolarizing noninvasive brain stimulation in this model decreased decision time, while hyperpolarizing stimulation increased it. This behavioral effect was caused by an increase in the rate of neural activity integration via recurrent connections, as well as changes in the susceptibility of the network to noisy background inputs which modulated population firing rate differences prior to the onset of the stimulus. These pre-stimulus differences biased the response to one or the other option, thus speeding or slowing decisions.

We then tested these model predictions in healthy participants performing a perceptual decision making task while receiving transcranial direct current stimulation (tDCS) over the left dlPFC, analogous to our simulated network stimulation. We found a striking match between model predictions and experimental results: depolarizing (inward) currents reduced and hyperpolarizing (outward) currents increased response times, but accuracy remained unaffected. Our results provide interventional evidence for the role of left dlPFC in perceptual decision making, and suggest that this region integrates and compares sensory evidence through competitive interactions between pyramidal cell populations which are selective for each response option. Mechanistically, our model suggests that stimulation of this region changes the rate at which evidence can be accumulated through recurrent activity and its susceptibility to background noise. More generally, our approach demonstrates that a linkage between computational modeling and noninvasive brain stimulation allows mechanistic accounts of brain function to be causally tested.
Isoform-level gene expression patterns in single-cell RNA-sequencing data
Authors: Vu Trung Nghia , Wills Quin F , Kalari Krishna R , Niu Nifang , Wang Liewei , Pawitan Yudi , Rantalainen Mattias
Published: January 2016

RNA-sequencing of single-cells enables characterization of transcriptional heterogeneity in seemingly homogenous cell populations. In this study we propose and apply a novel method, ISOform-Patterns (ISOP), based on mixture modeling, to characterize the expression patterns of pairs of isoforms from the same gene in single-cell isoform-level expression data. We define six principal patterns of isoform expression relationships and introduce the concept of differential pattern analysis. We applied ISOP for analysis of single-cell RNA-sequencing data from a breast cancer cell line, with replication in two independent datasets. In the primary dataset we detected and assigned pattern type of 16562 isoform-pairs from 4929 genes. Our results showed that 78% of the isoform pairs displayed a mutually exclusive expression pattern, 14% of the isoform pairs displayed bimodal isoform preference and 8% isoform pairs displayed isoform preference. 26% of the isoform-pair patterns were significant, while remaining isoform-pair patterns can be understood as effects of transcriptional bursting, drop-out and biological heterogeneity. 32% of genes discovered through differential pattern analysis were novel and not detected by differential expression analysis. ISOP provides a novel approach for characterization of isoform-level expression in single-cell populations. Our results reveal a common occurrence of isoform-level preference, commitment and heterogeneity in single-cell populations.
When Wavelengths Collide: Bias in Cell Abundance Measurements due to Expressed Fluorescent Proteins
Authors: Hecht Ariel , Endy Drew , Salit Marc , Munson Matthew S.
Published: January 2016

The abundance of bacteria in liquid culture is commonly inferred by measuring optical density at 600 nm. Red fluorescent proteins (RFP) can strongly absorb light at 600 nm. Increasing RFP expression can falsely inflate apparent cell density and lead to underestimations of mean per-cell fluorescence by up to 10%. Measuring optical density at 700 nm would allow estimation of cell abundance unaffected by the presence of nearly all fluorescent proteins.