bluuebunny/crossref_metadata_2025 huggingface dataset:
Metabolic connectivity as a driver of host and endosymbiont integration
Authors: Karkar Slim , Facchinelli Fabio , Price Dana C. , Weber Andreas P. M. , Bhattacharya Debashish
Published: April 2015

The origin of oxygenic photosynthesis in the Archaeplastida common ancestor was foundational for the evolution of multicellular life. It is very likely that the primary endosymbiosis that explains plastid origin relied initially on the establishment of a metabolic connection between the host cell and captured cyanobacterium. We posit that these connections were derived primarily from existing host-derived components. To test this idea, we used phylogenomic and network analysis to infer the phylogenetic origin and evolutionary history of 37 validated plastid innermost membrane (permeome) metabolite transporters from the model plant
Arabidopsis thaliana
. Our results show that 57% of these transporter genes are of eukaryotic origin and that the captured cyanobacterium made a relatively minor (albeit important) contribution to the process. We also tested the hypothesis that the bacterium-derived hexose-phosphate transporter UhpC might have been the primordial sugar transporter in the Archaeplastida ancestor. Bioinformatic and protein localization studies demonstrate that this protein in the extremophilic red algae
Galdieria sulphuraria
and
Cyanidioschyzon merolae
are plastid targeted. Given this protein is also localized in plastids in the glaucophyte alga
Cyanophora paradoxa
, we suggest it played a crucial role in early plastid endosymbiosis by connecting the endosymbiont and host carbon storage networks. In summary, our work significantly advances understanding of plastid integration and favors a host-centric view of endosymbiosis. Under this view, nuclear genes of either eukaryotic or bacterial (noncyanobacterial) origin provided key elements of the toolkit needed for establishing metabolic connections in the primordial Archaeplastida lineage.
A comprehensive method for detecting ubiquitinated substrates using TR-TUBE
Authors: Yoshida Yukiko , Saeki Yasushi , Murakami Arisa , Kawawaki Junko , Tsuchiya Hikaru , Yoshihara Hidehito , Shindo Mayumi , Tanaka Keiji
Published: April 2015

Significance

The identification of specific ubiquitin ligase–substrate pairs is crucial for understanding the roles of protein ubiquitination in the regulation of diverse biological processes. Despite the development of various methodologies for substrate identification, it remains challenging to determine ubiquitin ligase substrates. Based on previously described tandem ubiquitin-binding entity(ies) (TUBE), we designed the trypsin-resistant (TR)-TUBE for expression in cells. The coexpression of TR-TUBE with an ubiquitin ligase stabilizes the ubiquitinated substrates by masking the ubiquitin chains. Using a combination of two strategies for enriching ubiquitinated substrates, TR-TUBE and anti–Lys-ε-Gly-Gly antibody, we successfully identified specific ubiquitin ligase–substrate pairs. Our methodology provides an effective means for the identification of ubiquitin ligase substrates and the detection of ubiquitin ligase activity.
RNA-binding protein hnRNPLL regulates mRNA splicing and stability during B-cell to plasma-cell differentiation
Authors: Chang Xing , Li Bin , Rao Anjana
Published: April 2015

Significance

Plasma cells produce immunoglobulin and provide long-lasting protective immunity. Differentiation of B cells to plasma cells is accompanied by major changes in gene expression, which are regulated at both transcriptional and posttranscriptional levels. We have used genome-wide methods to identify the binding sites and RNA targets of heterogeneous nuclear RNA-binding protein LL (hnRNPLL), whose expression is up-regulated during B-cell to plasma-cell differentiation. In addition to its recognized function in promoting exon splicing, hnRNPLL shapes the transcriptome of plasma cells by regulating exon inclusion and promoting mRNA stability. hnRNPLL binds to preferred sequences in RNA and is critical for complete plasma-cell differentiation, by mediating the down-regulation of B-cell–specific transcription factors and maximizing immunoglobulin production.
dNTP pool levels modulate mutator phenotypes of error-prone DNA polymerase ε variants
Authors: Williams Lindsey N. , Marjavaara Lisette , Knowels Gary M. , Schultz Eric M. , Fox Edward J. , Chabes Andrei , Herr Alan J.
Published: April 2015

Significance

An increased rate of mutation, or “mutator phenotype,” generates genetic diversity that can accelerate cancer progression or confer resistance to chemotherapy drugs. New therapeutic strategies are needed that target mutator phenotypes directly. Mutator phenotypes due to defects in DNA polymerase ε have been implicated in colorectal and endometrial cancers and may emerge in other cancers during treatment. Here, we show in budding yeast that such mutator phenotypes are influenced by the levels of dNTPs, the building blocks of DNA. Lowering dNTP pool levels lessens the mutator phenotypes, whereas increasing dNTP pools accentuates the mutator phenotypes. These findings suggest that mutator phenotypes due to error-prone polymerases may be modulated by treatments that target dNTP pools.
Continental crust beneath southeast Iceland
Authors: Torsvik Trond H. , Amundsen Hans E. F. , Trønnes Reidar G. , Doubrovine Pavel V. , Gaina Carmen , Kusznir Nick J. , Steinberger Bernhard , Corfu Fernando , Ashwal Lewis D. , Griffin William L. , Werner Stephanie C. , Jamtveit Bjørn
Published: April 2015

Significance

The Iceland hotspot is widely thought to be the surface expression of a deep mantle plume from the core–mantle boundary that can be traced back in time at least 62 My. However, some lavas contain continental material, which has previously been proposed to have been recycled through the plume. Here, we argue that the plume split off a sliver of continent from Greenland in the Early Eocene. This sliver is now located beneath southeast Iceland where it locally contaminates some of the plume-derived magmas.
Chiral structures from achiral liquid crystals in cylindrical capillaries
Authors: Jeong Joonwoo , Kang Louis , Davidson Zoey S. , Collings Peter J. , Lubensky Tom C. , Yodh A. G.
Published: April 2015

Significance

Nematic liquid crystals (LCs) are arguably the simplest examples of partially ordered condensed matter, and they are core materials in many commercial products. Our experiments explore fundamental questions about how chiral configurations of LCs can arise from achiral building blocks. Left- and right-handed chiral structures are produced by a delicate balance of LC bulk elasticity and surface conditions in confinement. The key experimental ingredients are biocompatible aqueous lyotropic chromonic LCs that twist easily. Combined with the new constraints, this class of achiral LC exhibits chiral structures and a rich assortment of defects, which hint at applications in sensing and optics.
Phosphatidylinositol 4-phosphate and phosphatidylinositol 3-phosphate regulate phagolysosome biogenesis
Authors: Jeschke Andreas , Zehethofer Nicole , Lindner Buko , Krupp Jessica , Schwudke Dominik , Haneburger Ina , Jovic Marko , Backer Jonathan M. , Balla Tamas , Hilbi Hubert , Haas Albert
Published: April 2015

Significance

Phagocytes are key to innate immunity, as they ingest, kill, and degrade foreign particles, such as microbes. Particle uptake results in the formation of phagosomes that eventually fuse with lysosomes, the main degradative compartments in cells. Phagosome–lysosome fusion (PLF) is crucial for the degradation of phagosome contents and antigen presentation. Most pathogenic microbes that multiply within phagocytes and cause severe diseases (e.g. tuberculosis), prevent PLF. Deciphering the mechanisms that govern PLF will help to understand how phagocytic cells clear microbial infections and how pathogens evade being delivered to microbicidal phagolysosomes. Here, we identify specific phosphoinositide lipids [i.e. PI(4)P and PI(3)P] and the enzymes that produce them as regulators of PLF, which explains why these lipids are manipulated by some pathogens.
Islet 1 specifies the identity of hypothalamic melanocortin neurons and is critical for normal food intake and adiposity in adulthood
Authors: Nasif Sofia , de Souza Flavio S. J. , González Laura E. , Yamashita Miho , Orquera Daniela P. , Low Malcolm J. , Rubinstein Marcelo
Published: April 2015

Significance

Food intake and body weight regulation depend on a group of hypothalamic neurons that release satiety-induced neuropeptides known as melanocortins. Central melanocortins are encoded by the proopiomelanocortin gene (
Pomc
), and mice and humans carrying deleterious mutations in the
Pomc
gene display hyperphagia and severe obesity. Although the importance of these neurons is well understood, the genetic program that establishes hypothalamic melanocortin neurons and maintains normal
Pomc
expression levels remains unknown. Here, we combined molecular neuroanatomical and biochemical analyses with functional genetic studies in transgenic mice and zebrafish and discovered that the transcription factor Islet 1 determines the identity of central melanocortin neurons during early brain development and is critical for melanocortin-induced satiety and normal adiposity throughout the entire lifetime.
Using bimodal MRI/fluorescence imaging to identify host angiogenic response to implants
Authors: Berdichevski Alexandra , Simaan Yameen Haneen , Dafni Hagit , Neeman Michal , Seliktar Dror
Published: April 2015

Significance

The current investigation applies a bimodal imaging technique to uncover a newfound appreciation for the mode of implantation as it relates to the vascularization events associated with proangiogenic therapy. We apply our ability to noninvasively track the precise in vivo fate of an implanted proangiogenic vehicle to show that the subsequent vascular network formation is related directly to the mode of implantation vis-à-vis the biodegradation and bioresorption profiles. The findings in this study uncover important insights about angiogenesis, noninvasive in vivo monitoring, and biomaterials design that should be very beneficial to a wide scientific audience in the regenerative medicine field.
Hedgehog signaling activates a positive feedback mechanism involving insulin-like growth factors to induce osteoblast differentiation
Authors: Shi Yu , Chen Jianquan , Karner Courtney M. , Long Fanxin
Published: April 2015

Significance

Hedgehog (Hh) signaling is essential for embryonic bone formation in mammals. However, how Hh signaling executes the osteogenic function is not clear. We describe a positive feedback mechanism whereby Hh-Gli2 signaling induces expression of insulin-like growth factor 2 (Igf2), which signals via protein kinases mTORC2 and Akt to stabilize Gli2 and potentiate Hh induction of osteoblast differentiation. The Hh-Igf positive feedback loop may have general implications for Hh signaling in development and disease.
Analysis of cell division patterns in the
Arabidopsis
shoot apical meristem
Authors: Shapiro Bruce E. , Tobin Cory , Mjolsness Eric , Meyerowitz Elliot M.
Published: April 2015

Significance

Plant cells are incapable of sliding past each other, so generation of shape and structure in plant tissue is dependent on cells dividing and expanding in particular directions. Therefore, understanding how cells choose where to build new walls is critical in understanding how plant tissue is patterned. In the present study we expand on previous models of cell division to further understand what parameters of cell geometry and growth influence the position of new walls.
Memory, scene construction, and the human hippocampus
Authors: Kim Soyun , Dede Adam J. O. , Hopkins Ramona O. , Squire Larry R.
Published: April 2015

Significance

It has been suggested that the primary role of the hippocampus is to construct spatial scenes and further that memory impairments following hippocampal damage may be attributed to spatial processing demands in memory tasks. Two types of tasks have contributed evidence to this perspective: boundary extension and scene imagination. Boundary extension refers to the phenomenon whereby a scene is remembered as having an expanded background. Imagination tasks ask participants to mentally construct scenes. We tested patients with hippocampal damage on both types of tasks. They were intact at both boundary extension and imagination, although they remembered the tasks poorly. These results support the traditional view that the human hippocampus is primarily important for memory.
Task-driven intra- and interarea communications in primate cerebral cortex
Authors: Tauste Campo Adrià , Martinez-Garcia Marina , Nácher Verónica , Luna Rogelio , Romo Ranulfo , Deco Gustavo
Published: April 2015

Significance

How do multiple neurons communicate to solve a cognitive task? To answer this question, we investigate spike-train directional correlations across five primate cortical areas simultaneously recorded during a somatosensory discrimination task. Correlations are inferred using a nonparametric procedure that models spike trains as Markovian binary series and dynamically estimates the directed information between every neuron pair at different delays. We find that information processing during the discrimination task can be described by intra- and interarea decision-driven delayed correlations, which are no longer found when a monkey receives both stimuli but does not perform the task.
Balancing water resource conservation and food security in China
Authors: Dalin Carole , Qiu Huanguang , Hanasaki Naota , Mauzerall Denise L. , Rodriguez-Iturbe Ignacio
Published: April 2015

Significance

Agriculture represents the largest water-consuming sector in China, while industry and cities are growing competitors. To sustain a rapidly increasing population with richer diets, high levels of food production have come at significant environmental costs, such as groundwater overdraft and soil degradation. As socioeconomic growth and the associated pressure on water resources continue to increase, it is crucial to evaluate the effects of water-saving measures on agriculture, food trade, and water resources. This article estimates China’s future food trade patterns and associated water transfers and quantifies the effects of targeted irrigated land reductions on water consumption and food self-sufficiency, accounting for production displacement and local water productivity. Our findings provide important insights to policy-makers on trade-offs between environmental and agricultural objectives.
Egg and Larval Development Index for Lake Sturgeon
Authors: Eckes Orey T , Aloisi Douglas B , Sandheinrich Mark B
Published: April 2015

We developed an index of egg and larval maturation for Lake Sturgeon Acipenser fulvescens to incrementally chart development over time. To evaluate the relationship between temperature and development rate, eggs and larvae from the Wolf River were incubated at four constant water temperatures. The time required for neural tube closure, hatch, and exogenous feeding were monitored. The number of hours from incubation to each development stage and mean water temperature were related by predictive exponential regression equations for neural tube closure (R2 = 0.96), start hatch (R2 = 0.97), end hatch (R2 = 0.97), and exogenous feeding (R2 = 0.99). Calculated hourly development was used to create an index capable of predicting specific daily development. Daily development from incubation to exogenous feeding ranged from 2.0% to 8.3% at 10°C to 19.9°C. This index was used to predict the rate of development of sturgeon eggs and larvae from the St. Lawrence River reared in water with varying temperatures. All development stages occurred within 24 h of the time predicted by the index. This index may be used to accurately predict and manipulate the progress of development and assist with the culture and management of Lake Sturgeon populations.
The Effects of Diets Containing Standard Soybean Oil, Soybean Oil Enhanced with Conjugated Linoleic Acids, Menhaden Fish Oil, or an Algal Docosahexaenoic Acid Supplement on Juvenile Channel Catfish Performance, Hematology, Body Composition, and Nonspecific Immune Response
Authors: Faukner Jimmy , Rawles Steven D , Sink Todd D , Lochmann Rebecca , Proctor Andrew , Chen Ruguang , Phillips Harold
Published: April 2015

To reduce diet cost and address environmental concerns, current commercial diets for Channel Catfish Ictalurus punctatus contain little or no marine fish oil. However, there are conflicting data on the effects of fish oil and other lipid sources for juvenile Channel Catfish, and some novel lipids have not been tested against traditional ones. In this study, the effects of four different lipid sources for potential use in juvenile Channel Catfish diets were investigated by measuring fish growth performance, proximate and fatty acid composition of muscle, nonspecific immune response, and hematological parameters. In a 63-d feeding trial, juveniles (mean weight ± SE = 11.2 ± 0.0 g) were fed a commercial 32% protein diet supplemented with 2% lipid from standard soybean oil (SBO; control diet), SBO enriched with conjugated linoleic acids (CLAs; CLA diet), algal (Schizochytrium sp.) docosahexaenoic acid (DHA) extract (DHA diet), or menhaden fish oil (MFO diet). Fish that were fed the MFO diet had improved feed conversion compared with fish that were fed the SBO, CLA, or DHA diet. There were no other differences in fish growth performance or proximate composition and no differences among treatments in nonspecific immune responses or hematological parameters. As expected, fatty acid composition of fish muscle reflected that of the diets: fish that received the MFO, DHA, or CLA diet contained higher levels of healthful fatty acids (DHA or CLAs) than fish that were given the SBO control diet. Future trials will address methods for (1) increasing target levels of these fatty acids by using diets with little or no fish oil and (2) optimizing retention of desirable fatty acids to facilitate the production of Channel Catfish as a high-value functional food.
Quantum Mechanics as Classical Physics
Authors: Sebens Charles T.
Published: April 2015

Here I explore a novel no-collapse interpretation of quantum mechanics that combines aspects of two familiar and well-developed alternatives, Bohmian mechanics and the many-worlds interpretation. Despite reproducing the empirical predictions of quantum mechanics, the theory looks surprisingly classical. All there is at the fundamental level are particles interacting via Newtonian forces. There is no wave function. However, there are many worlds.
Big Data Biology: Between Eliminative Inferences and Exploratory Experiments
Authors: Ratti Emanuele
Published: April 2015

Recently, biologists have argued that data-driven biology fosters a new scientific methodology, namely, one that is irreducible to traditional methodologies of molecular biology defined as the discovery strategies elucidated by mechanistic philosophy. Here I show how data-driven studies can be included in the traditional mechanistic approach in two respects. On the one hand, some studies provide eliminative inferential procedures to prioritize and develop mechanistic hypotheses. On the other, different studies play an exploratory role in providing useful generalizations to complement the procedure of prioritization. Overall, this article aims to shed light on the structure of contemporary research in molecular biology.
Germs, Genes, and Memes: Function and Fitness Dynamics on Information Networks
Authors: Grim Patrick , Singer Daniel J. , Reade Christopher , Fisher Steven
Published: April 2015

Understanding the dynamics of information is crucial to many areas of research, both inside and outside of philosophy. Using computer simulations of three kinds of information, germs, genes, and memes, we show that the mechanism of information transfer often swamps network structure in terms of its effects on both the dynamics and the fitness of the information. This insight has both obvious and subtle implications for a number of questions in philosophy, including questions about the nature of information, whether there is genetic information, and how to arrange scientific communities.
On “Minimal Model Explanations”: A Reply to Batterman and Rice
Authors: Lange Marc
Published: April 2015

Batterman and Rice offer an account of “minimal model explanations” and argue against “common features accounts” of those explanations. This paper offers some objections to their proposals and arguments. It argues that their proposal cannot account for the apparent explanatory asymmetry of minimal model explanations. It argues that their account threatens ultimately to collapse into a “common features account.” Finally, it argues against their motivation for thinking that an explanation appealing to “common features” would have to explain the common features’ own prevalence.
Divisibility of Weil sums of binomials
Authors: Katz Daniel
Published: April 2015

Consider the Weil sum

W

F
,
d

(
u
)
=

∑

x
∈
F

ψ
(

x
d

+
u
x
)

W_{F,d}(u)=\sum _{x \in F} \psi (x^d+u x)

, where

F
F

is a finite field of characteristic

p
p

,

ψ
\psi

is the canonical additive character of

F
F

,

d
d

is coprime to

|

F
∗

|

|F^*|

, and

u
∈

F
∗

u \in F^*

. We say that

W

F
,
d

(
u
)

W_{F,d}(u)

is three-valued when it assumes precisely three distinct values as

u
u

runs through

F
∗

F^*

: this is the minimum number of distinct values in the nondegenerate case, and three-valued

W

F
,
d

W_{F,d}

are rare and desirable. When

W

F
,
d

W_{F,d}

is three-valued, we give a lower bound on the

p
p

-adic valuation of the values. This enables us to prove the characteristic

3
3

case of a 1976 conjecture of Helleseth: when

p
=
3

p=3

and

[
F
:

F

3

]

[F:{\mathbb F}_3]

is a power of

2
2

, we show that

W

F
,
d

W_{F,d}

cannot be three-valued.
Remarks on the nonlinear stability of the Kuramoto model with inertia
Authors: Choi Young-Pil , Ha Seung-Yeal , Noh Se
Published: April 2015

In this short note, we present an a priori nonlinear stability estimate for the Kuramoto model with finite inertia in

ℓ

∞

\ell ^{\infty }

-norm under some a priori condition on the size of the phase diameter. As a direct corollary of our nonlinear stability estimate, we show that phase-locked states obtained in Choi, Ha, and Yun (2011) are orbital-stable in

ℓ

∞

\ell ^{\infty }

-norm, which means that the perturbed phase-locked state approaches the phase-shift of the given phase-locked state. The phase-shift is explicitly determined by the averages of initial phase and frequency distribution and the strength of inertia

m
m

.
New canonical triple covers of surfaces
Authors: Rito Carlos
Published: April 2015

We construct a surface of general type with canonical map of degree

12
12

which factors as a triple cover and a bidouble cover of

P

2

\mathbb {P}^2

. We also show the existence of a smooth surface with

q
=
0
,

q=0,

χ
=
13

\chi =13

and

K
2

=
9
χ

K^2=9\chi

such that its canonical map is either of degree

3
3

onto a surface of general type or of degree

9
9

onto a rational surface.
Detecting fast solvability of equations via small powerful Galois groups
Authors: Chebolu S. , Mináč J. , Quadrelli C.
Published: April 2015

Fix an odd prime

p
p

, and let

F
F

be a field containing a primitive

p
p

th root of unity. It is known that a

p
p

-rigid field

F
F

is characterized by the property that the Galois group

G
F

(
p
)

G_F(p)

of the maximal

p
p

-extension

F
(
p
)

/

F

F(p)/F

is a solvable group. We give a new characterization of

p
p

-rigidity which says that a field

F
F

is

p
p

-rigid precisely when two fundamental canonical quotients of the absolute Galois groups coincide. This condition is further related to analytic

p
p

-adic groups and to some Galois modules. When

F
F

is

p
p

-rigid, we also show that it is possible to solve for the roots of any irreducible polynomials in

F
[
X
]

F[X]

whose splitting field over

F
F

has a

p
p

-power degree via non-nested radicals. We provide new direct proofs for hereditary

p
p

-rigidity, together with some characterizations for

G
F

(
p
)

G_F(p)

– including a complete description for such a group and for the action of it on

F
(
p
)

F(p)

– in the case

F
F

is

p
p

-rigid.
Observations on the vanishing viscosity limit
Authors: Kelliher James
Published: April 2015

Whether, in the presence of a boundary, solutions of the Navier-Stokes equations converge to a solution to the Euler equations in the vanishing viscosity limit is unknown. In a seminal 1983 paper, Tosio Kato showed that the vanishing viscosity limit is equivalent to having sufficient control of the gradient of the Navier-Stokes velocity in a boundary layer of width proportional to the viscosity. In a 2008 paper, the present author showed that the vanishing viscosity limit is equivalent to the formation of a vortex sheet on the boundary. We present here several observations that follow from these two papers.
Periodic points and the measure of maximal entropy of an expanding Thurston map
Authors: Li Zhiqiang
Published: April 2015

In this paper, we show that each expanding Thurston map

f
:

S
2

→

S
2

f\colon S^2\!\rightarrow S^2

has

1
+
deg
⁡
f

1+\deg f

fixed points, counted with appropriate weight, where

deg
⁡
f

\deg f

denotes the topological degree of the map

f
f

. We then prove the equidistribution of preimages and of (pre)periodic points with respect to the unique measure of maximal entropy

μ
f

\mu _f

for

f
f

. We also show that

(

S
2

,
f
,

μ
f

)

(S^2,f,\mu _f)

is a factor of the left shift on the set of one-sided infinite sequences with its measure of maximal entropy, in the category of measure-preserving dynamical systems. Finally, we prove that

μ
f

\mu _f

is almost surely the weak

∗

^*

limit of atomic probability measures supported on a random backward orbit of an arbitrary point.
Can surface oxygen abundances of red giants be explained by the canonical mixing theory?
Authors: Takeda Yoichi , Sato Bun'ei , Omiya Masashi , Harakawa Hiroki
Published: April 2015

Extensive oxygen abundance determinations were carried out for 239 late-G/early-K giant stars of 1.5–5 M⊙ by applying the spectrum-fitting technique to O i 7771–5 and [O i] 6300/6363 lines based on the high-dispersion spectra in the red region newly obtained at the Okayama Astrophysical Observatory. Our main purpose was to clarify whether any significantly large (≲ 0.4–0.5 dex) O-deficit really exists in these evolved stars, which was once suspected by Takeda et al. (2008, PASJ, 60, 781) from the analysis of the [O i] 5577 line, since it (if real) cannot be explained by the current theory and may require the necessity of special non-canonical deep mixing in the envelope. We found, however, that the previous [O/H]5577 results (differential abundances relative to the Sun) were systematically underestimated compared to the more reliable [O/H]7773 (from O i 7771–5 triplet lines) or [O/H]6300 (from [O i] 6300 line) obtained in this study. Comparing the updated [O/Fe] ratios with the theoretically predicted surface abundance changes caused by mixing of nuclear-processed products dredged-up from the interior, we concluded that the oxygen deficiency in these red giants is insignificantly marginal (only by ≲ 0.1 dex), which does not contradict the expectation from the recent theoretical simulation. This consequence of reasonable consistency between theory and observation also applies to the extent of peculiarity in [C/Fe] and [Na/Fe], which were also examined by re-analyzing the previous equivalent-width data of C i 5052/5380 and Na i 6160 lines.
Coupling of the magnetic field and gas flows inferred from the net circular polarization in a sunspot penumbra
Authors: Shaltout Abdelrazek M. K. , Ichimoto Kiyoshi
Published: April 2015

We analyze penumbral fine structure using high-resolution spectropolarimetric data obtained by the Solar Optical Telescope on board the Hinode satellite. The spatial correlation between the net circular polarization (NCP) and Evershed flow is investigated in detail. Here we obtain that negative NCP structures are correlated with the Evershed flow channels in the limb-side penumbra, and that negative NCP or depressions of positive NCP are associated with the Evershed flow channels in the disk center-side of the penumbra for a negative-polarity sunspot in NOAA 10923. The positive NCP dominant in the disk center-side penumbra is essentially attributed to interflow channels instead of Evershed flow channels. The stratification of magnetic field and velocity are investigated by using SIR-JUMP inversion with a one-component atmosphere, and the NCP of spectral lines in the limb-side and disk center-side of the penumbra is successfully reproduced. The inversion results show that an increased Evershed flow is associated with a strong magnetic field located in the deep photosphere. Our result does not match with the simple two-component penumbral models in which the penumbra consists of Evershed flow and interflow channels and the global NCP is attributed only to the Evershed flow channels.
Moonlight pollination in the gymnospermEphedra(Gnetales)
Authors: Rydin Catarina , Bolinder Kristina
Published: April 2015

Most gymnosperms are wind-pollinated, but some are insect-pollinated, and inEphedra(Gnetales), both wind pollination and insect pollination occur. Little is, however, known about mechanisms and evolution of pollination syndromes in gymnosperms. Based on four seasons of field studies, we show an unexpected correlation between pollination and the phases of the moon in one of our studied species,Ephedra foeminea. It is pollinated by dipterans and lepidopterans, most of them nocturnal, and its pollination coincides with the full moon of July. This may be adaptive in two ways. Many nocturnal insects navigate using the moon. Further, the spectacular reflection of the full-moonlight in the pollination drops is the only apparent means of nocturnal attraction of insects in these plants. In the sympatric but wind-pollinatedEphedra distachya, pollination is not correlated to the full moon but occurs at approximately the same dates every year. The lunar correlation has probably been lost in most species ofEphedrasubsequent an evolutionary shift to wind pollination in the clade. When the services of insects are no longer needed for successful pollination, the adaptive value of correlating pollination with the full moon is lost, and conceivably also the trait.
Transoceanic migration by a 12 g songbird
Authors: DeLuca William V. , Woodworth Bradley K. , Rimmer Christopher C. , Marra Peter P. , Taylor Philip D. , McFarland Kent P. , Mackenzie Stuart A. , Norris D. Ryan
Published: April 2015

Many fundamental aspects of migration remain a mystery, largely due to our inability to follow small animals over vast spatial areas. For more than 50 years, it has been hypothesized that, during autumn migration, blackpoll warblers (
Setophaga striata
) depart northeastern North America and undertake a non-stop flight over the Atlantic Ocean to either the Greater Antilles or the northeastern coast of South America. Using miniaturized light-level geolocators, we provide the first irrefutable evidence that the blackpoll warbler, a 12 g boreal forest songbird, completes an autumn transoceanic migration ranging from 2270 to 2770 km (mean ± s.d.: 2540 ± 257) and requiring up to 3 days (62 h ± 10) of non-stop flight. This is one of the longest non-stop overwater flights recorded for a songbird and confirms what has long been believed to be one of the most extraordinary migratory feats on the planet.
Predicting electromyographic signals under realistic conditions using a multiscale chemo–electro–mechanical finite element model
Authors: Mordhorst Mylena , Heidlauf Thomas , Röhrle Oliver
Published: April 2015

This paper presents a novel multiscale finite element-based framework for modelling electromyographic (EMG) signals. The framework combines (i) a biophysical description of the excitation–contraction coupling at the half-sarcomere level, (ii) a model of the action potential (AP) propagation along muscle fibres, (iii) a continuum-mechanical formulation of force generation and deformation of the muscle, and (iv) a model for predicting the intramuscular and surface EMG. Owing to the biophysical description of the half-sarcomere, the model inherently accounts for physiological properties of skeletal muscle. To demonstrate this, the influence of membrane fatigue on the EMG signal during sustained contractions is investigated. During a stimulation period of 500 ms at 100 Hz, the predicted EMG amplitude decreases by 40% and the AP propagation velocity decreases by 15%. Further, the model can take into account contraction-induced deformations of the muscle. This is demonstrated by simulating fixed-length contractions of an idealized geometry and a model of the human tibialis anterior muscle (TA). The model of the TA furthermore demonstrates that the proposed finite element model is capable of simulating realistic geometries, complex fibre architectures, and can include different types of heterogeneities. In addition, the TA model accounts for a distributed innervation zone, different fibre types and appeals to motor unit discharge times that are based on a biophysical description of theαmotor neurons.
Stochastic modelling of muscle recruitment during activity
Authors: Martelli Saulo , Calvetti Daniela , Somersalo Erkki , Viceconti Marco
Published: April 2015

Muscle forces can be selected from a space of muscle recruitment strategies that produce stable motion and variable muscle and joint forces. However, current optimization methods provide only a single muscle recruitment strategy. We modelled the spectrum of muscle recruitment strategies while walking. The equilibrium equations at the joints, muscle constraints, static optimization solutions and 15-channel electromyography (EMG) recordings for seven walking cycles were taken from earlier studies. The spectrum of muscle forces was calculated using Bayesian statistics and Markov chain Monte Carlo (MCMC) methods, whereas EMG-driven muscle forces were calculated using EMG-driven modelling. We calculated the differences between the spectrum and EMG-driven muscle force for 1–15 input EMGs, and we identified the muscle strategy that best matched the recorded EMG pattern. The best-fit strategy, static optimization solution and EMG-driven force data were compared using correlation analysis. Possible and plausible muscle forces were defined as within physiological boundaries and within EMG boundaries. Possible muscle and joint forces were calculated by constraining the muscle forces between zero and the peak muscle force. Plausible muscle forces were constrained within six selected EMG boundaries. The spectrum to EMG-driven force difference increased from 40 to 108 N for 1–15 EMG inputs. The best-fit muscle strategy better described the EMG-driven pattern (
R
2
= 0.94; RMSE = 19 N) than the static optimization solution (
R
2
= 0.38; RMSE = 61 N). Possible forces for 27 of 34 muscles varied between zero and the peak muscle force, inducing a peak hip force of 11.3 body-weights. Plausible muscle forces closely matched the selected EMG patterns; no effect of the EMG constraint was observed on the remaining muscle force ranges. The model can be used to study alternative muscle recruitment strategies in both physiological and pathophysiological neuromotor conditions.
Towards causally cohesive genotype–phenotype modelling for characterization of the soft-tissue mechanics of the heart in normal and pathological geometries
Authors: Nordbø Øyvind , Gjuvsland Arne B. , Nermoen Anders , Land Sander , Niederer Steven , Lamata Pablo , Lee Jack , Smith Nicolas P. , Omholt Stig W. , Vik Jon Olav
Published: April 2015

A scientific understanding of individual variation is key to personalized medicine, integrating genotypic and phenotypic information via computational physiology. Genetic effects are often context-dependent, differing between genetic backgrounds or physiological states such as disease. Here, we analyse
in silico
genotype–phenotype maps (GP map) for a soft-tissue mechanics model of the passive inflation phase of the heartbeat, contrasting the effects of microstructural and other low-level parameters assumed to be genetically influenced, under normal, concentrically hypertrophic and eccentrically hypertrophic geometries. For a large number of parameter scenarios, representing mock genetic variation in low-level parameters, we computed phenotypes describing the deformation of the heart during inflation. The GP map was characterized by variance decompositions for each phenotype with respect to each parameter. As hypothesized, the concentric geometry allowed more low-level parameters to contribute to variation in shape phenotypes. In addition, the relative importance of overall stiffness and fibre stiffness differed between geometries. Otherwise, the GP map was largely similar for the different heart geometries, with little genetic interaction between the parameters included in this study. We argue that personalized medicine can benefit from a combination of causally cohesive genotype–phenotype modelling, and strategic phenotyping that captures effect modifiers not explicitly included in the mechanistic model.
The entropic basis of collective behaviour
Authors: Mann Richard P. , Garnett Roman
Published: April 2015

We identify a unique viewpoint on the collective behaviour of intelligent agents. We first develop a highly general abstract model for the possible future lives these agents may encounter as a result of their decisions. In the context of these possibilities, we show that the
causal entropic principle
, whereby agents follow behavioural rules that maximize their entropy over all paths through the future, predicts many of the observed features of social interactions among both human and animal groups. Our results indicate that agents are often able to maximize their future path entropy by remaining cohesive as a group and that this cohesion leads to collectively intelligent outcomes that depend strongly on the distribution of the number of possible future paths. We derive social interaction rules that are consistent with maximum entropy group behaviour for both discrete and continuous decision spaces. Our analysis further predicts that social interactions are likely to be fundamentally based on Weber's law of response to proportional stimuli, supporting many studies that find a neurological basis for this stimulus–response mechanism and providing a novel basis for the common assumption of linearly additive ‘social forces’ in simulation studies of collective behaviour.
Experimental evolution gone wild
Authors: Scheinin M. , Riebesell U. , Rynearson T. A. , Lohbeck K. T. , Collins S.
Published: April 2015

Because of their large population sizes and rapid cell division rates, marine microbes have, or can generate, ample variation to fuel evolution over a few weeks or months, and subsequently have the potential to evolve in response to global change. Here we measure evolution in the marine diatom
Skeletonema marinoi
evolved in a natural plankton community in CO
2
-enriched mesocosms deployed
in situ
. Mesocosm enclosures are typically used to study how the species composition and biogeochemistry of marine communities respond to environmental shifts, but have not been used for experimental evolution to date. Using this approach, we detect a large evolutionary response to CO
2
enrichment in a focal marine diatom, where population growth rate increased by 1.3-fold in high CO
2
-evolved lineages. This study opens an exciting new possibility of carrying out
in situ
evolution experiments to understand how marine microbial communities evolve in response to environmental change.
Analysis of unstable modes distinguishes mathematical models of flagellar motion
Authors: Bayly P. V. , Wilson K. S.
Published: April 2015

The mechanisms underlying the coordinated beating of cilia and flagella remain incompletely understood despite the fundamental importance of these organelles. The axoneme (the cytoskeletal structure of cilia and flagella) consists of microtubule doublets connected by passive and active elements. The motor protein dynein is known to drive active bending, but dynein activity must be regulated to generate oscillatory, propulsive waveforms. Mathematical models of flagellar motion generate quantitative predictions that can be analysed to test hypotheses concerning dynein regulation. One approach has been to seek periodic solutions to the linearized equations of motion. However, models may simultaneously exhibit both periodic and unstable modes. Here, we investigate the emergence and coexistence of unstable and periodic modes in three mathematical models of flagellar motion, each based on a different dynein regulation hypothesis: (i) sliding control; (ii) curvature control and (iii) control by interdoublet separation (the ‘geometric clutch’ (GC)). The unstable modes predicted by each model are used to critically evaluate the underlying hypothesis. In particular, models of flagella with ‘sliding-controlled’ dynein activity admit unstable modes with non-propulsive, retrograde (tip-to-base) propagation, sometimes at the same parameter values that lead to periodic, propulsive modes. In the presence of these retrograde unstable modes, stable or periodic modes have little influence. In contrast, unstable modes of the GC model exhibit switching at the base and propulsive base-to-tip propagation.
Obstacle avoidance in social groups: new insights from asynchronous models
Authors: Croft Simon , Budgey Richard , Pitchford Jonathan W. , Wood A. Jamie
Published: April 2015

For moving animals, the successful avoidance of hazardous obstacles is an important capability. Despite this, few models of collective motion have addressed the relationship between behavioural and social features and obstacle avoidance. We develop an asynchronous individual-based model for social movement which allows social structure within groups to be included. We assess the dynamics of group navigation and resulting collision risk in the context of information transfer through the system. In agreement with previous work, we find that group size has a nonlinear effect on collision risk. We implement examples of possible network structures to explore the impact social preferences have on collision risk. We show that any social heterogeneity induces greater obstacle avoidance with further improvements corresponding to groups containing fewer influential individuals. The model provides a platform for both further theoretical investigation and practical application. In particular, we argue that the role of social structures within bird flocks may have an important role to play in assessing the risk of collisions with wind turbines, but that new methods of data analysis are needed to identify these social structures.
Three-dimensional cellular automata modelling of cleavage propagation across crystal boundaries in polycrystalline microstructures
Authors: Shterenlikht A. , Margetts L.
Published: April 2015

A three-dimensional cellular automata (CA) with rectilinear layout is used in this work to create and cleave polycrystalline microstructures. Each crystal is defined by a unique randomly generated orientation tensor. Separate states for grains, grain boundaries, crack flanks and crack fronts are created. Algorithms for progressive cleavage propagation through crystals and across grain boundaries are detailed. The mesh independent cleavage criterion includes the critical cleavage stress and the length scale. Resolution of an arbitrary crystallographic plane within a 26-cell Moore neighbourhood is considered. The model is implemented in Fortran 2008 coarrays. The model gives realistic predictions of grain size and mis-orientation distributions, grain boundary topology and crack geometry. Finally, we show how the proposed CA model can be linked to a finite-element model to produce a multi-scale fracture framework.
Sex-chromosome differentiation and ‘sex races’ in the common frog (
Rana temporaria
)
Authors: Rodrigues Nicolas , Vuille Yvan , Loman Jon , Perrin Nicolas
Published: April 2015

Sex-chromosome differentiation was recently shown to vary among common frog populations in Fennoscandia, suggesting a trend of increased differentiation with latitude. By rearing families from two contrasted populations (respectively, from northern and southern Sweden), we show this disparity to stem from differences in sex-determination mechanisms rather than in XY-recombination patterns. Offspring from the northern population display equal sex ratios at metamorphosis, with phenotypic sexes that correlate strongly with paternal LG
2
haplotypes (the sex chromosome); accordingly, Y haplotypes are markedly differentiated, with male-specific alleles and depressed diversity testifying to their smaller effective population size. In the southern population, by contrast, a majority of juveniles present ovaries at metamorphosis; only later in development do sex ratios return to equilibrium. Even at these later stages, phenotypic sexes correlate only mildly with paternal LG
2
haplotypes; accordingly, there are no recognizable Y haplotypes. These distinct patterns of gonadal development fit the concept of ‘sex races’ proposed in the 1930s, with our two populations assigned to the ‘differentiated’ and ‘semi-differentiated’ races, respectively. Our results support the suggestion that ‘sex races’ differ in the genetic versus epigenetic components of sex determination. Analysing populations from the ‘undifferentiated race’ with high-density genetic maps should help to further test this hypothesis.
Biotic interactions govern genetic adaptation to toxicants
Authors: Becker Jeremias Martin , Liess Matthias
Published: April 2015

The genetic recovery of resistant populations released from pesticide exposure is accelerated by the presence of environmental stressors. By contrast, the relevance of environmental stressors for the spread of resistance during pesticide exposure has not been studied. Moreover, the consequences of interactions between different stressors have not been considered. Here we show that stress through intraspecific competition accelerates microevolution, because it enhances fitness differences between adapted and non-adapted individuals. By contrast, stress through interspecific competition or predation reduces intraspecific competition and thereby delays microevolution. This was demonstrated in mosquito populations (
Culex quinquefasciatus
) that were exposed to the pesticide chlorpyrifos. Non-selective predation through harvesting and interspecific competition with
Daphnia magna
delayed the selection for individuals carrying the

ace-1
R

resistance allele. Under non-toxic conditions, susceptible individuals without

ace-1
R

prevailed. Likewise, predation delayed the reverse adaptation of the populations to a non-toxic environment, while the effect of interspecific competition was not significant. Applying a simulation model, we further identified how microevolution is generally determined by the type and degree of competition and predation. We infer that interactions with other species—especially strong in ecosystems with high biodiversity—can delay the development of pesticide resistance.