bluuebunny/crossref_metadata_2025 huggingface dataset:
Traumatic Globe Luxation With Chiasmal Avulsion
Authors: Zhou Sandy Wenting , Pang Audrey Yuan Ching , Poh Eugenie Wei Ting , Chin Chee Fang
Published: June 2018

Background:

To describe an unusual case of traumatic globe luxation with optic chiasmal avulsion and review the existing literature on this rare condition for further discussion of mechanisms, diagnosis, and management.

Methods:

Case report and review of existing case reports and case series identified through literature search.

Results:

A 28-year-old woman, with no previous medical history, had left globe luxation and optic chiasm avulsion after being stabbed directly into the left orbit with the use of the stiletto high heel of a shoe. Automated visual field testing detected a temporal hemianopia in the unaffected eye despite normal central visual acuity. Chiasmal avulsion was demonstrated by MRI.

Conclusions:

This case suggests that perimetry and MRI should always be considered in traumatic globe luxation to localize the site of injury. Temporal hemianopia in the fellow eye indicates a concomitant chiasmal injury.
Individual repeatability and heritability of divorce in a wild population
Authors: Germain Ryan R. , Wolak Matthew E. , Reid Jane M.
Published: June 2018

Understanding micro-evolutionary responses of mating systems to contemporary selection requires estimating sex-specific additive genetic variances and cross-sex genetic covariances in key reproductive strategy traits. One key trait comprises the occurrence of divorce versus mate fidelity across sequential reproductive attempts. If divorce represents an evolving behavioural strategy that responds to selection it must have non-zero individual repeatability and heritability, but quantitative estimates from wild populations are scarce. We used 39 years of individual breeding records and pedigree data from free-living song sparrows (Melospiza melodia) to quantify sex-specific permanent individual and additive genetic variances, and hence estimate repeatability and heritability, in liability for divorce. We estimated moderate repeatability among females, but little repeatability among males. Estimates of additive genetic variance were small in both sexes, and the cross-sex genetic covariance was close to zero. Consequently, the total heritability was small but likely non-zero, indicating low potential for micro-evolutionary response to selection. Rapid micro-evolutionary change of divorce rate, therefore, appears unlikely, even if there were substantial fitness benefits of divorce and resulting selection.
Reduced telomere length in offspring of old fathers in a long-lived seabird
Authors: Bouwhuis Sandra , Verhulst Simon , Bauch Christina , Vedder Oscar
Published: June 2018

Evidence for transgenerational effects of senescence, whereby offspring from older parents have a reduced lifetime reproductive success, is increasing. Such effects could arise from compromised germline maintenance in old parents, potentially reflected in reduced telomere length in their offspring. We test the relationship between parental age and offspring early-life telomere length in a natural population of common terns and find a significant negative correlation between paternal age and offspring telomere length. Offspring telomere length is reduced by 35 base pairs for each additional year of paternal age. We find no correlation with maternal age. These results fit with the idea of compromised germline maintenance in males, whose germline stem cells require continued division.
Round-trip across the Sahara: Afrotropical Painted Lady butterflies recolonize the Mediterranean in early spring
Authors: Talavera Gerard , Bataille Clément , Benyamini Dubi , Gascoigne-Pees Martin , Vila Roger
Published: June 2018

The Palearctic–African migratory circuit has been typically associated with birds. Very few insects are known to endure annual trans-Saharan circuits, but the Painted Lady butterfly (
Vanessa cardui
) is an exception. While it was demonstrated that this species massively migrates from Europe to the Afrotropics during the autumn, the existence of a reverse migration from the Afrotropics to Europe in the early spring remains hypothetical. Here, we analysed wing stable hydrogen isotope values (δ
2
H) of
V. cardui
migrants collected from February to April across the circum-Mediterranean region. We assessed their region of natal origin by comparing their wing isotope signature predicted δ
2
H values (isoscape). The results unambiguously demonstrate a sub-Saharan origin for many individuals, especially those collected in February, representing the first tangible evidence for a reverse northwards trans-Saharan migration in spring. This work supports the view that the Afrotropics (mostly exploited from September to February) is key in the
V. cardui
Palearctic–African population dynamics. This species relies on both temperate and tropical habitats to complete their multigenerational cycle, an unprecedented adaptation for butterflies and for most migratory insects. Such a migratory circuit has strong parallelisms with those of migratory birds.
Structural stress response of segmented natural shells: a numerical case study on the clypeasteroid echinoidEchinocyamus pusillus
Authors: Grun Tobias B. , von Scheven Malte , Bischoff Manfred , Nebelsick James H.
Published: June 2018

The skeleton ofEchinocyamus pusillusis considered as an exceptional model organism for structural strength and skeletal integrity within the echinoids as demonstrated by the absence of supportive collagenous fibres between single plates and the high preservation potential of their skeletons. The structural principles behind this remarkably stable, multi-plated, light-weight construction remain hardly explored. In this study, high-resolution X-ray micro-computed tomography, finite-element analysis and physical crushing tests are used to examine the structural mechanisms of this echinoid's skeleton. The virtual model ofE. pusillusshows that the material is heterogeneously distributed with high material accumulations in the internal buttress system and at the plate boundaries. Finite-element analysis indicates that the heterogeneous material distribution has no effect on the skeleton's strength. This numerical approach also demonstrates that the internal buttress system is of high significance for the overall skeletal stability of this flattened echinoid. Results of the finite-element analyses with respect to the buttress importance were evaluated by physical crushing tests. These uniaxial compression experiments support the results of the simulation analysis. Additionally, the crushing tests demonstrate that organic tissues do not significantly contribute to the skeletal stability. The strength of the echinoid shell, hence, predominantly relies on the structural design.
Scaling in biomechanical experimentation: a finite similitude approach
Authors: Ochoa-Cabrero Raul , Alonso-Rasgado Teresa , Davey Keith
Published: June 2018

Biological experimentation has many obstacles: resource limitations, unavailability of materials, manufacturing complexities and ethical compliance issues; any approach that resolves all or some of these is of some interest. The aim of this study is applying the recently discovered concept of finite similitude as a novel approach for the design of scaled biomechanical experiments supported with analysis using a commercial finite-element package and validated by means of image correlation software. The study of isotropic scaling of synthetic bones leads to the selection of three-dimensional (3D) printed materials for the trial-space materials. These materials conforming to the theory are analysed in finite-element models of a cylinder and femur geometries undergoing compression, tension, torsion and bending tests to assess the efficacy of the approach using reverse scaling of the approach. The finite-element results show similar strain patterns in the surface for the cylinder with a maximum difference of less than 10% and for the femur with a maximum difference of less than 4% across all tests. Finally, the trial-space, physical-trial experimentation using 3D printed materials for compression and bending testing provides a good agreement in a Bland–Altman statistical analysis, providing good supporting evidence for the practicality of the approach.
Structural centrosome aberrations sensitize polarized epithelia to basal cell extrusion
Authors: Ganier Olivier , Schnerch Dominik , Nigg Erich A.
Published: June 2018

Centrosome aberrations disrupt tissue architecture and may confer invasive properties to cancer cells. Here we show that structural centrosome aberrations, induced by overexpression of either Ninein-like protein (NLP) or CEP131/AZI1, sensitize polarized mammalian epithelia to basal cell extrusion. While unperturbed epithelia typically dispose of damaged cells through apical dissemination into luminal cavities, certain oncogenic mutations cause a switch in directionality towards basal cell extrusion, raising the potential for metastatic cell dissemination. Here we report that NLP-induced centrosome aberrations trigger the preferential extrusion of damaged cells towards the basal surface of epithelial monolayers. This switch in directionality from apical to basal dissemination coincides with a profound reorganization of the microtubule cytoskeleton, which in turn prevents the contractile ring repositioning that is required to support extrusion towards the apical surface. While the basal extrusion of cells harbouring NLP-induced centrosome aberrations requires exogenously induced cell damage, structural centrosome aberrations induced by excess CEP131 trigger the spontaneous dissemination of dying cells towards the basal surface from MDCK cysts. Thus, similar to oncogenic mutations, structural centrosome aberrations can favour basal extrusion of damaged cells from polarized epithelia. Assuming that additional mutations may promote cell survival, this process could sensitize epithelia to disseminate potentially metastatic cells.
Exploring the potential pharmacodynamic material basis and pharmacologic mechanism of the
Fufang-Xialian-Capsule
in chronic atrophic gastritis by network pharmacology approach based on the components absorbed into the blood
Authors: Li Shizhe , Xu Tengfei , Liu Shu , Liu Zhiqiang , Pi Zifeng , Song Fenrui , Jin Yongri
Published: June 2018

In this study, a new network pharmacology approach based on the components absorbed into the blood was used to investigate the pharmacodynamic material basis and the pharmacologic mechanism of the
Fufang-Xialian-Capsule
(
FXL
) in treating chronic atrophic gastritis (CAG). Initially, we confirmed the components absorbed into the blood by ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. Then, the network approach, which was based on the results of components absorbed into the blood, was used to analyse the pharmacodynamic material basis and the pharmacologic mechanism of
FXL
on treating CAG. As a result, 22 absorbed components were found in rat plasma. Given the results of the absorption analysis of the components, eight pathways associated with CAG development were found. The targets linked to these pathways are the drug targets of
FXL
in CAG treatment. The components associated with these targets are the potential pharmacodynamic material basis and exert synergy in regulating pathways during CAG treatment.
Material composition of the mouthpart cuticle in a damselfly larva (Insecta: Odonata) and its biomechanical significance
Authors: Büsse Sebastian , Gorb Stanislav N.
Published: June 2018

Odonata larvae are key predators in their habitats. They catch prey with a unique and highly efficient apparatus, the prehensile mask. The mandibles and maxillae, however, play the lead in handling and crushing the food. The material composition of the cuticle in the biomechanical system of the larval mouthparts has not been studied so far. We used confocal laser scanning microscopy (CLSM) to detect material gradients in the cuticle by differences in autofluorescence. Our results show variations of materials in different areas of the mouthparts: (i) resilin-dominated pads within the membranous transition between the labrum and the anteclypeus, which support mobility and might provide shock absorption, an adaptation against mechanical damage; (ii) high degrees of sclerotization in the incisivi of the mandibles, where high forces occur when crushing the prey's body wall. The interaction of the cuticle geometry, the material composition and the related musculature determine the complex concerted movements of the mouthparts. The material composition influences the strength, mobility and durability of the cuticular components of the mouthparts. Applying CLSM for extracting information about material composition and material properties of arthropod cuticles will considerably help improve finite-element modelling studies.
Phylogenomic history of enigmatic pygmy perches: implications for biogeography, taxonomy and conservation
Authors: Buckley Sean J. , Domingos Fabricius M. C. B. , Attard Catherine R. M. , Brauer Chris J. , Sandoval-Castillo Jonathan , Lodge Ryan , Unmack Peter J. , Beheregaray Luciano B.
Published: June 2018

Pygmy perches (Percichthyidae) are a group of poorly dispersing freshwater fishes that have a puzzling biogeographic disjunction across southern Australia. Current understanding of pygmy perch phylogenetic relationships suggests past east–west migrations across a vast expanse of now arid habitat in central southern Australia, a region lacking contemporary rivers. Pygmy perches also represent a threatened group with confusing taxonomy and potentially cryptic species diversity. Here, we present the first study of the evolutionary history of pygmy perches based on genome-wide information. Data from 13 991 ddRAD loci and a concatenated sequence of 1 075 734 bp were generated for all currently described and potentially cryptic species. Phylogenetic relationships, biogeographic history and cryptic diversification were inferred using a framework that combines phylogenomics, species delimitation and estimation of divergence times. The genome-wide phylogeny clarified the biogeographic history of pygmy perches, demonstrating multiple east–west events of divergence within the group across the Australian continent. These results also resolved discordance between nuclear and mitochondrial data from a previous study. In addition, we propose three cryptic species within a southwestern species complex. The finding of potentially new species demonstrates that pygmy perches may be even more susceptible to ecological and demographic threats than previously thought. Our results have substantial implications for improving conservation legislation of pygmy perch lineages, especially in southwestern Western Australia.
Response of
Prochilodus nigricans
to flood pulse variation in the central Amazon
Authors: Bayley Peter B. , Castello Leandro , Batista Vandick S. , Fabré Nidia N.
Published: June 2018

The influence of the flood pulse on fish populations has been posited, but infrequently tested or quantified. Here, we tested the effect of habitat on population size, using
Prochilodus nigricans
as a case study species. Floodplain habitat was based on the littoral zone area occupied by
P. nigricans
to feed. The magnitude of this habitat in each hydrological year, the moving littoral (ML), was expressed as the sum of daily littoral areas during the advancing flood pulse, using satellite-based passive microwave data. Annual population size was estimated by age class, using a dynamic age-structured model (MULTIFAN-CL) based on catches, effort and fish length frequencies from the Manaus-based fishery over 12.75 years. The principal null hypothesis was that the ML, using three lag times, had no effect on population size of a single age class of
P. nigricans
. The population size at 29 months of age was positively related (
p
 = 0.00030) to floodplain habitat (ML) earlier in the same year, when the fish were 21–27 months old. The result implies a density-dependent relationship for the population with respect to its feeding habitat. Potential mechanisms governed by flood pulse variation and habitat quality for this and other species using floodplain habitats are discussed.
The effect of static versus dynamic stimuli on visual processing of sexual cues in androphilic women and gynephilic men
Authors: Dawson Samantha J. , Chivers Meredith L.
Published: June 2018

Models of sexual response posit that attentional processing of sexual cues is requisite for sexual responding. Despite hypothesized similarities in the underlying processes resulting in sexual response, gender differences in sexual arousal patterns are abundant. One such gender difference relates to the stimulus features (e.g. gender cues, sexual activity cues) that elicit a response in men and women. In this study, we examined how stimulus modality (static visual images versus dynamic audiovisual films) and stimulus features (gender, sexual activity and nonsexual contextual cues) influences attentional (i.e. gaze) and elaborative (i.e. self-reported attraction (SRA), self-reported arousal) processing of sexual stimuli. Men's initial and controlled attention was consistently gender-specific (i.e. greater attention towards female targets), and this was not influenced by stimulus modality or the presence of sexual activity cues. By contrast, gender-specificity of women's attention patterns differed as a function of attentional stage, stimulus modality and the features within the stimulus. Degree of specificity was positively predictive of SRA in both genders; however, it was not significantly predictive of self-reported arousal. These findings are discussed in the context of gendered processing of visual sexual information, including a discussion of implications for research designs.
A phenomenological model for structural phase transitions in incommensurate alkane/urea inclusion compounds
Authors: Couzi Michel , Guillaume François , Harris Kenneth D. M.
Published: June 2018

n-Alkane/urea inclusion compounds are crystalline materials in whichn-alkane ‘guest’ molecules are located within parallel one-dimensional ‘host’ tunnels formed by a helical hydrogen-bonded arrangement of urea molecules. The periodic repeat distance of the guest molecules along the host tunnels is incommensurate with the periodic repeat distance of the host substructure. The structural properties of the high-temperature phase of these materials (phase I), which exist at ambient temperature, are described by a (3 + 1)-dimensional superspace. Recent publications have suggested that, in the prototypical incommensurate composite systems,n-nonadecane/urea andn-hexadecane/urea, two low-temperature phases II and ‘III’ exist and that one or both of these phases are described by a (3 + 2)-dimensional superspace. We present a phenomenological model based on symmetry considerations and developed in the frame of a pseudo-spin–phonon coupling mechanism, which accounts for the mechanisms responsible for the I ↔ II ↔ ‘III’ phase sequence. With reference to published experimental data, we demonstrate that, in all phases of these incommensurate materials, the structural properties are described by (3 + 1)-dimensional superspace groups. Around the temperature of the II ↔ ‘III’ transition, the macroscopic properties of the material are not actually associated with a phase transition, but instead represent a ‘crossover’ between two regimes involving different couplings between relevant order parameters.
Intramolecular hydrogen bonds in 1,4-dihydropyridine derivatives
Authors: Petrova M. , Muhamadejev R. , Vigante B. , Duburs G. , Liepinsh Edvards
Published: June 2018

1,4-Dihydropyridine (1,4-DHP) derivatives have been synthesized and characterized by
1
H,
13
C,
15
N nuclear magnetic resonance (NMR) spectroscopy, secondary proton/deuterium
13
C isotope shifts, variable temperature
1
H NMR experiments and quantum-chemical calculation. The intramolecular hydrogen bonds NH⋯O=C and CH⋯O=C in these compounds were established by NMR and quantum-chemical studies The downfield shift of the NH proton
,
accompanied by the upfield shift of the
15
N nuclear magnetic resonance signals, the shift to the higher wavenumbers of the NH stretching vibration in the infrared spectra and the increase of the
1
J(
15
N,
1
H) values may indicate the shortening of the N–H bond length upon intramolecular NH⋯O=C hydrogen bond formation.
Transition mechanism for a periodic bar-and-joint framework with limited degrees of freedom controlled by uniaxial load and internal stiffness
Authors: Tanaka H. , Hamada K. , Shibutani Y.
Published: June 2018

A specific periodic bar-and-joint framework with limited degrees of freedom is shown to have a transition mechanism when subjected to an external force. The static nonlinear elasticity of this framework under a uniaxial load is modelled with the two angular variables specifying the rotation and distortion of the linked square components. Numerically exploring the equilibrium paths then reveals a transition state of the structure at a critical value of the internal stiffness. A simplified formulation of the model with weak nonlinear terms yields an exact solution of its transition state. Load–displacement behaviour and stability for the two systems with or without approximation are analysed and compared.
Muscle–tendon unit length changes differ between young and adult sprinters in the first stance phase of sprint running
Authors: Aeles Jeroen , Jonkers Ilse , Debaere Sofie , Delecluse Christophe , Vanwanseele Benedicte
Published: June 2018

The aim of this study was to compare young and adult sprinters on several biomechanical parameters that were previously highlighted as performance-related and to determine the behaviour of several muscle–tendon units (MTU) in the first stance phase following a block start in sprint running. The ground reaction force (GRF) and kinematic data were collected from 16 adult and 21 young well-trained sprinters. No difference between the groups was found in some of the previously highlighted performance-related parameters (ankle joint stiffness, the range of dorsiflexion and plantar flexor moment). Interestingly, the young sprinters showed a greater maximal and mean ratio of horizontal to total GRF, which was mainly attributed to a greater horizontal GRF relative to body mass and resulted in a greater change in horizontal centre of mass (COM) velocity during the stance phase in the young compared with the adult sprinters. Results from the MTU length analyses showed that adult sprinters had more MTU shortening and higher maximal MTU shortening velocities in all plantar flexors and the rectus femoris. Although previously highlighted performance-related parameters could not explain the greater 100 m sprinting times in the adult sprinters, differences were found in the behaviour of the MTU of the plantar flexors and rectus femoris during the first stance phase. The pattern of length changes in these MTUs provides ideal conditions for the use of elastic energy storage and release for power enhancement.
An algorithm to explore entanglement in small systems
Authors: Reuvers R.
Published: June 2018

A quantum state’s entanglement across a bipartite cut can be quantified with entanglement entropy or, more generally, Schmidt norms. Using only Schmidt decompositions, we present a simple iterative algorithm to maximize Schmidt norms. Depending on the choice of norm, the optimizing states maximize or minimize entanglement, possibly across several bipartite cuts at the same time and possibly only among states in a specified subspace. Recognizing that convergence but not success is certain, we use the algorithm to explore topics ranging from fermionic reduced density matrices and varieties of pure quantum states to absolutely maximally entangled states and minimal output entropy of channels.
Tension-dependent transverse buckles and wrinkles in twisted elastic sheets
Authors: Kudrolli A. , Chopin J.
Published: June 2018

We investigate with experiments the twist-induced transverse buckling instabilities of an elastic sheet of length
L
, width
W
and thickness
t
, that is clamped at two opposite ends while held under a tension
T
. Above a critical tension
T
λ
and critical twist angle
η
tr
, we find that the sheet buckles with a mode number
n
≥1 transverse to the axis of twist. Three distinct buckling regimes characterized as clamp-dominated, bendable and stiff are identified, by introducing a bendability length
L
B
and a clamp length
L
C
(<
L
B
). In the stiff regime (
L
>
L
B
), we find that mode
n
=1 develops above
η
tr
≡
η
S
∼(
t
/
W
)
T
−1/2
, independent of
L
. In the bendable regime
L
C
<
L
<
L
B
,
n
=1 as well as
n
>1 occur above

η

tr

≡

η

B

∼

t

/

L

T

−
1

/

4

. Here, we find the wavelength

λ

B

∼

L
t

T

−
1

/

4

, when
n
>1. These scalings agree with those derived from a covariant form of the Föppl-von Kármán equations, however, we find that the
n
=1 mode also occurs over a surprisingly large range of
L
in the bendable regime. Finally, in the clamp-dominated regime (
L
<
L
C
), we find that
η
tr
is higher compared to
η
B
due to additional stiffening induced by the clamped boundary conditions.
Individual-specific mortality is associated with how individuals evaluate future discounting decisions
Authors: Lee Anthony J. , DeBruine Lisa M. , Jones Benedict C.
Published: June 2018

How organisms discount the value of future rewards is associated with many important outcomes, and may be a central component of theories of life-history. According to life-history theories, prioritizing immediacy is indicative of an accelerated strategy (i.e. reaching reproductive maturity quickly and producing many offspring at the cost of long-term investment). Previous work extrapolating life-history theories to facultative calibration of life-history traits within individuals has theorized that cues to mortality can trigger an accelerated strategy; however, compelling evidence for this hypothesis in modern humans is lacking. We assessed whether country-level life expectancy predicts individual future discounting behaviour across multiple intertemporal choice items in a sample of 13 429 participants from 54 countries. Individuals in countries with lower life expectancy were more likely to prefer an immediate reward to one that is delayed. Individuals from countries with greater life expectancy were especially more willing to wait for a future reward when the relative gain in choosing the future reward was large and/or the delay period was short. These results suggest that cues to mortality can influence the way individuals evaluate intertemporal decisions, which in turn can inform life-history trade-offs. We also found that older (but not very old) participants were more willing to wait for a future reward when there is a greater relative gain and/or shorter delay period, consistent with theoretical models that suggest individuals are more future-orientated at middle age.
Whisker touch sensing guides locomotion in small, quadrupedal mammals
Authors: Grant Robyn A. , Breakell Vicki , Prescott Tony J.
Published: June 2018

All small mammals have prominent facial whiskers that they employ as tactile sensors to guide navigation and foraging in complex habitats. Nocturnal, arboreal mammals tend to have the longest and most densely packed whiskers, and semi-aquatic mammals have the most sensitive. Here we present evidence to indicate that many small mammals use their whiskers to tactually guide safe foot positioning. Specifically, in 11, small, non-flying mammal species, we demonstrate that forepaw placement always falls within the ground contact zone of the whisker field and that forepaw width is always smaller than whisker span. We also demonstrate commonalities of whisker scanning movements (whisking) and elements of active control, associated with increasing contact with objects of interest, across multiple small mammal species that have previously only been shown in common laboratory animals. Overall, we propose that guiding locomotion, alongside environment exploration, is a common function of whisker touch sensing in small, quadrupedal mammals.
What is cumulative cultural evolution?
Authors: Mesoudi Alex , Thornton Alex
Published: June 2018

In recent years, the phenomenon of cumulative cultural evolution (CCE) has become the focus of major research interest in biology, psychology and anthropology. Some researchers argue that CCE is unique to humans and underlies our extraordinary evolutionary success as a species. Others claim to have found CCE in non-human species. Yet others remain sceptical that CCE is even important for explaining human behavioural diversity and complexity. These debates are hampered by multiple and often ambiguous definitions of CCE. Here, we review how researchers define, use and test CCE. We identify a core set of criteria for CCE which are both necessary and sufficient, and may be found in non-human species. We also identify a set of extended criteria that are observed in human CCE but not, to date, in other species. Different socio-cognitive mechanisms may underlie these different criteria. We reinterpret previous theoretical models and observational and experimental studies of both human and non-human species in light of these more fine-grained criteria. Finally, we discuss key issues surrounding information, fitness and cognition. We recommend that researchers are more explicit about what components of CCE they are testing and claiming to demonstrate.
The distribution of bacterial doubling times in the wild
Authors: Gibson Beth , Wilson Daniel J. , Feil Edward , Eyre-Walker Adam
Published: June 2018

Generation time varies widely across organisms and is an important factor in the life cycle, life history and evolution of organisms. Although the doubling time (DT) has been estimated for many bacteria in the laboratory, it is nearly impossible to directly measure it in the natural environment. However, an estimate can be obtained by measuring the rate at which bacteria accumulate mutations per year in the wild and the rate at which they mutate per generation in the laboratory. If we assume the mutation rate per generation is the same in the wild and in the laboratory, and that all mutations in the wild are neutral, an assumption that we show is not very important, then an estimate of the DT can be obtained by dividing the latter by the former. We estimate the DT for five species of bacteria for which we have both an accumulation and a mutation rate estimate. We also infer the distribution of DTs across all bacteria from the distribution of the accumulation and mutation rates. Both analyses suggest that DTs for bacteria in the wild are substantially greater than those in the laboratory, that they vary by orders of magnitude between different species of bacteria and that a substantial fraction of bacteria double very slowly in the wild.
Regulation between personality traits: individual social tendencies modulate whether boldness and leadership are correlated
Authors: Bevan Peggy A. , Gosetto Isabella , Jenkins Eliza R. , Barnes Isobel , Ioannou Christos C.
Published: June 2018

Although consistent behavioural differences between individuals (i.e. personality variation) are now well established in animals, these differences are not always expressed when individuals interact in social groups. This can be key in important social dynamics such as leadership, which is often positively related to personality traits such as boldness. Individuals consistently differ in how social they are (their sociability), so if other axes of personality variation, such as boldness, can be suppressed during social interactions, this suppression should be stronger in more sociable individuals. We measured boldness (latency to leave a refuge when alone) and sociability (time spent with a conspecific) in three-spined sticklebacks (
Gasterosteus aculeatus
) and tested the boldness–leadership association in pairs of these fish. Both boldness and sociability were repeatable, but were not correlated. When splitting the data between the 50% most sociable and 50% less sociable fish, boldness was more strongly associated with leadership in less rather than more sociable individuals. This is consistent with more sociable fish conforming to their partner's behaviour due to their greater social tendency. One axis of personality variation (sociability) can thus modulate the relationship between others (boldness and leadership), with potential implications for selection on personality variation in social animals.
To adapt or go extinct? The fate of megafaunal palm fruits under past global change
Authors: Onstein Renske E. , Baker William J. , Couvreur Thomas L. P. , Faurby Søren , Herrera-Alsina Leonel , Svenning Jens-Christian , Kissling W. Daniel
Published: June 2018

Past global change may have forced animal-dispersed plants with megafaunal fruits to adapt or go extinct, but these processes have remained unexplored at broad spatio-temporal scales. Here, we combine phylogenetic, distributional and fruit size data for more than 2500 palm (Arecaceae) species in a time-slice diversification analysis to quantify how extinction and adaptation have changed over deep time. Our results indicate that extinction rates of palms with megafaunal fruits have increased in the New World since the onset of the Quaternary (2.6 million years ago). In contrast, Old World palms show a Quaternary increase in transition rates towards evolving small fruits from megafaunal fruits. We suggest that Quaternary climate oscillations and concurrent habitat fragmentation and defaunation of megafaunal frugivores in the New World have reduced seed dispersal distances and geographical ranges of palms with megafaunal fruits, resulting in their extinction. The increasing adaptation to smaller fruits in the Old World could reflect selection for seed dispersal by ocean-crossing frugivores (e.g. medium-sized birds and bats) to colonize Indo-Pacific islands against a background of Quaternary sea-level fluctuations. Our macro-evolutionary results suggest that megafaunal fruits are increasingly being lost from tropical ecosystems, either due to extinctions or by adapting to smaller fruit sizes.
O-GlcNAc modification of oncogenic transcription factor Sox2 promotes protein stability and regulates self-renewal in pancreatic cancer
Authors: Sharma Nikita S , Gupta Vineet K , Dauer Patricia , Kesh Kousik , Hadad Roey , Giri Bhuwan , Chandra Anjali , Dudeja Vikas , Slawson Chad , Banerjee Santanu , Vickers Selwyn M , Saluja Ashok , Banerjee Sulagna
Published: June 2018

Pancreatic cancer is among the 3rdleading cause of cancer related deaths in the United States along with a 5-year survival rate of 7%. The aggressive biology of the disease is responsible for such dismal outcome and is manifested by an increase in self-renewal capacity of the cancer cells, which leads to an increased rate of tumor-recurrence, contributing to poor prognosis. Transcription factor SOX2 maintains a critical balance between differentiation and “stemness” and is thus tightly regulated within a cell. In cancer, SOX2 is aberrantly “turned-on” leading to activation of self-renewal pathways in cancer. Regulation of Sox2 in cancer is poorly understood. In the current study, we show for the first time that in pancreatic cancer, Sox2 is modified by addition of O-GlcNAc moiety, catalyzed by OGT (O-GlcNAc Transferase) at S246. This activates Sox2 transcriptional activity by stabilizing the protein in the nucleus. A CRISPR-OGT knockout in pancreatic cancer cell line S2VP10 resulted in a delayed tumor initiation. We further showed that mutation of this site (S246A) prevents the modification of Sox2 and its downstream activity. Our study also demonstrated that targeting OGTin vivowith a small molecule inhibitor OSMI, results in decreased tumor burden, delayed tumor progression and a decreased expression of SOX2 in pancreatic cancer cells. Our study highlights for the first time that that the O-GlcNAc transferase dependent SOX2 glycosylation has a profound effect on the transcriptional activity of SOX2 and is instrumental in determining self-renewal in pancreatic cancer.

Significance

Our study highlights for the first time that that the O-GlcNAc transferase dependent SOX2 glycosylation determines self-renewal in pancreatic cancer which is responsible for tumor initiation.
Predict plant-derived xenomiRs from plant miRNA sequences using random forest and one-dimensional convolutional neural network models
Authors: Zhao Qi , Mao Qian , Zhao Zheng , Dou Tongyi , Wang Zhiguo , Cui Xiaoyu , Liu Yuanning , Fan Xiaoya
Published: June 2018

Background

An increasing number of studies reported that exogenous miRNAs (xenomiRs) can be detected in animal bodies, however, some others reported negative results. Some attributed this divergence to the selective absorption of plant-derived xenomiRs by animals.

Results

Here, we analyzed 166 plant-derived xenomiRs reported in our previous study and 942 non-xenomiRs extracted from miRNA expression profiles of four species of commonly consumed plants. Employing statistics analysis and cluster analysis, our study revealed the potential sequence specificity of plant-derived xenomiRs. Furthermore, a random forest model and a one-dimensional convolutional neural network model were trained using miRNA sequence features and raw miRNA sequences respectively and then employed to predict unlabeled plant miRNAs in miRBase. A total of 241 possible plant-derived xenomiRs were predicted by both models. Finally, the potential functions of these possible plant-derived xenomiRs along with our previously reported ones in human body were analyzed.

Conclusions

Our study, for the first time, presents the systematic plant-derived xenomiR sequences analysis and provides evidence for selective absorption of plant miRNA by human body, which could facilitate the future investigation about the mechanisms underlying the transference of plant-derived xenomiR.
Topographic Organization of Extraoccipital Visual Processing Areas in the Macaque
Authors: Patel Gaurav H. , Snyder Lawrence H. , Corbetta Maurizio
Published: June 2018

The macaque visual system has long been used as a model for investigating the processing of incoming visual stimuli results from the coordinated work of a distributed network of areas interacting at many different levels (Felleman and Van Essen, 1991). While much is known about the organization and layout of the occipital visual areas, there are still substantial gaps in our understanding of layout and organization of the higher-level areas. The goal of this study is to describe the whole brain functional anatomy using BOLD-fMRI in macaques performing a series of demanding visuospatial attention tasks. We wish to study the spatial specificity of visual responses in terms of contralateral preference, i.e. stronger responses to contralateral visual stimuli, as well as retinotopic organization both in terms of polar angle and eccentricity. We found that most visuospatial processing areas only respond to contralaterally presented stimuli; ipsilaterally presented stimuli evoked little or no activity in these areas. Additionally, we found that LIP, MT, and possibly PITd contained polar-angle maps of the contralateral hemifield. These same areas, plus FEF and area 46, appear to have separate representations of the fovea and periphery. When compared to previous human fMRI studies, these results indicate that there may be significant differences between macaque visual processing areas and their putative human homologues.
Live calcium imaging ofAedes aegyptineuronal tissues reveals differential importance of chemosensory systems for life-history-specific foraging strategies
Authors: Bui Michelle , Shyong Jennifer , Lutz Eleanor K. , Yang Ting , Li Ming , Truong Kenneth , Arvidson Ryan , Buchman Anna , Riffell Jeffrey A. , Akbari Omar S.
Published: June 2018

Aedes aegyptihave a wide variety of sensory pathways that have supported success as a species as well as a highly competent vector of numerous debilitating infectious pathogens. Investigations into mosquito sensory systems and their effects on behavior are valuable resources for the advancement of mosquito control strategies. Numerous studies have elucidated key aspects of mosquito sensory systems, however there remains critical gaps within the field. In particular, compared to that of the adult form, there has been a lack of studies directed towards the immature life stages. Additionally, although numerous studies have pinpointed specific sensory receptors as well as relevant response behaviors, there has been a lack of studies able to monitor both concurrently. To begin filling aforementioned gaps, here we engineeredAe. aegyptito ubiquitously express a genetically encoded calcium indicator, GCaMP6s. Using this strain, combined with advanced confocal microscopy, we were able to simultaneously measure live stimulus-evoked calcium responses in both neuronal and muscle cells with a wide spatial range and resolution. Moreover, by couplingin vivocalcium imaging with behavioral assays we were able to gain functional insights into how stimulus-evoked neural and muscle activities are represented, modulated, and transformed in mosquito larvae enabling us to elucidate mosquito sensorimotor properties important for life-history-specific foraging strategies.

Significance Statement

Understanding mosquito sensory systems and resulting behavior has been a major factor in the advancement of mosquito control innovations.Aedes aegyptilarvae offer an effective life stage for further elucidating information on mosquito sensory systems. Due to their relatively simplified nervous system, mosquito larvae are ideal for studying neural signal transduction, coding, and behavior. Moreover, a better understanding of the larval sensory system may enable the development of novel control methodologies able to target mosquitoes before they reach a vector-competent stage. Here we engineerAe. aegyptito ubiquitously express a genetically encoded calcium indicator, GCaMP6s and use this tool to observe links between sensorimotor responses and behavior by exploiting live calcium imaging as well as live tracking based behavioral assays.
Sexual Conflict through Mother’s Curse and Father’s Curse
Authors: Arvid Ågren J. , Munasinghe Manisha , Clark Andrew G.
Published: June 2018

In contrast with autosomes, lineages of sex chromosomes reside for different amounts of time in males and females, and this transmission asymmetry makes them hotspots for sexual conflict. Similarly, the maternal inheritance of the mitochondrial genome (mtDNA) means that mutations that are beneficial in females can spread in a population even if they are deleterious in males, a form of sexual conflict known as Mother’s Curse. While both Mother’s Curse and sex chromosome induced sexual conflict have been well studied on their own, the interaction between mitochondrial genes and genes on sex chromosomes is poorly understood. Here, we use analytical models and computer simulations to perform a comprehensive examination of how transmission asymmetries of nuclear, mitochondrial, and sex chromosome-linked genes may both cause and resolve sexual conflicts. For example, the accumulation of male-biased Mother’s Curse mtDNA mutations will lead to selection in males for compensatory nuclear modifier loci that alleviate the effect. We show how the Y chromosome, being strictly paternally transmitted provides a particularly safe harbor for such modifiers. This analytical framework also allows us to discover a novel kind of sexual conflict, by which Y chromosome-autosome epistasis may result in the spread of male beneficial but female deleterious mutations in a population. We christen this phenomenon Father’s Curse. Extending this analytical framework to ZW sex chromosome systems, where males are the heterogametic sex, we also show how W-autosome epistasis can lead to a novel kind of nuclear Mother’s Curse. Overall, this study provides a comprehensive framework to understand how genetic transmission asymmetries may both cause and resolve sexual conflicts.
CRISPR-SURF: Discovering regulatory elements by deconvolution of CRISPR tiling screen data
Authors: Hsu Jonathan Y. , Fulco Charles P. , Cole Mitchel A. , Canver Matthew C. , Pellin Danilo , Sher Falak , Farouni Rick , Clement Kendell , Guo James A. , Biasco Luca , Orkin Stuart H. , Engreitz Jesse M. , Lander Eric S. , Keith Joung J. , Bauer Daniel E. , Pinello Luca
Published: June 2018

Tiling screens using CRISPR-Cas technologies provide a powerful approach to map regulatory elements to phenotypes of interest, but computational methods that effectively model these experimental approaches for different CRISPR technologies are not readily available. Here we present CRISPR-SURF, a deconvolution framework to identify functional regulatory regions in the genome from data generated by CRISPR-Cas nuclease, CRISPR interference (CRISPRi), or CRISPR activation (CRISPRa) tiling screens. We validated CRISPR-SURF on previously published and new data, identifying both experimentally validated and new potential regulatory elements. With CRISPR tiling screens now being increasingly used to elucidate the regulatory architecture of the non-coding genome, CRISPRSURF provides a generalizable and accessible solution for the discovery of regulatory elements.
Breaking the “unbreakable” ZIKA virus envelope
Authors: Pindi Chinmai , Chirasani Venkat R , Homaidur Rahman Mohd. , Ahsan Mohd. , Revanasiddappa Prasanna D , Senapati Sanjib
Published: June 2018

The rapid spread of zika virus (ZIKV) and its association with microcephaly and Guillain-Barre syndrome have raised major concerns worldwide. Studies have shown that ZIKV can survive in harsh conditions, e.g. high fever; in sharp contrast to the dengue virus (DENV) of same Flaviviridae family. In spite of recent cryo-EM structures that showed similar architecture of the ZIKV and DENV envelopes, little is known of what makes ZIKV envelope so robust and unique. Here, we present a detailed analysis of the constituent raft-raft and protein-protein interactions on ZIKV and DENV envelopes to undermine their differential stability at near-atomic to atomic level using coarse-grained (CG) and all-atom (AA) molecular dynamics simulations. Our results from CG simulations show that, at high temperatures, ZIKV envelope retains its structural integrity, while DENV2 disintegrate through the formation of holes at 5- and 3-fold vertices. Protein structural network from AA simulations shows a stronger inter-raft communications in ZIKV through multiple electrostatic and H-bond interactions. Particularly, the intricate network of interlocking DE-loop and FG-loop among five DIII domains in ZIKA vertices was exceedingly robust that makes this envelope stable, even at high temperatures. Our results are validated by alanine mutations to the CD-loop residues Gln350 and Thr351 that showed no effect on ZIKA stability, in close accordance with a recent mutagenesis study. These detailed information, which were difficult to extract experimentally, broadened our understanding of the flaviviruses and can accelerate the structure-based drug designing processes aiming ZIKA and DENV therapeutics.

IMPORTANCE

The rapid spread of zika virus (ZIKV) and its association with severe birth defects have raised worldwide concern. Recent studies have shown that ZIKV can survive in harsh conditions, e.g. high fever, unlike dengue (DENV) and other flaviviruses. Here, we unravel the molecular basis of ZIKV unprecedented stability over DENV at high temperatures, mimicking fever. Our study, based on coarse-grained and all-atom molecular dynamics simulations, could not only explore the mechanism of DENV envelope breaking at high temperatures, but also captured atomic-level contacts and interactions at raft-raft and protein-protein interfaces that keep ZIKV envelope intact in similar conditions. The obtained results are validated by in-silico and reported in-vitro mutagenesis studies by showing the presence of specific H-bonding and electrostatic interactions among ZIKV E protein residues. At the end, our study was successful to define potential ZIKV epitopes and provide residue-level insights for designing specific ZIKV antibodies and small molecule inhibitors.