bluuebunny/crossref_metadata_2025 huggingface dataset:
Design principles of hair-like structures as biological machines
Authors: Seale Madeleine , Cummins Cathal , Viola Ignazio Maria , Mastropaolo Enrico , Nakayama Naomi
Published: May 2018

Hair-like structures are prevalent throughout biology and frequently act to sense or alter interactions with an organism's environment. The overall shape of a hair is simple: a long, filamentous object that protrudes from the surface of an organism. This basic design, however, can confer a wide range of functions, owing largely to the flexibility and large surface area that it usually possesses. From this simple structural basis, small changes in geometry, such as diameter, curvature and inter-hair spacing, can have considerable effects on mechanical properties, allowing functions such as mechanosensing, attachment, movement and protection. Here, we explore how passive features of hair-like structures, both individually and within arrays, enable diverse functions across biology. Understanding the relationships between form and function can provide biologists with an appreciation for the constraints and possibilities on hair-like structures. Additionally, such structures have already been used in biomimetic engineering with applications in sensing, water capture and adhesion. By examining hairs as a functional mechanical unit, geometry and arrangement can be rationally designed to generate new engineering devices and ideas.
Atom economy and green elimination of nitric oxide using ZrN powders
Authors: Chen Ning , Wang Jigang , Yin Wenyan , Li Zhen , Li Peishen , Guo Ming , Wang Qiang , Li Chunlei , Wang Changzheng , Chen Shaowei
Published: May 2018

Nitric oxide (NO) may cause serious environmental problems, such as acid rain, haze weather, global warming and even death. Herein, a new low-cost, highly efficient and green method for the elimination of NO using zirconium nitride (ZrN) is reported for the first time, which does not produce any waste or any by-product. Relevant experimental parameters, such as reaction temperature and gas concentration, were investigated to explore the reaction mechanism. Interestingly, NO can be easily decomposed into nitrogen (N
2
) by ZrN powders at 600°C with ZrN simultaneously transformed into zirconium dioxide (ZrO
2
) gradually. The time for the complete conversion of NO into N
2
was approximately 14 h over 0.5 g of ZrN at a NO concentration of 500 ppm. This green elimination process of NO demonstrated good atom economy and practical significance in mitigating environmental problems.
Archaeopedological analysis of colluvial deposits in favourable and unfavourable areas: reconstruction of land use dynamics in SW Germany
Authors: Henkner Jessica , Ahlrichs Jan , Downey Sean , Fuchs Markus , James Bruce , Junge Andrea , Knopf Thomas , Scholten Thomas , Kühn Peter
Published: May 2018

Colluvial deposits, as the correlate sediments of human-induced soil erosion, depict an excellent archive of land use and landscape history as indicators of human–environment interactions. This study establishes a chronostratigraphy of colluvial deposits and reconstructs past land use dynamics in the Swabian Jura, the Baar and the Black Forest in SW Germany. In the agriculturally favourable Baar area multiple main phases of colluvial deposition, and thus intensified land use, can be identified from the Neolithic to the Modern times. In the unfavourable Swabian Jura increased colluvial deposition began later compared to the more favourable areas in the Baar. The same holds true for the unfavourable areas of the Black Forest, but intensified land use can only be reconstructed for the Middle Ages and Early Modern times instead of for the Bronze and Iron Age as in the Swabian Jura. Land use intensity and settlement dynamics represented by thick, multilayered colluvial deposits increase in the Baar and the Black Forest during the Middle Ages. In between those phases of geomorphodynamic activity and colluviation, stable phases occur, interpreted as phases with sustainable land use or without human presence.
A novel environmental restoration method for an abandoned limestone quarry with a deep open pit and steep palisades: a case study
Authors: Wang Hanxun , Zhang Bin , Bai Xueliang , Shi Lei
Published: May 2018

In general, exploitation of rock materials, such as limestone or granite exploitation, can cause serious damage to the environment near a mine area. With economic development and the ever-increasing demand for ore resources, mining activities have induced very serious environmental issues in China. Therefore, environmental restoration work around mines in China is urgently required. This study explores the Chuankou open-pit limestone quarry in Tongchuan City, Shaanxi Province, Northwest China, as the engineering case. The environmental issues caused by over 40 years of limestone exploitation, including land degradation, land occupation, dust pollution and potential geological disasters, were investigated. Combining the characteristics of this quarry with a summary of previous studies on environmental restoration work, this paper proposes a novel and systematic method that was comprehensively carried out through engineering and revegetation measures. The engineering measure, that is, the construction of an artificial slope by using local abandoned construction materials, solved the environmental problems in this quarry and provided site conditions favourable for revegetation. The revegetation measure restored the local ecosystem. This method provides both a new idea for the sustainable development of a mining area and a useful reference for analogous engineering cases.
How do microalgae perceive light in a high-rate pond? Towards more realistic Lagrangian experiments
Authors: Demory David , Combe Charlotte , Hartmann Philipp , Talec Amélie , Pruvost Eric , Hamouda Raouf , Souillé Fabien , Lamare Pierre-Olivier , Bristeau Marie-Odile , Sainte-Marie Jacques , Rabouille Sophie , Mairet Francis , Sciandra Antoine , Bernard Olivier
Published: May 2018

Hydrodynamics in a high-rate production reactor for microalgae cultivation affects the light history perceived by cells. The interplay between cell movement and medium turbidity leads to a complex light pattern, whose forcing effects on photosynthesis and photoacclimation dynamics are non-trivial. Hydrodynamics of high density algal ponds mixed by a paddle wheel has been studied recently, although the focus has never been on describing its impact on photosynthetic growth efficiency. In this multidisciplinary downscaling study, we first reconstructed single cell trajectories in an open raceway using an original hydrodynamical model offering a powerful discretization of the Navier–Stokes equations tailored to systems with free surfaces. The trajectory of a particular cell was selected and the associated high-frequency light pattern was computed. This light pattern was then experimentally reproduced in an Arduino-driven computer controlled cultivation system with a low density
Dunaliella salina
culture. The effect on growth and pigment content was recorded for various frequencies of the light pattern, by setting different paddle wheel velocities. Results show that the frequency of this realistic signal plays a decisive role in the dynamics of photosynthesis, thus revealing an unexpected photosynthetic response compared to that recorded under the on/off signals usually used in the literature. Indeed, the light received by a single cell contains signals from low to high frequencies that nonlinearly interact with the photosynthesis process and differentially stimulate the various time scales associated with photoacclimation and energy dissipation. This study highlights the need for experiments with more realistic light stimuli to better understand microalgal growth at high cell densities. An experimental protocol is also proposed, with simple, yet more realistic, step functions for light fluctuations.
Quantum correlations are weaved by the spinors of the Euclidean primitives
Authors: Christian Joy
Published: May 2018

The exceptional Lie group
E
8
plays a prominent role in both mathematics and theoretical physics. It is the largest symmetry group associated with the most general possible normed division algebra, namely, that of the non-associative real octonions, which—thanks to their non-associativity—form the only possible closed set of spinors (or rotors) that can parallelize the 7-sphere. By contrast, here we show how a similar 7-sphere also arises naturally from the algebraic interplay of the graded Euclidean primitives, such as points, lines, planes and volumes, which characterize the three-dimensional conformal geometry of the ambient physical space, set within its eight-dimensional Clifford-algebraic representation. Remarkably, the resulting algebra remains associative, and allows us to understand the origins and strengths of all quantum correlations locally, in terms of the geometry of the compactified physical space, namely, that of a quaternionic 3-sphere,
S
3
, with
S
7
being its algebraic representation space. Every quantum correlation can thus be understood as a correlation among a set of points of this
S
7
, computed using manifestly local spinors within
S
3
, thereby extending the stringent bounds of ±2 set by Bell inequalities to the bounds of

±
2

2

on the strengths of all possible strong correlations, in the same quantitatively precise manner as that predicted within quantum mechanics. The resulting geometrical framework thus overcomes Bell’s theorem by producing a strictly deterministic and realistic framework that allows a locally causal understanding of all quantum correlations, without requiring either remote contextuality or backward causation. We demonstrate this by first proving a general theorem concerning the geometrical origins of the correlations predicted by arbitrarily entangled quantum states, and then reproducing the correlations predicted by the EPR-Bohm and the GHZ states. The
raison d’être
of strong correlations turns out to be the Möbius-like twists in the Hopf bundles of
S
3
and
S
7
.
Periodic behaviour in ground-level environmental radioactivity: fingerprints of solar activity?
Authors: Babić Dinko , Senčar Jasminka
Published: May 2018

Long-term data on ground-level environmental radioactivity are analysed, these referring to daily records of the total β activity in air and absorbed dose rate between 1976 and 2016 in Zagreb, Croatia. A Fourier analysis of these two datasets reveals a periodic behaviour with numerous periods ranging from approximately four months to roughly 21 years. Ninety per cent of the periods agree remarkably well with known periodicities in solar activity throughout solar cycles 21–24, which suggests that the observed modulations were most probably caused by variations in the cosmogenic radionuclide production in the upper atmosphere. Hence, one can extract the fine structure of solar activity from environmental radioactivity monitoring data, which implies that it could be possible to supplement the existing information on the exposure of Earth to cosmic rays by analysing results from radioactivity monitoring stations all over the world. These datasets cover Earth densely due to the existence of a global radioecological network and are complementary to those resulting from dedicated cosmic ray detection experiments. Because of that, such analyses might possibly lead to new findings.
Avoiding/inducing dynamic buckling in a thermomechanically coupled plate: a local and global analysis of slow/fast response
Authors: Settimi Valeria , Rega Giuseppe , Saetta Eduardo
Published: May 2018

The nonlinear response of a reduced model of an orthotropic single-layered plate with thermomechanical coupling is investigated in the presence of thermal excitations, in addition to mechanical ones. Different issues are addressed via accurate and extended local and global analyses. (i) Assessing the possible occurrence, disappearance or modification of mechanical buckling as a result of thermal aspects; (ii) exploiting global dynamics to unveil the effects of coupling; (iii) highlighting the crucial role played by the slow thermal transient evolution in modifying the fast steady mechanical response; (iv) framing the influence of coupling and underlining the need to use a thermomechanical model to grasp the actual plate dynamics; and (v) getting hints of technical interest as to the outcome robustness with respect to variations in the external/internal thermal parameters.
Poor geographical match between the distributions of host diversity and parasite discovery effort
Authors: Jorge Fátima , Poulin Robert
Published: May 2018

Mapping global parasite diversity is crucial to identify geographical hotspots of emerging disease, and guide public health and conservation efforts. In principle, assuming a bottom-up coupling between the diversity of resources and consumers, the geographical distribution of parasite diversity should match that of host diversity. We test the expected spatial congruence between host and parasite diversity for helminth parasites of vertebrate hosts, across grid cells of a global map. Using high-resolution databases on host species distributions and newly compiled data on the geographical distribution of parasite species discovery, we found positive covariation between host species richness and the number of parasite species discovered, for all vertebrate groups, regardless of the analytical method used, spatial autocorrelation, and spatial resolution. However, all associations were very weak, indicating a poor match between host species richness and parasite species discovery. The research deficit in parasite discovery peaks in areas corresponding to hotspots of host diversity, where disproportionately fewer new parasites are discovered than expected based on local host richness. This spatially biased research effort prevents a full inventory of parasite biodiversity, and impedes predictions of where new diseases may emerge. The host taxon-specific maps we produced, however, can guide future efforts to uncover parasite biodiversity.
Melanin-based coloration and host–parasite interactions under global change
Authors: Côte J. , Boniface A. , Blanchet S. , Hendry A. P. , Gasparini J. , Jacquin L.
Published: May 2018

The role of parasites in shaping melanin-based colour polymorphism, and the consequences of colour polymorphism for disease resistance, remain debated. Here we review recent evidence of the links between melanin-based coloration and the behavioural and immunological defences of vertebrates against their parasites. First we propose that (1) differences between colour morphs can result in variable exposure to parasites, either directly (certain colours might be more or less attractive to parasites) or indirectly (variations in behaviour and encounter probability). Once infected, we propose that (2) immune variation between differently coloured individuals might result in different abilities to cope with parasite infection. We then discuss (3) how these different abilities could translate into variable sexual and natural selection in environments varying in parasite pressure. Finally, we address (4) the potential role of parasites in the maintenance of melanin-based colour polymorphism, especially in the context of global change and multiple stressors in human-altered environments. Because global change will probably affect both coloration and the spread of parasitic diseases in the decades to come, future studies should take into account melanin-based coloration to better predict the evolutionary responses of animals to changing disease risk in human-altered environments.
Full allogeneic fusion of embryos in a holothuroid echinoderm
Authors: Gianasi Bruno L. , Hamel Jean-François , Mercier Annie
Published: May 2018

Whole-body chimaeras (organisms composed of genetically distinct cells) have been directly observed in modular/colonial organisms (e.g. corals, sponges, ascidians); whereas in unitary deuterostosmes (including mammals) they have only been detected indirectly through molecular analysis. Here, we document for the first time the step-by-step development of whole-body chimaeras in the holothuroid
Cucumaria frondosa
, a unitary deuterostome belonging to the phylum Echinodermata. To the best of our knowledge, this is the most derived unitary metazoan in which direct investigation of zygote fusibility has been undertaken. Fusion occurred among hatched blastulae, never during earlier (unhatched) or later (larval) stages. The fully fused chimaeric propagules were two to five times larger than non-chimaeric embryos. Fusion was positively correlated with propagule density and facilitated by the natural tendency of early embryos to agglomerate. The discovery of natural chimaerism in a unitary deuterostome that possesses large externally fertilized eggs provides a framework to explore key aspects of evolutionary biology, histocompatibility and cell transplantation in biomedical research.
Heritable variation in prey defence provides refuge for subdominant predators
Authors: Lenhart Paul A. , Jackson Kelly A. , White Jennifer A.
Published: May 2018

Generalist predators with broadly overlapping niches commonly coexist on seemingly identical sets of prey. Here, we provide empirical demonstration that predators can differentially exploit fine-grained niches generated by variable, heritable and selective defences within a single prey species. Some, but not all, clones of the aphid
Aphis craccivora
are toxic towards the dominant invasive predatory ladybeetle,
Harmonia axyridis
. However, other less competitive ladybeetle species are not affected by the aphid's toxic trait. In laboratory and open field experiments, we show: (i) that subdominant ladybeetle species were able to exploit the toxic aphids, benefitting from the suppression of the dominant predator; and (ii) that this narrow-spectrum toxicity can function as an anti-predator defence for the aphid, but depends on enemy community context. Our results demonstrate that niche differentiation among generalist predators may hinge upon previously underappreciated heritable variation in prey defence, which, in turn, may promote diversity and stability of enemy communities invaded by a dominant predator.
Quantifying uncertainty due to fission–fusion dynamics as a component of social complexity
Authors: Ramos-Fernandez Gabriel , King Andrew J. , Beehner Jacinta C. , Bergman Thore J. , Crofoot Margaret C. , Di Fiore Anthony , Lehmann Julia , Schaffner Colleen M. , Snyder-Mackler Noah , Zuberbühler Klaus , Aureli Filippo , Boyer Denis
Published: May 2018

Groups of animals (including humans) may show flexible grouping patterns, in which temporary aggregations or subgroups come together and split, changing composition over short temporal scales, (i.e. fission and fusion). A high degree of fission–fusion dynamics may constrain the regulation of social relationships, introducing uncertainty in interactions between group members. Here we use Shannon's entropy to quantify the predictability of subgroup composition for three species known to differ in the way their subgroups come together and split over time: spider monkeys (Ateles geoffroyi), chimpanzees (Pan troglodytes) and geladas (Theropithecus gelada). We formulate a random expectation of entropy that considers subgroup size variation and sample size, against which the observed entropy in subgroup composition can be compared. Using the theory of set partitioning, we also develop a method to estimate the number of subgroups that the group is likely to be divided into, based on the composition and size of single focal subgroups. Our results indicate that Shannon's entropy and the estimated number of subgroups present at a given time provide quantitative metrics of uncertainty in the social environment (within which social relationships must be regulated) for groups with different degrees of fission–fusion dynamics. These metrics also represent an indirect quantification of the cognitive challenges posed by socially dynamic environments. Overall, our novel methodological approach provides new insight for understanding the evolution of social complexity and the mechanisms to cope with the uncertainty that results from fission–fusion dynamics.
Flexible memory controls sperm competition responses in maleDrosophila melanogaster
Authors: Rouse J. , Watkinson K. , Bretman A.
Published: May 2018

Males of many species use social cues to predict sperm competition (SC) and tailor their reproductive strategies, such as ejaculate or behavioural investment, accordingly. While these plastic strategies are widespread, the underlying mechanisms remain largely unknown. Plastic behaviour requires individuals to learn and memorize cues associated with environmental change before using this experience to modify behaviour.Drosophila melanogasterrespond to an increase in SC threat by extending mating duration after exposure to a rival male. This behaviour shows lag times between environmental change and behavioural response suggestive of acquisition and loss of memory. Considering olfaction is important for a male's ability to assess the SC environment, we hypothesized that an olfactory learning and memory pathway may play a key role in controlling this plastic behaviour. We assessed the role of genes and brain structures known to be involved in learning and memory. We show that SC responses depend on anaesthesia-sensitive memory, specifically the genesrutandamn. We also show that theγlobes of the mushroom bodies are integral to the control of plastic mating behaviour. These results reveal the genetic and neural properties required for reacting to changes in the SC environment.
Sun-basking fish benefit from body temperatures that are higher than ambient water
Authors: Nordahl Oscar , Tibblin Petter , Koch-Schmidt Per , Berggren Hanna , Larsson Per , Forsman Anders
Published: May 2018

In terrestrial environments, cold-blooded animals can attain higher body temperatures by sun basking, and thereby potentially benefit from broader niches, improved performance and higher fitness. The higher heat capacity and thermal conductivity of water compared with air have been universally assumed to render heat gain from sun basking impossible for aquatic ectotherms, such that their opportunities to behaviourally regulate body temperature are largely limited to choosing warmer or colder habitats. Here we challenge this paradigm. Using physical models we first show that submerged objects exposed to natural sunlight attain temperatures in excess of ambient water. We next demonstrate that free-ranging carp (
Cyprinus carpio
) can increase their body temperature during aquatic sun basking close to the surface. The temperature excess gained by basking was larger in dark than in pale individuals, increased with behavioural boldness, and was associated with faster growth. Overall, our results establish aquatic sun basking as a novel ecologically significant mechanism for thermoregulation in fish. The discovery of this previously overlooked process has practical implications for aquaculture, offers alternative explanations for behavioural and phenotypic adaptations, will spur future research in fish ecology, and calls for modifications of models concerning climate change impacts on biodiversity in marine and freshwater environments.
Springtail community structure is influenced by functional traits but not biogeographic origin of leaf litter in soils of novel forest ecosystems
Authors: Raymond-Léonard Laura J. , Gravel Dominique , Reich Peter B. , Handa I. Tanya
Published: May 2018

With ongoing global change, shifts in the ranges of non-native species and resulting novel communities can modify biotic interactions and ecosystem processes. We hypothesized that traits and not biogeographic origin of novel plant communities will determine community structure of organisms that depend on plants for habitat or as a food resource. We tested the functional redundancy of novel tree communities by verifying if six pairs of congeneric European and North American tree species bearing similar leaf litter traits resulted in similar ecological filters influencing the assembly of springtail (Collembola) communities at two sites. Litter biogeographic origin (native versus non-native) did not influence springtail community structure, but litter genus, which generally reflected trait differences, did. Our empirical evidence suggests that a functional trait approach may be indeed as relevant as, and complementary to, studying biogeographic origin to understand the ecological consequences of non-native tree species in soils of novel forest ecosystems.
Cumulative culture in the laboratory: methodological and theoretical challenges
Authors: Miton Helena , Charbonneau Mathieu
Published: May 2018

In the last decade, cultural transmission experiments (transmission chains, replacement, closed groups and seeded groups) have become important experimental tools in investigating cultural evolution. However, these methods face important challenges, especially regarding the operationalization of theoretical claims. In this review, we focus on the study of cumulative cultural evolution, the process by which traditions are gradually modified and, for technological traditions in particular, improved upon over time. We identify several mismatches between theoretical definitions of cumulative culture and their implementation in cultural transmission experiments. We argue that observed performance increase can be the result of participants learning faster in a group context rather than effectively leading to a cumulative effect. We also show that in laboratory experiments, participants are asked to complete quite simple tasks, which can undermine the evidential value of the diagnostic criterion traditionally used for cumulative culture (i.e. that cumulative culture is a process that produces solutions that no single individual could have invented on their own). We show that the use of unidimensional metrics of cumulativeness drastically curtail the variation that may be observed, which raises specific issues in the interpretation of the experimental evidence. We suggest several solutions to these mismatches (learning times, task complexity and variation) and develop the use of design spaces in experimentally investigating old and new questions about cumulative culture.
The coevolution of cooperation and cognition in humans
Authors: dos Santos Miguel , West Stuart A.
Published: May 2018

Cooperative behaviours in archaic hunter–gatherers could have been maintained partly due to the gains from cooperation being shared with kin. However, the question arises as to how cooperation was maintained after early humans transitioned to larger groups of unrelated individuals. We hypothesize that after cooperation had evolved via benefits to kin, the consecutive evolution of cognition increased the returns from cooperating, to the point where benefits to self were sufficient for cooperation to remain stable when group size increased and relatedness decreased. We investigate the theoretical plausibility of this hypothesis, with both analytical modelling and simulations. We examine situations where cognition either (i) increases the benefits of cooperation, (ii) leads to synergistic benefits between cognitively enhanced cooperators, (iii) allows the exploitation of less intelligent partners, and (iv) the combination of these effects. We find that cooperation and cognition can coevolve—cooperation initially evolves, favouring enhanced cognition, which favours enhanced cooperation, and stabilizes cooperation against a drop in relatedness. These results suggest that enhanced cognition could have transformed the nature of cooperative dilemmas faced by early humans, thereby explaining the maintenance of cooperation between unrelated partners.
Dissociating cognitive and motoric precursors of human self-initiated action
Authors: Khalighinejad N. , Brann E. , Dorgham A , Haggard P.
Published: May 2018

Across-trial variability of EEG decreases more markedly prior to self-initiated than prior to externally-triggered actions, providing a novel neural precursor for volitional action. However, it remains unclear whether this neural convergence is an early, deliberative stage, or a late, execution-related stage in the chain of cognitive processes that transform intentions to actions. We report two experiments addressing these questions. Self-initiated actions were operationalized as endogenous ‘skip’ responses while waiting for target stimuli in a perceptual decision task. These self-initiated ‘skips’ were compared to blocks where participants were instructed to skip. EEG variability decreased more markedly prior to self-initiated compared to externally-triggered ‘skip’ actions, replicating previous findings.

Importantly, this EEG convergence was stronger at fronto-midline electrodes than at either the electrode contralateral or ipsilateral to the hand assigned to the ‘skip’ action in each block (Experiment 1). Further, convergence was stronger when availability of skip responses was ‘rationed’, encouraging deliberate planning before skipping (Experiment 2). This suggests that the initiation of voluntary actions involves a bilaterally-distributed, effector-independent process related to deliberation. A consistent process of volition is detectable during early, deliberative planning, and not only during late, execution-related time windows.
The Human RNA-Binding Proteome and Its Dynamics During Arsenite-Induced Translational Arrest
Authors: Trendel Jakob , Schwarzl Thomas , Prakash Ananth , Bateman Alex , Hentze Matthias W. , Krijgsveld Jeroen
Published: May 2018

Proteins and RNA functionally and physically intersect in multiple biological processes, however, currently no universal method is available to purify protein-RNA complexes. Here we introduce XRNAX, a method for the generic purification of protein-crosslinked RNA, and demonstrate its versatility to study the composition and dynamics of protein-RNA interactions by various transcriptomic and proteomic approaches. We show that XRNAX captures all RNA biotypes, and use this to characterize the sub-proteomes that interact with coding and non-coding RNAs (ncRNAs), and to identify hundreds of protein-RNA interfaces. Exploiting the quantitative nature of XRNAX, we observe drastic remodeling of the RNA-bound proteome during arsenite-induced stress, distinct from autophagy-induced changes in the total proteome. In addition, we combine XRNAX with CLIP-seq to validate the interaction of ncRNA with Lamin B and EXOSC2. Thus, XRNAX is a resourceful approach to study structural and compositional aspects of protein-RNA interactions to address fundamental questions in RNA-biology.
Face Viewing Behavior Predicts Multisensory Gain During Speech Perception
Authors: Rennig Johannes , Wegner-Clemens Kira , Beauchamp Michael S
Published: May 2018

During face viewing, some individuals prefer to fixate the mouth while others fixate the eyes. Individuals who have a history of mouth fixation might have stronger associations between visual and auditory speech, resulting in improved comprehension. First, we measured eye movements during face-viewing and observed high interindividual variability in mouth fixation time. Next, we measured eye movements and comprehension during perception of noisy auditory speech with or without visual speech. When visual speech was present, participants primarily fixated the mouth, but derived substantial benefit compared to noisy auditory speech with high interindividual variability. The benefit of visual speech was predicted by the eye movements made during the initial face-viewing task, but not by eye movements during the noisy speech task. These findings suggest a link between eye movements during face viewing and audiovisual speech perception and suggest that individual histories of visual exposure shape abilities across cognitive domains.
Neural evidence for age-related differences in representational quality and strategic retrieval processes
Authors: Trelle Alexandra N. , Henson Richard N. , Simons Jon S.
Published: May 2018

Mounting behavioral evidence suggests that declines in both representational quality and controlled retrieval processes contribute to episodic memory decline with age. The present study sought neural evidence for age-related change in these factors by measuring neural differentiation during encoding of paired associates, and changes in regional BOLD activity and functional connectivity during retrieval conditions that placed low (intact pairs) and high (recombined pairs) demands on controlled retrieval processes. Pattern similarity analysis revealed age-related declines in the differentiation of stimulus representations at encoding, manifesting as both reduced pattern similarity between closely related events, and increased pattern similarity between distinct events. During retrieval, both groups exhibited increased recruitment of areas within the core recollection network, including the hippocampus and angular gyrus, when endorsing studied pairs, whereas younger adults exhibited increased recruitment of, and hippocampal connectivity with, lateral prefrontal regions during correct rejections of recombined pairs. These results provide evidence for age-related changes in representational quality and in the neural mechanisms supporting memory retrieval under conditions of high, but not low, control demand.
Weber’s law is the result of exact temporal accumulation of evidence
Authors: Pardo-Vazquez Jose L. , Castiñeiras Juan , Valente Mafalda , Costa Tiago , Renart Alfonso
Published: May 2018

Weber’s law states that the discriminability between two stimulus intensities depends only on their ratio. Despite its status as the cornerstone of psychophysics, the mecha-nisms underlying Weber’s law are still debated, as no principled way exists to choose between its many proposed alternative explanations. We studied this problem training rats to discriminate the lateralization of sounds of different overall level. We found that the rats’ discrimination accuracy in this task is level-invariant, consistent with Weber’s law. Surprisingly, the shape of the reaction time distributions is also level-invariant, implying that the only behavioral effect of changes in the overall level of the sounds is a uniform scaling of time. Furthermore, we demonstrate that Weber’s law breaks down if the stimulus duration is capped at values shorter than the typical reaction time. Together, these facts suggest that Weber’s law is associated to a process of bounded evidence accumulation. Consistent with this hypothesis, we show that, among a broad class of sequential sampling models, the only robust mechanism consistent with reaction time scale-invariance is based on perfect accumulation of evidence up to a constant bound, Poisson-like statistics, and a power-law encoding of stimulus intensity. Fits of a minimal diffusion model with these characteristics describe the rats performance and reaction time distributions with virtually no error. Various manipulations of motivation were unable to alter the rats’ psychometric function, demonstrating the stability of the just-noticeable-difference and suggesting that, at least under some conditions, the bound for evidence accumulation can set a hard limit on discrimination accuracy. Our results establish the mechanistic foundation of the process of intensity discrimination and clarify the factors that limit the precision of sensory systems.
Deconvoluting Virome-Wide Antiviral Antibody Profiling Data
Authors: Monaco Daniel R. , Kottapalli Sanjay V. , Yuan Tiezheng , Breitwieser Florian P. , Anderson Danielle E. , Wijaya Limin , Tan Kevin , Chia Wan Ni , Kammers Kai , Caturegli Mario , Waugh Kathleen , Rewers Marian , Wang Lin-Fa , Benjamin Larman H.
Published: May 2018

The ability to comprehensively characterize exposures and immune responses to viral infections will be critical to better understanding human health and disease. We previously described the VirScan system, a phage-display based technology for profiling antibody binding to a comprehensive library of peptides designed to represent the human virome. The previous VirScan analytical approach did not fully account for disproportionate representation of viruses in the library or for antibody cross-reactivity among sequences shared by related viruses. Here we present the ‘AntiViral Antibody Response Deconvolution Algorithm’ (‘AVARDA’), a multi-module software package for analyzing VirScan datasets. AVARDA provides a probabilistic assessment of infection at species-level resolution by considering alignment of all library peptides to each other and to all human viruses. We employed AVARDA to analyze VirScan data from a cohort of encephalitis patients with either known viral infections or undiagnosed etiologies. By comparing acute and convalescent sera, AVARDA successfully confirmed or detected antibody responses to human herpesviruses 1, 3, 4, 5, and 6, thereby improving the rate of diagnosing viral encephalitis in this cohort by 62.5%. We further assessed AVARDA’s utility in the setting of an epidemiological study, demonstrating its ability to determine infections acquired in a child followed prospectively from infancy. We consider ways in which AVARDA’s conceptual framework may be further developed in the future and describe how its analyses may be extended beyond investigations of viral infection. AVARDA, in combination with VirScan and other pan-pathogen serological techniques, is likely to find broad utility in the epidemiology and diagnosis of infectious diseases.
Expression-based analyses indicate a central role for hypoxia in driving tumor plasticity through microenvironment remodeling and chromosomal instability
Authors: Jing Anqi , Vizeacoumar Frederick S. , Parameswaran Sreejit , Haave Bjorn , Cunningham Chelsea E. , Wu Yuliang , Arnold Roland , Bonham Keith , Freywald Andrew , Han Jie , Vizeacoumar Franco J.
Published: May 2018

Can transcriptomic alterations drive the evolution of tumors? We rationalize that expressional changes found in all patients arise earlier in tumor development compared to alterations that occur only in limited subsets of patients. Our analyses of non-mutated genes from the non-amplified regions of the genome of 158 triple negative breast cancer (TNBC) cases identified 219 exclusively expression-altered (EEA) genes that may play important role in TNBC. Phylogenetic analyses of these genes predict a “punctuated burst” of multiple gene up-regulation events occurring at early stages of tumor development, followed by minimal subsequent changes later in tumor progression. Remarkably, this punctuated burst of expressional changes is instigated by hypoxia-related molecular events, predominantly in two groups of genes that control chromosomal instability (CIN) and remodel tumor microenvironment (TME). We conclude that alterations in the transcriptome are not stochastic and that early stage hypoxia induces CIN and TME remodeling to permit further tumor evolution.
xMD-miRNA-seq to generate near in vivo miRNA expression estimates in colon epithelial cells
Authors: Rosenberg Avi Z. , Wright Carrie , Fox-Talbot Karen , Rajpurohit Anandita , Williams Courtney , Porter Corey , Kovbasnjuk Olga , McCall Matthew N. , Shin Joo Heon , Halushka Marc K.
Published: May 2018

Accurate, RNA-seq based, microRNA (miRNA) expression estimates from primary cells have recently been described. However, this in vitro data is mainly obtained from cell culture, which is known to alter cell maturity/differentiation status, significantly changing miRNA levels. What is needed is a robust method to obtain in vivo miRNA expression values directly from cells. We introduce expression microdissection miRNA small RNA sequencing (xMD-miRNA-seq), a method to isolate cells directly from formalin fixed paraffin-embedded (FFPE) tissues. xMD-miRNA-seq is a low-cost, high-throughput, immunohistochemistry-based method to capture any cell type of interest. As a proof-of-concept, we isolated colon epithelial cells from two specimens and performed low-input small RNA-seq. We generated up to 600,000 miRNA reads from the samples. Isolated epithelial cells, had abundant epithelial-enriched miRNA expression (miR-192; miR-194; miR-200b; miR-200c; miR-215; miR-375) and overall similar miRNA expression patterns to other epithelial cell populations (colonic enteroids and flow-isolated colon epithelium). xMD-derived epithelial cells were generally not contaminated by other adjacent cells of the colon as noted by t-SNE analysis. xMD-miRNA-seq allows for simple, economical, and efficient identification of cell-specific miRNA expression estimates. Further development will enhance rapid identification of cell-specific miRNA expression estimates in health and disease for nearly any cell type using archival FFPE material.
Identification of a Chimeric M4 Protein and Novel Emm Pattern in Currently Circulating Strains of Emm4 Group A Streptococcus
Authors: DebRoy Sruti , Li Xiqi , Kalia Awdhesh , Galloway Peña Jessica , Shah Brittany J. , Fowler Vance G. , Flores Anthony R. , Shelburne Samuel A.
Published: May 2018

Group A Streptococcus (GAS) is classified by sequence of the gene encoding the M protein (emm) and the patterns into which emm types are grouped. We discovered a novel emm pattern in emm4 GAS, historically considered pattern E, arising from a fusion event between emm and the adjacent enn gene. We identified the emm/enn fusion event in 51/52 emm4 GAS strains isolated by national surveillance in 2015. GAS isolates with an emm/enn fusion event completely replaced pattern E emm4 strains over a 4-year span in Houston (2013-2017). The novel emm/enn gene fusion and new emm pattern has potential vaccine implications.
Chromatin-informed inference of transcriptional programs in gynecologic and basal breast cancers
Authors: Osmanbeyoglu Hatice U. , Shimizu Fumiko , Rynne-Vidal Angela , Jelinic Petar , Mok Samuel C. , Chiosis Gabriela , Levine Douglas A. , Leslie Christina S.
Published: May 2018

Epigenomic data on transcription factor occupancy and chromatin accessibility can elucidate the developmental origin of cancer cells and reveal the enhancer landscape of key oncogenic transcriptional regulators. However, in many cancers, epigenomic analyses have been limited, and computational methods to infer regulatory networks in tumors typically use expression data alone, or rely on transcription factor (TF) motifs in annotated promoter regions. Here, we develop a novel machine learning strategy called PSIONIC (patient-specific inference of networks informed by chromatin) to combine cell line chromatin accessibility data with large tumor expression data sets and model the effect of enhancers on transcriptional programs in multiple cancers. We generated a new ATAC-seq data set profiling chromatin accessibility in gynecologic and basal breast cancer cell lines and applied PSIONIC to 723 RNA-seq experiments from ovarian, uterine, and basal breast tumors as well as 96 cell line RNA-seq profiles. Our computational framework enables us to share information across tumors to learn patient-specific inferred TF activities, revealing regulatory differences between and within tumor types. Many of the identified TF regulators were significantly associated with survival outcome in basal breast, uterine serous and endometrioid carcinomas. Moreover, PSIONIC-predicted activity for MTF1 in cell line models correlated with sensitivity to MTF1 inhibition. Therefore computationally dissecting the role of TFs in gynecologic cancers may ultimately advance personalized therapy.
Aggregation ofVibrio choleraeby cationic polymers enhances quorum sensing but over-rides biofilm dissipation in response to autoinduction
Authors: Perez-Soto Nicolas , Creese Oliver , Fernandez-Trillo Francisco , Krachler Anne-Marie
Published: May 2018

Vibrio choleraeis a Gram-negative bacterium found in aquatic environments and a human pathogen of global significance. Its transition between host-associated and environmental life styles involves the tight regulation of niche-specific phenotypes such as motility, biofilm formation and virulence.V. cholerae’s transition from the host to environmental dispersal usually involves suppression of virulence and dispersion of biofilm communities. In contrast to this naturally occurring transition, bacterial aggregation by cationic polymers triggers a unique response, which is to suppress virulence gene expression while also triggering biofilm formation byV. cholerae, an artificial combination of traits that is potentially very useful to bind and neutralize the pathogen from contaminated water. Here, we set out to uncover the mechanistic basis of this polymer-triggered bacterial behavior. We found that bacteria-polymer aggregates undergo rapid autoinduction and achieve quorum sensing at bacterial densities far below those required for autoinduction in the absence of polymers. We demonstrate this induction of quorum sensing is due both to a rapid formation of autoinducer gradients and local enhancement of autoinducer concentrations within bacterial clusters, as well as the stimulation of CAI-1 and AI-2 production by aggregated bacteria. We further found that polymers cause an induction of the biofilm specific regulator VpsR and the biofilm structural protein RbmA, bypassing the usual suppression of biofilm during autoinduction. Overall, this study highlights that synthetic materials can be used to cross-wire natural bacterial responses to achieve a combination of phenotypes with potentially useful applications.
LMO7 deficiency reveals the significance of the cuticular plate for hearing function
Authors: Du Ting-Ting , Dewey James B. , Wagner Elizabeth L. , Francis Shimon P. , Perez-Reyes Edward , Xu Wenhao , Oghalai John S , Shin Jung-Bum
Published: May 2018

Sensory hair cells, the mechanoreceptors of the auditory and vestibular system, harbor two specialized organelles, the hair bundle and the cuticular plate. Both subcellular structures have adapted to facilitate the remarkable sensitivity and speed of hair cell mechanotransduction. While the mechanosensory hair bundle is extensively studied, the molecules and mechanisms mediating the development and function of the cuticular plate are poorly understood. The cuticular plate is believed to provide a rigid foundation for stereociliar pivot movements, but specifics about its function, especially the significance of its integrity for long-term maintenance of hair cell mechanotransduction, are not known. In this study, we describe the discovery of a hair cell protein called LIM only protein 7 (LMO7). In the hair cell, LMO7 is specifically localized in the cuticular plate.Lmo7 KOmice suffer multiple deficiencies in the cuticular plate, including reduced filamentous actin density and abnormal length and distribution of stereociliar rootlets. In addition to the cuticular plate defects, olderLmo7 KOmice develop abnormalities in inner hair cell stereocilia. Together, these defects affect cochlear tuning and sensitivity and give rise to late-onset progressive hearing loss.