bluuebunny/crossref_metadata_2025 huggingface dataset:
Cartan ribbonization and a topological inspection
Authors: Raffaelli Matteo , Bohr Jakob , Markvorsen Steen
Published: February 2019

We develop the concept of Cartan ribbons together with a rolling-based method to ribbonize and approximate any given surface in space by intrinsically flat ribbons. The rolling requires that the geodesic curvature along the contact curve on the surface agrees with the geodesic curvature of the corresponding Cartan development curve. Essentially, this follows from the orientational alignment of the two co-moving Darboux frames during rolling. Using closed contact centre curves, we obtain closed approximating Cartan ribbons that contribute zero to the total curvature integral of the ribbonization. This paves the way for a particularly simple topological inspection—it is reduced to the question of how the ribbons organize their edges relative to each other. The Gauss–Bonnet theorem leads to this topological inspection of the vertices. Finally, we display two examples of ribbonizations of surfaces, namely of a torus using two ribbons and of an ellipsoid using closed curvature lines as centre curves for the ribbons.
Foam–liquid front motion in Eulerian coordinates
Authors: Torres-Ulloa C. , Berres S. , Grassia P.
Published: February 2019

A mathematical model formulated as a system of Hamilton–Jacobi equations describes implicitly the propagation of a foam–liquid front in an oil reservoir, as the zero-level set of the solution variable. The conceptual model is based on the ‘pressure-driven growth’ model in Lagrangian coordinates. The Eulerian mathematical model is solved numerically, where the marching is done via a finite volume scheme with an upwind flux. Periodic reinitialization ensures a more accurate implicit representation of the front. The numerical level set contour values are initially formed to coincide with an early time asymptotic analytical solution of the pressure-driven growth model. Via the simulation of the Eulerian numerical model, numerical data are obtained from which graphical representations are generated for the location of the propagating front, the angle that the front normal makes with respect to the horizontal and the front curvature, all of which are compared with the Lagrangian model predictions. By making this comparison, it is possible to confirm the existence of a concavity in the front shape at small times, which physically corresponds to an abrupt reorientation of the front over a limited length scale.
The adjoint equations for thermochemical compressible mantle convection: derivation and verification by twin experiments
Authors: Ghelichkhan S. , Bunge H-.P.
Published: February 2019

The adjoint method is an efficient way to obtain gradient information in a mantle convection model relative to past flow structure, allowing one to retrodict mantle flow from observations of the present-day mantle state. While adjoint equations for isochemical mantle flow have been derived for both incompressible and compressible flows, here we extend the method to thermochemical mantle flow models, and present thermochemical adjoint equations in the elastic-liquid approximation. We verify the method with twin experiments, and retrodict the flow history of a thermochemical reference model (reference twin) assuming for the final state, either a consistent thermochemical interpretation, using the thermochemical adjoint equations, or an inconsistent purely thermal interpretation, using the isochemical adjoint equations. The consistent simulation correctly retrodicts the flow evolution of the reference twin. The inconsistent case, instead, restores a false flow history whereby internal buoyancy forces and convectively maintained topography are overestimated. Because the cost function is reduced in either case, our results suggest that the adjoint method can be used to link assumptions on the role of chemical mantle heterogeneity to geologic inferences of dynamic topography, thus providing additional means to test hypotheses on mantle composition and dynamics.
Not all interactions are positive: testing how antagonistic interactions impact the robustness of plant-pollinator networks
Authors: Briggs Heather M. , Ayers Carolyn A. , Armsworth Paul R. , Brosi Berry J.
Published: February 2019

Given ongoing pollinator declines, it is important to understand the dynamics of linked extinctions of plants driven by pollinator extinctions. Topological robustness models focused on this question suggest relatively high robustness of plant species to pollinator species extinctions. Still, existing robustness models typically assume that all interactions in plant-pollinator networks are positive, which is clearly not always the case. For example, many pollinators remove floral resources with-out transferring pollen, or even damage floral structures in the case of nectar robbing. Here we introduce antagonistic interactions into plant-pollinator networks and assess the resilience of plant communities to pollinator species losses. Incorporating antagonistic interactions leads to lower network robustness, i.e. an increased rate of plant species loss (as compared to networks with only mutualistic interactions) in empirical plant-pollinator networks. In conjunction with extinction order, the addition of increasingly antagonistic interactions was idiosyncratic in that it did not always magnify the effects of extinction order across the three networks. These results underscore the importance of considering the full spectrum of interaction outcomes when assessing robustness to coextinctions in plant-pollinator networks, as well as other ecological systems.
Audiograms of howling monkeys: are extreme loud calls the result of runaway selection?
Authors: Ramsier Marissa A. , Cunningham Andrew J. , Patiño May R. , Glander Kenneth E. , Dominy Nathaniel J.
Published: February 2019

The eponymous vocalizations of howling monkeys (genusAlouatta) are associated with territorial defense and male-male competition, yet the extreme loudness of howls, which are among the loudest vocalizations of any terrestrial mammal, have yet to be fully explained. Loudness facilitates long-distance sound propagation but the effectiveness of any vocal signal depends in part on the auditory capabilities of the intended receiver, and the auditory sensitivities of howling monkeys are unknown. To better understand the evolution of loud calls, we used the auditory brainstem response (ABR) method to estimate the auditory sensitivities ofAlouatta palliata. The mean estimated audiogram of four wild-caught adults displayed a w-shaped pattern with two regions of enhanced sensitivity centered at 0.7-1.0 and 11.3 kHz. The lower-frequency region of auditory sensitivity is pitched moderately higher than the fundamental frequencies of howling, whereas the higher-frequency region corresponds well with harmonics in an infant distress call, thewrah-ha. Fitness advantages from detecting infants amid low-frequency background noise, including howling, could explain the incongruity between our ABR thresholds and the fundamental frequencies of howling. Attending to infant calls is expected to enhance reproductive success within an infanticidal genus, and we suggest that the extraordinary loudness of male howling is an indirect (runaway) result of positive feedback between the selective pressures of hearing infant distress calls and deterring infanticide.
MoMI-G: Modular Multi-scale Integrated Genome Graph Browser
Authors: Yokoyama Toshiyuki T. , Sakamoto Yoshitaka , Seki Masahide , Suzuki Yutaka , Kasahara Masahiro
Published: February 2019

Long-read sequencing allows more sensitive and accurate discovery of structural variants (SVs). While more and more SVs are being identified, a number of them are difficult to visualize using existing SV visualization tools. Therefore, methods to visualize SVs such as nested or large SVs of over a megabase pair need to be developed. To this end, we developed MOdular Multi-scale Integrated Genome graph browser, MoMI-G, a web-based genome browser to visualize SVs, genes, repeats, and other annotations as a variation graph with paths. This browser allows more intuitive recognition of large, nested, and potentially more complex SVs. MoMI-G has view modules for different scales, which allow users to view the whole genome down to nucleotide-level alignments of long reads. Alignments spanning reference alleles and those spanning alternative alleles are shown in the same view. Users can customize the view, if they are not satisfied with the preset views. In addition, MoMI-G has Interval Card Deck, a feature for rapid manual inspection of hundreds of SVs. Herein, we describe the utility of MoMI-G by using representative examples of large and nested SVs found in two cell lines, LC-2/ad and CHM1. MoMI-G is freely available at https://github.com/MoMI-G/MoMI-G under the MIT license.
A scalar Poincaré map for struggling in Xenopus tadpoles
Authors: Olenik Mark , Houghton Conor
Published: February 2019

Short-term synaptic plasticity is widely found in many areas of the central nervous system. In particular, it is believed that synaptic depression can act as a mechanism to allow simple networks to generate a range of different firing patterns. The locomotor circuit of hatchling Xenopus tadpoles produces two types of behaviours: swimming and the slower, stronger struggling movement that is associated with rhythmic bends of the whole body. Struggling is accompanied by anti-phase bursts in neurons on each side of the spinal cord and is believed to be governed by a short-term synaptic depression of commissural inhibition. To better understand burst generation in struggling, we study a minimal network of two neurons coupled through depressing inhibitory synapses. Depending on the strength of the synaptic conductance between the two neurons, such a network can produce symmetric n – n anti-phase bursts, where neurons fire n spikes in alternation, with the period of such solutions increasing with the strength of the synaptic conductance. Relying on the timescale disparity in the model, we reduce the eight-dimensional network equations to a fully explicit scalar Poincaré burst map. This map tracks the state of synaptic depression from one burst to the next, and captures the complex bursting dynamics of the network. Fixed points of this map are associated with stable burst solutions of the full network model, and are created through fold bifurcations of maps. We derive conditions that describe period increment bifurcations between stable n – n and (n + 1) – (n + 1) bursts, producing a full bifurcation diagram of the burst cycle period. Predictions of the Poincaré map fit excellently with numerical simulations of the full network model, and allow the study of parameter sensitivity for rhythm generation.
Mutagenesis oforcoimpairs foraging but not oviposition in the hawkmothManduca sexta
Authors: Fandino Richard A. , Haverkamp Alexander , Bisch-Knaden Sonja , Zhang Jin , Bucks Sascha , Thi Tu-Anh Nguyen , Werkenthin Achim , Ryback Jürgen , Stengl Monika , Knaden Markus , Hansson Bill S. , Große-Wilde Ewald
Published: February 2019

Plant volatile detection through olfaction plays a crucial role in insect behaviors.In vivo, the odorant receptor co-receptororcois an obligatory component for the function of odorant receptors (ORs), a major receptor family involved in insect olfaction. We used CRISPR-Cas9 targeted mutagenesis to knock-out (KO)orcoin a neurophysiological model species, the hawkmothManduca sexta. M. sextaand its host, the Sacred Datura (Datura wrightii) share a model insect-plant relationship based on mutualistic and antagonistic life history traits.D. wrightiiis the innately preferred nectar-source and oviposition host forM. sexta. Hence, the hawkmoth is an important pollinator while theM. sextalarvae are specialized herbivores of the plant. We generated anorcoKO through CRISPR-Cas9 to test the consequences of a loss of OR-mediated olfaction in this insect-plant relationship. Neurophysiological characterization revealed severely reduced antennal and antennal lobe responses to representative odorants emitted byD. wrightii. In a wind-tunnel setting with a flowering plant,orcoKO hawkmoths showed disrupted flight orientation and an ablated proboscis extension response to the natural stimulus. However, when testing the oviposition behavior of mated females encountering a non-flowering plant, there was no difference betweenorcoKO and wild type females regarding upwind flight orientation and number of eggs laid. Overall, OR-mediated olfaction is essential for foraging and pollination behaviors, but plant-seeking and oviposition behaviors appear largely unaffected.

Significance statement

Insects detect plant volatiles mainly through the expression of ORs and IRs on the antennal olfactory sensory neurons (OSNs). In vivo, Orco is an obligate partner for OR, but not IR function and ORs mediate a vast spectrum of olfactory perception. We applied CRISPR-Cas9 inM. sextato mutate theorcogene and determine the physiological and behavioral implication of a loss of Orco receptor function in a semi-ecological interaction with D. wrightii. We found that while behaviors related to foraging were largely disrupted, other sensory modalities outside Orco function determine the relationship between an ovipositing female and its plant host. These results have implications toward understanding the olfactory basis of insect-plant interactions shaping our ecological and agricultural landscapes.
A quantitative model of human neurodegenerative diseases involving protein aggregation
Authors: Kepp Kasper P.
Published: February 2019

Human neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease, and Amyotrophic lateral sclerosis involve protein aggregation and share many other similarities. It is widely assumed that the protein aggregates exhibit a specific molecular mode of toxic action. This paper presents a simple mathematical model arguing that clinical cognitive status relates to the energy available after subtracting cell maintenance due to general turnover of the misfolded proteins, rather than a specific toxic molecular action per se. Proteomic cost minimization can explain why highly expressed proteins changed less during evolution, leaving more energy for reproducing microorganisms on longer evolutionary timescales. In higher organisms, the excess energy instead defines cognitive capability, and the same equations remarkably apply. Proteomic cost minimization can explain why late-onset neurodegenerative diseases involve protein aggregation. The model rationalizes clinical ages of symptom onset for patients carrying pathogenic protein mutations: Unstable or aggregation-prone mutations confer a direct energy cost of turnover, but other risk modifiers also change the available cellular energy as ultimately defining clinical outcome. Proteomic cost minimization is consistent with current views on biomarker histories, explains conflicting data on overexpression models, and is supported by specific experiments showing that proteasome activity is required to confer toxicity to pathogenic mutants. The mechanism and model lend promise to a quantitative personalized medicine of neurodegenerative disease.
Stimulus-aware spatial filtering for single-trial neural response and temporal response function estimation in high-density EEG with applications in auditory research
Authors: Das Neetha , Vanthornhout Jonas , Francart Tom , Bertrand Alexander
Published: February 2019

Objective. Neural responses recorded using electroencephalography (EEG) and magnetoencephalography (MEG) can be used to study how our brain functions, as well as for various promising brain computer interface (BCI) applications. However, a common problem is the low signal to noise ratio (SNR) which makes it challenging to estimate task-related neural responses or the temporal response function (TRF) describing the linear relationship between the stimulus and the neural response, particularly over short data windows. To address these, we present an algorithm that takes advantage of the multi-channel nature of the recordings, and knowledge of the presented stimulus, to achieve a joint noise reduction and dimensionality reduction using spatial filtering. Methods. Forward modeling is used to project the stimulus onto the electrode space. The second-order statistics of this estimated desired signal and the raw neural data are used to estimate spatial filters that maximize the SNR of the neural response, based on a generalized eigenvalue decomposition. Main Results. 1. For synthesized EEG data, over a range of SNRs, our filtering resulted in significantly better TRF estimates from 20 s trials, compared to unfiltered EEG data. 2. On a dataset from 28 subjects who listened to a single-talker stimulus, our method resulted in correlations between predicted neural responses and the original EEG data that were significantly higher compared to standard approaches. 3. On a dataset of 16 subjects attending to 1 speaker in a two-speaker scenario, our method resulted in attention decoding accuracies which were higher compared to existing forward modelling methods. Significance. Our algorithm presents a data-driven way to denoise and reduce dimensionality of neural data, thus aiding further analysis, by utilizing the knowledge of the stimulus. The method is computationally efficient, and does not require repeated trials, thereby relieving experiment design from the necessity of presenting repeated stimuli to the subjects.
The IDH-Tau-EGFR triad defines diffuse glioma pathology by controlling mesenchymal differentiation and neo-vascular fitness
Authors: Gargini Ricardo , Segura-Collar Berta , Hernández-SanMiguel Esther , Garcia-Escudero Vega , Romero-Bravo Andrés , Herránz Beatriz , Núñez Felipe J , García-Pérez Daniel , Ayuso-Sacido Angel , Seoane Joan , Sepúlveda-Sánchez Juan M. , Hernández-Laín Aurelio , Castro María G. , García-Escudero Ramón , Ávila Jesús , Sánchez-Gómez Pilar
Published: February 2019

Classification of gliomas as wild-type or mutantIDH1/2tumors has profound clinical implications. However, how these two groups of gliomas progress, in a microenvironment-dependent manner, is still a pending question. Here we describe that the expression of Tau is epigenetically induced by mutant IDH1/2, whereas is almost absent from tumors withEGFR/PTENmutations. Moreover,Tau (MAPT)expression is inversely correlated with overall survival inEGFR-amplified gliomas. Using orthotopicEGFR-related models, we have observed that Tau overexpression or microtubule stabilizers impair the mesenchymal transformation of glioma cells, with profound changes in tumor vasculature and a significant decrease in tumor burden. However, epithelial-to-mesenchymal transformedEGFR-mutant cells, acting as pericytes, induce neo-vasculogenesis and favor aggressive glioma growth, a process that is no longer sensitive to Tau. Altogether our data indicate that the genomic background controls glioma aggressiveness by modifying the vascular microenvironment.

GRAPHICAL ABSTRACT
Papillomavirus can be transmitted through the blood and produce infections in blood recipients: Evidence from two animal models
Authors: Cladel Nancy M. , Jiang Pengfei , Li Jingwei J. , Peng Xuwen , Cooper Timothy K. , Majerciak Vladimir , Balogh Karla K. , Meyer Thomas J. , Brendle Sarah A. , Budgeon Lynn R. , Shearer Debra A. , Munden Regina , Cam Maggie , Vallur Raghavan , Christensen Neil D. , Zheng Zhi-Ming , Hu Jiafen
Published: February 2019

Human papillomavirus (HPV) infections are commonly thought to be strictly sexually transmitted. However, studies have demonstrated the presence of HPV in cancers of many non-sexual internal organs, raising the question as to how the viruses gain access to these sites. A possible connection between blood transfusion and HPV-associated disease has not received much attention. We show, in two animal models, that blood infected with papillomavirus yields infections at permissive sites. Furthermore, we demonstrate that blood from actively infected mice can transmit the infection to naïve animals. Finally, we report papillomavirus infections in the stomach tissues of animals infected via the blood. Stomach tissues are not known to be permissive for papillomavirus infection, although the literature suggests that HPVs may be associated with a subset of gastric cancers. These results indicate that the human blood supply, which is not screened for papillomaviruses, could be a potential source of HPV infection and subsequent cancers.

Human papillomaviruses cause 5% of human cancers. Currently, blood banks do not screen for these viruses. We demonstrate that blood transfused from papillomavirus-infected animals produces infections in recipients. Public health implications are significant if the same is true for humans.

Definitions

Local papillomavirus infection:An infection initiated by the direct application of virus or viral DNA to the site of infection

Intravenous (IV) papillomavirus infection:An infection resulting from blood-borne delivery of virus or viral DNA to the site of infection.
Formalin Tissue Fixation Biases Myelin-Sensitive MRI
Authors: Seifert Alan C. , Umphlett Melissa , Hefti Marco , Fowkes Mary , Xu Junqian
Published: February 2019

Purpose

Chemical fixatives, such as formalin, form cross-links between proteins and affect the relaxation times and diffusion properties of tissue. These fixation-induced changes likely also affect myelin density measurements produced by quantitative magnetization transfer (qMT) and myelin water imaging (MWI). In this work, we evaluate these myelin-sensitive MRI methods for fixation-induced biases.

Methods

We perform qMT, MWI, and D2O-exchanged zero echo-time (ZTE) imaging on unfixed human spinal cord tissue, and repeat these measurements after 1 day and 31 days of formalin fixation.

Results

The qMT bound pool fraction increased by 30.7±21.1% after 1 day of fixation and by 42.6±33.9% after 31 days of fixation. Myelin water fraction increased by 39.7±15.5% and 37.0±15.9% at these same time points, and mean T2of the myelin water pool nearly doubled. Reference-normalized D2O-exchanged ZTE signal intensity increased by 8.17±6.03% after 31 days of fixation, but did not change significantly after 1 day of fixation. After fixation, specimen cross-sectional area decreased by approximately 5%; after correction for shrinkage, changes in D2O-exchanged ZTE intensity were nearly eliminated.

Conclusion

F and MWF are significantly increased by formalin fixation, while D2O-exchanged ZTE intensity is minimally affected. Changes in qMT and MWI may be due, in part, to delamination and formation of vacuoles in the myelin sheath. D2O-exchanged signal intensity may be altered by fixation-induced changes in myelin lipid solid-state1H T1. We urge caution in the comparison of these measurements across subjects or specimens in different states, especially unfixed vs. fixed tissue.
Seasonal changes of airborne bacterial communities over Tokyo and influence of local meteorology
Authors: Uetake Jun , Tobo Yutaka , Uji Yasushi , Hill Thomas C. J. , DeMott Paul J. , Kreidenweis Sonia M. , Misumi Ryohei
Published: February 2019

Recent progress in Next Generation Sequencing allows us to explore the diversity of airborne microorganisms across time and space. However, few studies have used consecutive short-period samples to explore correlations between the seasonal variation of the microbiota and meteorology. In order to understand airborne bacterial community dynamics over Tokyo, including fine-scale correlations between airborne microorganisms and meteorological conditions, and the influence of local versus long-range transport of microbes, air samples were continuously taken from a platform at the 458-m level of the Tokyo Skytree (a 634-m-high broadcasting tower in Tokyo) from August 2016 to February 2017. Predicted source regions of airborne particles, from back trajectory analyses, changed abruptly from the Pacific Ocean to the Eurasian Continent in the beginning of October. However, microbial community composition and alpha and beta diversities were not affected by this meteorological regime shift, suggesting that long-range transport from ocean or continent was not the principal determinant controlling the local airborne microbiome. By contrast, local meteorology, especially relative humidity and wind speed, had significant relationships with both alpha diversities and beta diversity. Among four potential local source categories (soil, bay seawater, river, and pond), bay seawater and soil were constant and predominant sources. Statistical analyses suggest humidity is the most influential meteorological factor, most likely because it is correlated with soil moisture and hence negatively correlated with the dispersal of particles from the land surface.
MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome
Authors: Tian Dechao , Zhang Ruochi , Zhang Yang , Zhu Xiaopeng , Ma Jian
Published: February 2019

The composition of the cell nucleus is highly heterogeneous, with different constituents forming complex interactomes. However, the global patterns of these interwoven heterogeneous interactomes remain poorly understood. Here we focus on two different interactomes, chromatin interaction network and gene regulatory network, as a proof-of-principle, to identify heterogeneous interactome modules (HIMs) in the nucleus. Each HIM represents a cluster of gene loci that are in spatial contact more frequently than expected and that are regulated by the same group of transcription factor proteins. We develop a new algorithm MOCHI to facilitate the discovery of HIMs based on network motif clustering in heterogeneous interactomes. By applying MOCHI to five different cell types, we found that HIMs have strong spatial preference within the nucleus and exhibit distinct functional properties. Through integrative analysis, this work demonstrates the utility of MOCHI to identify HIMs, which may provide new perspectives on 3D genome organization and function.
Elucidating the short and long-term mechanical response of the cell nucleus with a hybrid-viscoelastic model
Authors: Pérez-Calixto Daniel , González-Villa Erika , Jiménez-Díaz Edgar , Serna-Márquez Nathalia , Vázquez-Victorio Genaro , Hautefeuille Mathieu
Published: February 2019

The mechanical properties of the nucleus play an important role in all the processes of a cell and impact greatly its decisions, functions and phenotype. It is then important to understand how internal and external stresses can modify them. To study the mechanical response of the nucleus at different timescales, a hybrid viscoelastic model integrating both continuum mechanics and soft glass matter theory is developed. It indeed accounts for the instantaneous viscoelastic response of the structural components of the nucleus as well as the active response of the nuclear envelope and the dynamic reorganization of the cytoskeleton at different timescales. This model can describe adequately the nuclear deformation caused by substrate stiffness in primary hepatocytes and HepG2 cells in culture up to 5 days. It also reveals that the increase of nuclear strain in the long term implies nuclear softening (a phenomenon intensified on stiffer substrates), simultaneously with an increase of the dissipative properties of the nucleus, offering stability. Finally, in the context of soft glassy theory, the model suggests that processes of aging and mechanical memory of the cell may be originated by the dissipative capacity of the nuclei.
Quantification of multicellular colonization in tumor metastasis using exome sequencing data
Authors: Nishino Jo , Watanabe Shuichi , Miya Fuyuki , Kamatani Takashi , Boroevich Keith A , Tsunoda Tatsuhiko
Published: February 2019

Metastasis is a major cause of cancer-related mortality, and it is essential to understand how metastasis occurs in order to overcome it. One relevant question is the origin of a metastatic tumor cell population. Although the hypothesis of a single-cell origin for metastasis from a primary tumor has long been prevalent, several recent studies using mouse models have supported a multi-cellular origin of metastasis. Human bulk whole-exome sequencing (WES) studies also have demonstrated a multiple ‘clonal’ origin of metastasis, with different mutational compositions. Specifically, there has not yet been strong research to determine how many founder cells colonize a metastatic tumor. To address this question, we developed a method to quantify the ‘founder cell population size’ in a metastasis using paired WES data from primary and metachronous metastatic tumors. Simulation studies demonstrated the proposed method gives unbiased results with sufficient accuracy in the range of realistic settings. Applying the proposed method to real WES data from four colorectal cancer patients, all samples supported a multi-cellular origin of metastasis and the founder size was quantified, ranging from 3 to 15 cells. Such a wide-ranging founder sizes estimated by the proposed method suggests that there are large variations in genetic similarity between primary and metastatic tumors in the same subjects, which might be involved in (dis)similarity of drug responses between tumors.
Relationships between depressive symptoms and brain responses during emotional movie viewing emerge in adolescence
Authors: Gruskin David C. , Rosenberg Monica D. , Holmes Avram J.
Published: February 2019

Affective disorders such as major depression are common but serious illnesses characterized by altered processing of emotional information. Although the frequency and severity of depressive symptoms increase dramatically over the course of childhood and adolescence, much of our understanding of their neurobiological bases comes from work characterizing adults’ responses to static emotional information. As a consequence, relationships between depressive brain phenotypes and naturalistic emotional processing, as well as the manner in which these associations emerge over the lifespan, remain poorly understood. Here, we apply static and dynamic inter-subject correlation analyses to examine how brain function is associated with clinical and non-clinical depressive symptom severity in 112 children and adolescents (7-21 years old) who viewed an emotionally evocative clip from the film Despicable Me during functional MRI. Our results reveal that adolescents with greater depressive symptom severity exhibit atypical fMRI responses during movie viewing, and that this effect is stronger during less emotional moments of the movie. Furthermore, adolescents with more similar item-level depressive symptom profiles showed more similar brain responses during movie viewing. In contrast, children’s depressive symptom severity and profiles were unrelated to their brain response typicality or similarity. Together, these results indicate a developmental change in the relationships between brain function and depressive symptoms from childhood through adolescence. Our findings suggest that depressive symptoms may shape how the brain responds to complex emotional information in a dynamic manner sensitive to both developmental stage and affective context.
Marked compositional changes in harvestmen assemblages in Amazonian forest islands induced by a mega dam
Authors: Lúcia Tourinho Ana , Benchimol Maíra , Porto Willians , Peres Carlos A. , Storck-Tonon Danielle
Published: February 2019

Mega hydroelectric dams have become one of the main drivers of habitat loss in tropical forests, converting large tracts of pristine forests into isolated forest islands. Understanding how biodiversity cope with landscape modification in these archipelagic landscapes is of paramount importance to assess the environmental consequences of dam infrastructure and propose mitigation actions for biodiversity conservation. In this context, harvestmen (Opiliones, Arachnida) comprise a good indicator taxon of habitat quality, given their high sensitivity to desiccation and microclimatic change. Here, we investigate the effects of landscape change induced by a mega hydropower dam on forest harvestmen species richness, abundance and composition within the Balbina Hydroelectric Dam, Central Brazilian Amazon. Using both nocturnal search and diurnal beating tray surveys, we sampled 20 islands and five mainland continuous forests, relating our biological response variables to local, patch and landscape scale metrics. We captured 783 harvestmen representing 31 species, 22 genera and 9 families considering all sampling sites, with species composition differing across islands and mainland sites. Although species richness was unaffected by any local, patch and landscape variables, species composition and abundance were differentially affected by a set of predictor variables at different scales. Forest cover and fallen woody stems were significant predictors of species composition patterns, whereas vegetation density, forest cover, island area, abundance of palm trees, and fallen woody stems best explained harvestmen abundance. We recommend retaining large forest habitat patches surrounded by a great amount of forest cover to prevent the rapid decay in tree communities and minimize forest disturbance effects in large hydroelectric dams.
Remarkable genetic diversity of Trypanosoma cruzi and Trypanosoma rangeli in two localities of southern Ecuador identified via deep sequencing of mini-exon gene amplicons
Authors: Maiguashca Sánchez Jalil , Sueto Salem Oduro Beffi , Schwabl Philipp , Grijalva Mario J. , Llewellyn Martin S. , Costales Jaime Alfredo
Published: February 2019

Trypanosoma cruzi, causative agent of Chagas disease, and T. rangeli are kinetoplastid parasites endemic to Latin America. Although closely-related to T. cruzi and capable of infecting humans, T. rangeli is non-pathogenic. Both parasite species are transmitted by triatomine bugs, and the presence of T. rangeli constitutes a confounding factor in the study of Chagas prevalence and transmission dynamics. T. cruzi possesses high molecular heterogeneity: six discrete typing units (DTUs) are currently recognized. In Ecuador, TcI predominates while other DTUs are seldom reported. Here, infection by T. cruzi and/or T. rangeli in triatomine bugs from two communities of southern Ecuador was evaluated via PCR product size polymorphism of kinetoplast-minicircle sequences and the non-transcribed spacer region of the mini-exon gene. Additionally, mini-exon amplicons were deep-sequenced to analyze single nucleotide polymorphisms and mixed infections. As a control, mini-exon products from several monoclonal reference strains were included. T. cruzi genetic diversity was significantly greater in adult vectors than in nymphal stage V vectors. Among infected triatomines, deep sequencing revealed one T. rangeli infection (3%), 9 T. cruzi infections (27.3%) and 23 T. cruzi / T. rangeli mixed infections (69.7%), suggesting that T. rangeli prevalence has been largely underestimated in the region. Furthermore, deep-sequencing detected TcIV sequences in six samples (first TcIV record in southern Ecuador). Our data indicate that amplicon size analysis alone is not reliable for parasite identification/typing in mixed infections containing both T. cruzi and T. rangeli, or when multiple T. cruzi DTUs are present. Additionally, our analysis showed extensive overlap among the parasite populations present in the two studied localities (ca. 28 km apart); suggesting active parasite dispersal over the study area. Our results highlight the value of amplicon sequencing methodologies to clarify the population dynamics of kinetoplastid parasites in endemic regions and inform control campaigns in southern Ecuador.
Evolution of leaf-cutter behavior in bees (Hymenoptera: Megachilidae) as inferred from total-evidence tip-dating analyses
Authors: Gonzalez Victor H. , Gustafson Grey T. , Engel Michael S.
Published: February 2019

A unique feature among bees is the ability of some species ofMegachile s.l. to cut and process fresh leaves for nest construction. The presence of razors between the female mandibular teeth (interdental laminae) to facilitate leaf-cutting (LC) is a morphological novelty that might have triggered a subsequent diversification in this group. However, we have a limited understanding of the evolutionary origins of this behavior and associated structures. Herein, we use total-evidence tip-dating analyses to infer the origin of LC bees and patterns of variation of interdental laminae. Our datasets included five nuclear genes, representatives of all fossil taxa, 80% of the extant generic-level diversity of Megachilidae, and the full range of generic and subgeneric diversity of Megachilini. Our analyses support the notion of a recent origin of LC bees (15–25 Ma), casting doubts on Eocene trace fossils attributed to these bees. We demonstrate that interdental laminae developed asynchronicaly from two different structures in the mandible (teeth or fimbrial ridge), and differ in their phenotypic plasticity. Based on the phylogenetic results, we propose robust classificatory solutions to long-standing challenges in the systematics of Megachilidae. We discuss the implications of our findings as a foundational framework to develop novel evolutionary, ecological, and functional hypotheses on this behavior.
SwiftOrtho: a Fast, Memory-Efficient, Multiple Genome Orthology Classifier
Authors: Hu Xiao , Friedberg Iddo
Published: February 2019

Introduction

Gene homology type classification is a requisite for many types of genome analyses, including comparative genomics, phylogenetics, and protein function annotation. A large variety of tools have been developed to perform homology classification across genomes of different species. However, when applied to large genomic datasets, these tools require high memory and CPU usage, typically available only in costly computational clusters. To address this problem, we developed a new graph-based orthology analysis tool, SwiftOrtho, which is optimized for speed and memory usage when applied to large-scale data.

Results

In our tests, SwiftOrtho is the only tool that completed orthology analysis of 1,760 bacterial genomes on a computer with only 4GB RAM. Using various standard orthology datasets, we also show that SwiftOrtho has a high accuracy. SwiftOrtho enables the accurate comparative genomic analyses of thousands of genomes using low memory computers.

Availability

https://github.com/Rinoahu/SwiftOrtho
Networked information interactions of epileptic EEG based on symbolic transfer entropy
Authors: Yao Wenpo , Wang Jun
Published: February 2019

Identifying networked information exchanges among brain regions is important for understanding the brain structure. We employ symbolic transfer entropy to facilitate the construction of networked information interactions for EEGs of 22 epileptics and 22 healthy subjects. The epileptic patients during seizure-free interval have lower information transfer in each individual and whole brain regions than the healthy subjects. Among all of the brain regions, the information flows out of and into the brain area of O1 of the epileptic EEGs are significantly lower than those of the healthy (p<0.0005), and the information flow from F7 to F8 (p<0.00001) is particularly promising to discriminate the two groups of EEGs. Moreover, Shannon entropy of probability distributions of information exchanges suggests that the healthy EEGs have higher complexity and irregularity than the epileptic brain electrical activities. By characterizing the brain networked information interactions, our findings highlight the long-term reduced information exchanges, degree of brain interactivities and informational complexity of the epileptic EEG.
Who Are The Traditional Healers Treating Mental Illnesses In Rural Ethiopia? A population-Based Descriptive Study
Authors: Belachew Ayele , Molla Mitikie , Fekadu Abebaw
Published: February 2019

Background

Ethiopia is a traditional country with a pluralistic health care system where people use the traditional health care systems in combination with the modern health care. In view of this, we assessed the profile of faith and traditional healers and their experience in treating people with mental illness in rural district Ethiopia so that inform the health minister to consider working towards integration with modern biomedical care to improve access.

Methods

We conducted a descriptive cross-sectional study among 173 traditional healers in Sodo district of Ethiopia. Data were collected through face-to-face interviews by trained enumerators using pretested structured questionnaires and analyzed using SPSS version 20.

Result

The median age of traditional and faith based healers was 55 (IQR=48.5, 67 years), about a third (29.5%) of them were female and 54(31.2%) earned their living exclusively from traditional healing practice. Eighty six (48.6%) healers didn’t attend formal education. Four types of healers were identified-herbalists accounted for 59% (n=102), faith healers were 36 (20.8%) mixed herbal and faith practitioners were 19(11.0%) and 16 (9.2%) were diviners. Most, 119(69%) had been practicing for an average of 15 years. Half of healers entered into the healing practice due to family kinship, whereas 26(15%) because of ancestral spirit.

Seventy one (41%) of the healers reported that they have ever treated patients with mental illness in their lifetime. Sixty three(36.4%) reported that they had treated mental illness within the past one year, of which 30(47%) treat only mental illness while 33(52%) treat both mental and physical illnesses. All faith healers and divine healers reported treating mental illness while 11(57.9%) of mixed healers, and no herbalists reported treating mental illness. Only 58(33.5%) believed that mental illness can be cured completely.

Conclusion

Significant proportion of traditional healers manages mental illness and remains an important part of the healthcare system in the rural setting of Ethiopia. Herbalists believed that biomedical treatments are preferable for mental illnesses, while faith healers and diviners believed traditional practices alone or in combination with biomedical practices is the treatment of choice.
Remodeling gut microbiota by Streptococcus thermophilus 19 attenuates inflammation in septic mice
Authors: Han Fu , Zhang Yijie , Yang Xuekang , Fang Zhuoqun , Han Shichao , Li Xiaoqiang , Cai Weixia , Xiao Dan , Liu Jiaqi , Zhang Wanfu , Wu Gaofeng , Hu Dahai
Published: February 2019

Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection and is the leading cause of death in burn patients. Streptococcus thermophilus 19 is a highly effective probiotic, with well-studied health benefits, but its role in protecting viscera against injury caused by sepsis and the underlying mechanism is poorly understood. The goal of this study was to evaluate protection potency of S. thermophilus against inflammation in mice and evaluate the influence of sepsis and S. thermophilus on microbial community. We tested the utility of S. thermophilus 19 in attenuating inflammation in vitro and vivo of LPS-induced sepsis mouse model. We also evaluated the influence of sepsis and S. thermophilus on microbial community. In vitro, S. thermophilus 19 decrease the expression of inflammatory factors. Additionally, in a lipopolysaccharide-induced septic mouse model, mice administered the probiotic 19 was highly resistant to Lps and exhibited decreased expression of inflammatory factors compared to Lps-treated control mice. A MiSeq-based sequence analysis revealed that gut microbiota alterations in mice intraperitoneally injected with 1 mg/ml LPS were mitigated by the administration of oral probiotics 19. Together these findings indicate that S. thermophilus 19 may be a new avenue for interventions against inflammation caused by sepsis and other systemic inflammatory diseases. In an analysis of the gut microbiota of the all group mice, we found that sepsis is associated with gut microbiota and probiotics attenuate the inflammation through remodeling gut microbiota.

Importance

Sepsis is life-threatening organ dysfunction which is the leading cause of death in burn patients. Although our understanding of sepsis has increased substantially in recent years, it’s still reported to be the leading cause of death in seriously ill patients. Evidences showed that gut microbiota play an important role in sepsis. Moreover, probiotics have been used to prevent numbers of gut health disorders and alleviate inflammation associated with some human diseases by promoting changes in the gut microbiota composition. Hence, to investigate the mechanism of probiotics in the treatment of sepsis has emerged. The significance of our research is in identifying the role of gut microbiota in sepsis and found an effective probiotic that reduces inflammation, S. thermophilus 19, and investigating the therapeutic effect and mechanism of S. thermophilus 19 on sepsis, which might be a new avenue for interventions against inflammation caused by sepsis and other systemic inflammatory diseases.
Amyloid conformers of the FXR1 protein prevent mRNA degradation in cortical neurons
Authors: Sopova J.V. , Koshel E. I , Belashova T.A. , Zadorsky S.P. , Sergeeva A.V. , Siniukova V.A. , Shenfeld A.A. , Velizhanina M.E. , Volkov K.V. , Nizhnikov A.A. , Gaginskaya E.R. , Galkin A.P.
Published: February 2019

Functional amyloids regulate vital processes in a variety of organisms from bacteria to higher eukaryotes. The development of methods enabling large-scale screening for amyloids opens up opportunity for systemic analysis of the prevalence of amyloids in nature. Using an original proteomic approach, we identified several proteins forming amyloid-like detergent-resistant aggregates in the rat brain. One of them is the FXR1 protein, which is known to regulate memory and emotions (1, 2). We demonstrated that in brain FXR1 forms amyloid oligomers and insoluble detergent-resistant aggregates that strongly colocalize with amyloid-specific dye Thioflavin S and bind mRNA molecules. Moreover, we demonstrated that mRNAs colocalized with FXR1 amyloid particles are completely resistant to treatment with RNAse A. Taking into consideration that the members of ribonuclease A superfamily function in neurons (3) we can conclude that amyloid conformers of FXR1 control RNA stability in brain. Thus, in contrast to pathological amyloids that cause neurodegeneration, FXR1 is the functional amyloid in forebrain. We showed that amyloid properties of FXR1 depend on its N-terminal part from 1 to 379 amino acids. This fragment forms amyloid fibrils in vitro that bind Congo red and manifest apple-green birefringence when assayed by polarization microscopy. The amyloid-forming region of FXR1 is highly conserved in mammals. These data suggest that the ability of amyloid conformers of FXR1 to protect mRNAs is characteristic of different mammalian species, including humans.

Significance Statement

Amyloids are highly ordered cross-β sheet protein fibrils associated with many neurodegenerative diseases including Alzheimer’s disease. However, some amyloid proteins regulate vital processes. We identified a set of proteins that form amyloid-like aggregates in the brain of healthy rats. One of them - the FXR1 protein is known to regulate memory and emotions. FXR1 forms amyloid fibrils that bind RNA molecules and prevent their degradation in brain cortex neurons. Amyloid-forming sequence of FXR1 is highly conserved across mammals including human. Discovery of functional amyloids in mammalian brain shows that strategy aimed at the development of universal anti-amyloid drugs is unpromising. Such potential drugs should prevent or suppress formation of pathological aggregates of a certain protein, but not affect functional amyloids.