bluuebunny/crossref_metadata_2025_split huggingface dataset:
Capsule Networks as Recurrent Models ofGrouping and Segmentation
Authors: Doerig Adrien , Schmittwilken Lynn , Sayim Bilge , Manassi Mauro , Herzog Michael H. 
Published: August 2019

AbstractClassically, visual processing is described as a cascade of local feedforward computations. Feedforward Convolutional Neural Networks (ffCNNs) have shown how powerful such models can be. However, using visual crowding as a well-controlled challenge, we previously showed that no classic model of vision, including ffCNNs, can explain human global shape processing (1). Here, we show that Capsule Neural Networks (CapsNets; 2), combining ffCNNs with recurrent grouping and segmentation, solve this challenge. We also show that ffCNNs and standard recurrent CNNs do not, suggesting that the grouping and segmentation capabilities of CapsNets are crucial. Furthermore, we provide psychophysical evidence that grouping and segmentation are implemented recurrently in humans, and show that CapsNets reproduce these results well. We discuss why recurrence seems needed to implement grouping and segmentation efficiently. Together, we provide mutually reinforcing psychophysical and computational evidence that a recurrent grouping and segmentation process is essential to understand the visual system and create better models that harness global shape computations.Author SummaryFeedforward Convolutional Neural Networks (ffCNNs) have revolutionized computer vision and are deeply transforming neuroscience. However, ffCNNs only roughly mimic human vision. There is a rapidly expanding body of literature investigating differences between humans and ffCNNs. Several findings suggest that, unlike humans, ffCNNs rely mostly on local visual features. Furthermore, ffCNNs lack recurrent connections, which abound in the brain. Here, we use visual crowding, a well-known psychophysical phenomenon, to investigate recurrent computations in global shape processing. Previously, we showed that no model based on the classic feedforward framework of vision can explain global effects in crowding. Here, we show that Capsule Neural Networks (CapsNets), combining ffCNNs with recurrent grouping and segmentation, solve this challenge. ffCNNs and recurrent CNNs with lateral and top-down recurrent connections do not, suggesting that grouping and segmentation are crucial for human-like global computations. Based on these results, we hypothesize that one computational function of recurrence is to efficiently implement grouping and segmentation. We provide psychophysical evidence that, indeed, grouping and segmentation is based on time consuming recurrent processes in the human brain. CapsNets reproduce these results too. Together, we provide mutually reinforcing computational and psychophysical evidence that a recurrent grouping and segmentation process is essential to understand the visual system and create better models that harness global shape computations.
Autophagy mediates temporary reprogramming and dedifferentiation in plant somatic cells
Authors: Rodriguez Eleazar , Chevalier Jonathan , Olsen Jakob , Ansbøl Jeppe , Kapousidou Vaitsa , Zuo Zhangli , Svenning Steingrim , Loefke Christian , Koemeda Stefanie , Drozdowskyj Pedro Serrano , Jez Jakub , Durnberger Gerhard , Kuenzl Fabian , Schutzbier Michael , Mechtler Karl , Lolle Signe , Dagdas Yasin , Petersen Morten 
Published: August 2019

AbstractSomatic cells acclimate to changes in the environment by temporary reprogramming. Much has been learned about transcription factors that induce these cell-state switches in both plants and animals, but how cells rapidly modulate their proteome remains elusive. Here, we show rapid induction of autophagy during temporary reprogramming in plants triggered by phytohormones, immune and danger signals. Quantitative proteomics following sequential reprogramming revealed that autophagy is required for timely decay of previous cellular states and for tweaking the proteome to acclimate to the new conditions. Signatures of previous cellular programs thus persist in autophagy deficient cells, affecting cellular decision-making. Concordantly, autophagy deficient cells fail to acclimatize to dynamic climate changes. Similarly, they have defects in dedifferentiating into pluripotent stem cells, and redifferentiation during organogenesis. These observations indicate that autophagy mediates cell state switches that underlie somatic cell reprogramming in plants and possibly other organisms, and thereby promotes phenotypic plasticity.
Sex chromosomes control vertical transmission of feminizing Wolbachia symbionts in an isopod
Authors: Becking Thomas , Chebbi Mohamed Amine , Giraud Isabelle , Moumen Bouziane , Laverré Tiffany , Caubet Yves , Peccoud Jean , Gilbert Clément , Cordaux Richard 
Published: August 2019

AbstractMicrobial endosymbiosis is widespread in animals, with major ecological and evolutionary implications. Successful symbiosis relies on efficient vertical transmission through host generations. However, when symbionts negatively affect host fitness, hosts are expected to evolve suppression of symbiont effects or transmission. Here we show that sex chromosomes control vertical transmission of feminizing Wolbachia endosymbionts in the isopod Armadillidium nasatum. Theory predicts that the invasion of an XY/XX species by cytoplasmic sex ratio distorters is unlikely because it leads to fixation of the unusual (and often lethal or infertile) YY genotype. We demonstrate that A. nasatum X and Y sex chromosomes are genetically highly similar and YY individuals are viable and fertile, thereby enabling Wolbachia spread in this XY-XX species. Nevertheless, we show that Wolbachia cannot drive fixation of YY individuals because infected YY females do not transmit Wolbachia to their offspring, unlike XX and XY females. The genetic basis fits the model of a Y-linked recessive allele (associated with an X-linked dominant allele), in which the homozygous state suppresses Wolbachia transmission. Moreover, production of all-male progenies by infected YY females restores a balanced sex ratio at the host population level. This suggests that blocking of Wolbachia transmission by YY females may have evolved to suppress feminization, thereby offering a whole new perspective on the evolutionary interplay between microbial symbionts and host sex chromosomes.
The genome of a subterrestrial nematode reveals an evolutionary strategy for adaptation to heat
Authors: Weinstein Deborah J. , Allen Sarah E. , Lau Maggie C. Y. , Erasmus Mariana , Asalone Kathryn C. , Walters-Conte Kathryn , Deikus Gintaras , Sebra Robert , Borgonie Gaetan , van Heerden Esta , Onstott Tullis C. , Bracht John R. 
Published: August 2019

AbstractThe nematodeHalicephalobus mephistowas originally discovered inhabiting a deep terrestrial aquifer 1.3 km underground.H. mephistocan thrive under conditions of abiotic stress including heat and minimal oxygen, where it feeds on a community of both chemolithotrophic and heterotrophic prokaryotes in an unusual ecosystem isolated from the surface biosphere. Here we report the comprehensive genome and transcriptome of this organism, identifying a signature of adaptation: an expanded repertoire of 70 kilodalton heat-shock proteins (Hsp70) and avrRpt2 induced gene 1 (AIG1) proteins. We find that positive selection has driven the expansion of Hsp70 genes, which are also transcriptionally induced upon growth under heat stress. We further show that AIG1 may have been acquired by horizontal gene transfer (HGT) from a rhizobial fungus. Over one-third of the genes ofH. mephistoare novel, highlighting the divergence of this nematode from other sequenced organisms. This work sheds light on the genomic strategies of adaptation to heat in the first complete subterrestrial eukaryotic genome.
Suppression of membranous LRP5 recycling, WNT/β-catenin signaling, and colorectal tumorigenesis by 15-LOX-1 peroxidation of PI3P_linoleic acid
Authors: Liu Fuyao , Zuo Xiangsheng , Liu Yi , Deguchi Yasunori , Moussalli Micheline J. , Chen Weidong , Yang Peiying , Wei Bo , Tan Lin , Lorenzi Philip L. , Gao Shen , Jaoude Jonathan C. , Mehdizadeh Amir , Ann Valentin Lovie , Wei Daoyan , Shureiqi Imad 
Published: August 2019

SUMMARYAberrant Wnt/β-catenin activation is a major driver of colorectal cancer (CRC), which is typically initiated byAPCmutations. Additional modifiable factors beyondAPCmutations have been recognized to be important for further potentiation of aberrant β-catenin activation to promote colorectal tumorigenesis. These factors have yet to be clearly identified. Western-type diets are increasingly enriched in linoleic acid (LA). LA-enriched diet however promotes chemically-induced colorectal tumorigenesis in rodent models. Furthermore, the main metabolizing enzyme of LA, 15-lipoxygenase-1 (15-LOX-1), is transcriptionally silenced in CRC. Whether LA and 15-LOX-1 affect Wnt/β-catenin signaling to modulate colorectal tumorigenesis is poorly understood. Herein, we report that high dietary LA promoted colorectal tumorigenesis in mice with intestinally targetedAPCmutation (ApcΔ580) by upregulating a Wnt receptor, LRP5 expression, and β-catenin activation. 15-LOX-1 transgenic expression in intestinal epithelial cells suppressed LRP5 expression, β-catenin activation and subsequently CRC in these mice. In particular, 15-LOX-1 peroxidation of LA in phosphatidylinositol-3-phosphates (PI3P_LA) into PI3P_13-HODE decreased PI3P binding to SNX17and LRP5, which inhibited LRP5 recycling from endosomes to the plasma membrane, thereby leading to an increase of LRP5 lysosomal degradation. Our findings demonstrate for the first time that 15-LOX-1 metabolism of LA in PI3P to regulate LRP5 membrane abundance is a modifiable factor of Wnt/β-catenin aberrant signaling that could be potentially therapeutically targeted to suppress colorectal tumorigenesis and progression.
Genome sequencing for early-onset dementia: high diagnostic yield and frequent observation of multiple contributory alleles
Authors: Cochran J. Nicholas , McKinley Emily C. , Cochran Meagan , Amaral Michelle D. , Moyers Bryan A. , Lasseigne Brittany N. , Gray David E. , Lawlor James M.J. , Prokop Jeremy W. , Geier Ethan G. , Holt James M. , Thompson Michelle L. , Newberry J. Scott , Yokoyama Jennifer S. , Worthey Elizabeth A. , Geldmacher David S. , Love Marissa Natelson , Cooper Gregory M. , Myers Richard M. , Roberson Erik D. 
Published: August 2019

ABSTRACTWe assessed the utility of genome sequencing for early-onset dementia. Participants were selected from a memory disorders clinic. Genome sequencing was performed along withC9orf72repeat expansion testing. All returned sequencing results were Sanger validated clinically. Prior clinical diagnoses included Alzheimer’s disease, frontotemporal dementia, and unspecified dementia. The mean age-of-onset was 54 (41–76). 50% of patients had a strong family history, 37.5% had some, and 12.5% had no known family history. Nine of 32 patients (28%) had a variant defined as pathogenic or likely pathogenic (P/LP) by American College of Medical Genetics standards, including variants inAPP,C9orf72,CSF1R, andMAPT. Nine patients (including three with P/LP variants) harbored established risk alleles with moderate penetrance (odds ratios of about 2–5) inABCA7,AKAP9,GBA,PLD3,SORL1, andTREM2. All six patients harboring these moderate penetrance variants but not P/LP variants also had one or twoAPOEε4 alleles. One patient had twoAPOEε4 alleles with no other established contributors. In total, 16 patients (50%) harbored one or more genetic variants likely to explain symptoms. We identified variants of uncertain significance (VUSs) inABI3, ADAM10, ARSA, GRID2IP, MME, NOTCH3, PLCD1, PSEN1, TM2D3, TNK1, TTC3, and VPS13C, also often along with other variants. In summary, genome sequencing for early-onset dementia demonstrated high utility, with particular advantages where targeted testing may fail such as atypical variant-disease associations or presence of multiple moderate impact alleles. One or more established contributory alleles is often present in early-onset dementia, supporting an oligogenic model.
Exogenous alginate protectsStaphylococcus aureusfrom killing byPseudomonas aeruginosa
Authors: Price Courtney E. , Brown Dustin G. , Limoli Dominique H. , Phelan Vanessa V. , O’Toole George A. 
Published: August 2019

ABSTRACTCystic fibrosis (CF) patients chronically infected with bothPseudomonas aeruginosaandStaphylococcus aureushave worse health outcomes than patients who are mono-infected with eitherP. aeruginosaorS. aureus. We showed previously that mucoid strains ofP. aeruginosacan co-exist withS. aureus in vitrodue to transcriptional downregulation of several toxic exoproducts typically produced byP. aeruginosa, including siderophores, rhamnolipids, and HQNO (2-heptyl-4-hydroxyquinoline N-oxide). Here we demonstrate that exogenous alginate protectsS. aureusfromP. aeruginosain both planktonic and biofilm co-culture models under a variety of nutritional conditions.S. aureusprotection in the presence of exogenous alginate is due to transcriptional downregulation ofpvdA, a gene required for the production of the iron scavenging siderophore pyoverdine, as well as down-regulation of the PQS (Pseudomonas quinolone signal; 2-heptyl-3,4-dihydroxyquinoline) quorum sensing system. The impact of exogenous alginate is independent of endogenous alginate production. We further demonstrate that co-culture of mucoidP. aeruginosawith non-mucoidP. aeruginosacan mitigate the killing ofS. aureusby the non-mucoid strain ofP. aeruginosa, indicating that the mechanism we describe here may functionin vivoin the context of mixed infections. Finally, we investigated a panel of mucoid clinical isolates that retain the ability killS. aureusat late time points, and show that each strain has a unique expression profile, indicating that mucoid isolates can overcome the effects of mucoidy in a strain-specific manner.IMPORTANCECF patients are chronically infected by polymicrobial communities of microorganisms. The two dominant bacterial pathogens that infect CF patient lungs areP. aeruginosaandS. aureus, with ∼30% of patients co-infected by both species. Patients infected with bothP. aeruginosaandS. aureushave worse outcomes than mono-infected patients, and both species persist within the same physical space in the lungs of CF patients. A variety of host and environmental factors have been demonstrated to promoteP. aeruginosa-S. aureusco-existence, despite evidence thatP. aeruginosakillsS. aureuswhen these organisms are co-culturedin vitro. Thus, a better understanding ofP. aeruginosa-S. aureusinteractions, particularly mechanisms by which these microorganisms are able to co-exist in proximal physical space, will lead to better informed treatments for chronic polymicrobial infections.
Higher order interactions and coexistence theory
Authors: Singh Pragya , Baruah Gaurav 
Published: August 2019

AbstractHigher order interactions (HOIs) have been suggested to stabilize diverse ecological communities. However, their role in maintaining species coexistence from the perspective of modern coexistence theory is unknown. Here, using a three-species Lotka-Volterra model, we derive a general rule for species coexistence modulated by HOIs. We show that negative HOIs that intensify pairwise competition, can promote coexistence across a wide range of fitness differences, provided that HOIs strengthen intraspecific competition more than interspecific competition. In contrast, positive HOIs that alleviate pairwise competition can also stabilize coexistence across a wide range of fitness differences, irrespective of differences in strength of inter- and intraspecific competition. Furthermore, we extend our three-species analytical result to multispecies competitive community and show, using simulations, that feasible multispecies coexistence is possible provided that strength of negative intraspecific HOIs is higher than interspecific HOIs. In addition, multispecies communities, however, become unstable with positive HOIs as such higher-order interactions could lead to disproportionately infeasible growth rates. This work provides crucial insights on the underlying mechanisms that could maintain species diversity and links HOIs with modern coexistence theory.
Baroreceptor denervation reduces inflammatory status and worsens cardiovascular collapse during systemic inflammation
Authors: Amorim Mateus R. , de Deus Júnia L. , Pereira Camila A. , da Silva Luiz E. V. , Borges Gabriela S. , Ferreira Nathanne S. , Batalhão Marcelo E. , Antunes-Rodrigues José , Cárnio Evelin C. , Tostes Rita C. , Branco Luiz G. S. 
Published: August 2019

ABSTRACTBeyond the regulation of cardiovascular function, baroreceptor afferents play polymodal roles. We hypothesized that baroreceptor denervation affects lipopolysaccharide (LPS)-induced systemic inflammation (SI) and hemodynamic collapse in conscious rats, and that these parameters are interconnected. We combine: a) hemodynamic and thermoregulatory recordings after LPS administration at a septic-like dose b) analysis of the cardiovascular complexity, c) evaluation of vascular function in mesenteric resistance vessels, and d) measurements of inflammatory cytokines (plasma and spleen). LPS-induced drop in blood pressure was higher in sino-aortic denervated (SAD) rats. LPS-induced hemodynamic collapse was associated with SAD-dependent autonomic disbalance. LPS-induced vascular dysfunction was not affected by SAD. Surprisingly, SAD blunted LPS-induced surges of plasma and spleen cytokines. These data indicate that sino-aortic afferents are key to alleviate LPS-induced cardiovascular collapse, affecting the autonomic cardiovascular control, without affecting resistance blood vessels. Moreover, baroreflex modulation of the LPS-induced SI and hemodynamic collapse seem not to be interconnected.
Reassessing the validity of slow-wave dynamics as a proxy for NREM sleep homeostasis
Authors: Hubbard Jeffrey , Gent Thomas C. , Hoekstra Marieke M. B. , Emmenegger Yann , Mongrain Valerie , Landolt Hans-Peter , Adamantidis Antoine R. , Franken Paul 
Published: August 2019

AbstractSleep-wake driven changes in NREM sleep (NREMS) EEG delta (δ: ∼0.75-4.5Hz) power are widely used as proxy for a sleep homeostatic process. We noted frequency increases in δ-waves in sleep-deprived (SD) mice, prompting us to re-evaluate how slow-wave characteristics relate to prior sleep-wake history. We discovered two types of δ-waves; one responding to SD with high initial power and fast, discontinuous decay (δ2: ∼2.5-3.5Hz) and another unrelated to time-spent-awake with slow, linear decays (δ1: ∼0.75-1.75Hz). Human experiments confirmed this δ-band heterogeneity. Similar to SD, silencing of centromedial thalamus neurons boosted δ2-waves, specifically. δ2-dynamics paralleled that of temperature, muscle tone, heart-rate, and neuronal UP/DOWN state lengths, all reverting to characteristic NREMS levels within the first recovery hour. Thus, prolonged waking seems to necessitate a physiological recalibration before typical NREMS can be reinstated. These short-lasting δ2-dynamics challenge accepted models of sleep regulation and function based on the merged δ-band as sleep-need proxy.
Diversity amongst human cortical pyramidal neurons revealed via their sag currents and frequency preferences
Authors: Chameh Homeira Moradi , Rich Scott , Wang Lihua , Chen Fu-Der , Zhang Liang , Carlen Peter L. , Tripathy Shreejoy J. , Valiante Taufik A. 
Published: August 2019

AbstractIn the human neocortex coherent interlaminar theta oscillations are driven by deep cortical layers, suggesting neurons in these layers exhibit distinct electrophysiological properties. To characterize this potential distinctiveness, we use in vitro whole-cell recordings from cortical layers 2 and 3 (L2&3), layer 3c (L3c) and layer 5 (L5) of the human cortex. Across all layers we observe notable heterogeneity, indicating human cortical pyramidal neurons are an electrophysiologically diverse population. L5 pyramidal cells are the most excitable of these neurons and exhibit the most prominent sag current (abolished by blockade of the hyperpolarization activated cation current, Ih). While subthreshold resonance is more common in L3c and L5, we rarely observe this resonance at frequencies greater than 2Hz. However, the frequency dependent gain of L5 neurons reveals they are most adept at tracking both delta and theta frequency inputs, a unique feature that may indirectly be important for the generation of cortical theta oscillations.
Climatic sensitivity of species’ vegetative and reproductive phenology in a Hawaiian montane wet forest
Authors: Pau Stephanie , Cordell Susan , Ostertag Rebecca , Sack Lawren , Inman-Narahari Faith 
Published: August 2019

ABSTRACTUnderstanding the way tropical tree phenology (i.e., the timing and amount of seed and leaf production) responds to climate is vital for predicting how climate change may alter ecological functioning of tropical forests. We examined the effects of temperature, rainfall, and photosynthetically active radiation (PAR) on seed and leaf phenology in a montane wet forest on Hawaiʻi using monthly data collected over ∼6 years. We expected that species’ phenologies were more sensitive to temperature and PAR than to rainfall at this wet tropical site because rainfall is not limiting. Seed production declined with increasing temperatures for two foundational species in Hawaiian forests (Acacia koaandMetrosideros polymorpha). Seed production also declined with rainfall for two species, and greater PAR for one species. One species showed relatively flat responses to climate. Community-level leaf phenology was not strongly seasonal. Unlike seed phenology, we found no effect of temperature on leaf phenology. However, leaf fall increased with rainfall. Climatic factors explained a low to moderate proportion of variance for both seed and leaf litterfall, thus the impact of future climate change on this forest will depend on how climate change interacts with other factors such as daylength, biotic, and/or evolutionary constraints. Our results nonetheless provide insight into how climate change may differentially affect different species with potential consequences for shifts in species distributions and community composition.
Sensitivity in the antioxidant system of discus fish (Symphysodonspp.) to cold temperature: evidence for species-specific cold resistance
Authors: Jin Shi-Rong , Wen Bin , Chen Zai-Zhong , Gao Jian-Zhong , Wang Lei , Liu Ying , Liu Han-Peng 
Published: August 2019

ABSTRACTThe discus fish (Symphysodonspp.) is an endemic species of the Amazon that is among the most popular ornamental fish around the world, and is usually used as the model animal for studying the diversification of Amazon fish. Here, a comparative analysis of two species of discus fish, i.e.,S. haraldiandS. aequifasciatus, based on several antioxidant indexes was conducted, to test the hypothesis that cold resistance might correlate with the diversification of discus fish. We set up a continuous sequence of three temperature programs, namely cooling (28 °C to 14 °C; -1 °C/h), cold maintenance (14 °C for 12 h) and recovery (14 °C to 28 °C; +1 °C/h). Subordinate function (SF) combined with principal component analysis (PCA) showed that the cold hardiness ofS. haraldiduring cold treatment was in the order of cooling > cold maintenance ≈ recovery, but the cold hardiness ofS. aequifasciatusduring cold treatment was in the order of cold maintenance > cooling > recovery. Specifically, the lowest cold hardiness was observed inS. aequifasciatusduring recovery, indicating that cold stress resulted in more seriously oxidative stress inS. aequifasciatusthan inS. haraldi. Overall, these results show a significant interspecific variation, indicating the correlation between environmental adaptation and the diversification of discus fish.