bluuebunny/crossref_metadata_2025_split huggingface dataset:
Soil nutrient stoichiometry affects the initial response of microbial community to trophic perturbation
Authors: Mise Kazumori , Maruyama Runa , Miyabara Yuichi , Kunito Takashi , Senoo Keishi , Otsuka Shigeto 
Published: May 2018

AbstractSoil microbes are drivers of global ecosystem functionality and are continuously subjected to external perturbations. It is fundamental for ecologists and environmental scientists to understand and further predict the microbes’ responses to these perturbations. A major and ubiquitous perturbation is the addition of chemical nutrients, including fertilizers and animal urine, to soil. Recent biogeographical studies suggest that soil nutrient stoichiometry (i.e., nutritional balance) determines microbial community structure and its functions with regard to material circulation. Given this information, here, we show that soil nutrient stoichiometry, or the bioavailable C:P ratio, determines the impact of nutrient addition on the soil’s microbial communities. We sampled two soils with similar carbon and nitrogen concentrations but with a 20-fold difference in phosphorus bioavailability. Soil microcosms with carbon and nitrogen amendments were constructed for both the soils. The phosphorus-depleted soil received prolonged effect from carbon and nitrogen amendments: the phosphatase activity gradually increased over a 24-day incubation period and the microbial community structure did not present recovery to its initial state. In contrast, in the other soil, both phosphatase activity and microbial community structure gradually returned to those of the control samples. Phosphorus depletion mitigated carbon and nitrogen intake; therefore, the effects of carbon and nitrogen amendment lasted longer. Our results demonstrate that nutritional stoichiometry is a strong predictor of microbial community dynamics in response to trophic perturbation, particularly when considering the length of time the trait of perturbation persists in the soil.
Identifying lncRNA-mediated regulatory modules via ChIA-PET network analysis
Authors: Thiel Denise , Conrad Nataša Djurdjevac , Peschutter Ria X , Siebert Heike , Marsico Annalisa 
Published: May 2018

AbstractBackgroundAlthough several studies have provided insights into the role of long non-coding RNAs (lncRNAs), the majority of them has unknown function. Recent evidence has shown the importance of both lncR-NAs and chromatin interactions in transcriptional regulation. Although network-based methods, mainly exploiting gene-lncRNA co-expression, have been applied to characterize lncRNA of unknown function by means of ‘guilt-by-association’ strategies, no method exists which combines co-expression analysis with 3D chromatin interaction data.ResultsTo better understand the function of chromatin interactions in the context of lncRNA-mediated gene regulation, we have developed a multi-step graph analysis approach to examine the RNA polymerase II ChIA-PET chromatin interaction network in the K562 human cell line. We have annotated the network with gene and lncRNA coordinates, and chromatin states from the ENCODE project. We used centrality measures, as well as an adaptation of our previously developed Markov State Models (MSM) clustering method, to gain a better understanding of lncRNAs in transcriptional regulation. The novelty of our approach resides into the detection of fuzzy regulatory modules based on network properties and their optimization based on co-expression analysis between genes and gene-lncRNA pairs. This results in our method returning morebona fideregulatory modules than other state-of-the art approaches for clustering on graphs.ConclusionsInterestingly, we find that lncRNA network hubs tend to be significantly enriched in disease association, positional conservation and enhancer-like functions. We validated regulatory functions for well known lncRNAs, such as MALAT1 and the enhancer-like lncRNA FALEC. In addition, by investigating the modular structure of bigger components we show that we can propose regulatory functional mechanisms for uncharacterized lncRNAs, such FLJ37453, RP11442N24 B.1 and LINC00910.
Deep Neural Network for Protein Contact Prediction by Weighting Sequences in a Multiple Sequence Alignment
Authors: Fukuda Hiroyuki , Tomii Kentaro 
Published: May 2018

AbstractProtein contact prediction is a crucially important step for protein structure prediction. To predict a contact, approaches of two types are used: evolutionary coupling analysis (ECA) and supervised learning. ECA uses a large multiple sequence alignment (MSA) of homologue sequences and extract correlation information between residues. Supervised learning uses ECA analysis results as input features and can produce higher accuracy. As described herein, we present a new approach to contact prediction which can both extract correlation information and predict contacts in a supervised manner directly from MSA using a deep neural network (DNN). Using DNN, we can obtain higher accuracy than with earlier ECA methods. Simultaneously, we can weight each sequence in MSA to eliminate noise sequences automatically in a supervised way. It is expected that the combination of our method and other meta-learning methods can provide much higher accuracy of contact prediction.
Developmental “awakening” of primary motor cortex to the sensory consequences of movement
Authors: Dooley James C. , Blumberg Mark S. 
Published: May 2018

ABSTRACTBefore primary motor cortex (M1) develops its motor functions, it functions like a somatosensory area. Here, by recording from neurons in the forelimb representation of M1 in postnatal day (P) 8-12 rats, we demonstrate a rapid shift in its sensory responses. At P8-10, M1 neurons respond overwhelmingly to feedback from sleep-related twitches of the forelimb, but the same neurons do not respond to wake-related movements. By P12, M1 neurons suddenly respond to wake movements, a transition that results from opening the sensory gate in the external cuneate nucleus. Also at P12, few M1 neurons respond to twitches, but the full complement of twitch-related feedback observed at P8 can be unmasked through local disinhibition. Finally, through P12, M1 sensory responses originate in the deep thalamorecipient layers, not primary somatosensory cortex. These findings demonstrate that M1 initially establishes a sensory framework upon which its later-emerging role in motor control is built.
UPA-Seq: Prediction of Functional LncRNAs Using Differential Sensitivity to UV Crosslinking
Authors: Komatsu Taiwa , Mito Mari , Fujii Koichi , Iwasaki Shintaro , Nakagawa Shinichi 
Published: May 2018

SummaryWhile a large number of long noncoding RNAs (lncRNAs) are transcribed from the genome of higher eukaryotes, systematic prediction of their functionality has been challenging due to the lack of conserved sequence motifs or structures. Assuming that lncRNAs function as large ribonucleoprotein complexes and thus are easily crosslinked to proteins upon UV irradiation, we performed RNA-Seq analyses of RNAs recovered from the aqueous phase after UV irradiation and phenol-chloroform extraction (UPA-Seq). As expected, the numbers of UPA-Seq reads mapped to known functional lncRNAs were remarkably reduced upon UV irradiation. Comparison with ENCODE eCLIP data revealed that lncRNAs that exhibited greater decreases upon UV irradiation preferentially associated with proteins containing prion-like domains (PrLDs). Fluorescent in situ hybridization (FISH) analyses revealed the nuclear localization of novel functional lncRNA candidates, including one that accumulated at the site of transcription. We propose that UPA-Seq provides a useful tool for the selection of lncRNA candidates to be analyzed in depth in subsequent functional studies.
Higher rostral locus coeruleus integrity is associated with better memory performance in older adults
Authors: Dahl Martin J. , Mather Mara , Düzel Sandra , Bodammer Nils C. , Lindenberger Ulman , Kühn Simone , Werkle-Bergner Markus 
Published: May 2018

AbstractFor decades, research into memory decline in human cognitive aging has focused on neocortical regions, the hippocampus, and dopaminergic neuromodulation. Recent findings indicate that the locus coeruleus (LC) and noradrenergic neuromodulation may also play an important role in shaping memory development in later life. However, technical challenges in quantifying LC integrity have hindered the study of LC-cognition associations in humans. Using high-resolution neuromelanin-sensitive magnetic resonance imaging, we found that individual differences in learning and memory were positively associated with LC integrity across a variety of memory tasks in younger (n = 66), and older adults (n = 228). Moreover, we observed functionally relevant age differences confined to rostral LC. Older adults with a more youth-like rostral LC also showed higher memory performance. These findings link non-invasive, in vivo indices of LC integrity to memory in aging and highlight the role of the LC norepinephrine system in the decline of cognition.
Preferred walking speed on rough terrain; is it all about energetics?
Authors: Gast Koren , Kram Rodger , Riemer Raziel 
Published: May 2018

AbstractHumans have evolved the ability to walk very efficiently. Further, humans prefer to walk at speeds that approximately minimize their metabolic energy expenditure per unit distance (i.e. gross cost of transport, COT). This has been found in a variety of population groups and other species. However, these studies were performed on smooth, level ground or on treadmills. We hypothesized that the objective function for walking is more complex than only minimizing the COT. To test this idea, we compared the preferred speeds and the relationships between COT and speed for people walking on both a smooth, level floor and a rough, natural terrain trail. Rough terrain presumably introduces other factors, such as stability, to the objective function. 10 healthy men walked on both a straight, flat, smooth floor and on an outdoor trail strewn with rocks and boulders. In both locations, subjects performed 6-8 trials at different speeds relative to their preferred speed. The COT-speed relationships were similarly U-shaped for both surfaces, but the COT values on rough terrain were approximately 215% greater. On the smooth surface, the preferred speed (1.24+/-0.14 m/sec) was 5.1% faster (p>0.05) than the speed that minimized COT (1.18 m/sec) but on rough terrain, the preferred speed (1.06+/-0.07 m/sec) was 6.2% slower (p>0.05) than the COT minimum speed (1.13 m/sec). This suggests that the objective function when walking on rough terrain includes additional factors such as stability.Summary statement: On rough terrain, humans do not choose their walking speed based on metabolic energy minimization alone.
Polygenic adaptation fuels genetic redundancy inDrosophila
Authors: Barghi Neda , Tobler Raymond , Nolte Viola , Jaksic Ana Marija , Mallard Francois , Otte Kathrin Anna , Dolezal Marlies , Taus Thomas , Kofler Robert , Schlöetterer Christian 
Published: May 2018

AbstractThe genetic architecture of adaptive traits is of key importance to predict evolutionary responses. Most adaptive traits are polygenic – i.e. result from selection on a large number of genetic loci – but most molecularly characterized traits have a simple genetic basis. This discrepancy is best explained by the difficulty in detecting small allele frequency changes across many contributing loci. To resolve this, we use laboratory natural selection, a framework that is powerful enough to detect signatures for selective sweeps and polygenic adaptation. We exposed 10 replicates of aDrosophila simulanspopulation to a new temperature regime and uncovered a polygenic architecture of an adaptive trait with high genetic redundancy among adaptive alleles. We observed convergent phenotypic responses, e.g. fitness, metabolic rate and fat content, and a strong polygenic response (99 selected alleles; means=0.061). However, each of these selected alleles increased in frequency only in a subset of the evolving replicates. Our results show that naturalD. simulanspopulations harbor a vast reservoir of adaptive variation facilitating rapid evolutionary responses. The observed genetic redundancy potentiates this genotypic variation through multiple genetic pathways leading to phenotypic convergence. This key property of adaptive alleles requires the modification of testing strategies in natural populations beyond the search for convergence on the molecular level.
Asymmetrical interference between number and item size perception provide evidence for a domain specific impairment in dyscalculia
Authors: Castaldi Elisa , Mirassou Anne , Dehaene Stanislas , Piazza Manuela , Eger Evelyn 
Published: May 2018

AbstractDyscalculia, a specific learning disability that impacts arithmetical skills, has previously been associated to a deficit in the precision of the system that estimates the approximate number of objects in visual scenes (the so called ‘number sense’ system). However, because in tasks involving numerosity comparisons dyscalculics’ judgements appears disproportionally affected by continuous quantitative dimensions (such as the size of the items), an alternative view linked dyscalculia to a domain-general difficulty in inhibiting task-irrelevant responses.To arbitrate between these views, we evaluated the degree of reciprocal interference between numerical and non-numerical quantitative dimensions in adult dyscalculics and matched controls. We used a novel stimulus set orthogonally varying in mean item size and numerosity, putting particular attention into matching both features’ perceptual discriminability. Participants compared those stimuli based on each of the two dimensions. While control subjects showed no significant size interference when judging numerosity, dyscalculics’ numerosity judgments were strongly biased by the unattended size dimension. Importantly however, both groups showed the same degree of interference from number when judging mean size. Moreover, only the ability to discard the irrelevant size information when comparing numerosity (but not the reverse) significantly predicted calculation ability across subjects.Overall, our results show that numerosity discrimination is less prone to interference than discrimination of another quantitative feature (mean item size) when the perceptual discriminability of these features is matched, as here in control subjects. By quantifying, for the first time, dyscalculic subjects’ degree of interference on another orthogonal dimension of the same stimuli, we are able to exclude a domain-general inhibition deficit as explanation for their poor / biased numerical judgement. We suggest that enhanced reliance on non-numerical cues during numerosity discrimination can represent a strategy to cope with a less precise number sense.
Human vicarious trial and error is predictive of spatial navigation performance
Authors: Santos-Pata Diogo , Verschure Paul FMJ 
Published: May 2018

ABSTRACTWhen learning new environments, rats often pause at decision points and look back and forth over their possible trajectories as if they were imagining the future outcome of their actions, a behavior termed “Vicarious trial and error” (VTE). As the animal learns the environmental configuration, rats change from deliberative to habitual behavior, and VTE tends to disappear, suggesting a functional relevance in the early stages of learning. Despite the extensive research on spatial navigation, learning and VTE in the rat model, fewer studies have focused on humans. Here, we tested whether head-scanning behaviors that humans typically exhibit during spatial navigation are as predictive of spatial learning as in the rat. Subjects performed a goal-oriented virtual navigation task in a symmetric environment. Spatial learning was assessed through the analysis of trajectories, timings, and head orientations, under habitual and deliberative spatial navigation conditions. As expected, we found that trajectory length and duration decreased with the trial number, implying that subjects learned the spatial configuration of the environment over trials. Interestingly, IdPhi (a standard metric of VTE) also decreased with the trial number, suggesting that humans benefit from the same head-orientation scanning behavior as rats at spatial decision-points. Moreover, IdPhi captured exclusively at the first decision-point of each trial, was correlated with trial trajectory duration and length. Our findings demonstrate that in VTE is a signature of the stage of spatial learning in humans, and can be used to predict performance in navigation tasks with high accuracy.
Overt social interaction and resting state in young adult males with autism: core and contextual neural features
Authors: Jasmin Kyle , Gotts Stephen J. , Xu Y. , Liu S. , Riddell Cameron , Ingeholm John , Kenworthy Lauren , Wallace Gregory L. , Braun Allen R. , Martin Alex 
Published: May 2018

AbstractConversation is an important and ubiquitous social behavior. Individuals with Autism Spectrum Disorder (autism) without intellectual disability often have normal structural language abilities but deficits in social aspects of communication like pragmatics, prosody, and eye contact. Previous studies of resting state activity suggest that intrinsic connections among neural circuits involved with social processing are disrupted in autism, but to date no neuroimaging study has examined neural activity during the most commonplace yet challenging social task: spontaneous conversation. Here we used functional MRI to scan autistic males (N=19) without intellectual disability and age- and IQ-matched typically developing controls (N=20) while they engaged in a total of 193 face-to-face interactions. Participants completed two kinds of tasks: Conversation, which had high social demand, and Repetition, which had low social demand. Autistic individuals showed abnormally increased task-driven inter-regional temporal correlation relative to controls, especially among social processing regions and during high social demand. Furthermore, these increased correlations were associated with parent ratings of participants’ social impairments. These results were then compared with previously-acquired resting-state data (56 Autism, 62 Control participants). While some inter-regional correlation levels varied by task or rest context, others were strikingly similar across both task and rest, namely increased correlation among the thalamus, dorsal and ventral striatum, somatomotor, temporal and prefrontal cortex in the autistic individuals, relative to the control groups. These results suggest a basic distinction. Autistic cortico-cortical interactions vary by context, tending to increase relative to controls during Task and decrease during Rest. In contrast, striato- and thalamocortical relationships with socially engaged brain regions are increased in both Task and Rest, and may be core to the condition of autism.
A systematic genetic analysis and visualization of phenotypic heterogeneity among orofacial cleft GWAS signals
Authors: Carlson Jenna C. , Anand Deepti , Butali Azeez , Buxo Carmen J. , Christensen Kaare , Deleyiannis Frederic , Hecht Jacqueline T. , Moreno Lina M. , Orioli Ieda M. , Padilla Carmencita , Shaffer John R. , Vieira Alexandre R. , Wehby George L. , Weinberg Seth M. , Murray Jeffrey C. , Beaty Terri H. , Saadi Irfan , Lachke Salil A. , Marazita Mary L. , Feingold Eleanor , Leslie Elizabeth J. 
Published: May 2018

AbstractPhenotypic heterogeneity is a hallmark of complex traits, and genetic studies of such traits may focus on them as a single diagnostic entity or by analyzing specific components. For example, in orofacial clefting (OFC), three subtypes – cleft lip (CL), cleft lip and palate (CLP), and cleft palate (CP) have been studied separately and in combination. To further dissect the genetic architecture of OFCs and how a given associated locus may be contributing to distinct subtypes of a trait we developed a framework for quantifying and interpreting evidence of subtype-specific or shared genetic effects in complex traits. We applied this technique to create a “cleft map” of the association of 30 genetic loci with three OFC subtypes. In addition to new associations, we found loci with subtype-specific effects (e.g., GRHL3 (CP), WNT5A (CLP)), as well as loci associated with two or all three subtypes. We cross-referenced these results with mouse craniofacial gene expression datasets, which identified additional promising candidate genes. However, we found no strong correlation between OFC subtypes and expression patterns. In aggregate, the cleft map revealed that neither subtype-specific nor shared genetic effects operate in isolation in OFC architecture. Our approach can be easily applied to any complex trait with distinct phenotypic subgroups.
Genetic tools weed out misconceptions of strain reliability inCannabis sativa: Implications for a budding industry
Authors: Schwabe Anna L. , McGlaughlin Mitchell E. 
Published: May 2018

AbstractCannabis sativais listed as a Schedule I substance by the United States Drug Enforcement Agency and has been federally illegal in the United States since 1937. However, the majority of states in the United States, as well as several countries, now have various levels of legalCannabis. Products are labeled with identifying strain names but there is no official mechanism to registerCannabisstrains, therefore the potential exists for incorrect identification or labeling. This study uses genetic analyses to investigate strain reliability from the consumer point of view. Ten microsatellite regions were used to examine samples from strains obtained from dispensaries in three states. Samples were examined for genetic similarity within strains, and also a possible genetic distinction between Sativa, Indica, or Hybrid types. The analyses revealed genetic inconsistencies within strains. Additionally, although there was strong statistical support dividing the samples into two genetic groups, the groups did not correspond to commonly reported Sativa/Hybrid/Indica types. Genetic differences have the potential to lead to phenotypic differences and unexpected effects, which could be surprising for the recreational user, but have more serious implications for patients relying on strains that alleviate specific medical symptoms.
Absence of surface IgD does not impair naive B cell homeostasis and memory B cell formation in humans
Authors: Nechvatalova J. , Bartol S.J.W. , Chovancova Z. , Boon L. , Vlkova M. , van Zelm M.C. 
Published: May 2018

One Sentence SummaryHuman B cells with a genetic defect inIGHDdevelop normallyin vivo, and do not have a competitive disadvantage to IgD-expressing B cells for developing into memory B cells.AbstractSurface immunoglobulin D (IgD) is co-expressed with IgM on naive mature B cells. Still, the role of surface IgD remains enigmatic even 50 years after its initial discovery. We here examined thein vivorole of surface IgD in human B-cell homeostasis and antibody responses in four individuals with heterozygous nonsense mutations inIGHD. AllIGHDheterozygous individuals had normal numbers of B cells and serum immunoglobulins, and did not show signs of immunodeficiency or immune dysregulation. IgD+and IgD– naive mature B cells were present in equal numbers and showed similar immunophenotypes, except for decreased expression of CD79b in the IgD– subset. Furthermore, both IgD+ and IgD– naive mature B cells had normal replication histories, similar capacities to differentiate into plasma cells uponin vitrostimulation, and Ig switched memory B cells showed similar levels of somatic hypermutations. Thus human B cells lacking IgD expression develop normally and generate immunological memoryin vivo, suggesting that surface IgD might function more restricted in regulating of B-cell activation to specific antigenic structures.