bluuebunny/crossref_metadata_2025_split huggingface dataset:
A multidimensional framework for measuring biotic novelty: How novel is a community?
Authors: Schittko Conrad , Bernard-Verdier Maud , Heger Tina , Buchholz Sascha , Kowarik Ingo , von der Lippe Moritz , Seitz Birgit , Joshi Jasmin , Jeschke Jonathan M. 
Published: October 2019

AbstractAnthropogenic changes in climate, land use and disturbance regimes, as well as introductions of non-native species can lead to the transformation of many ecosystems. The resulting novel ecosystems are usually characterized by species assemblages that have not occurred previously in a given area. Quantifying the ecological novelty of communities (i.e. biotic novelty) would enhance the understanding of environmental change. However, quantification remains challenging since current novelty metrics, such as the number and/or proportion of non-native species in a community, fall short of considering both functional and evolutionary aspects of biotic novelty. Here, we propose the Biotic Novelty Index (BNI), an intuitive and flexible multidimensional measure that combines (1) functional differences between native and non-native introduced species with (2) temporal dynamics of species introductions. We show that the BNI is an additive partition of Rao’s quadratic entropy, capturing the novel interaction component of the community’s functional diversity. Simulations show that the index varies predictably with the relative amount of functional novelty added by recently arrived species, and they illustrate the need to provide an additional standardized version of the index. We present a detailed R-code and two applications of the BNI by (1) measuring changes of biotic novelty of dry grassland plant communities along an urbanization gradient in a metropolitan region and (2) determining the biotic novelty of plant species assemblages at a national scale. Results illustrate the applicability of the index across scales and its flexibility in the use of data of different quality. Both case studies revealed strong connections between biotic novelty and increasing urbanization, a measure of abiotic novelty. We conclude that the BNI framework may help in building a basis for a better understanding of the ecological and evolutionary consequences of global change.
Dissociation between Frontal and Temporal-Parietal Contributions to Connected Speech in Acute Stroke
Authors: Ding Junhua , Martin Randi , Hamilton A. Cris , Schnur Tatiana T. 
Published: October 2019

AbstractHumans are uniquely able to retrieve and combine words into syntactic structure to produce connected speech. Previous identification of focal brain regions necessary for production focused primarily on associations with the content produced by speakers with chronic stroke, where function may have shifted to other regions after reorganization occurred. Here, we relate patterns of brain damage with deficits to the content and structure of spontaneous connected speech in 52 speakers during the acute stage of a left hemisphere stroke. Multivariate lesion behavior mapping demonstrated that damage to temporal-parietal regions impacted the ability to retrieve words and produce them within increasingly complex combinations. Damage primarily to inferior frontal cortex affected the production of syntactically accurate structure. In contrast to previous work, functional-anatomical dissociations did not depend on lesion size likely because acute lesions were smaller than typically found in chronic stroke. These results are consistent with predictions from theoretical models based primarily on evidence from language comprehension and highlight the importance of investigating individual differences in brain-language relationships in speakers with acute stroke.
TSA-Seq reveals a largely “hardwired” genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes
Authors: Zhang Liguo , Zhang Yang , Chen Yu , Gholamalamdari Omid , Wang Yuchuan , Ma Jian , Belmont Andrew S. 
Published: October 2019

AbstractGenome-wide mapping of chromosomal distances relative to nuclear compartments using TSA-Seq suggests a more deterministic relationship between intranuclear gene position and expression as a function of nuclear speckle distance than radial position. Gene activity increases overall with decreasing distance to nuclear speckles, with active chromosomal regions forming the apex of chromosome loops protruding from the nuclear periphery into the interior. Interestingly, genomic distances to the nearest lamina-associated domain are larger for loop apexes mapping very close to nuclear speckles, suggesting the possibility of genomic “hardwiring” and conservation of speckle-associated regions. To facilitate comparison of genome organization relative to nuclear speckles in human K562, HCT116, HFFc6, and H1 cell lines, here we describe reducing the required cell number 10-20-fold for TSA-Seq by deliberately saturating protein-labeling while preserving distance mapping by the still unsaturated DNA-labeling. Surprisingly, in pair-wise cell line comparisons, only ∼10% of the genome shows a statistically significant shift in relative nuclear speckle distances. These modest shifts in nuclear speckle distance, however, tightly correlate with changes in cell-type specific gene expression. Similarly, half of all loci that contain induced heat-shock protein genes appear pre-positioned close to nuclear speckles, with the remaining showing small shifts towards speckles with transcriptional induction. Speckle association together with chromatin decondensation correlates with expression amplification upon HSPH1 activation. Our results demonstrate a largely “hardwired” genome organization and specific genes moving small mean distances relative to speckles during cell differentiation or physiological transition, suggesting an important role of nuclear speckles in gene expression regulation.
Computational and experimental investigation of biofilm disruption dynamics induced by high velocity gas jet impingement
Authors: Prades Lledó , Fabbri Stefania , Dorado Antonio D. , Gamisans Xavier , Stoodley Paul , Picioreanu Cristian 
Published: October 2019

ABSTRACTExperimental data showed that high-speed micro-sprays can effectively disrupt biofilms on their support substratum, producing a variety of dynamic reactions such as elongation, displacement, ripples formation and fluidization. However, the mechanics underlying the impact of high-speed turbulent flows on biofilm structure is complex in such extreme conditions, since direct measurements of viscosity at these high shear rates are not possible using dynamic testing instruments. Here we used computational fluid dynamics simulations to assess the complex fluid interactions of ripple patterning produced by high-speed turbulent air jets impacting perpendicular to the surface of Streptococcus mutans biofilms, a dental pathogen causing caries, captured by high speed imaging. The numerical model involved a two-phase flow of air over a non-Newtonian biofilm, whose viscosity as a function of shear rate was estimated using the Herschel-Bulkley model. The simulation suggested that inertial, shear and interfacial tension forces governed biofilm disruption by the air jet. Additionally, the high shear rates generated by the jet impacts coupled with shear-thinning biofilm property resulted in rapid liquefaction (within milliseconds) of the biofilm, followed by surface instability and travelling waves from the impact site. Our findings suggest that rapid shear-thinning in the biofilm reproduces dynamics under very high shear flows that elasticity can be neglected under these conditions, behaving the biofilm as a Newtonian fluid. A parametric sensitivity study confirmed that both applied force intensity (i.e. high jet-nozzle air velocity) and biofilm properties (i.e. low viscosity, low air-biofilm surface tension and thickness) intensify biofilm disruption, by generating large interfacial instabilities.IMPORTANCEKnowledge of mechanisms promoting disruption though mechanical forces is essential in optimizing biofilm control strategies which rely on fluid shear. Our results provide insight into how biofilm disruption dynamics is governed by applied forces and fluid properties, revealing a mechanism for ripples formation and fluid-biofilm mixing. These findings have important implications for the rational design of new biofilms cleaning strategies with fluid jets, such as determining optimal parameters (e.g. jet velocity and position) to remove the biofilm from a certain zone (e.g. in dental hygiene or debridement of surgical site infections), or using antimicrobial agents which could increase the interfacial area available for exchange, as well as causing internal mixing within the biofilm matrix, thus disrupting the localized microenvironment which is associated with antimicrobial tolerance. The developed model also has potential application in predicting drag and pressure drop caused by biofilms on bioreactor, pipeline and ship hull surfaces.
Ecological character displacement destabilizes food webs
Authors: Barbour Matthew A. 
Published: October 2019

AbstractEcological character displacement is an adaptive process that generally increases phenotypic diversity. Despite the fact that this diversification is due to an eco-evolutionary feedback between consumers competing for shared resources, its consequences for food-web dynamics have received little attention. Here, I study a model of two consumers competing for two shared resources to examine how character displacement in consumer attack rates affects resource abundances and the resilience of food webs to perturbations. I found that character displacement always strengthened consumer-resource interactions whenever consumers competed for resources that occurred in different habitats. This increase in interaction strength resulted in lower resource abundances and less resilient food webs. This occurred under different evolutionary tradeoffs and in both simple and more realistic foraging scenarios. Taken together, my results show that the adaptive process of character displacement may come with the ecological cost of decreasing food-web resilience.
Harmonization of diffusion MRI datasets with adaptive dictionary learning
Authors: St-Jean Samuel , Viergever Max A. , Leemans Alexander 
Published: October 2019

AbstractDiffusion magnetic resonance imaging can indirectly infer the microstructure of tissues and provide metrics subject to normal variability in a population. Potentially abnormal values may yield essential information to support analysis of controls and patients cohorts, but subtle confounds could be mistaken for purely biologically driven variations amongst subjects. In this work, we propose a new harmonization algorithm based on adaptive dictionary learning to mitigate the unwanted variability caused by different scanner hardware while preserving the natural biological variability of the data. Our harmonization algorithm does not require paired training datasets, nor spatial registration or matching spatial resolution. Overcomplete dictionaries are learned iteratively from all datasets at the same time with an adaptive regularization criterion. removing variability attributable to the scanners in the process. The obtained mapping is applied directly in the native space of each subject towards a scanner-space. The method is evaluated with a public database which consists of two different protocols acquired on three different scanners. Results show that the effect size of the four studied diffusion metrics is preserved while removing variability attributable to the scanner. Experiments with alterations using a free water compartment, which is not simulated in the training data, shows that the modifications applied to the diffusion weighted images are preserved in the diffusion metrics after harmonization, while still reducing global variability at the same time. The algorithm could help multicenter studies pooling their data by removing scanner specific confounds, and increase statistical power in the process.
Preparation of single-cell suspension from mouse breast cancer focusing on preservation of original cell state information and cell type composition
Authors: Pavel Abaffy , Sandra Lettlova , Jaroslav Truksa , Mikael Kubista , Radek Sindelka 
Published: October 2019

SUMMARYSingle-cell analysis of gene expression has become a very popular method during the last decade. Unfortunately, appropriate standardization and workflow optimization remain elusive. The first step of the single cell analysis requires that the solid tissue be disassociated into a suspension of individual cells. However, during this step several technical bias can arise which can later result in the misinterpretation of the data. The goal of this study was to identify and quantify the effect of these technical factors on the quality of the single-cell suspension and the subsequent interpretation of the produced expression data. We tested the effects of various enzymes used for dissociation, several centrifugation forces, dissociation temperatures and the addition of Actinomycin D, a gene expression inhibitor. RT-qPCR was used to assess the effect from each parameter alteration, while a single-cell RNA sequencing experiment was used to confirm the optimized factors. Our concluding results provide a complete protocol for the tissue dissociation of mouse mammary tumour from 4T1 cells that preserves the original cell state and is suitable for any single-cell RNA sequencing analysis. Furthermore, our workflow may serve as a guide for the optimization of the dissociation procedure of any other tissue of interest, which would ultimately improve the reproducibility of the reported data.
Interaction of YAP with the Myb-MuvB (MMB) complex defines a transcriptional program to promote the proliferation of cardiomyocytes
Authors: Gründl Marco , Walz Susanne , Hauf Laura , Schwab Melissa , Werner Kerstin Marcela , Spahr Susanne , Ade Carsten P. , Gaubatz Stefan 
Published: October 2019

ABSTRACTThe Hippo signalling pathway and its central effector YAP regulate proliferation of cardiomyocytes and growth of the heart. Using genetic models in mice we show that the increased proliferation of cardiomyocytes due to loss of the Hippo-signaling component SAV1 depends on the Myb-MuvB (MMB) complex. Similarly, proliferation of postnatal cardiomyocytes induced by constitutive active YAP requires MMB. Genome studies revealed that YAP and MMB regulate an overlapping set of cell cycle genes in cardiomyocytes. We find that YAP binds directly to B-MYB, a subunit of MMB, in a manner dependent on the YAP WW domains and a PPXY motif in B-MYB. Disruption of the interaction by overexpression of the YAP binding domain of B-MYB strongly inhibits the proliferation of cardiomyocytes. Our results point to MMB as a critical downstream effector of YAP in the control of cardiomyocyte proliferation.
Native Electrospray-based Metabolomics Enables the Detection of Metal-binding Compounds
Authors: Aron Allegra , Petras Daniel , Schmid Robin , Gauglitz Julia M. , Büttel Isabell , Antelo Luis , Zhi Hui , Saak Christina C. , Malarney Kien P. , Thines Eckhard , Dutton Rachel J. , Raffatellu Manuela , Dorrestein Pieter C. 
Published: October 2019

AbstractMetals are essential for the molecular machineries of life, and microbes have evolved a variety of small molecules to acquire, compete for, and utilize metals. Systematic methods for the discovery of metal-small molecule complexes from biological samples are limited. Here we describe a two-step native electrospray ionization mass spectrometry method, in which double-barrel post-column metal-infusion and pH adjustment is combined with ion identity molecular networking, a rule-based informatics workflow. This method can be used to identify metal-binding compounds in complex samples based on defined mass (m/z) offsets of ion features with the same chromatographic profiles. As this native metal metabolomics approach can be easily implemented on any liquid chromatography-based mass spectrometry system, this method has the potential to become a key strategy for elucidating and understanding the role of metal-binding molecules in biology.
Ecological divergence and hybridization of Neotropical Leishmania parasites
Authors: Van den Broeck Frederik , Savill Nicholas J. , Imamura Hideo , Sanders Mandy , Maes Ilse , Cooper Sinclair , Mateus David , Jara Marlene , Adaui Vanessa , Arevalo Jorge , Llanos-Cuentas Alejandro , Garcia Lineth , Cupolillo Elisa , Miles Michael , Berriman Matthew , Schnaufer Achim , Cotton James A. , Dujardin Jean-Claude 
Published: October 2019

ABSTRACTThe tropical Andes is an important natural laboratory to understand speciation and diversification in many taxa. Here, we examined the evolutionary history of parasites of the Leishmania braziliensis species complex based on whole genome sequencing of 67 isolates from 47 localities in Peru. We firstly show the origin of near-clonal Andean Leishmania lineages that diverged from admixed Amazonian ancestors, accompanied by a significant reduction in genome diversity and large structural variations implicated in host-parasite interactions. Beside a clear dichotomy between Andean and Amazonian species, patterns of population structure were strongly associated with biogeographical origin. Molecular clock analyses and ecological niche modeling suggested that the history of diversification of the Andean lineages is limited to the Late Pleistocene and intimately associated with habitat contractions driven by climate change. These results support a wider model on trypanosomatid evolution where major parasite lineages emerge through ecological fitting. Second, genome-scale analyses provided evidence of meiotic recombination between Andean and Amazonian Leishmania species, resulting in full-genome hybrids. The mitochondrial genome of these hybrids consisted of homogeneous uniparental maxicircles, but minicircles originated from both parental species, leaving a mosaic ancestry of minicircle-encoded guide RNA genes. We further show that mitochondrial minicircles - but not maxicircles - show a similar evolutionary pattern as the nuclear genome, suggesting that biparental inheritance of minicircles is universal and may be important to alleviate maxicircle-nuclear incompatibilities. By comparing full nuclear and mitochondrial genome ancestries, our data expands our appreciation on the genetic consequences of diversification and hybridization in parasitic protozoa.
MutantZp1results in Zona Pellucida Lacking and Female Infertility in Rats and Humans
Authors: Lv Chao , Huang Hua-Lin , Wang Yan , Peng Tian-Liu , Tan Hang-Jing , Zeng Ming-Hua , Quan Ru-Ping , Deng Hong-Wen , Xiao Hong-Mei 
Published: October 2019

AbstractZona pellucida (ZP) plays a vital role in reproductive processes including oogenesis, fertilization and preimplantation development of embryo. The ZP of humans is composed of four glycoproteins (ZP1-ZP4), same as rats ZP. Our previous research reported a first case of human infertility due toZP1mutation, but the mechanism was unclear. Here we developed a genome editingin vivorat model and a co-transfectedin vitrocell model to investigate the pathogenic effect. In rat homozygous for the homologous mutation, ZP were absent in all of collected eggs. Further the growing and fully grown oocytes in the mutant ovaries completely lack a ZP but with detectable intracellular ZP1 protein. After mating with male rats, none of the mutant female rats got pregnant. Moreover, the co-transfected cell experiments and the ovarian experiments showed that the truncated ZP1 sequestered intracellularly ZP3 and ZP4 to impede their release outside, resulting in an intracellular accumulation of ZP1, ZP3 and ZP4, leading to absence of ZP in mutant oocytes. Our results clearly establish the causal role ofZP1mutation on ZP defects and female infertility.Summary statementRat model mirrored completely the phenotypes observed in humans, infertility and abnormal eggs that lack a zona pellucida, through the negative effects ofZP1mutation.
The Role of Gene Encoding Variation ofDRD4in the Relationship between Inattention and Seasonal Daylight
Authors: Vollebregt M.A. , Franke B. , Buitelaar J.K. , Arnold L.E. , Faraone S.V. , Grevet E.H. , Reif A. , Zayats T. , Bralten J. , Bau C.H.D. , Haavik J. , Kuntsi J. , Cupertino R.B. , Loo S.K. , Lundervold A.J. , Ribasés M. , Sánchez-Mora C. , Ramos-Quiroga J.A. , Asherson P. , Swanson J.M. , Arns M. 
Published: October 2019

ABSTRACTDaylight is the strongest synchronizer of human circadian rhythms. The circadian pathway hypothesis posits that synchrony between daylight and the circadian system relates to (in)attention. The dopamine neurotransmitter system is implicated in regulating the circadian system as well as in (attention)-deficit hyperactivity disorder [ADHD]. We studied the role of functional genetic variation in the gene encoding of dopamine-receptor-D4 (DRD4) in the relationship between inattention and seasonal daylight (changes). Gene-by-environment (GxE) mega-analyses were performed across eight studies including 3757 adult participants (with and without ADHD). We tested 1) theSpring-focus hypothesis, in which attention in 7R-carriers normalizes with increasing daylight levels preceding measurement, 2) theSummer-born ADHD hypothesis, in which 7R-carriers report more inattention when born in spring/summer than in autumn/winter, 3) theWinter-born ADHD hypothesis, opposing the second hypothesis. TheSpring-focus hypothesiswas upheld (1386 ADHD, 760 controls;d=-0.16 between periods); 7R-carriers reported evenlessinattention than 7R-non-carriers after winter solstice (d=0.27 between genotype-groups). Results were diagnosis-independent. Sensitivity analyses at individual study level confirmed the circannual patterns for 7R-carriers. Incorporating geographic changes into the independent measure, we also calculated changes in sunlight levels. This approach likewise showed that inattention correlated negatively with increasing light levels in 7R-carriers (r=-.135). Results emphasize peripheral effects of dopamine and the effects of (seasonal) daylight changes on cognition.