bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emergent honeycomb topology of the leaf spongy mesophyll
Authors: Borsuk Aleca M. , Roddy Adam B. , Théroux-Rancourt Guillaume , Brodersen Craig R. 
Published: November 2019

AbstractThe spongy mesophyll layer in leaves is ubiquitous among vascular plants, yet its structure is relatively unknown and typically described as a disordered assemblage of isodiametric cells. We characterized spongy mesophyll structure among diverse taxa using X-ray microCT imaging and found that leaves with small cell sizes, high cell packing densities, and close vein spacing were congruent with the isodiametric paradigm. When these structural traits exceeded well-defined thresholds, the spongy mesophyll domain was instead tessellated with an emergent topological motif of an irregular honeycomb that minimizes cellular investment and obeys Euler’s Law of space filling. Our data suggest spongy mesophyll is governed by allometric scaling laws, with two distinct topologies optimized for either photosynthetic performance or minimal resource investment.One Sentence SummaryConserved topological motifs in the spongy mesophyll are coordinated with leaf photosynthetic performance.
Ectomycorrhizal fungi induce systemic resistance against insects on a non-mycorrhizal plant in a CERK1-dependent manner
Authors: Vishwanathan Kishore , Zienkiewicz Krzysztof , Liu Yang , Janz Dennis , Feussner Ivo , Polle Andrea , Haney Cara H. 
Published: November 2019

ABSTRACTBelow-ground microbes can induce systemic resistance (ISR) against foliar pests and pathogens on diverse plant hosts. The prevalence of ISR among plant-microbe-pest systems raises the question of host specificity in microbial induction of ISR. To test whether ISR is limited by plant host range, we tested the ISR-inducing ectomycorrhizal (ECM) fungus Laccaria bicolor on the non-mycorrhizal plant Arabidopsis. We found that root inoculation with L. bicolor triggered ISR against the insect herbivore Trichoplusia ni and induced systemic susceptibility (ISS) against the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (Pto). We found that L. bicolor-triggered ISR against T. ni was dependent on jasmonic acid (JA) signaling and salicylic acid (SA) biosynthesis and signaling. We found that heat killed L. bicolor and chitin are sufficient to trigger ISR against T. ni and ISS against Pto and that the chitin receptor CERK1 is necessary for L. bicolor-mediated effects on systemic immunity. Collectively our findings suggest that some ISR responses might not require intimate co-evolution of host and microbe, but rather might be the result of root perception of conserved microbial signals.
Divergent strategies for learning in males and females
Authors: Chen Cathy S. , Ebitz R. Becket , Bindas Sylvia R. , Redish A. David , Hayden Benjamin Y. , Grissom Nicola M. 
Published: November 2019

AbstractA frequent assumption in value-based decision-making tasks is that agents make decisions based on the feature dimension that reward probabilities vary on. However, in complex, multidimensional environments, stimuli can vary on multiple dimensions at once, meaning that the feature deserving the most credit for outcomes is not always obvious. As a result, individuals may vary in the strategies used to sample stimuli across dimensions, and these strategies may have an unrecognized influence on decision-making. Sex is a proxy for multiple genetic and endocrine influences that can influence decision-making strategies, including how environments are sampled. In this study, we examined the strategies adopted by female and male mice as they learned the value of stimuli that varied in both image and location in a visually-cued two-armed bandit, allowing two possible dimensions to learn about. Female mice acquired the correct image-value associations more quickly than male mice, and they used a fundamentally different strategy to do so. Female mice constrained their decision-space early in learning by preferentially sampling one location over which images varied. Conversely, male strategies were inconsistent, changing frequently and strongly influenced by the immediate experience of stochastic rewards. Individual strategies were related to sex-gated changes in neuronal activation in early learning. Together, we find that in mice, sex is linked with divergent strategies for sampling and learning about the world, revealing substantial unrecognized variability in the approaches implemented during value-based decision-making.
Enabling FIB-SEM Systems for Large Volume Connectomics and Cell Biology
Authors: Xu C. Shan , Pang Song , Hayworth Kenneth J. , Hess Harald F. 
Published: November 2019

AbstractIsotropic high-resolution imaging of large volumes provides unprecedented opportunities to advance connectomics and cell biology research. Conventional Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) offers unique benefits such as high resolution (< 10 nm in x, y, and z), robust image alignment, and minimal artifacts for superior tracing of neurites. However, its prevailing deficiencies in imaging speed and duration cap the maximum possible image volume. We have developed technologies to overcome these limitations, thereby expanding the image volume of FIB-SEM by more than four orders of magnitude from 103µm3to 3 x 107µm3while maintaining an isotropic resolution of 8 x 8 x 8 nm3voxels. These expanded volumes are now large enough to support connectomic studies, in which the superior z resolution enables automated tracing of fine neurites and reduces the time-consuming human proofreading effort. Moreover, by trading off imaging speed, the system can readily be operated at even higher resolutions achieving voxel sizes of 4 x 4 x 4 nm3, thereby generating ground truth of the smallest organelles for machine learning in connectomics and providing important insights into cell biology. Primarily limited by time, the maximum volume can be greatly extended.Here we provide a detailed description of the enhanced FIB-SEM technology, which has transformed the conventional FIB-SEM from a laboratory tool that is unreliable for more than a few days to a robust imaging platform with long term reliability: capable of years of continuous imaging without defects in the final image stack. An in-depth description of the systematic approach to optimize operating parameters based on resolution requirements and electron dose boundary conditions is also explicitly disclosed. We further explore how this technology unleashes the full potential of FIB-SEM systems, revolutionizing volume electron microscopy (EM) imaging for biology by gaining access to large sample volumes with single-digit nanoscale isotropic resolution.
Insilico Analysis Reveal Three novel nsSNPs May effect onGM2Aprotein Leading to AB variant of GM2 gangliosidosis
Authors: Abdelhameed Tebyan A. , Mustafa Mujahed I. , Abdelrahman Dina N. , Abdelrhman Fatima A. , Hassan Mohamed A. 
Published: November 2019

ABSTRACTBackgroundAB variant of GM2 gangliosidosis caused as a result of mutations in GM2 activator gene (GM2A) which is regarded as neurodegenerative disorder. This study aimed to predict the possible damaging SNPs of this gene and their impact on the protein using different bioinformatics tools.MethodsSNPs retrieved from the NCBI database were analyzed using several bioinformatics tools. The different tools collectively predicted the effect of single nucleotide substitution on both structure and function of GM2 activator.ResultsThree novel mutations were found to be highly damaging to the structure and function of theGM2Agene.ConclusionFour SNPs were found to be highly damaging SNPs that affect function, structure and stability ofGM2Aprotein, which they are: C99Y, C112F, C138S and C138R, three of them are novel SNPs (C99Y, C112F and C138S). Also 46 SNPs were predicted to affect miRNAs binding sites on 3’UTR leading to abnormal expression of the resulting protein. These SNPs should be considered as important candidates in causing AB variant of GM2 gangliosidosis and may help in diagnosis and genetic screening of the disease.
Reference-free deconvolution of complex DNA methylation data – a systematic protocol
Authors: Scherer Michael , Nazarov Petr V. , Toth Reka , Sahay Shashwat , Kaoma Tony , Maurer Valentin , Plass Christoph , Lengauer Thomas , Walter Jörn , Lutsik Pavlo 
Published: November 2019

AbstractEpigenomic profiling enables unique insights into human development and diseases. Often the analysis of bulk samples remains the only feasible option for studying complex tissues and organs in large patient cohorts, masking the signatures of important cell populations in convoluted signals. DNA methylomes are highly cell type-specific, and enable recovery of hidden components using advanced computational methods without the need for reference profiles. We propose a three-stage protocol for reference-free deconvolution of DNA methylomes comprising: (i) data preprocessing, confounder adjustment and feature selection, (ii) deconvolution with multiple parameters, and (iii) guided biological inference and validation of deconvolution results. Our protocol simplifies the analysis and integration of DNA methylomes derived from complex samples, including tumors. Applying this protocol to lung cancer methylomes from TCGA revealed components linked to stromal cells, tumor-infiltrating immune cells, and associations with clinical parameters. The protocol takes less than four days to complete and requires basic R skills.
A New approximate matching compression algorithm for DNA sequences
Authors: Lázaro-Guevara J.M. , Garrido K.M. 
Published: November 2019

1.AbstractUndeveloped countries like Guatemala, where access to high-speed internet connections is limited, downloading and sharing Biological information of thousands of Mega Bits is a huge problem for the beginning and development of Bioinformatics. Based on that information is an urgent necessity to find a better way to share this biological data. There is when the compression algorithms become relevant. With all this information in mind, born the idea of creating a new algorithm using redundancy and approximate selection.Methods:Using the probability given by the transition matrix of the three-word tuple and relative frequencies. Calculating the relative and total frequencies given by the permutation formula (nr) and compressing 6 bits of information into 1 implementing the ASCII table code (0…255 characters, 28), using clusters of 102 DNA bases compacted into 17 string sequences. For decompressing, the inverse process must be done, except that the triplets must be selected randomly (or use a matrix dictionary, 4102).Conclusion:The compression algorithm has a better compression ratio than LZW and Huffman’s algorithm. However, the time needed for decompressing makes this algorithm incompatible for massive data. The functionality as MD5sum need more research but is a promising helpful tool for DNA checking.
Spexin and a novel cichlid-specific spexin paralog both inhibit FSH and LH through a specific galanin receptor (Galr2b) in tilapia
Authors: Cohen Yaron , Hausken Krist , Bonfil Yoav , Gutnick Michael , Levavi-Sivan Berta 
Published: November 2019

AbstractSpexin (SPX) is a 14 amino acid peptide hormone that has pleiotropic functions across vertebrates, one of which is involvement in the brain-pituitary-gonad axis of fish. SPX(1) has been identified in each class of vertebrates, and a second SPX (named SPX2) has been found in some non-mammalian species. We have cloned two spexin paralogs, designated as Spx1a and Spx1b, from Nile tilapia (Oreochromis niloticus) that have varying tissue distribution patterns. Spx1b is a novel peptide only identified in cichlid fish, and is more closely related to Spx1 than Spx2 homologs as supported by phylogenetic, synteny, and functional analyses. Kisspeptin, Spx, and galanin (Gal) peptides and their corresponding kiss receptors and Gal receptors (Galrs), respectively, are evolutionarily related. Cloning of six tilapia Galrs (Galr1a, Galr1b, Galr2a, Galr2b, Galr type 1, and Galr type 2) and subsequentin vitrosecond-messenger reporter assays for Gαs, Gαq, and Gαisuggests that Gal and Spx activate Galr1a/Galr2a and Galr2b, respectively. A decrease in plasma follicle stimulating hormone and luteinizing hormone concentrations was observed with injections of Spx1a or Spx1bin vivo. Additionally, application of Spx1a to pituitary slices decreased the firing rate of LH cells, suggesting direct inhibition at the pituitary level. These data collectively suggest an inhibitory mechanism of action against the secretion of gonadotropins for a traditional and a novel spexin paralog in cichlid species.
Event-related dynamics of brain oscillations during perception of verbal information in patients with paranoid schizophrenia
Authors: Garakh Zhanna V. , Larionova Ekaterina V. 
Published: November 2019

AbstractWe studied the evoked changes in brain rhythmic activity during reading semantic (words) and meaningless verbal information (pseudowords) in patients with paranoid schizophrenia (n= 40) and in control group of healthy subjects (n= 64). Patients with paranoid schizophrenia showed the decrease in the event-related synchronization (ERS) of alpha and theta rhythms compared to controls when reading semantic verbal information. Reduced event-related synchronization of the alpha rhythm in time window 105 – 145 ms may be associated with the severity of hallucinations (P3 scale) by PANSS. In contrast to the control group, the patients had no differences in the gamma range when reading words and pseudowords. This fact may indicate that patients with paranoid schizophrenia assign significance to those stimuli that are not normally considered as significant (pseudowords).
Visual landmarks calibrate auditory space across eye movements
Authors: Aagten-Murphy David , Szinte Martin , Taylor Robert , Deubel Heiner 
Published: November 2019

AbstractVisual objects that are present both before and after eye movements can act as landmarks, aiding localization of other visual stimuli. We investigated whether visual landmarks would also influence auditory localization – despite participants’ head position remaining unchanged. Participants made eye-movements from central fixation to a peripheral visual landmark, which either remained stationary or was covertly displaced. Following the movement, participants judged whether a stimulus (auditory or visual) was shifted in location relative to before the movement. Visual localization estimates shifted along with the landmark, although the landmark displacement itself went unnoticed. Interestingly, auditory localization estimates were also displaced. Thus, despite identical auditory input reaching the ears, two auditory stimuli originating from the same position were perceived as spatially distinct when the visual landmark moved. These results are consistent with the idea that auditory spatial information is encoded within an eye-centered reference frame and subject to spatial recalibration by visual landmarks.HighlightsVisual landmarks affect stimulus localization across eye movementsWe show this also for auditory stimuli, even when the head remains stableDue to a visual landmark displacement, identical auditory stimuli are perceived as shiftedThis suggests that auditory space is calibrated on eye-centered maps across saccades
Analysis of the effects of related fingerprints on molecular similarity using an eigenvalue entropy approach
Authors: Kuwahara Hiroyuki , Gao Xin 
Published: November 2019

AbstractTwo-dimensional (2D) chemical fingerprints are widely used as numerical features for the quantification of structural similarity of chemical compounds, which is an important step in similarity-based virtual screening (VS). Here, using an eigenvalue-based entropy approach, we sought to identify 2D fingerprints with little to no contribution to shaping the eigenvalue distribution of the feature matrix as related fingerprints and examined the degree to which these related 2D fingerprints influence molecular similarity scores via Tanimoto coefficient. We found that there are many related fingerprints in publicly available fingerprint schemes and that their presence in the feature set tends to decrease the similarity scores. Our results have implication in the optimal selection of 2D fingerprints and the identification of potential hits for compounds with target biological activity in VS.
On the spillover effect and optimal size of marine reserves for sustainable fishing yields
Authors: Takashina Nao 
Published: November 2019

AbstractMarine reserves are an essential component of modern fishery management. Marine reserves, which represent a management tradeoff between harvesting and conservation, are fundamental to maintenance of fisheries. Finding optimal reserve sizes that improve fishing yields is not only of theoretical interest, but also of practical importance to facilitate decision making. Also, since the migratory behavior of some species influences the spillover effect of a marine reserve, this is a key consideration when assessing performance of marine reserves. The relationship between optimal reserve size and migration rate/mode has not been well studied, but it is fundamental to management success. Here, I investigate optimal reserve size and its management outcome with different levels of spillover via a simple two-patch mathematical model. In this model, one patch is open to fishing, and the other is closed. The two-patch model is aggregated by single-population dynamics when the migration rate is sufficiently larger than the growth rate of a target species. At this limit, I show that an optimal reserve size exists when pre-reserve fishing occurs at fishing mortality larger thanfMSY, the fishing mortality at the maximum sustainable yield (MSY). Also, the fishing yield at an optimal reserve size becomes as large as MSY at the limit. Numerical simulations at various migration rates between the two patches suggest that the maximum harvest under management with a marine reserve is achieved at this limit. This contrasts with the conservation benefit which is maximized at an intermediate migration rate. Numerical simulations show that the above-mentioned condition derived from the aggregated model is necessary when the migration rate is not sufficiently large, and that a moderate migration rate is further necessary for an optimal reserve size to exist. However, high fishing mortality reduces this requirement.
Dynamics of host glutathione and glutathione related enzymes in Macrophomina phaseolina-sorghum bicolor interaction
Authors: Bandara Ananda Y. , Weerasooriya Dilooshi K. , Liu Sanzhen , Little Christopher R. 
Published: November 2019

SUMMARYGlutathione and its related enzymes play an integral role in cellular detoxification processes and redox buffering. A genome wide transcriptome profiling was conducted through RNA sequencing to investigate the dynamics of glutathione and related enzymes in sorghum bicolor (L.) Moench in response to Macrophomina phaseolina (MP) infection. Compared to mock inoculated control treatment, MP significantly upregulated the glutathione synthetase, glutamate cysteine ligase (involved in glutathione biosynthesis), glutathione s-transferase (GST), glutathione peroxidase (GPX), and glutathione reductase (GR) genes in a charcoal rot susceptible sorghum genotype (Tx7000), but not in a resistant genotype (SC599) at 7 days post- inoculation. The net log2 fold up-regulation of the aforesaid genes in MP-inoculated Tx7000 was 1.9, 0.9, 120.0, 9.0, and 4.5, respectively. To confirm the gene expression data, cell extracts were acquired from MP- and mock-inoculated resistant (SC599, SC35) and susceptible (Tx7000, BTx3042) sorghum genotypes and their reduced (GSH), oxidized (GSSG) glutathione, GST, GPX, and GR activities were measured using standard protocols. A significantly reduced GSH/GSSG ratio was observed in Tx7000 and BTx3042 indicating the strong oxidative stress experienced by charcoal rot susceptible genotypes under MP infection. MP significantly increased the GST, GPX, and GR activities of Tx7000 and BTx3042. Although augmented GR activity contributes to cellular GSH restoration, the enhanced GST activity leads to diminishing GSH pools through vacuolar sequestration of GSH-S-conjugates. This eases the oxidative stress confronted by susceptible genotypes under MP infection and in turn contributes to reduced charcoal rot susceptibility. The importance of GSH in controlling the MP infection associated oxidative stress was further supported by the significantly reduced disease severity observed in Tx7000 and BTx3042 upon exogenous GSH application.
CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single-cells
Authors: Perez-Rathke Alan , Sun Qiu , Wang Boshen , Boeva Valentina , Shao Zhifeng , Liang Jie 
Published: November 2019

AbstractChromatin interactions are important for gene regulation and cellular specialization. Emerging evidence suggests many-body spatial interactions can play important roles in condensing super-enhancer regions into a cohesive transcriptional apparatus. Chromosome conformation studies using Hi-C are limited to pairwise, population-averaged interactions; therefore, not suitable for direct assessment of many-body interactions. We describe a computational model, CHROMATIX, that reconstructs structural ensembles based on Hi-C data and identifies significant many-body interactions. For a diverse set of highly-active transcriptional loci with at least 2 super-enhancers, we detail the many-body functional landscape and show DNase-accessibility, POLR2A binding, and decreased H3K27me3 are predictive of interaction-enriched regions.
Addressing dereplication crisis: Taxonomy-free reduction of massive genome collections using embeddings of protein content
Authors: Viehweger A. , Hoelzer M. , Brandt C. 
Published: November 2019

AbstractMany recent microbial genome collections curate hundreds of thousands of genomes. This volume complicates many genomic analyses such as taxon assignment because the associated computational burden is substantial. However, the number of representatives of each species is highly skewed towards human pathogens and model organisms. Thus many genomes contain little additional information and could be removed. We created a frugal dereplication method that can reduce massive genome collections based on genome sequence alone, without the need for manual curation nor taxonomic information.We recently created a genome representation for bacteria and archaea called “nanotext”. This method embeds each genome in a low-dimensional vector of numbers. Extending nanotext, our proposed algorithm called “thinspace” uses these vectors to group and dereplicate similar genomes.We dereplicated the Genome Taxonomy Database (GTDB) from about 150 thousand genomes to less than 22 thousand. The resulting collection increases the percent of classified reads in a metagenomic dataset by a factor of 5 compared to NCBI RefSeq and performs equal to both a larger as well as a manually curated GTDB subset.With thinspace, massive genome collections can be dereplicated on regular hardware, without affecting downstream results. It is released under a BSD-3 license (github.com/phiweger/thinspace).