bluuebunny/crossref_metadata_2025_split huggingface dataset:
Depth in convolutional neural networks solves scene segmentation
Authors: Seijdel N , Tsakmakidis N , De Haan EHF , Bohte SM , Scholte HS 
Published: December 2019

AbstractFeedforward deep convolutional neural networks (DCNNs) are, under specific conditions, matching and even surpassing human performance in object recognition in natural scenes. This performance suggests that the analysis of a loose collection of image features could support the recognition of natural object categories, without dedicated systems to solve specific visual subtasks. Research in humans however suggests that while feedforward activity may suffice for sparse scenes with isolated objects, additional visual operations (‘routines’) that aid the recognition process (e.g. segmentation or grouping) are needed for more complex scenes. Linking human visual processing to performance of DCNNs with increasing depth, we here explored if, how, and when object information is differentiated from the backgrounds they appear on. To this end, we controlled the information in both objects and backgrounds, as well as the relationship between them by adding noise, manipulating background congruence and systematically occluding parts of the image. Results indicate that with an increase in network depth, there is an increase in the distinction between object- and background information. For more shallow networks, results indicated a benefit of training on segmented objects. Overall, these results indicate that, de facto, scene segmentation can be performed by a network of sufficient depth. We conclude that the human brain could perform scene segmentation in the context of object identification without an explicit mechanism, by selecting or “binding” features that belong to the object and ignoring other features, in a manner similar to a very deep convolutional neural network.
iucn_sim: A new program to simulate future extinctions based on IUCN threat status
Authors: Andermann Tobias , Faurby Søren , Cooke Robert , Silvestro Daniele , Antonelli Alexandre 
Published: December 2019

AbstractThe ongoing environmental crisis poses an urgent need to forecast thewho,where, andwhenof future species extinctions, as such information is crucial for targeting conservation efforts. Commonly, such forecasts are made based on conservation status assessments produced by the International Union for Conservation of Nature (IUCN). However, when researchers apply these IUCN conservation status data for predicting future extinctions, important information is often omitted, which can impact the accuracy of these predictions.Here we present a new approach and a software for simulating future extinctions based on IUCN conservation status information, which incorporates generation length information of individual species when modeling extinction risks. Additionally, we explicitly model future changes in conservation status for each species, based on status transition rates that we estimate from the IUCN assessment history of the last decades. Finally, we apply a Markov chain Monte Carlo algorithm to estimate extinction rates for each species, based on the simulated future extinctions. These estimates inherently incorporate the chances of conservation status changes and the generation length for each given species and are specific to the simulated time frame.We demonstrate the utility of our approach by estimating extinction rates for all bird species. Our average extinction risk estimate for the next 100 years across all birds is 6.98 × 10−4extinctions per species-year, and we predict an expected biodiversity loss of between 669 to 738 bird species within that time frame. Further, the rate estimates between species sharing the same IUCN status show larger variation than the rates estimated with alternative approaches, which reflects expected differences in extinction risk among taxa of the same conservation status. Our method demonstrates the utility of applying species-specific information to the estimation of extinction rates, rather than assuming equal extinction risks for species assigned to the same conservation status.
Mountain stoneflies may tolerate warming streams: evidence from organismal physiology and gene expression
Authors: Hotaling Scott , Shah Alisha A. , McGowan Kerry L. , Tronstad Lusha M. , Giersch J. Joseph , Finn Debra S. , Woods H. Arthur , Dillon Michael E. , Kelley Joanna L. 
Published: December 2019

AbstractRapid glacier recession is altering the physical conditions of headwater streams. Stream temperatures are predicted to rise and become increasingly variable, putting entire meltwater-associated biological communities at risk of extinction. Thus, there is a pressing need to understand how thermal stress affects mountain stream insects, particularly where glaciers are likely to vanish on contemporary timescales. In this study, we tested the critical thermal maximum (CTMAX) of stonefly nymphs representing multiple species and a range of thermal regimes in the high Rocky Mountains, USA. We then collected RNA-sequencing data to assess how organismal thermal stress translated to the cellular level. Our focal species included the meltwater stonefly,Lednia tumana, which was recently listed under the U.S. Endangered Species Act due to climate-induced habitat loss. For all study species, critical thermal maxima (CTMAX> 20°C) far exceeded the stream temperatures mountain stoneflies experience (< 10°C). Moreover, while evidence for a cellular stress response was present, we also observed constitutive expression of genes encoding proteins known to underlie thermal stress (i.e., heat shock proteins) even at low temperatures that reflected natural conditions. We show that high-elevation aquatic insects may not be physiologically threatened by short-term exposure to warm temperatures and that longer term physiological responses or biotic factors (e.g., competition) may better explain their extreme distributions.
Neuropeptide F receptor acts in theDrosophilaprothoracic gland to regulate growth and developmental timing
Authors: Kannangara Jade R. , Henstridge Michelle A. , Parsons Linda M. , Kondo Shu , Mirth Christen K. , Warr Coral G. 
Published: December 2019

SUMMARYAs juvenile animals grow, their behaviour, physiology, and development need to be matched to environmental conditions to ensure they survive to adulthood. However, we know little about how behaviour and physiology are integrated with development to achieve this outcome. Neuropeptides are prime candidates for achieving this due to their well-known signalling functions in controlling many aspects of behaviour, physiology and development in response to environmental cues. In the growingDrosophilalarva, while several neuropeptides have been shown to regulate feeding behaviour, and a handful to regulate growth, it is unclear if any of these play a global role in coordinating feeding behaviour with developmental programs. Here, we demonstrate that Neuropeptide F Receptor (NPFR), best studied as a conserved regulator of feeding behaviour from insects to mammals, also regulates development inDrosophila. Knocking downNPFRin the prothoracic gland, which produces the steroid hormone ecdysone, generates developmental delay and an extended feeding period, resulting in increased body size. We show that these effects are due to decreased ecdysone production, as these animals have reduced expression of ecdysone biosynthesis genes and lower ecdysone titres. Moreover, these phenotypes can be rescued by feeding larvae food supplemented with ecdysone. Further, we show that NPFR negatively regulates the insulin signalling pathway in the prothoracic gland to achieve these effects. Taken together, our data demonstrate that NPFR signalling plays a key role in regulating animal development and may thus play a global role in integrating feeding behaviour and development inDrosophila.
Structural clusters of histone H3 and H4 residues regulate chronological lifespan inSaccharomyces cerevisiae
Authors: Ngubo Mzwanele , Reid Jessica , Patterton Hugh -G 
Published: December 2019

AbstractWe have performed a comprehensive analysis of the involvement of histone H3 and H4 residues in the regulation of chronological lifespan in yeast, and identify four structural groups in the nucleosome that influence lifespan. We also identify residues where substitution with an epigenetic mimic extends lifespan, providing evidence that a simple epigenetic switch, without possible additional background modifications, causes longevity. Residues where substitution result in the most pronounced lifespan extension are all on the exposed face of the nucleosome, with the exception of H3E50, which is present on the lateral surface, between two DNA gyres. Other residues that have a more modest effect on lifespan extension are concentrated at the extremities of the H3-H4 dimer, suggesting a role in stabilizing the dimer in its nucleosome frame. Residues that reduce lifespan are buried in the histone handshake motif, suggesting that these mutations destabilize the octamer structure.All residues exposed on the nucleosome disk face and that cause lifespan extension are known to interact with Sir3. We find that substitution of H4K16 and H4H18 cause Sir3 to redistribute from telomeres and silent mating loci to secondary positions, often enriched for Rap1, Abf1 or Reb1 binding sites, whereas H3E50 does not. The redistribution of Sir3 in the genome can be reproduced by an equilibrium model based on primary and secondary binding sites with different affinities for Sir3. The redistributed Sir3 cause transcriptional repression at most of the new loci, including of genes where null mutants were previously shown to extend chronological lifespan. The transcriptomic profiles of H4K16 and H4H18 mutant strains are very similar, and compatible with a DNA replication stress response. This is distinct from the transcriptomic profile of H3E50, which matches strong induction of oxidative phosphorylation. We propose that the different groups of residues are involved in binding to heterochromatin proteins, in destabilizing the association of the nucleosome DNA, disrupting binding of the H3-H4 dimer in the nucleosome, or disrupting the structural stability of the octamer, each category impacting on chronological lifespan by a different mechanism.
A sulfoglycolytic Entner-Doudoroff pathway inRhizobium leguminosarumbv.trifoliiSRDI565
Authors: Li Jinling , Epa Ruwan , Scott Nichollas E. , Skoneczny Dominic , Sharma Mahima , Snow Alexander J.D. , Lingford James P. , Goddard-Borger Ethan D. , Davies Gideon J. , McConville Malcolm J. , Williams Spencer J. 
Published: December 2019

AbstractRhizobia are nitrogen fixing bacteria that engage in symbiotic relationships with plant hosts but can also persist as free-living bacteria with the soil and rhizosphere. Here we show that free livingRhizobium leguminosarumSRDI565 can grow on the sulfosugar sulfoquinovose (SQ) using a sulfoglycolytic Entner-Doudoroff (sulfo-ED) pathway resulting in production of sulfolactate (SL) as the major metabolic end-product. Comparative proteomics supports the involvement of a sulfo-ED operon encoding an ABC transporter cassette, sulfo-ED enzymes and an SL exporter. Consistent with an oligotrophic lifestyle, proteomics data revealed little change in expression of the sulfo-ED proteins during growth on SQ versus mannitol, a result confirmed through biochemical assay of sulfoquinovosidase activity in cell lysates (data are available via ProteomeXchange with identifier PXD015822). Metabolomics analysis showed that growth on SQ involves gluconeogenesis to satisfy metabolic requirements for glucose-6-phosphate and fructose-6-phosphate. Metabolomics analysis also revealed the unexpected production of small amounts of sulfofructose and 2,3-dihydroxypropanesulfonate, which are proposed to arise from promiscuous activities of the glycolytic enzyme phosphoglucose isomerase and a non-specific aldehyde reductase, respectively. This work shows that rhizobial metabolism of the abundant sulfosugar SQ may contribute to persistence of the bacteria in the soil and to mobilization of sulfur in the pedosphere.
Yeast ATM and ATR use different mechanisms to spread histone H2A phosphorylation around a DNA double-strand break
Authors: Li Kevin , Bronk Gabriel , Kondev Jane , Haber James E. 
Published: December 2019

AbstractOne of the hallmarks of DNA damage is the rapid spreading of phosphorylated histone H2A (γ-H2AX) around a DNA double-strand break (DSB). In the budding yeastS. cerevisiae, nearly all H2A isoforms can be phosphorylated, either by Mec1ATRor Tel1ATMcheckpoint kinases. We induced a site-specific DSB with HO endonuclease at theMATlocus on chromosome III and monitored the formation of γ-H2AX by ChIP-qPCR in order to uncover the mechanisms by which Mec1ATRand Tel1ATMpropagate histone modifications across chromatin. With either kinase, γ-H2AX spreads as far as ∼50 kb on both sides of the lesion within 1 h; but the kinetics and distribution of modification around the DSB are significantly different. The total accumulation of phosphorylation is reduced by about half when either of the two H2A genes is mutated to the nonphosphorylatable S129A allele. Mec1 activity is limited by the abundance of its ATRIP partner, Ddc2. Moreover, Mec1 is more efficient than Tel1 at phosphorylating chromatin intrans– at distant undamaged sites that are brought into physical proximity to the DSB. We compared experimental data to mathematical models of spreading mechanisms to determine whether the kinases search for target nucleosomes by primarily moving in three dimensions through the nucleoplasm or in one dimension along the chromatin. Bayesian model selection indicates that Mec1 primarily uses a 3D diffusive mechanism, whereas Tel1 undergoes directed motion along the chromatin.
Bifidobacterium breveUCC2003 exopolysaccharide modulates the early life microbiota by acting as a dietary substrate
Authors: Puengel D , Treveil A , Dalby MJ , Caim S , Colquhoun IJ , Booth C , Ketskemety J , Korcsmaros T , van Sinderen D , Lawson MAE , Hall LJ 
Published: December 2019

AbstractMembers of the genusBifidobacteriumrepresent an important bacterial group for promoting health during early life. Previous studies have indicated that bifidobacterial exopolysaccharides (EPS) are involved in host interactions, with purified EPS also suggested to modulate microbe-microbe interactions by acting as a nutrient substrate. To further explore the role of EPS as a potential dietary component, we determined the longitudinal effects of bifidobacterial EPS on microbial communities and metabolite profiles using an infant model colon system.Bifidobacterium breveUCC2003 was utilised as a representative early life bifidobacterial strain, and a corresponding isogenic EPS-deletion mutant (B. breveUCC2003 EPS-). Initial transcriptomics analysis of the EPS mutant vs. parentB. breveUCC2003 strain highlighted differential expression in a discrete number of genes, including theepsbiosynthetic cluster, though overall growth dynamics between the two strains were unaffected. Model colon vessels were inoculated withB. brevestrains and microbiome dynamics were monitored using metataxonomic (via 16S rRNA sequencing) and metabolomic (via1H NMR) approaches. Baseline early life microbiota profiles were similar between vessels, with persistence ofB. breve(EPS+ and EPS-) observed between 0-36h. Within the EPS-positive vessel there was a significant shift in microbiome and metabolite profiles until the end of the study (405h); we observed increases ofEscherichiaandTyzzerella, and short-chain fatty acids including acetate, propionate and formate, including further correlations between taxa and metabolites which were not observed in the EPS-negative vessel. These data indicate that theB. breveUCC2003 EPS is potentially being metabolised by members of the infant microbial community, leading to differential microbial metabolism and altered metabolite by-products. Overall, these findings may allow for development of EPS-specific strategies to beneficially alter the early life microbiota to promote infant health.
14-3-3β paralog is inhibited by acetylation during differentiation to the osteogenic lineage
Authors: Frontini-Lopez Yesica R , Gojanovich Aldana D , Uhart Marina , Bustos Diego M 
Published: December 2019

Abstract14-3-3 protein family binds and regulate hundred of serine/threonine phosphorylated proteins. Considered as redundant, ubiquitous and constantly expressed this protein family was treated as an accessory for many signaling systems. Here we studied the reversible inhibition by acetylation of its essential N-ε-lysine 49/51 residue during the osteogenic differentiation of human adipose-derived stem cells (ASC). We found that during the differentiation of ASC the levels of 14-3-3 acK49/51 increase showing that inhibition of 14-3-3 is necessary for this process. Among the 7 paralogs of this family, the inhibition by this posttranslational modification occurs mostly on the paralog β located specifically in the nucleus where 14-3-3 was described to binds to H3 histone and many transcription factors. Short hairpin RNA silencing of 14-3-3β gene but not 14-3-3γ increases significantly the osteogenic potential of the cells. These results show that specifically 14-3-3β is a negative regulator of osteogenesis and its inhibition by acetylation on lysine 51 is the cellular mechanism to regulate it.
Sexual Differences in Mitochondrial Proteins in Rat Cerebral Microvessels: A Proteomic Approach
Authors: Cikic Sinisa , Chandra Partha K. , Harman Jarrod C. , Rutkai Ibolya , Katakam Prasad V.G. , Guidry Jessie J. , Gidday Jeffrey M. , Busija David W. 
Published: December 2019

ABSTRACTSex differences in mitochondrial numbers and function are present in large cerebral arteries, but it is unclear whether these differences extend to the microcirculation. We performed an assessment of mitochondria-related proteins in cerebral microvessels (MVs) isolated from young, male and female, Sprague-Dawley rats. MVs composed of arterioles, capillaries, and venules were isolated from the cerebrum and used to perform a 3 vs. 3 quantitative, multiplexed proteomics experiment utilizing tandem mass tags (TMT), coupled with liquid chromatography/mass spectrometry (LC/MS). MS data and bioinformatic analyses were performed using Proteome Discoverer version 2.2 and Ingenuity Pathway Analysis. We identified a total of 1,969 proteins, of which 1,871 were quantified by TMT labels. Sixty-four proteins were expressed significantly (p < 0.05) higher in female samples compared with male samples. Females expressed more mitochondrial proteins involved in energy production, mitochondrial membrane structure, anti-oxidant enzyme proteins, and those involved in fatty acid oxidation. Conversely, males had higher expression levels of mitochondria-destructive proteins. We validated our key Proteomics results with western blotting. Our findings reveal, for the first time, the full extent of sexual dimorphism in the mitochondrial metabolic protein profiles of MVs, which may contribute to sex-dependent cerebrovascular and neurological pathologies.SynopsisEnergy-producing proteins in the cerebral microvessels (MVs) of male and female rats were examined by quantitative discovery-based proteomics to gain insight into the sex-dependent etiology of cardiovascular and neurological diseases. Females expressed more mitochondrial proteins involved in energy production, membrane structure, anti-oxidant activity, and fatty acid oxidation. In contrast, males exhibited more mitochondria-destructive proteins such as mitochondrial eating protein. Our findings reveal for the first time the sexual dimorphism of mitochondria-related proteins in cerebral MVs, which may explain functional sex-related differences in MVs during health and in the etiology of neurological pathologies of cerebrovascular origin.
Transcriptome sequencing and screening of genes related to sex determination ofTrichosanthes kirilowiiMaxim
Authors: Hu Xiuqin , Zhu Jinkai , Ji Guanjie , Wang Zhen , Xin Jie 
Published: December 2019

AbstractTrichosanthes kirilowiiMaxim. (TK) is a dioecious plant in the Cucurbitaceae for which different sexes have separate medicinal uses. In order to study the genes related to sex determination, transcriptome sequencing was performed on flower buds and leaves of male and female plants using the high-throughput sequencing technology. A total of 145,975 unigenes and 7110 DEGs were obtained. There were 6776 DEGs annotated to 1234 GO terms and enriched to 18 functional groups, including five biological processes related to sugar metabolism. KEGG pathway analysis indicated genes involved in hormone transduction, hormone synthesis and carbohydrate metabolism. The sex determination genes ofTKare different from known sex determination mechanisms (ACS11, ACS7(2), WIP1). Many DEGs ofTKare involved in reproductive organ formation, hormone signal transduction and regulatory networks. In combination with the previous study of sex differentiation of Cucurbitaceae, the results of GO, KEGG and the expression of related genes in male and female plants, 18 candidate genes for sex determining ofTKwere screened from 151 hormone-related differentially expressed genes. The genes includedMYB80, MYB108andMYB21of the MYB family,CER1, CBL, ABCB199, SERK1andHSP81-3. The results provide a foundation for the study of sex differentiation inTK.
Accuracy of a deep convolutional neural network in the detection of myopic macular diseases using swept-source optical coherence tomography
Authors: Sogawa Takahiro , Tabuchi Hitoshi , Nagasato Daisuke , Masumoto Hiroki , Ikuno Yasushi , Ohsugi Hideharu , Ishitobi Naofumi , Mitamura Yoshinori 
Published: December 2019

AbstractThis study examined and compared outcomes of deep learning (DL) in identifying swept-source optical coherence tomography (OCT) images without myopic macular lesions [i.e., no high myopia (nHM) vs. high myopia (HM)], and OCT images with myopic macular lesions [e.g., myopic choroidal neovascularization (mCNV) and retinoschisis (RS)]. A total of 796 SS-OCT images were included in the study as follows and analyzed by k-fold cross-validation (k = 5) using DL’s renowned model, Visual Geometry Group-16: nHM, 107 images; HM, 456 images; mCNV, 122 images; and RS, 111 images (n = 796). The binary classification of OCT images with or without myopic macular lesions; the binary classification of HM images and images with myopic macular lesions (i.e., mCNV and RS images); and the ternary classification of HM, mCNV, and RS images were examined. Additionally, sensitivity, specificity, and the area under the curve (AUC) for the binary classifications as well as the correct answer rate for ternary classification were examined.The classification results of OCT images with or without myopic macular lesions were as follows: AUC, 0.983; sensitivity, 0.953; specificity, 0.940. The classification results of HM images and images with myopic macular lesions were as follows: AUC, 0.976; sensitivity, 0.940; specificity, 0.941. The correct answer rate in the ternary classification of HM images, mCNV images, and RS images were as follows: HM images, 93.7%; mCNV images, 82.4%; and RS, 92.3% with mean, 91.4%. Using noninvasive, easy-to-obtain swept-source OCT images, the DL model was able to classify OCT images without myopic macular lesions and OCT images with myopic macular lesions such as mCNV and RS with high accuracy. The study results suggest the possibility of conducting highly accurate screening of ocular diseases using artificial intelligence, which may improve the prevention of blindness and reduce workloads for ophthalmologists.