bluuebunny/crossref_metadata_2025_split huggingface dataset:
Culturable diversity of Arctic phytoplankton during pack ice melting
Authors: Ribeiro Catherine Gérikas , dos Santos Adriana Lopes , Gourvil Priscillia , Gall Florence Le , Marie Dominique , Tragin Margot , Probert Ian , Vaulot Daniel 
Published: May 2019

AbstractMassive phytoplankton blooms develop at the Arctic ice edge, sometimes extending far under the pack ice. An extensive culturing effort was conducted before and during a phytoplankton bloom in Baffin Bay between April and July 2016. Different isolation strategies were applied, including flow cytometry cell sorting, manual single cell pipetting and serial dilution. Although all three techniques yielded the most common organisms, each technique retrieved specific taxa, highlighting the importance of using several methods to maximize the number and diversity of isolated strains. More than 1,000 cultures were obtained, characterized by 18S rRNA sequencing and optical microscopy and de-replicated to a subset of 276 strains presented in this work. Strains grouped into 57 genotypes defined by 100% 18S rRNA sequence similarity. These genotypes spread across five divisions: Heterokontophyta, Chlorophyta, Cryptophyta, Haptophyta and Dinophyta. Diatoms were the most abundant group (193 strains), mostly represented by the generaChaetocerosandAttheya. The generaRhodomonasandPyramimonaswere the most abundant non-diatom nanoplankton strains, whileMicromonas polarisdominated the picoplankton. Diversity at the class level was higher during the peak of the bloom. Potentially new species were isolated, in particular within the generaNavicula,Nitzschia,Coscinodiscus,Thalassiosira,Pyramimonas,MantoniellaandIsochrysis.Submitted to: Elementa: Science of the Anthropocene Date: May 17, 2019
Extensive Transcriptional and Translational Regulation Occur During the Maturation of Malaria Parasite Sporozoites
Authors: Lindner Scott E. , Swearingen Kristian E. , Shears Melanie J. , Walker Michael P. , Vrana Erin N. , Hart Kevin J. , Minns Allen M. , Sinnis Photini , Moritz Robert L. , Kappe Stefan H.I. 
Published: May 2019

AbstractPlasmodium sporozoites are transmitted from an infected mosquito to mammals in which they infect the liver. The infectivity profile of sporozoites changes as they egress from oocysts on the mosquito midgut into the hemocoel, and then invade the salivary glands, where they maintain a poised and infectious state until transmission occurs. Upon transmission, the sporozoite must then navigate the host skin, vasculature, and liver. All of these feats require distinct repertoires of proteins and capabilities that are coordinated in an appropriate temporal manner. Here, we report the comprehensive and dynamic transcriptomes and proteomes of both oocyst sporozoite and salivary gland sporozoite stages in both rodent-infectious Plasmodium yoelii parasites and human-infectious Plasmodium falciparum parasites. These data robustly define mRNAs and proteins that are Upregulated in Oocyst Sporozoites (UOS) or Upregulated in Infectious Sporozoites (UIS), which include critical gene products for sporozoite functions, as well as many of unknown importance that are similarly regulated. Moreover, we found that Plasmodium uses two overlapping, extensive, and independent programs of translational repression across sporozoite maturation to temporally regulate specific genes necessary to successfully navigate the mosquito vector and mammalian host environments. Finally, gene-specific validation experiments of selected, translationally repressed transcripts in P. yoelii confirmed the interpretations of the global transcriptomic and proteomic datasets. Together, these data indicate that two waves of translational repression are implemented and relieved at different times in sporozoite maturation to promote its successful life cycle progression.
Older adults benefit from more widespread brain network integration during working memory
Authors: Crowell C.A. , Davis S.W. , Beynel L. , Deng L. , Lakhlani D. , Hilbig S.A. , Palmer H. , Brito A. , Wang J. , Peterchev A. V , Luber B. , Lisanby S.H. , Appelbaum L.G. , Cabeza R. 
Published: May 2019

AbstractNeuroimaging evidence suggests that the aging brain relies on a more distributed set of cortical regions than younger adults in order to maintain successful levels of performance during demanding cognitive tasks. However, it remains unclear how task demands give rise to this age-related expansion in cortical networks. To investigate this issue, we used functional magnetic resonance imaging to measure univariate activity, network connectivity, and cognitive performance in younger and older adults during a working memory (WM) task. In the WM task investigated, participants hold letters online (maintenance) while reordering them alphabetically (manipulation). WM load was titrated to obtain four individualized difficulty levels. Network integration—defined as the ratio of within-versus between-network connectivity—was linked to individual differences in WM capacity. The study yielded three main findings. First, as task difficulty increased, network integration decreased in younger adults, whereas it increased in older adults. Second, age-related increases in network integration were driven by increases in right hemispheric connectivity to both left and right cortical regions, a finding that helps to reconcile extant theories of compensatory recruitment in aging to address the multivariate dynamics of global network functioning. Lastly, older adults with higher WM capacity demonstrated higher levels of network integration in the most difficult condition. These results shed light on the mechanisms of age-related network reorganization by suggesting that changes in network connectivity may act as an adaptive form of compensation, with older adults recruiting a more distributed cortical network as task demands increase.Significance statementOlder adults often activate brain regions not engaged by younger adults, but the circumstances under which this widespread network emerges are unclear. Here, we examined the effects of aging on network connectivity between task regions recruited during a working memory (WM) manipulation task, and the rest of the brain. We found an age-related increase in the more global network integration in older adults, and an association between this integration and working memory capacity in older adults. The findings are generally consistent with the compensatory interpretation of these effects.
Genotype Imputation and Reference Panel: A Systematic Evaluation
Authors: Bai Wei-Yang , Zhu Xiao-Wei , Cong Pei-Kuan , Zhang Xue-Jun , Richards J Brent , Zheng Hou-Feng 
Published: May 2019

AbstractHere, 622 imputations were conducted with 394 customized reference panels for Han Chinese and European populations. Besides validating the fact that the imputation accuracy could always benefit from the increased panel size when the reference panel was population-specific, the results brought two new thoughts as follows. First, when the haplotype size of reference panel was fixed, the imputation accuracy of common and low-frequency variants (MAF>0.5%) decreased while the population-diversity of reference panel increased, but for rare variants (MAF<0.5%), a fraction of diversity (<20%) of panel could improve the imputation accuracy. Second, when the haplotype size of reference panel was increased with extra population-diverse samples, the imputation accuracy of common variants (MAF>5%) for European population could always benefit from the expanding sample size. But for Han Chinese population, the accuracy of all imputed variants reached the highest when reference panel contained a fraction of extra diverse sample (15%∼21%). In addition, we evaluated the existing reference panels such as the HRC and 1000G Phase3 and CONVERGE. For European population, HRC was the best reference panel. For Han Chinese population, we proposed an optimum constituent ratio for the Han Chinese imputation if researchers would like to customize their own sequenced reference panel, but a high quality and large-scale Chinese reference panel was still needed. Our findings could be generalized to the other populations with conservative genome, a tool was provided to investigate other populations of interest (https://github.com/Abyss-bai/reference-panel-reconstruction).Highlights (Key points)A total of 394 reference panels were designed and customized by three strategies, and large-scale genotype imputations were performed with these panels for systematic evaluation in Han Chinese and European populations.The accuracy of imputed variants reached the highest when reference panel contains a fraction of extra diverse sample (15%∼21%) for Han Chinese population, if the haplotype size of the reference panel was increased with extra samples, which is the most common cases.The imputation accuracy showed the different trends between Han Chinese and European populations. In a sense, the European genome may more diverse than Han Chinese genome by itself.Existing reference panels were not the best choice for Chinese imputation, a high quality and large-scale Chinese reference panel was still needed.
miRNA-encoded peptide, miPEP858, regulates plant growth and development in Arabidopsis
Authors: Sharma Ashish , Badola Poorwa Kamal , Bhatia Chitra , Sharma Deepika , Trivedi Prabodh Kumar 
Published: May 2019

AbstractMicroRNAs (miRNAs), small non-coding endogenous RNAs, are processed product of primary miRNAs (pri-miRNAs) and regulate target gene expression. pri-miRNAs have also been reported to encode small peptides, miRNA-Encoded Peptides (miPEPs). Though regulatory role of miPEPs has been speculated, no detailed study has been carried out to elucidate their function through developing knock-out mutants. Here, we report that pri-miR858a ofArabidopsis thalianaencodes a small peptide (miPEP858a) which regulates the expression of pri-miR858a leading to modulation in the expression of target genes involved in the plant growth and development as well as phenylpropanoid pathway. CRISPR-based miPEP858a-edited plants developed phenotypes similar to that of mature miR858-edited plants suggesting crucial role of miPEP858a in mediating miR585a function. miPEP858a-edited and miPEP858a overexpressing lines altered plant development and accumulated modulated levels of flavonoids due to changes in expression of associated genes. Exogenous treatment of synthetic-miPEP858a to the miPEP858a-edited plants complemented phenotypes and the gene function suggesting a significant role of miPEP858a in controlling the miR858 function and plant development.One sentence summarySmall peptide, miPEP858a, encoded by primary miRNA for miR858a regulates plant growth, development and flavonoid biosynthesisThe authors responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors
Identifying dynamic, partially occupied residues using anomalous scattering
Authors: Rocchio Serena , Duman Ramona , El Omari Kamel , Mykhaylyk Vitaliy , Yan Zhen , Wagner Armin , Bardwell James C. A. , Horowitz Scott 
Published: May 2019

AbstractX-ray crystallography is generally used to take single snapshots of a protein’s conformation. The important but difficult task of characterizing structural ensembles in crystals is typically limited to small conformational changes, such as multiple side-chain conformations. A crystallographic method was recently introduced that utilizes Residual Anomalous and Electron Density (READ) to characterize structural ensembles encompassing large-scale structural changes. Key to this method is an ability to accurately measure anomalous signals and distinguish them from noise or other anomalous scatterers. This report presents an optimized data collection and analysis strategy for partially occupied iodine anomalous signals. Using the long wavelength-optimized beamline I23 at Diamond Light Source, the ability to accurately distinguish the positions of anomalous scatterers with as low as ~12% occupancy is demonstrated. The number and position of these anomalous scatterers are consistent with previous biophysical, kinetic and structural data that suggest the protein Im7 binds to the chaperone Spy in multiple partially occupied conformations. This study shows that a long-wavelength beamline results in easily validated anomalous signals that are strong enough to be used to detect and characterize highly dynamic sections of crystal structures.SynopsisStructural studies on partially occupied, dynamic protein systems by crystallography are difficult. We present methods here for detecting these states in crystals.
Structural analysis ofde novoSTXBP1 mutation in complex with syntaxin 1A reveals a major alteration in the interaction interface in a child with developmental delay and spasticity
Authors: Banne Ehud , Falik-Zaccai Tzipora , Brielle Esther , Kalfon Limor , Ladany Hagay , Klinger Danielle , Schneidman-Duhovny Dina , Linial Michal 
Published: May 2019

AbstractSTXBP1, also known as Munc-18, is a master regulator of neurotransmitter release and synaptic function in the human brain through its direct interaction with syntaxin 1A. STXBP1 related disorders are well characterized and cover a diverse range of neurological and neurodevelopmental conditions. Through exome sequencing of a child with developmental delay, hypotonia and spasticity, we found a novelde novoinsertion mutation of three nucleotides in the STXBP1 coding region, resulting in an additional arginine after position 39 (R39dup). Inconclusive results from state-of-the-art variant prediction tools mandated a structure-based approach using molecular dynamics (MD) simulations of the STXBP1-syntaxin 1A complex. Comparison of the interaction interfaces of the wild type and the R39dup complexes revealed a reduced interaction surface area in the mutant, leading to destabilization of the interaction. We applied the same MD methodology to 7 additional previously reported STXBP1 mutations. We find that the stability of the STXBP1-syntaxin 1A interface correlates with the reported clinical phenotypes. We illustrate a direct link between a patient’s genetic variations and the observed clinical phenotype through protein structure, dynamics, and function.
Performance Evaluation of Traditional Signal Processing Methods in LocalizingTursiops truncatusWhistles in a Reverberant Aquatic Environment
Authors: Woodward SF , Magnasco MO 
Published: May 2019

AbstractRelative to individually distinctivesignature whistles, little is known about the “non-signature” calls – particularly the non-signature whistles – of the common Atlantic bottlenose dolphin,Tursiops truncatus. While such calls are suspected to serve social function, tracking their exchange among conspecifics and correlating their usage with non-acoustic behavior has proven challenging, given both their relative scarcity in the dolphin repertoire and their characteristic shared use among dolphins, which precludes the unique identification of callers on the basis of whistle properties alone. Towards the goal of robustly identifying the callers of non-signature whistles (equivalently, attributing non-signature whistles to callers), we present a new, long-term audiovisual monitoring system designed for and tested at the Dolphin Discovery exhibit of the National Aquarium in Baltimore, Maryland. In this paper, we confirm the system’s ability to spatially localize impulse-like sounds using traditional signal processing approaches that have already been used to localize dolphin echolocation clicks. We go on to provide the first rigorous experimental evaluation of the component time-difference-of-arrival-(TDOA) extraction methods on whistle-like tonal sounds in a (reverberant) aquatic environment, showing that they are generally not suited to sound localization. Nevertheless, we find that TDOA extraction under these circumstances is performed significantly better using a Generalized Cross-Correlation with Phase Transform (GCC-PHAT) method than a standard circular cross-correlation method, a potentially important result.
Incorporating neuronal fatigue in deep neural networks captures dynamics of adaptation in neurophysiology and perception
Authors: Vinken Kasper , Boix Xavier , Kreiman Gabriel 
Published: May 2019

AbstractAdaptation is a fundamental property of the visual system that molds how an object is processed and perceived in its temporal context. It is unknown whether adaptation requires a circuit level implementation or whether it emerges from neuronally intrinsic biophysical processes. Here we combined neurophysiological recordings, psychophysics, and deep convolutional neural network computational models to test the hypothesis that a neuronally intrinsic, biophysically plausible, fatigue mechanism is sufficient to account for the hallmark properties of adaptation. The proposed model captured neural signatures of adaptation including repetition suppression and novelty detection. At the behavioral level, the proposed model was consistent with perceptual aftereffects. Furthermore, adapting to prevailing but irrelevant inputs improves object recognition and the adaptation computations can be trained in a network trained to maximize recognition performance. These results show that an intrinsic fatigue mechanism can account for key neurophysiological and perceptual properties and enhance visual processing by incorporating temporal context.
Benchmarking of computational error-correction methods for next-generation sequencing data
Authors: Mitchell Keith , Brito Jaqueline J. , Mandric Igor , Wu Qiaozhen , Knyazev Sergey , Chang Sei , Martin Lana S. , Karlsberg Aaron , Gerasimov Ekaterina , Littman Russell , Hill Brian L. , Wu Nicholas C. , Yang Harry , Hsieh Kevin , Chen Linus , Littman Eli , Shabani Taylor , Enik German , Yao Douglas , Sun Ren , Schroeder Jan , Eskin Eleazar , Zelikovsky Alex , Skums Pavel , Pop Mihai , Mangul Serghei 
Published: May 2019

AbstractBackgroundRecent advancements in next-generation sequencing have rapidly improved our ability to study genomic material at an unprecedented scale. Despite substantial improvements in sequencing technologies, errors present in the data still risk confounding downstream analysis and limiting the applicability of sequencing technologies in clinical tools. Computational error-correction promises to eliminate sequencing errors, but the relative accuracy of error correction algorithms remains unknown.ResultsIn this paper, we evaluate the ability of error-correction algorithms to fix errors across different types of datasets that contain various levels of heterogeneity. We highlight the advantages and limitations of computational error correction techniques across different domains of biology, including immunogenomics and virology. To demonstrate the efficacy of our technique, we apply the UMI-based high-fidelity sequencing protocol to eliminate sequencing errors from both simulated data and the raw reads. We then perform a realistic evaluation of error correction methods.ConclusionsIn terms of accuracy, we find that method performance varies substantially across different types of datasets with no single method performing best on all types of examined data. Finally, we also identify the techniques that offer a good balance between precision and sensitivity
A diversity of traits contributes to salinity tolerance of wild Galapagos tomatoes seedlings
Authors: Pailles Yveline , Awlia Mariam , Julkowska Magdalena , Passone Luca , Zemmouri Khadija , Negrão Sónia , Schmöckel Sandra M. , Tester Mark 
Published: May 2019

AbstractTraits of modern crops have been heavily selected in agriculture, causing the commercial lines to be more susceptible to harsh conditions, which their wild relatives are naturally better able to withstand. Understanding the developed mechanisms of tolerance present in wild relatives can enhance crop performance under stress. In this study, salinity tolerance traits of two species of wild tomato endemic to the Galapagos Islands, Solanum cheesmaniae and Solanum galapagense, were investigated. Since these tomatoes grow well despite being constantly splashed with seawater, they could be a valuable genetic resource for improving salinity tolerance in commercial tomatoes. To explore their potential, over 20 traits reflecting plant growth, physiology and ion content were recorded in 67 accessions of S. cheesmaniae and S. galapagense and two commercial tomato lines of Solanum lycopersicum. Salt treatments of 200 mM NaCl were applied for ten days, using supported hydroponics. Great natural variation was evident in the responses of the Galapagos tomatoes to salt stress and they also displayed greater tolerance to salt stress than the commercial lines tested, based on multivariate trait analyses. Although Galapagos tomatoes in general exhibited better tolerance to salt stress than the commercial lines tested, the accessions LA0317, LA1449 and LA1403 showed particularly high salinity tolerance based on growth maintenance under stress. Thus, Galapagos tomatoes should be further explored using forward genetic studies to identify and investigate the genes underlying their high tolerance and be used as a resource for increasing salinity tolerance of commercial tomatoes. The generated data, along with useful analysis tools, have been packaged and made publicly available via an interactive online application (https://github.com/mmjulkowska/La_isla_de_tomato) to facilitate trait selection and the use of Galapagos tomatoes for the development of salt tolerant commercial tomatoes.
White Matter Connectometry Among Individuals with Self-Reported Family History of Drug and Alcohol Use Disorders
Authors: Waters Abigail B. , Sawyer Kayle S. , Gansler David A. 
Published: May 2019

AbstractHeredity is an important risk factor for alcoholism. Several studies have been conducted on small groups of alcohol naïve adolescents which show lowered fractional anisotropy of frontal white matter in FH+ groups. We sought to compare large FH+ and FH-groups using white matter connectometry, as opposed to the previously used global tractography method, as it is more sensitive to regional variability. Imaging and behavioral data from the Human Connectome Project (WU-MINN HCP 1200) was used. Groups of participants were positive (n=109) and negative (n=109) for self-reported drug and alcohol use disorders in at least one parent. Groups were matched on gender, age, education, current alcohol usage, and alcohol use disorders (AUD). Connectometry was performed on diffusion MRI in DSI-Studio using q-space diffeomorphic reconstruction, and multiple regression was completed with 5000 permutations. Analyses showed decreased major tract (>40 mm) connectivity in the FH+ group in left inferior longitudinal fasciculus, bilateral cortico-striatal pathway, left cortico-thalamic pathway, and corpus callosum, compared to the FH- group. For cognitive tasks related to reward processing, inhibition, and monitoring, there were a number of interactions, such that the relationship between identified networks and behavior differed significantly between groups. Positive self-report of family history of alcoholism was associated with decreased connectivity in reward signaling pathways, controlling for alcohol consumption and AUD. This is the first connectometry study of FH+, and extends the neural basis of the hereditary diathesis of alcoholism beyond that demonstrated with global tractography. Regions associated with FH+ are similar to those associated with AUD.