bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular mechanisms of temperature acclimation and adaptation in marine diatoms
Authors: Liang Yue , Koester Julie A , Liefer Justin D , Irwin Andrew J , Finkel Zoe V 
Published: May 2019

Abstract
Diatoms are important contributors to marine primary production and the ocean carbon cycle, yet the molecular mechanisms that regulate their acclimation and adaptation to temperature are poorly understood. Here we use a transcriptomic approach to investigate the molecular mechanisms associated with temperature acclimation and adaptation in closely related colder- and warmer-adapted diatom species. We find evidence that evolutionary changes in baseline gene expression, which we termed transcriptional investment or divestment, is a key mechanism used by diatoms to adapt to different growth temperatures. Invested and divested pathways indicate that the maintenance of protein processing machinery and membrane structure, important short-term physiological mechanisms used to respond to temperature changes, are key elements associated with adaptation to different growth temperatures. Our results also indicate that evolutionary changes in the transcriptional regulation of acetyl-CoA associated pathways, including lipid and branched chain amino acid metabolism, are used by diatoms to balance photosynthetic light capture and metabolism with changes in growth temperature. Transcriptional investment and divestment can provide a framework to identify mechanisms of acclimation and adaption to temperature.
Commonality in dysregulated expression of gene sets in cortical brains of individuals with autism, schizophrenia, and bipolar disorder
Authors: Guan Jinting , Cai James J. , Ji Guoli , Sham Pak Chung 
Published: May 2019

AbstractIndividuals affected with different neuropsychiatric disorders such as autism (AUT), schizophrenia (SCZ) and bipolar disorder (BPD), may share similar clinical manifestations, suggesting shared genetic influences and common biological mechanisms underlying these disorders. Using brain transcriptome data gathered from postmortem donors affected with AUT, SCZ and BPD, it is now possible to identify shared dysregulated gene sets, i.e., those abnormally expressed in brains of neuropsychiatric patients, compared to non-psychiatric controls. Here, we apply a novel aberrant gene expression analysis method, coupled with consensus co-expression network analysis, to identify gene sets with shared dysregulated expression in cortical brains of individuals affected with AUT, SCZ and BPD. We identify eight gene sets with dysregulated expression shared by AUT, SCZ and BPD, 23 by AUT and SCZ, four by AUT and BPD, and two by SCZ and BPD. The identified genes are enriched with functions relevant to amino acid transport, synapse, neurotransmitter release, oxidative stress, nitric oxide synthase biosynthesis, immune response, protein folding, lysophosphatidic acid-mediated signaling and glycolysis. Our method has been proven to be effective in discovering and revealing multigene sets with dysregulated expression shared by different neuropsychiatric disorders. Our findings provide new insights into the common molecular mechanisms underlying the pathogenesis and progression of AUT, SCZ and BPD, contributing to the study of etiological overlap between these neuropsychiatric disorders.
A novel hydrolase with a pro-death activity from the protozoan parasite Leishmania major
Authors: Basmaciyan Louise , Jacquet Pauline , Azas Nadine , Casanova Magali 
Published: May 2019

AbstractApoptosis is a cell death process generally described as involving a cascade of caspase activation, death receptors and/or pro- and antiapoptotic molecules from the BcL-2 family. But about 20 years ago, a caspase-independent apoptotic pathway has been described. Regarding this pathway, we can learn a lot from Leishmania parasites. Indeed, these parasitic protozoa enter, in response to different stimuli, in a form of cell death phenotypically similar to mammalian apoptosis but without involving caspases or death receptors. So far, only two proteins have been clearly identified as being involved in Leishmania-regulated cell death: the metacaspase and the endonuclease G. We report here the identification of a new protein modeled as a potential hydrolase, highly conserved among Leishmania species and absent in the very close parasite Trypanosoma brucei. This protein is involved in L. major-regulated cell death induced by curcumin, miltefosine and pentamidine, after gene overexpression and/or protein translocation to the nucleus. The identification of proteins involved in Leishmania-regulated cell death will provide a better understanding of nonconventional apoptotic pathways in higher eukaryotes. It will also allow the development of new therapeutic tools via the identification of new specific targets.
Schistosoma mansoni treatment reduces HIV entry into cervical CD4+ T cells and induces IFN-I pathways
Authors: Yegorov Sergey , Joag Vineet , Galiwango Ronald M. , Good Sara V. , Mpendo Juliet , Tannich Egbert , Boggild Andrea K. , Kiwanuka Noah , Bagaya Bernard S. , Kaul Rupert 
Published: May 2019

AbstractSchistosoma mansoni(Sm) infection has been linked with an increased risk of HIV acquisition in women. Therefore, defining the mechanism(s) by whichSmalters HIV susceptibility might lead to new HIV prevention strategies. Here, we analyze the impact of standardSmtherapy in HIV-uninfectedSm+ Ugandan adult women on genital HIV susceptibility and mucosal and systemic immunology. Schistosomiasis treatment induces a profound reduction of HIV entry into cervical and blood CD4+ T cells that is sustained for up to two months, despite transient systemic and mucosal immune activation and elevated genital IL-1α levels. Genital IFN-α2a levels are also elevated post-treatment, and IFN-α2a blocks HIV entry into primary CD4+ T cells ex vivo. Transcriptomic analysis of blood mononuclear cells post-Smtreatment shows IFN-I pathway up-regulation and partial reversal ofSm-dysregulated interferon signaling. These findings indicate thatSmtherapy may reduce HIV susceptibility for women withSminfection, potentially through de-repression of IFN-I pathways.
A soft photopolymer cuboid that computes with binary strings of white light
Authors: Hudson Alexander D. , Ponte Matthew R. , Mahmood Fariha , Pena Ventura Thomas , Saravanamuttu Kalaichelvi 
Published: May 2019

AbstractNext-generation stimuli–responsive materials must be configured with local computational ability so that instead of a discrete on-off responsiveness, they sense, process and interact reciprocally with environmental stimuli. Because of their varied architectures and tunable responsiveness to a range of physical and chemical stimuli, polymers hold particular promise in the generation of such “materials that compute”. Here, we present a photopolymer cuboid that autonomously performs pattern recognition and transfer, volumetric encoding and binary arithmetic with incandescent beams. The material’s nonlinear response to incident beams generates one, two or three mutually orthogonal ensembles of white-light filaments, which respectively self-organize into disordered, 1-D and 2-D periodic geometries. Data input as binary (dark-bright) strings generate a unique distribution of filament geometries, which corresponds to the result of a specific operation. The working principles of this material that computes with light is transferrable to other nonlinear systems and incoherent sources including light emitting diodes.
A pistil-expressed pectin methylesterase confers cross-incompatibility between strains of Zea mays
Authors: Lu Yongxian , Hokin Samuel A. , Kermicle Jerry L. , Hartwig Thomas , Evans Mathew M. S. 
Published: May 2019

AbstractA central problem in speciation is the origin and mechanisms of reproductive barriers that block gene flow between sympatric populations. Wind-pollinated plant species that flower in synchrony with one another rely on post-pollination interactions to maintain reproductive isolation. In some locations in Mexico, sympatric populations of domesticated maize and annual teosinte grow in intimate associate and flower synchronously, but rarely produce hybrids. This trait is typically conferred by a single haplotype, Teosinte crossing barrier1-s. Here, we show that the Teosinte crossing barrier1-s haplotype contains a pistil-expressed, potential speciation gene, encoding a pectin methylesterase homolog. The modification of the pollen tube cell wall by the pistil, then, is likely a key mechanism for pollen rejection in Zea and may represent a general mechanism for reproductive isolation in grasses.
Uncovering the structure of self-regulation through data-driven ontology discovery
Authors: Eisenberg Ian W. , Bissett Patrick G. , Zeynep Enkavi A. , Li Jamie , MacKinnon David P. , Marsch Lisa A. , Poldrack Russell A. 
Published: May 2019

AbstractPsychological sciences have identified a wealth of cognitive processes and behavioral phenomena, yet struggle to produce cumulative knowledge. Progress is hamstrung by siloed scientific traditions and a focus on explanation over prediction, two issues that are particularly damaging for the study of multifaceted constructs like self-regulation. Here, we derive a psychological ontology from a study of individual differences across a broad range of behavioral tasks, self-report surveys, and self-reported real-world outcomes associated with self-regulation. Though both tasks and surveys putatively measure self-regulation, they show little empirical relationship. Within tasks and surveys, however, the ontology identifies reliable individual traits and reveals opportunities for theoretic synthesis. We then evaluate predictive power of the psychological measurements and find that while surveys modestly and heterogeneously predict real-world outcomes, tasks largely do not. We conclude that self-regulation lacks coherence as a construct, and that data-driven ontologies lay the groundwork for a cumulative psychological science.
Resting brain dynamics at different timescales capture distinct aspects of human behavior
Authors: Liégeois Raphaël , Li Jingwei , Kong Ru , Orban Csaba , Van De Ville Dimitri , Ge Tian , Sabuncu Mert R. , Yeo B. T. Thomas 
Published: May 2019

AbstractLinking human behavior to resting-state brain function is a central question in systems neuroscience. In particular, the functional timescales at which different types of behavioral factors are encoded remain largely unexplored. The behavioral counterparts of static functional connectivity (FC), at the resolution of several minutes, have been studied but behavioral correlates of dynamic measures of FC at the resolution of a few seconds remain unclear. Here, using resting-state fMRI and 58 phenotypic measures from the Human Connectome Project, we find that dynamic FC captures task-based phenotypes (e.g., processing speed or fluid intelligence scores), whereas self-reported measures (e.g., loneliness or life satisfaction) are equally well explained by static and dynamic FC. Furthermore, behaviorally relevant dynamic FC emerges from the interconnections across all resting-state networks, rather than within or between pairs of networks. Our findings shed new light on the timescales of cognitive processes involved in distinct facets of behavior.
qDSB-Seq is a general method for genome-wide quantification of DNA double-strand breaks using sequencing
Authors: Zhu Yingjie , Biernacka Anna , Pardo Benjamin , Dojer Norbert , Forey Romain , Skrzypczak Magdalena , Fongang Bernard , Nde Jules , Yousefi Razie , Pasero Philippe , Ginalski Krzysztof , Rowicka Maga 
Published: May 2019

AbstractDNA double-strand breaks (DSBs) are among the most lethal types of DNA damage and frequently cause genome instability. Sequencing-based methods for mapping DSBs have been developed but they allow measurement only of relative frequencies of DSBs between loci, which limits our understanding of the physiological relevance of detected DSBs. Here we propose quantitative DSB sequencing (qDSB-Seq), a method providing both DSB frequencies per cell and their precise genomic coordinates. We induce spike-in DSBs by a site-specific endonuclease and use them to quantify detected DSBs (labeled, e.g., using i-BLESS). Utilizing qDSB-Seq, we determine numbers of DSBs induced by a radiomimetic drug and replication stress, and reveal two orders of magnitude differences in DSB frequencies. We also measure absolute frequencies of Top1-dependent DSBs at natural replication fork barriers. qDSB-Seq is compatible with various DSB labeling methods in different organisms and allows accurate comparisons of absolute DSB frequencies across samples.
Proton mediated spin state transition of cobalt heme analogs
Authors: Zhao Jianping , Peng Qian , Wang Zijian , Xu Wei , Xiao Hongyan , Wu Qi , Sun Hao-Ling , Ma Fang , Zhao Jiyong , Sun Cheng-Jun , Zhao Jianzhang , Li Jianfeng 
Published: May 2019

AbstractThe spin state transition from low spin to high spin upon substrate addition is one of the key steps in cytochrome P450 catalysis. External perturbations such as pH and hydrogen bonding can also trigger the spin state transition of hemes through deprotonated histidine (e.g. Cytochrome c). In this work, we report the isolated 2-methylimidazole Cobalt(II) [Co(TPP)(2-MeHIm)] and [Co(TTP)(2-MeHIm)], and the corresponding 2-methylimidazolate derivatives where the N−H proton of axial 2-MeHIm is removed. Interestingly, various spectroscopies including EPR and XAFS determine a high-spin state (S = 3/2) for the imidazolate derivatives, in contrast to the low-spin state (S = 1/2) of all known imidazole analogs. DFT assisted stereoelectronic investigations are applied to understand the metal-ligand interactions, which suggest that the dramatically displaced metal center allowing a promotion eg(dπ) → b1g($$d_{x^2 - y^2}$$

d

x

2

-

y

2

) is crucial for the occurrence of the spin state transition.
Publisher Correction: GWAS of bone size yields twelve loci that also affect height, BMD, osteoarthritis or fractures
Authors: Styrkarsdottir Unnur , Stefansson Olafur A. , Gunnarsdottir Kristbjorg , Thorleifsson Gudmar , Lund Sigrun H. , Stefansdottir Lilja , Juliusson Kristinn , Agustsdottir Arna B. , Zink Florian , Halldorsson Gisli H. , Ivarsdottir Erna V. , Benonisdottir Stefania , Jonsson Hakon , Gylfason Arnaldur , Norland Kristjan , Trajanoska Katerina , Boer Cindy G. , Southam Lorraine , Leung Jason C. S. , Tang Nelson L. S. , Kwok Timothy C. Y. , Lee Jenny S. W. , Ho Suzanne C. , Byrjalsen Inger , Center Jacqueline R. , Lee Seung Hun , Koh Jung-Min , Lohmander L. Stefan , Ho-Pham Lan T. , Nguyen Tuan V. , Eisman John A. , Woo Jean , Leung Ping-C. , Loughlin John , Zeggini Eleftheria , Christiansen Claus , Rivadeneira Fernando , van Meurs Joyce , Uitterlinden Andre G. , Mogensen Brynjolfur , Jonsson Helgi , Ingvarsson Thorvaldur , Sigurdsson Gunnar , Benediktsson Rafn , Sulem Patrick , Jonsdottir Ingileif , Masson Gisli , Holm Hilma , Norddahl Gudmundur L. , Thorsteinsdottir Unnur , Gudbjartsson Daniel F. , Stefansson Kari 
Published: May 2019

The original HTML version of this Article was updated shortly after publication to add links to the Peer Review file.In addition, affiliations 16 and 17 incorrectly read ‘School of Medicine Sydney, University of Notre Dame Australia, Sydney, WA, 6160, Australia’ and ‘St Vincent’s Clinical School, University of New South Wales Medicine, University of New South Wales, Sydney, NSW, 2052, Australia.’ This has now been corrected in both the PDF and HTML versions of the Article.
High-resolution phase-contrast imaging of biological specimens using a stable betatron X-ray source in the multiple-exposure mode
Authors: Guo Bo , Zhang Xiaohui , Zhang Jie , Hua Jianfei , Pai Chih-Hao , Zhang Chaojie , Chu Hsu-Hsin , Mori Warren , Joshi Chan , Wang Jyhpyng , Lu Wei 
Published: May 2019

AbstractPhase-contrast imaging using X-ray sources with high spatial coherence is an emerging tool in biology and material science. Much of this research is being done using large synchrotron facilities or relatively low-flux microfocus X-ray tubes. An alternative high-flux, ultra-short and high-spatial-coherence table-top X-ray source based on betatron motions of electrons in laser wakefield accelerators has the promise to produce high quality images. In previous phase-contrast imaging studies with betatron sources, single-exposure images with a spatial resolution of 6–70 μm were reported by using large-scale laser systems (60–200 TW). Furthermore, images obtained with multiple exposures tended to have a reduced contrast and resolution due to the shot-to-shot fluctuations. In this article, we demonstrate that a highly stable multiple-exposure betatron source, with an effective average source size of 5 μm, photon number and pointing jitters of <5% and spectral fluctuation of <10%, can be obtained by utilizing ionization injection in pure nitrogen plasma using a 30–40 TW laser. Using this source, high quality phase-contrast images of biological specimens with a 5-μm resolution are obtained for the first time. This work shows a way for the application of high resolution phase-contrast imaging with stable betatron sources using modest power, high repetition-rate lasers.
Atomic replacement effects on the band structure of doped perovskite thin films
Authors: Cheng S. L. , Du C. H. , Chuang T. H. , Lin J. G. 
Published: May 2019

AbstractThe potential applications of perovskite manganite R1-xAxMnO3 (R = rare earth element; A = Sr, Ca) thin films have been continuously explored due to their multi-functional properties. In particular, the optimally hole-doped La0.67Ca0.33MnO3 thin film demonstrates a colossal magneto-resistance that is beneficial to the performance of spintronic devices. To understand the effect of R and A ions on the material properties, we systematically measure the resistivity, magnetization, and electronic energy states for three optimally hole-doped R0.67A0.33MnO3 thin films with R = La, Sm and A = Sr, Ca. Various energy parameters are derived based on the X-ray absorption and X-ray photoelectron spectra, including the band gap, the charge frustration energy and the magnetic exchange energy. It is interesting to find that the replacement of La with Sm is more effective than that of Sr with Ca in terms of tuning the electrical property, the Curie temperature, and the band gap. The strain-induced reduction of the O 2p- Mn 3d hybridization and the interplay of R/A site disorder and strain effect are discussed. The results of this study provide useful information for the band design of perovskite oxide films.
Little evidence for switches to environmental sex determination and turnover of sex chromosomes in lacertid lizards
Authors: Rovatsos Michail , Vukić Jasna , Mrugała Agata , Suwala Grzegorz , Lymberakis Petros , Kratochvíl Lukáš 
Published: May 2019

AbstractAmniotes possess variability in sex determination, from environmental sex determination (ESD), where no sex chromosomes are present, to genotypic sex determination (GSD) with highly differentiated sex chromosomes. Some evolutionary scenarios postulate high stability of differentiated sex chromosomes and rare transitions from GSD to ESD. However, sex chromosome turnovers and two independent transitions from highly differentiated ZZ/ZW sex chromosomes to ESD were previously reported in the lacertid lizards. Here, we examined the homology of sex chromosomes in the wide phylogenetic spectrum of lacertids and their outgroups by comparing gene copy numbers between sexes in genes previously found to be Z-specific in some lacertids. Our current sampling covers 45 species from 26 genera including lineages supposed to possess a derived sex determining systems. We found that all tested lacertids share homologous differentiated ZZ/ZW sex chromosomes, which were present already in their common ancestor living around 85 million years ago. These differentiated sex chromosomes are not present in amphisbaenians and teiid lizards, the close relatives of lacertids. Our study demonstrates how inaccuracies in data can influence the outcome of phylogenetic reconstructions of evolution of sex determination, in this case they overestimated the number of shifts from GSD to ESD and the rate in turnovers of sex chromosomes.
Multi-timescale phase-amplitude couplings in transitions of anesthetic-induced unconsciousness
Authors: Tsai Feng-Fang , Fan Shou-Zen , Cheng Hsiao-Liang , Yeh Jia-Rong 
Published: May 2019

AbstractUnder general anesthesia (GA), advanced analysis methods enhance the awareness of the electroencephalography (EEG) signature of transitions from consciousness to unconsciousness. For nonlinear and nonstationary signals, empirical mode decomposition (EMD) works as a dyadic filter bank to reserve local dynamical properties in decomposed components. Moreover, cross-frequency phase-amplitude coupling analysis illustrates that the coupling between the phase of low-frequency components and the amplitude of high-frequency components is correlated with the brain functions of sensory detection, working memory, consciousness, and attentional selection. To improve the functions of phase-amplitude coupling analysis, we utilized a multi-timescale approach based on EMD to assess changes in brain functions in anesthetic-induced unconsciousness using a measure of phase-amplitude coupling. Two groups of patients received two different anesthetic recipes (with or without ketamine) during the induction period of GA. Long-term (low-frequency) coupling represented a common transitional process of brain functions from consciousness to unconsciousness with a decay trend in both groups. By contrast, short-term coupling reflected a reverse trend to long-term coupling. However, the measures of short-term coupling also reflected a higher degree of coupling for the group with ketamine compared with that without ketamine. In addition, the coupling phase is a factor of interest. The phases for different combinations of coupling components showed significant changes in anesthetic-induced unconsciousness. The coupling between the delta-band phase and the theta-band amplitude changed from in-phase to out-phase coupling during the induction process from consciousness to unconsciousness. The changes in the coupling phase in EEG signals were abrupt and sensitive in anesthetic-induced unconsciousness.
Effect of elastic grading on fretting wear
Authors: Willert Emanuel , Dmitriev Andrey I. , Psakhie Sergey G. , Popov Valentin L. 
Published: May 2019

AbstractWe consider fretting wear in elastic frictional contact under influence of oscillations of small amplitude and investigate the question, how wear damage can be influenced by the introduction of material gradients. To achieve a general understanding we restrict our consideration to media with a power-law dependency of the elastic modulus on depth. In this case, a complete analytical solution can be found for the final worn shape. In the limiting case of small fretting oscillations we obtain a simple, closed-form asymptotic solution of the problem. We find that the optimum grading depends on the oscillation amplitude: for large amplitudes, the use of materials with a positive exponent decreases the wear volume whilst for very small amplitudes the use of graded materials with slightly negative exponent is beneficial. Especially interesting is the case of the Gibson-medium which may help avoiding both fretting wear and fretting fatigue.