bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial transcriptome remodeling during sequential co-culture with a marine dinoflagellate and diatom
Authors: Landa Marine , Burns Andrew S , Roth Selena J , Moran Mary Ann 
Published: July 2017

Abstract
In their role as primary producers, marine phytoplankton modulate heterotrophic bacterial activities through differences in the types and amounts of organic matter they release. This study investigates the transcriptional response of bacterium Ruegeria pomeroyi, a member of the Roseobacter clade known to affiliate with diverse phytoplankton groups in the ocean, during a shift in phytoplankton taxonomy. The bacterium was initially introduced into a culture of the dinoflagellate Alexandrium tamarense, and then experienced a change in phytoplankton community composition as the diatom Thalassiosira pseudonana gradually outcompeted the dinoflagellate. Samples were taken throughout the 30-day experiment to track shifts in bacterial gene expression informative of metabolic and ecological interactions. Transcriptome data indicate fundamental differences in the exometabolites released by the two phytoplankton. During growth with the dinoflagellate, gene expression patterns indicated that the main sources of carbon and energy for R. pomeroyi were dimethysulfoniopropionate (DMSP), taurine, methylated amines, and polyamines. During growth with the diatom, dihydroxypropanesulfonate (DHPS), xylose, ectoine, and glycolate instead appeared to fuel the bulk of bacterial metabolism. Expression patterns of genes for quorum sensing, gene transfer agent, and motility suggest that bacterial processes related to cell communication and signaling differed depending on which phytoplankton species dominated the co-culture. A remodeling of the R. pomeroyi transcriptome implicating more than a quarter of the genome occurred through the change in phytoplankton regime.
Genetic and neuronal mechanisms governing the sex-specific interaction between sleep and sexual behaviors in Drosophila
Authors: Chen Dandan , Sitaraman Divya , Chen Nan , Jin Xin , Han Caihong , Chen Jie , Sun Mengshi , Baker Bruce S. , Nitabach Michael N. , Pan Yufeng 
Published: July 2017

AbstractAnimals execute one particular behavior among many others in a context-dependent manner, yet the mechanisms underlying such behavioral choice remain poorly understood. Here we studied how two fundamental behaviors, sex and sleep, interact at genetic and neuronal levels in Drosophila. We show that an increased need for sleep inhibits male sexual behavior by decreasing the activity of the male-specific P1 neurons that coexpress the sex determination genes fru
M
and dsx, but does not affect female sexual behavior. Further, we delineate a sex-specific neuronal circuit wherein the P1 neurons encoding increased courtship drive suppressed male sleep by forming mutually excitatory connections with the fru
M
-positive sleep-controlling DN1 neurons. In addition, we find that FRUM regulates male courtship and sleep through distinct neural substrates. These studies reveal the genetic and neuronal basis underlying the sex-specific interaction between sleep and sexual behaviors in Drosophila, and provide insights into how competing behaviors are co-regulated.
Carbon stocks and changes of dead organic matter in China's forests
Authors: Zhu Jianxiao , Hu Huifeng , Tao Shengli , Chi Xiulian , Li Peng , Jiang Lai , Ji Chengjun , Zhu Jiangling , Tang Zhiyao , Pan Yude , Birdsey Richard A. , He Xinhua , Fang Jingyun 
Published: July 2017

AbstractForests play an important role in global carbon cycles. However, the lack of available information on carbon stocks in dead organic matter, including woody debris and litter, reduces the reliability of assessing the carbon cycles in entire forest ecosystems. Here we estimate that the national DOM carbon stock in the period of 2004–2008 is 925 ± 54 Tg, with an average density of 5.95 ± 0.35 Mg C ha−1. Over the past two decades from periods of 1984−1988 to 2004−2008, the national dead organic matter carbon stock has increased by 6.7 ± 2.2 Tg carbon per year, primarily due to increasing forest area. Temperature and precipitation increase the carbon density of woody debris, but decrease that of litter. Additionally, the woody debris increases significantly with above ground biomass and forest age. Our results can improve estimates of the carbon budget in China's forests and for better understanding of effects of climate and stand characteristics on dead organic matter distribution.
Afferent specific role of NMDA receptors for the circuit integration of hippocampal neurogliaform cells
Authors: Chittajallu R. , Wester J. C. , Craig M. T. , Barksdale E. , Yuan X. Q. , Akgül G. , Fang C. , Collins D. , Hunt S. , Pelkey K. A. , McBain C. J. 
Published: July 2017

AbstractAppropriate integration of GABAergic interneurons into nascent cortical circuits is critical for ensuring normal information processing within the brain. Network and cognitive deficits associated with neurological disorders, such as schizophrenia, that result from NMDA receptor-hypofunction have been mainly attributed to dysfunction of parvalbumin-expressing interneurons that paradoxically express low levels of synaptic NMDA receptors. Here, we reveal that throughout postnatal development, thalamic, and entorhinal cortical inputs onto hippocampal neurogliaform cells are characterized by a large NMDA receptor-mediated component. This NMDA receptor-signaling is prerequisite for developmental programs ultimately responsible for the appropriate long-range AMPAR-mediated recruitment of neurogliaform cells. In contrast, AMPAR-mediated input at local Schaffer-collateral synapses on neurogliaform cells remains normal following NMDA receptor-ablation. These afferent specific deficits potentially impact neurogliaform cell mediated inhibition within the hippocampus and our findings reveal circuit loci implicating this relatively understudied interneuron subtype in the etiology of neurodevelopmental disorders characterized by NMDA receptor-hypofunction.
Cognitive behavioral therapy for insomnia in Parkinson’s disease: a case series
Authors: Humbert Meghan , Findley James , Hernandez-Con Maria , Chahine Lana M. 
Published: July 2017

AbstractChronic insomnia is common in patients with Parkinson’s disease. There are limited data to guide its treatment in this patient population, especially in regards to non-pharmacologic interventions, some of which are highly effective in the non-Parkinson’s disease population. The aim of this study is to describe a series of Parkinson’s disease patients who underwent cognitive behavioral therapy for insomnia (CBTi). Parkinson’s disease patients who had undergone a baseline and at least one follow-up CBTi session were identified. Electronic medical records and pre-treatment and post-treatment patient sleep diaries were reviewed. Sleep measures of interest included wake time after sleep onset, sleep efficiency, sleep onset latency, and total sleep time. Pre-treatment and post-treatment values were compared within subjects using paired t-test. Five patients were included. Patients attended an average of eight sessions of CBTi (range 5–12). Significant increases in sleep efficiency (p = 0.02) and decreases in number of awakenings per night (p = 0.02) were found. Our data provide preliminary evidence that cognitive behavioral therapy is an effective treatment for insomnia in Parkinson’s disease, and is well tolerated and well received by patients. Given the limited data supporting use of medications to treat chronic insomnia in Parkinson’s disease, combined with their risks, randomized trials to demonstrate the efficacy of CBTi in Parkinson’s disease are warranted.
L

p
-Adaptation: Simultaneous Design Centering and Robustness Estimation of Electronic and Biological Systems
Authors: Asmus Josefine , Müller Christian L. , Sbalzarini Ivo F. 
Published: July 2017

AbstractThe design of systems or models that work robustly under uncertainty and environmental fluctuations is a key challenge in both engineering and science. This is formalized in the design-centering problem, which is defined as finding a design that fulfills given specifications and has a high probability of still doing so if the system parameters or the specifications fluctuate randomly. Design centering is often accompanied by the problem of quantifying the robustness of a system. Here we present a novel adaptive statistical method to simultaneously address both problems. Our method, L
p
-Adaptation, is inspired by the evolution of robustness in biological systems and by randomized schemes for convex volume computation. It is able to address both problems in the general, non-convex case and at low computational cost. We describe the concept and the algorithm, test it on known benchmarks, and demonstrate its real-world applicability in electronic and biological systems. In all cases, the present method outperforms the previous state of the art. This enables re-formulating optimization problems in engineering and biology as design centering problems, taking global system robustness into account.
Lower Cretaceous fossils from China shed light on the ancestral body plan of crown softshell turtles (Trionychidae, Cryptodira)
Authors: Brinkman Donald , Rabi Márton , Zhao Lijun 
Published: July 2017

AbstractPan-trionychids or softshell turtles are a highly specialized and widespread extant group of aquatic taxa with an evolutionary history that goes back to the Early Cretaceous. The earliest pan-trionychids had already fully developed the “classic” softshell turtle morphology and it has been impossible to resolve whether they are stem members of the family or are within the crown. This has hindered our understanding of the evolution of the two basic body plans of crown-trionychids. Thus it remains unclear whether the more heavily ossified shell of the cyclanorbines or the highly reduced trionychine morphotype is the ancestral condition for softshell turtles. A new pan-trionychid from the Early Cretaceous of Zhejiang, China,Perochelys hengshanensissp. nov., allows a revision of softshell-turtle phylogeny. Equal character weighting resulted in a topology that is fundamentally inconsistent with molecular divergence date estimates of deeply nested extant species. In contrast, implied weighting retrieved Lower Cretaceous Perochelysspp. andPetrochelys kyrgyzensisas stem trionychids, which is fully consistent with their basal stratigraphic occurrence and an Aptian-Santonian molecular age estimate for crown-trionychids. These results indicate that the primitive morphology for soft-shell turtles is a poorly ossified shell like that of crown-trionychines and that shell re-ossification in cyclanorbines (including re-acquisition of peripheral elements) is secondary.
Action-based Modeling of Complex Networks
Authors: Arora Viplove , Ventresca Mario 
Published: July 2017

AbstractComplex networks can model a wide range of complex systems in nature and society, and many algorithms (network generators) capable of synthesizing networks with few and very specific structural characteristics (degree distribution, average path length, etc.) have been developed. However, there remains a significant lack of generators capable of synthesizing networks with strong resemblance to those observed in the real-world, which can subsequently be used as a null model, or to perform tasks such as extrapolation, compression and control. In this paper, a robust new approach we term Action-based Modeling is presented that creates a compact probabilistic model of a given target network, which can then be used to synthesize networks of arbitrary size. Statistical comparison to existing network generators is performed and results show that the performance of our approach is comparable to the current state-of-the-art methods on a variety of network measures, while also yielding easily interpretable generators. Additionally, the action-based approach described herein allows the user to consider an arbitrarily large set of structural characteristics during the generator design process.
Minimal hepatic encephalopathy is associated with expansion and activation of CD4+CD28−, Th22 and Tfh and B lymphocytes
Authors: Mangas-Losada Alba , García-García Raquel , Urios Amparo , Escudero-García Desamparados , Tosca Joan , Giner-Durán Remedios , Serra Miguel Angel , Montoliu Carmina , Felipo Vicente 
Published: July 2017

AbstractPeripheral inflammation acts synergistically with hyperammonemia in inducing neurological alterations in cirrhotic patients with minimal hepatic encephalopathy (MHE). We hypothesized that appearance of MHE would be associated to some specific qualitative change in peripheral inflammation. The aim of this work was to characterize the changes in peripheral inflammation associated to appearance of MHE. We analyzed it by immunophenotyping and cytokine profile analysis, in cirrhotic patients without or with MHE and controls. The main alterations associated specifically with MHE are: 1) increased activation of all subtypes of CD4+T-lymphocytes, with the increased expression of CD69; 2) increased amount of CD4+CD28−T lymphocytes, associated with increased levels of CX3CL1 and of IL-15; 3) increased differentiation of CD4+T lymphocytes to Th follicular and Th22; 4) increased activation of B lymphocytes and serum IgG. This study has identified some specific alterations of the immune system associated with appearance of the neurological alterations in MHE patients.
Hobit expression by a subset of human liver-resident CD56bright Natural Killer cells
Authors: Lunemann Sebastian , Martrus Gloria , Goebels Hanna , Kautz Tobias , Langeneckert Annika , Salzberger Wilhelm , Koch Martina , J. Bunders Madeleine , Nashan Björn , van Gisbergen Klaas P. J. M. , Altfeld Marcus 
Published: July 2017

AbstractImmune responses show a high degree of tissue specificity shaped by factors influencing tissue egress and retention of immune cells. The transcription factor Hobit was recently shown to regulate tissue-residency in mice. Whether Hobit acts in a similar capacity in humans remains unknown. Our aim was to assess the expression and contribution of Hobit to tissue-residency of Natural Killer (NK) cells in the human liver. The human liver was enriched for CD56brightNK cells showing increased expression levels of the transcription factor Hobit. HobitposCD56brightNK cells in the liver exhibited high levels of CD49a, CXCR6 and CD69. HobitposCD56brightNK cells in the liver furthermore expressed a unique set of transcription factors with higher frequencies and levels of T-bet and Blimp-1 when compared to HobitnegCD56brightNK cells. Taken together, we show that the transcription factor Hobit identifies a subset of NK cells in human livers that express a distinct set of adhesion molecules and chemokine receptors consistent with tissue residency. These data suggest that Hobit is involved in regulating tissue-residency of human intrahepatic CD56brightNK cells in a subset of NK cells in inflamed livers.
Mass-spectrometry analysis of modifications at DNA termini induced by DNA polymerases
Authors: Smirnov Igor P. , Kolganova Natalia A. , Vasiliskov Vadim A. , Chudinov Alexander V. , Timofeev Edward N. 
Published: July 2017

AbstractNon-natural nucleotide substrates are widely used in the enzymatic synthesis of modified DNA. The terminal activity of polymerases in the presence of modified nucleotides is an important, but poorly characterized, aspect of enzymatic DNA synthesis. Here, we studied different types of polymerase activity at sequence ends using extendable and non-extendable synthetic models in the presence of the Cy5-dUTP analog Y. In primer extension reactions with selected exonuclease-deficient polymerases, nucleotide Y appeared to be a preferential substrate for non-templated 3′-tailing, as determined by MALDI mass-spectrometry and gel-electrophoresis. This result was further confirmed by the 3′-tailing of a non-extendable hairpin oligonucleotide model. Additionally, DNA polymerases induce an exchange of the 3′ terminal thymidine for a non-natural nucleotide via pyrophosphorolysis in the presence of inorganic pyrophosphate. In primer extension reactions, the proofreading polymerases Vent, Pfu, and Phusion did not support the synthesis of Y-modified primer strand. Nevertheless, Pfu and Phusion polymerases were shown to initiate terminal nucleotide exchange at the template. Unlike non-proofreading polymerases, these two enzymes recruit 3′–5′ exonuclease functions to cleave the 3′ terminal thymidine in the absence of pyrophosphate.
Static Magnetic Field Stimulation Enhances Oligodendrocyte Differentiation and Secretion of Neurotrophic Factors
Authors: Prasad Ankshita , Teh Daniel B. Loong , Blasiak Agata , Chai Chou , Wu Yang , Gharibani Payam M. , Yang In Hong , Phan Thang T. , Lim Kah Leong , Yang Hyunsoo , Liu Xiaogang , All Angelo H. 
Published: July 2017

AbstractThe cellular-level effects of low/high frequency oscillating magnetic field on excitable cells such as neurons are well established. In contrast, the effects of a homogeneous, static magnetic field (SMF) on Central Nervous System (CNS) glial cells are less investigated. Here, we have developed an in vitro SMF stimulation set-up to investigate the genomic effects of SMF exposure on oligodendrocyte differentiation and neurotrophic factors secretion. Human oligodendrocytes precursor cells (OPCs) were stimulated with moderate intensity SMF (0.3 T) for a period of two weeks (two hours/day). The differential gene expression of cell activity marker (c-fos), early OPC (Olig1, Olig2. Sox10), and mature oligodendrocyte markers (CNP, MBP) were quantified. The enhanced myelination capacity of the SMF stimulated oligodendrocytes was validated in a dorsal root ganglion microfluidics chamber platform. Additionally, the effects of SMF on the gene expression and secretion of neurotrophic factors- BDNF and NT3 was quantified. We also report that SMF stimulation increases the intracellular calcium influx in OPCs as well as the gene expression of L-type channel subunits-CaV1.2 and CaV1.3. Our findings emphasize the ability of glial cells such as OPCs to positively respond to moderate intensity SMF stimulation by exhibiting enhanced differentiation, functionality as well as neurotrophic factor release.
From powders to bulk metallic glass composites
Authors: Krämer Lisa , Champion Yannick , Pippan Reinhard 
Published: July 2017

AbstractOne way to adjust the properties of materials is by changing its microstructure. This concept is not easily applicable on bulk metallic glasses (BMGs), because they do not consist of grains or different phases and so their microstructure is very homogeneous. One obvious way to integrate inhomogeneities is to produce bulk metallic glass composites (BMGCs). Here we show how to generate BMGCs via high-pressure torsion (HPT) starting from powders (amorphous Zr-MG and crystalline Cu). Using this approach, the composition can be varied and by changing the applied shear strains, the refinement of the microstructure is adjustable. This process permits to produce amorphous/crystalline composites where the scale of the phases can be varied from the micro- to the nanometer regime. Even mixing of the two phases and the generation of new metallic glasses can be achieved. The refinement of microstructure increases the hardness and a hardness higher than the initial BMG can be obtained.
Signatures of a magnetic field-induced unconventional nematic liquid in the frustrated and anisotropic spin-chain cuprate LiCuSbO4
Authors: Grafe H.-J. , Nishimoto S. , Iakovleva M. , Vavilova E. , Spillecke L. , Alfonsov A. , Sturza M.-I. , Wurmehl S. , Nojiri H. , Rosner H. , Richter J. , Rößler U. K. , Drechsler S.-L. , Kataev V. , Büchner B. 
Published: July 2017

AbstractModern theories of quantum magnetism predict exotic multipolar states in weakly interacting strongly frustrated spin-1/2 Heisenberg chains with ferromagnetic nearest neighbor (NN) inchain exchange in high magnetic fields. Experimentally these states remained elusive so far. Here we report strong indications of a magnetic field-induced nematic liquid arising above a field of ~13 T in the edge-sharing chain cuprate LiSbCuO4 ≡ LiCuSbO4. This interpretation is based on the observation of a field induced spin-gap in the measurements of the 7Li NMR spin relaxation rate T1−1 as well as a contrasting field-dependent power-law behavior of T1−1 vs. T and is further supported by static magnetization and ESR data. An underlying theoretical microscopic approach favoring a nematic scenario is based essentially on the NN XYZ exchange anisotropy within a model for frustrated spin-1/2 chains and is investigated by the DMRG technique. The employed exchange parameters are justified qualitatively by electronic structure calculations for LiCuSbO4.
Ultrafast intersystem crossings in Fe-Co Prussian blue analogues
Authors: van Veenendaal Michel 
Published: July 2017

AbstractUltrafast spincrossover is studied in Fe-Co Prussian blue analogues using a dissipative quantum-mechanical model of a cobalt ion coupled to a breathing mode. All electronic interactions are treated on an equal footing. It is theoretically demonstrated that the divalent cobalt ion reaches 90% of the $$S{\boldsymbol{=}}\frac{{\bf{3}}}{{\bf{2}}}$$
S
=

3
2

value within 20 fs after photoexciting a low-spin Co3+ ion by an iron-to-cobalt charge transfer. The doublet-to-quartet spin crossover is significantly faster than the oscillation period of the breathing mode. The system relaxes to the lowest manifold of divalent cobalt (4T1) in 150–200 fs. Strong oscillations in spin-orbit coupling and the involvement of higher-lying quartets are found.
Comparison of micro-CT imaging and histology for approximal caries detection
Authors: Boca C. , Truyen B. , Henin L. , Schulte A. G. , Stachniss V. , De Clerck N. , Cornelis J. , Bottenberg P. 
Published: July 2017

AbstractHistological sectioning is a generally accepted in vitro validation method for caries detection techniques. However, it requires cumbersome sample preparation and induces irreversible sample destruction. Micro-Computer Tomography (micro-CT) allows non-destructive imaging of tooth structure. The aim of this study was to compare the performance of histological sectioning and micro-CT imaging in detecting approximal carious lesions. Unlike previous studies, evaluation is objectified by comparing visual appearance of exactly corresponding anatomical regions. Sixty extracted human teeth were scanned with a desktop micro CT system. Axial histological slices were prepared and photographed. Sample preparation, combined with dedicated image processing, ensured selection of identical anatomical regions on radiographic and histological images. Evaluation of the presence and extent of carious lesions was performed by four dentists using custom-designed software. Each section was scored independently (histo or micro CT). Scores of approximal surfaces were retained for further analysis. Spearman’s correlation coefficients (0.738 to 0.829, p < 0.0001) showed a good agreement between signs of carious lesions in the identical region obtained with both methods. Bland-Altman plots showed that 90.76% of the data points were within the limits of agreement. Micro-CT imaging was shown to provide an interesting alternative to histological sectioning as detection method for carious lesions.