bluuebunny/crossref_metadata_2025_split huggingface dataset:
Germination ecology of the perennial herb Xyris longiscapa: inter-annual variation in seed germination and seasonal dormancy cycles
Authors: Oliveira Túlio G. S. , Garcia Queila S. 
Published: July 2019

AbstractGermination ecology was investigated in a natural population of Xyris longiscapa, a perennial herbaceous species endemic to the Brazilian campo rupestre. Seeds were collected over four consecutive years (2014 to 2017) to evaluate germination responses to a range of temperatures (from 15 to 30°C). The light requirement was evaluated in seeds collected in 2014. Seeds collected in 2014 were also buried in soil in the natural habitat of the species to evaluate changes in germinability at different temperatures over the time. Seeds showed an absolute light requirement for germination. Seed germination was affected by temperature, collection year and the interaction between these two factors. Seeds collected in 2014 showed a narrower temperature range for germination (15–20°C), compared with the seeds collected in 2015, 2016 and 2017 that germinated in a temperature range of 15–25°C. Buried seeds remained viable in soil for at least 14 months and exhibited seasonal dormancy cycling. Secondary dormancy was induced during the rainy season and alleviated during the dry season, following a conditional dormancy/dormancy cycle. The degree of primary dormancy appeared to be influenced by the environmental conditions experienced by seeds during maturation. Primary dormancy (when present), seed persistence in soil and seasonal dormancy cycles are strategies of X. longiscapa to enhance regeneration success in the harsh environment of the Brazilian campo rupestre.
A role for PM19-Like 1 in seed dormancy in Arabidopsis
Authors: Barrero Jose M. , Dorr Marie M. , Talbot Mark J. , Ishikawa Shinnosuke , Umezawa Taishi , White Rosemary G. , Gubler Frank 
Published: July 2019

AbstractThe understanding of the genetic basis of grain dormancy in wheat has rapidly improved in the last few years, and a number of genes have been identified related to that trait. We recently identified the wheat genes TaPM19-A1 and -A2 and we have now taken the first step towards understanding the role of this class of genes in seeds. By investigating the Arabidopsis homologous PM19-Like 1 (PM19L1) we have found that it has a seed-specific expression pattern and, while its expression is higher in dormant than in non-dormant seeds, knock-out mutations produced seeds with increased dormancy. Not only primary dormancy, but also secondary dormancy in response to high temperature was increased by the loss-of-function. We have also examined the function of PM19L1 by localizing the PM19 protein primarily to the cotyledon cells in seeds, possibly in membranes. By investigating the co-expression network of this gene we have found that it is connected to a small group of abscisic acid (ABA)-induced seed maturation and storage-related genes. The function of PM19L1 represents a good opportunity to explore the interactions of key factors that can influence seed dormancy such as ABA, temperature and membrane properties.
Temporal phosphate gradients reveal diverse acclimation responses in phytoplankton phosphate uptake
Authors: Cáceres Carlos , Spatharis Sofie , Kaiserli Eirini , Smeti Evangelia , Flowers Hugh , Bonachela Juan A 
Published: July 2019

AbstractPhytoplankton face environmental nutrient variations that occur in the dynamic upper layers of the ocean. Phytoplankton cells are able to rapidly acclimate to nutrient fluctuations by adjusting their nutrient-uptake system and metabolism. Disentangling these acclimation responses is a critical step in bridging the gap between phytoplankton cellular physiology and community ecology. Here, we analyzed the dynamics of phosphate (P) uptake acclimation responses along different P temporal gradients by using batch cultures of the diatom Phaeodactylum tricornutum. We employed a multidisciplinary approach that combined nutrient-uptake bioassays, transcriptomic analysis, and mathematical models. Our results indicated that cells increase their maximum nutrient-uptake rate (Vmax) both in response to P pulses and strong phosphorus limitation. The upregulation of three genes coding for different P transporters in cells experiencing low intracellular phosphorus levels supported some of the observed Vmax variations. In addition, our mathematical model reproduced the empirical Vmax patterns by including two types of P transporters upregulated at medium-high environmental and low intracellular phosphorus levels, respectively. Our results highlight the existence of a sequence of acclimation stages along the phosphate continuum that can be understood as a succession of acclimation responses. We provide a novel conceptual framework that can contribute to integrating and understanding the dynamics and wide diversity of acclimation responses developed by phytoplankton.
Structure of amyloid-β (20-34) with Alzheimer’s-associated isomerization at Asp23 reveals a distinct protofilament interface
Authors: Warmack Rebeccah A. , Boyer David R. , Zee Chih-Te , Richards Logan S. , Sawaya Michael R. , Cascio Duilio , Gonen Tamir , Eisenberg David S. , Clarke Steven G. 
Published: July 2019

AbstractAmyloid-β (Aβ) harbors numerous posttranslational modifications (PTMs) that may affect Alzheimer’s disease (AD) pathogenesis. Here we present the 1.1 Å resolution MicroED structure of an Aβ 20–34 fibril with and without the disease-associated PTM, L-isoaspartate, at position 23 (L-isoAsp23). Both wild-type and L-isoAsp23 protofilaments adopt β-helix-like folds with tightly packed cores, resembling the cores of full-length fibrillar Aβ structures, and both self-associate through two distinct interfaces. One of these is a unique Aβ interface strengthened by the isoaspartyl modification. Powder diffraction patterns suggest a similar structure may be adopted by protofilaments of an analogous segment containing the heritable Iowa mutation, Asp23Asn. Consistent with its early onset phenotype in patients, Asp23Asn accelerates aggregation of Aβ 20–34, as does the L-isoAsp23 modification. These structures suggest that the enhanced amyloidogenicity of the modified Aβ segments may also reduce the concentration required to achieve nucleation and therefore help spur the pathogenesis of AD.
Passive optical time-of-flight for non line-of-sight localization
Authors: Boger-Lombard Jeremy , Katz Ori 
Published: July 2019

AbstractOptical imaging through diffusive, visually-opaque barriers and around corners is an important challenge in many fields, ranging from defense to medical applications. Recently, novel techniques that combine time-of-flight (TOF) measurements with computational reconstruction have allowed breakthrough imaging and tracking of objects hidden from view. These light detection and ranging (LiDAR)-based approaches require active short-pulsed illumination and ultrafast time-resolved detection. Here, bringing notions from passive radio detection and ranging (RADAR) and passive geophysical mapping approaches, we present an optical TOF technique that allows passive localization of light sources and reflective objects through diffusive barriers and around corners. Our approach retrieves TOF information from temporal cross-correlations of scattered light, via interferometry, providing temporal resolution that surpasses state-of-the-art ultrafast detectors by three orders of magnitude. While our passive approach is limited by signal-to-noise to relatively sparse scenes, we demonstrate passive localization of multiple white-light sources and reflective objects hidden from view using a simple setup.
The histone methyltransferase Setd2 is indispensable for V(D)J recombination
Authors: Ji Zhongzhong , Sheng Yaru , Miao Juju , Li Xiaoxia , Zhao Huifang , Wang Jinming , Cheng Chaping , Wang Xue , Liu Kaiyuan , Zhang Kai , Xu Longmei , Yao Jufang , Shen Lijing , Hou Jian , Zhou Wenhao , Sun Jinqiao , Li Li , Gao Wei-Qiang , Zhu Helen He 
Published: July 2019

AbstractThe diverse repertoire of T cell receptors (TCR) and immunoglobulins is generated through the somatic rearrangement of respective V, D and J gene segments, termed V(D)J recombination, during early T or B cell development. However, epigenetic regulation of V(D)J recombination is still not fully understood. Here we show that the deficiency of Setd2, a histone methyltransferase that catalyzes lysine 36 trimethylation on histone 3 (H3K36me3) in mice, causes a severe developmental block of thymocytes at the CD4−CD8−DN3 stage. While H3K36me3 is normally enriched at the TCRβ locus, Setd2 deficiency reduces TCRβ H3K36me3 and suppresses TCRβ V(D)J rearrangement by impairing RAG1 binding to TCRβ loci and the DNA double-strand break repair. Similarly, Setd2 ablation also impairs immunoglobulin V(D)J rearrangement to induce B cell development block at the pro-B stage. Lastly, SETD2 is frequently mutated in patients with primary immunodeficiency. Our study thus demonstrates that Setd2 is required for optimal V(D)J recombination and normal lymphocyte development.
Engineering electronic structure to prolong relaxation times in molecular qubits by minimising orbital angular momentum
Authors: Ariciu Ana-Maria , Woen David H. , Huh Daniel N. , Nodaraki Lydia E. , Kostopoulos Andreas K. , Goodwin Conrad A. P. , Chilton Nicholas F. , McInnes Eric J. L. , Winpenny Richard E. P. , Evans William J. , Tuna Floriana 
Published: July 2019

AbstractThe proposal that paramagnetic transition metal complexes could be used as qubits for quantum information processing (QIP) requires that the molecules retain the spin information for a sufficient length of time to allow computation and error correction. Therefore, understanding how the electron spin-lattice relaxation time (T1) and phase memory time (Tm) relate to structure is important. Previous studies have focused on the ligand shell surrounding the paramagnetic centre, seeking to increase rigidity or remove elements with nuclear spins or both. Here we have studied a family of early 3d or 4f metals in the +2 oxidation states where the ground state is effectively a2S state. This leads to a highly isotropic spin and hence makes the putative qubit insensitive to its environment. We have studied how this influencesT1andTmand show unusually long relaxation times given that the ligand shell is rich in nuclear spins and non-rigid.
Role of solvent-anion charge transfer in oxidative degradation of battery electrolytes
Authors: Fadel Eric R. , Faglioni Francesco , Samsonidze Georgy , Molinari Nicola , Merinov Boris V. , Goddard III William A. , Grossman Jeffrey C. , Mailoa Jonathan P. , Kozinsky Boris 
Published: July 2019

AbstractElectrochemical stability windows of electrolytes largely determine the limitations of operating regimes of lithium-ion batteries, but the degradation mechanisms are difficult to characterize and poorly understood. Using computational quantum chemistry to investigate the oxidative decomposition that govern voltage stability of multi-component organic electrolytes, we find that electrolyte decomposition is a process involving the solvent and the salt anion and requires explicit treatment of their coupling. We find that the ionization potential of the solvent-anion system is often lower than that of the isolated solvent or the anion. This mutual weakening effect is explained by the formation of the anion-solvent charge-transfer complex, which we study for 16 anion-solvent combinations. This understanding of the oxidation mechanism allows the formulation of a simple predictive model that explains experimentally observed trends in the onset voltages of degradation of electrolytes near the cathode. This model opens opportunities for rapid rational design of stable electrolytes for high-energy batteries.
Gallium arsenide solar cells grown at rates exceeding 300 µm h−1 by hydride vapor phase epitaxy
Authors: Metaferia Wondwosen , Schulte Kevin L. , Simon John , Johnston Steve , Ptak Aaron J. 
Published: July 2019

AbstractWe report gallium arsenide (GaAs) growth rates exceeding 300 µm h−1 using dynamic hydride vapor phase epitaxy. We achieved these rates by maximizing the gallium to gallium monochloride conversion efficiency, and by utilizing a mass-transport-limited growth regime with fast kinetics. We also demonstrate gallium indium phosphide growth at rates exceeding 200 µm h−1 using similar growth conditions. We grew GaAs solar cell devices by incorporating the high growth rate of GaAs and evaluated its material quality at these high rates. Solar cell growth rates ranged from 35 to 309 µm h−1 with open circuit voltages ranging from 1.04 to 1.07 V. The best devices exceeded 25% efficiency under the AM1.5 G solar spectrum. The high open-circuit voltages indicate that high material quality can be maintained at these extremely high growth rates. These results have strong implications toward lowering the deposition cost of III-V materials potentially enabling the deposition of high efficiency devices in mere seconds.
The influence of Echinacea purpurea leaf microbiota on chicoric acid level
Authors: Maggini Valentina , De Leo Marinella , Granchi Carlotta , Tuccinardi Tiziano , Mengoni Alessio , Gallo Eugenia Rosaria , Biffi Sauro , Fani Renato , Pistelli Luisa , Firenzuoli Fabio , Bogani Patrizia 
Published: July 2019

AbstractThe controversial anti-proliferative effects of Echinacea purpurea (L.) Moench (Asteraceae) might be related to different plant metabolites contained in plant samples, extracts and products. The influence of bacterial endophytes on the synthesis of bioactive compounds in the medicinal plants has been previously demonstrated but there are only few studies addressing anticancer effects and mechanisms of E. purpurea extracts following endophytic colonization. The present study aimed to test and compare the lactate dehydrogenase (LDH) inhibition potential of n-hexane and methanol extracts from in vitro endophyte non-inoculated and inoculated E. purpurea plants. An in vitro model was previously set up to perform the infection of axenic E. purpurea plants with bacterial endophytic strains isolated from E. purpurea aerial part. Only methanol extracts showed LDH5 inhibition, in particular the richest in chicoric acid and most strongly inhibiting extract was obtained from inoculated stem and leaves of E. purpurea (IC50 = 0.9 mg/ml). Chicoric acid showed an IC50 value (66.7 µM) in enzymatic assays better than that of the reference compound galloflavin. Modeling studies were carried out to suggest the putative interaction mode of chicoric acid in the enzyme active site. This in vitro model on plant-bacterial interaction may lead to obtain extracts from plants enriched in bioactive compounds and it is a new approach for the discovery of novel anticancer compounds.
The Henna pigment Lawsone activates the Aryl Hydrocarbon Receptor and impacts skin homeostasis
Authors: Lozza Laura , Moura-Alves Pedro , Domaszewska Teresa , Lage Crespo Carolina , Streata Ioana , Kreuchwig Annika , Puyskens Andreas , Bechtle Marina , Klemm Marion , Zedler Ulrike , Silviu Ungureanu Bogdan , Guhlich-Bornhof Ute , Koehler Anne-Britta , Stäber Manuela , Mollenkopf Hans-Joachim , Hurwitz Robert , Furkert Jens , Krause Gerd , Weiner January , Jacinto António , Mihai Ioana , Leite-de-Moraes Maria , Siebenhaar Frank , Maurer Marcus , Kaufmann Stefan H. E. 
Published: July 2019

AbstractAs a first host barrier, the skin is constantly exposed to environmental insults that perturb its integrity. Tight regulation of skin homeostasis is largely controlled by the aryl hydrocarbon receptor (AhR). Here, we demonstrate that Henna and its major pigment, the naphthoquinone Lawsone activate AhR, bothin vitroandin vivo. In human keratinocytes and epidermis equivalents, Lawsone exposure enhances the production of late epidermal proteins, impacts keratinocyte differentiation and proliferation, and regulates skin inflammation. To determine the potential use of Lawsone for therapeutic application, we harnessed human, murine and zebrafish models. In skin regeneration models, Lawsone interferes with physiological tissue regeneration and inhibits wound healing. Conversely, in a human acute dermatitis model, topical application of a Lawsone-containing cream ameliorates skin irritation. Altogether, our study reveals how a widely used natural plant pigment is sensed by the host receptor AhR, and how the physiopathological context determines beneficial and detrimental outcomes.
Computational Models Accurately Predict Multi-Cell Biomarker Profiles in Inflammation and Cancer
Authors: Fischer Carol L. , Bates Amber M. , Lanzel Emily A. , Guthmiller Janet M. , Johnson Georgia K. , Singh Neeraj Kumar , Kumar Ansu , Vidva Robinson , Abbasi Taher , Vali Shireen , Xie Xian Jin , Zeng Erliang , Brogden Kim A. 
Published: July 2019

AbstractIndividual computational models of single myeloid, lymphoid, epithelial, and cancer cells were created and combined into multi-cell computational models and used to predict the collective chemokine, cytokine, and cellular biomarker profiles often seen in inflamed or cancerous tissues. Predicted chemokine and cytokine output profiles from multi-cell computational models of gingival epithelial keratinocytes (GE KER), dendritic cells (DC), and helper T lymphocytes (HTL) exposed to lipopolysaccharide (LPS) or synthetic triacylated lipopeptide (Pam3CSK4) as well as multi-cell computational models of multiple myeloma (MM) and DC were validated using the observed chemokine and cytokine responses from the same cell type combinations grown in laboratory multi-cell cultures with accuracy. Predicted and observed chemokine and cytokine responses of GE KER + DC + HTL exposed to LPS and Pam3CSK4 matched 75% (15/20, p = 0.02069) and 80% (16/20, P = 0.005909), respectively. Multi-cell computational models became ‘personalized’ when cell line-specific genomic data were included into simulations, again validated with the same cell lines grown in laboratory multi-cell cultures. Here, predicted and observed chemokine and cytokine responses of MM cells lines MM.1S and U266B1 matched 75% (3/4) and MM.1S and U266B1 inhibition of DC marker expression in co-culture matched 100% (6/6). Multi-cell computational models have the potential to identify approaches altering the predicted disease-associated output profiles, particularly as high throughput screening tools for anti-inflammatory or immuno-oncology treatments of inflamed multi-cellular tissues and the tumor microenvironment.
Preferential phosphatidylinositol 5-phosphate binding contributes to a destabilization of the VHS domain structure of Tom1
Authors: Xiong Wen , Tang Tuo-Xian , Littleton Evan , Karcini Arba , Lazar Iulia M. , Capelluto Daniel G. S. 
Published: July 2019

AbstractTom1 transports endosomal ubiquitinated proteins that are targeted for degradation in the lysosomal pathway. Infection of eukaryotic cells by Shigella flexneri boosts oxygen consumption and promotes the synthesis of phosphatidylinositol-5-phosphate (PtdIns5P), which triggers Tom1 translocation to signaling endosomes. Removing Tom1 from its cargo trafficking function hinders protein degradation in the host and, simultaneously, enables bacterial survival. Tom1 preferentially binds PtdIns5P via its VHS domain, but the effects of a reducing environment as well as PtdIns5P on the domain structure and function are unknown. Thermal denaturation studies demonstrate that, under reducing conditions, the monomeric Tom1 VHS domain switches from a three-state to a two-state transition behavior. PtdIns5P reduced thermostability, interhelical contacts, and conformational compaction of Tom1 VHS, suggesting that the phosphoinositide destabilizes the protein domain. Destabilization of Tom1 VHS structure was also observed with other phospholipids. Isothermal calorimetry data analysis indicates that, unlike ubiquitin, Tom1 VHS endothermically binds to PtdIns5P through two noncooperative binding sites, with its acyl chains playing a relevant role in the interaction. Altogether, these findings provide mechanistic insights about the recognition of PtdIns5P by the VHS domain that may explain how Tom1, when in a different VHS domain conformational state, interacts with downstream effectors under S. flexneri infection.
Magnetic nanocomposites decorated on multiwalled carbon nanotube
for removal of Maxilon Blue 5G using the sono-Fenton method
Authors: Nas Mehmet Salih , Kuyuldar Esra , Demirkan Buse , Calimli Mehmet Harbi , Demirbaş Ozkan , Sen Fatih 
Published: July 2019

AbstractHerein, multiwalled carbon nanotube-based
Fe3O4 nano-adsorbents
(Fe3O4@MWCNT) were synthesized by
ultrasonic reduction method. The synthesized nano-adsorbent
(Fe3O4@MWCNT) exhibited efficient
sonocatalytic activity to remove Maxilon Blue 5G, a textile dye, and present in a
cationic form, in aqueous solution under ultrasonic irradiation. The magnetic
nano-adsorbent particles were characterized by high-resolution transmission electron
microscopy (HR-TEM), transmission electron microscopy (TEM), Raman spectroscopy and
X-ray diffraction (XRD). Some important parameters such as nano-adsorbent dosage,
solution pH, initial dye and H2O2
concentration, reaction time, ultrasonic power and temperature were tested to
determine the optimum conditions for the elimination of Maxilon Blue 5G dye. The
reusability results showed that
Fe3O4@MWCNT nano-adsorbent has a
decrease of about 32.15% in the removal efficiency of Maxilon Blue 5G under
ultrasonic irradiation after six times reuse. Additionally, in order to reveal the
sufficient kinetic explanation, various experiments were performed at different
temperatures and testing three kinetic models like the pseudo-first-order,
pseudo-second-order and intraparticle diffusion for removal adsorption process of
Maxilon Blue 5G using Fe3O4@MWCNT
nano-adsorbent. The experimental kinetic results revealed that the adsorption
process of Maxilon Blue 5G in the aquatic mediums using sono-Fenton method was found
to be compatible with the intraparticle diffusion. Using kinetic models and studies,
some activation parameters like enthalpy, entropy and Gibbs free energy for the
adsorption process were calculated. The activation parameters indicated that
Fe3O4@MWCNT nano-adsorbent could
be used as an effective adsorbent for the removal of Maxilon Blue 5G as a textile
dye and the adsorption process of Maxilon Blue 5G with
Fe3O4@MWCNT nano-adsorbent is
spontaneous.
Artificial intelligence and machine learning in clinical development: a translational perspective
Authors: Shah Pratik , Kendall Francis , Khozin Sean , Goosen Ryan , Hu Jianying , Laramie Jason , Ringel Michael , Schork Nicholas 
Published: July 2019

AbstractFuture of clinical development is on the verge of a major transformation due to convergence of large new digital data sources, computing power to identify clinically meaningful patterns in the data using efficient artificial intelligence and machine-learning algorithms, and regulators embracing this change through new collaborations. This perspective summarizes insights, recent developments, and recommendations for infusing actionable computational evidence into clinical development and health care from academy, biotechnology industry, nonprofit foundations, regulators, and technology corporations. Analysis and learning from publically available biomedical and clinical trial data sets, real-world evidence from sensors, and health records by machine-learning architectures are discussed. Strategies for modernizing the clinical development process by integration of AI- and ML-based digital methods and secure computing technologies through recently announced regulatory pathways at the United States Food and Drug Administration are outlined. We conclude by discussing applications and impact of digital algorithmic evidence to improve medical care for patients.