bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oxygen Transfer at the Sediment/Water Interface for Sediment Bed With Rough Surface
Authors: Higashino Makoto 
Published: September 2018

AbstractA model of sediment oxygen demand (SOD) for a sediment bed with a rough surface was presented. The equivalent sand roughness commonly used in hydraulics was chosen to express the size of roughness elements, and SOD was expressed as a function of the intensity of near‐bed turbulence described by the shear velocity; microbial oxygen uptake rate, that is, the maximum oxidation rate; and roughness height. The modeling results show that bed roughness enhances oxygen transfer from the water column to the sediment surface. The effects of bed roughness on SOD depend on both the shear velocity and microbial oxygen uptake rate. At low microbial oxygen uptake rate, SOD approaches a constant value rapidly as the shear velocity increases. Bed roughness barely influences SOD regardless of the shear velocity because SOD can substantially besediment side limiting. The roughness height plays an important role in determining SOD at high microbial oxygen uptake rate, because SOD can be controlled by oxygen transfer from the water column to the sediment surface, that is,transfer limiting. Increasing roughness height makes the oxygen transfer rate from flowing water to the sediment surface faster as well as increasing shear velocity, resulting in raised SOD. The proposed mode can substantially reproduce the experimental SOD for rough bed.
PAXX and its paralogs synergistically direct DNA polymerase λ activity in DNA repair
Authors: Craxton Andrew , Munnur Deeksha , Jukes-Jones Rebekah , Skalka George , Langlais Claudia , Cain Kelvin , Malewicz Michal 
Published: September 2018

AbstractPAXX is a recently identified component of the nonhomologous end joining (NHEJ) DNA repair pathway. The molecular mechanisms of PAXX action remain largely unclear. Here we characterise the interactomes of PAXX and its paralogs, XLF and XRCC4, to show that these factors share the ability to interact with DNA polymerase λ (Pol λ), stimulate its activity and are required for recruitment of Pol λ to laser-induced DNA damage sites. Stimulation of Pol λ activity by XRCC4 paralogs requires a direct interaction between the SP/8 kDa domain of Pol λ and their N-terminal head domains to facilitate recognition of the 5′ end of substrate gaps. Furthermore, PAXX and XLF collaborate with Pol λ to promote joining of incompatible DNA ends and are redundant in supporting Pol λ function in vivo. Our findings identify Pol λ as a novel downstream effector of PAXX function and show XRCC4 paralogs act in synergy to regulate polymerase activity in NHEJ.
BRWD1 orchestrates epigenetic landscape of late B lymphopoiesis
Authors: Mandal Malay , Maienschein-Cline Mark , Maffucci Patrick , Veselits Margaret , Kennedy Domenick E. , McLean Kaitlin C. , Okoreeh Michael K. , Karki Sophiya , Cunningham-Rundles Charlotte , Clark Marcus R. 
Published: September 2018

AbstractTranscription factor (TF) networks determine cell fate in hematopoiesis. However, how TFs cooperate with other regulatory mechanisms to instruct transcription remains poorly understood. Here we show that in small pre-B cells, the lineage restricted epigenetic reader BRWD1 closes early development enhancers and opens the enhancers of late B lymphopoiesis to TF binding. BRWD1 regulates over 7000 genes to repress proliferative and induce differentiation programs. However, BRWD1 does not regulate the expression of TFs required for B lymphopoiesis. Hypogammaglobulinemia patients with BRWD1 mutations have B-cell transcriptional profiles and enhancer landscapes similar to those observed in Brwd1-/- mice. These data indicate that, in both mice and humans, BRWD1 is a master orchestrator of enhancer accessibility that cooperates with TF networks to drive late B-cell development.
Towards exact molecular dynamics simulations with machine-learned force fields
Authors: Chmiela Stefan , Sauceda Huziel E. , Müller Klaus-Robert , Tkatchenko Alexandre 
Published: September 2018

AbstractMolecular dynamics (MD) simulations employing classical force fields constitute the cornerstone of contemporary atomistic modeling in chemistry, biology, and materials science. However, the predictive power of these simulations is only as good as the underlying interatomic potential. Classical potentials often fail to faithfully capture key quantum effects in molecules and materials. Here we enable the direct construction of flexible molecular force fields from high-level ab initio calculations by incorporating spatial and temporal physical symmetries into a gradient-domain machine learning (sGDML) model in an automatic data-driven way. The developed sGDML approach faithfully reproduces global force fields at quantum-chemical CCSD(T) level of accuracy and allows converged molecular dynamics simulations with fully quantized electrons and nuclei. We present MD simulations, for flexible molecules with up to a few dozen atoms and provide insights into the dynamical behavior of these molecules. Our approach provides the key missing ingredient for achieving spectroscopic accuracy in molecular simulations.
Contrasting effects on deep convective clouds by different types of aerosols
Authors: Jiang Jonathan H. , Su Hui , Huang Lei , Wang Yuan , Massie Steven , Zhao Bin , Omar Ali , Wang Zhien 
Published: September 2018

AbstractConvective clouds produce a significant proportion of the global precipitation and play an important role in the energy and water cycles. We quantify changes of the convective cloud ice mass-weighted altitude centroid (ZIWC) as a function of aerosol optical thickness (AOT). Analyses are conducted in smoke, dust and polluted continental aerosol environments over South America, Central Africa and Southeast Asia, using the latest measurements from the CloudSat and CALIPSO satellites. We find aerosols can inhibit or invigorate convection, depending on aerosol type and concentration. On average, smoke tends to suppress convection and results in lower ZIWC than clean clouds. Polluted continental aerosol tends to invigorate convection and promote higher ZIWC. The dust aerosol effects are regionally dependent and their signs differ from place to place. Moreover, we find that the aerosol inhibition or invigoration effects do not vary monotonically with AOT and the variations depend strongly on aerosol type. Our observational findings indicate that aerosol type is one of the key factors in determining the aerosol effects on convective clouds.
Acquired cancer resistance to combination immunotherapy from transcriptional loss of class I HLA
Authors: Paulson K. G. , Voillet V. , McAfee M. S. , Hunter D. S. , Wagener F. D. , Perdicchio M. , Valente W. J. , Koelle S. J. , Church C. D. , Vandeven N. , Thomas H. , Colunga A. G. , Iyer J. G. , Yee C. , Kulikauskas R. , Koelle D. M. , Pierce R. H. , Bielas J. H. , Greenberg P. D. , Bhatia S. , Gottardo R. , Nghiem P. , Chapuis A. G. 
Published: September 2018

AbstractUnderstanding mechanisms of late/acquired cancer immunotherapy resistance is critical to improve outcomes; cellular immunotherapy trials offer a means to probe complex tumor–immune interfaces through defined T cell/antigen interactions. We treated two patients with metastatic Merkel cell carcinoma with autologous Merkel cell polyomavirus specific CD8+ T cells and immune-checkpoint inhibitors. In both cases, dramatic remissions were associated with dense infiltration of activated CD8+s into the regressing tumors. However, late relapses developed at 22 and 18 months, respectively. Here we report single cell RNA sequencing identified dynamic transcriptional suppression of the specific HLA genes presenting the targeted viral epitope in the resistant tumor as a consequence of intense CD8-mediated immunologic pressure; this is distinguished from genetic HLA-loss by its reversibility with drugs. Transcriptional suppression of Class I loci may underlie resistance to other immunotherapies, including checkpoint inhibitors, and have implications for the design of improved immunotherapy treatments.
Eosinophil recruitment is dynamically regulated by interplay among lung dendritic cell subsets after allergen challenge
Authors: Yi Shuying , Zhai Jing , Niu Rui , Zhu Guangming , Wang Meixiang , Liu Jianguo , Huang Hua , Wang Yaping , Jing Xiuli , Kang Li , Song Wengang , Shi Yufang , Tang Hua 
Published: September 2018

AbstractEosinophil infiltration, a hallmark of allergic asthma, is essential for type 2 immune responses. How the initial eosinophil recruitment is regulated by lung dendritic cell (DC) subsets during the memory stage after allergen challenge is unclear. Here, we show that the initial eosinophil infiltration is dependent on lung cDC1s, which require nitric oxide (NO) produced by inducible NO synthase from lung CD24−CD11b+DC2s for inducing CCL17 and CCL22 to attract eosinophils. During late phase responses after allergen challenge, lung CD24+cDC2s inhibit eosinophil recruitment through secretion of TGF-β1, which impairs the expression of CCL17 and CCL22. Our data suggest that different lung antigen-presenting cells modulate lung cDC1-mediated eosinophil recruitment dynamically, through secreting distinct soluble factors during the memory stage of chronic asthma after allergen challenge in the mouse.
Identifying the missing link in catalyst transfer polymerization
Authors: He Weiying , Patrick Brian O. , Kennepohl Pierre 
Published: September 2018

AbstractNickel-catalyzed catalyst transfer polycondensation (CTP) of thiophenes is an efficient strategy for the controlled synthesis of polythiophenes. However, a detailed view of its reaction mechanism has remained elusive with unresolved questions regarding the geometry and bonding of critical Ni(0) thiophene intermediates. Herein, we provide experimental and computational evidence of structurally characterized square planar η2-Ni(0)–thiophene species and their relevance to the mechanism of CTP. These results confirm the viability of C,C-η2 bound intermediates in CTP of thiophenes, providing an electronic rationale for the stability of such species, and thus that such processes can proceed as living polymerizations. We further show that C,S-κ2 species may also be relevant in nickel-catalyzed CTP of thiophenes, providing new avenues for exploitation and optimization.
Microfluidic deposition for resolving single-molecule protein architecture and heterogeneity
Authors: Ruggeri Francesco Simone , Charmet Jerome , Kartanas Tadas , Peter Quentin , Chia Sean , Habchi Johnny , Dobson Christopher M. , Vendruscolo Michele , Knowles Tuomas P. J. 
Published: September 2018

AbstractScanning probe microscopy provides a unique window into the morphology, mechanics, and structure of proteins and their complexes on the nanoscale. Such measurements require, however, deposition of samples onto substrates. This process can affect conformations and assembly states of the molecular species under investigation and can bias the molecular populations observed in heterogeneous samples through differential adsorption. Here, we show that these limitations can be overcome with a single-step microfluidic spray deposition platform. This method transfers biological solutions to substrates as microdroplets with subpicoliter volume, drying in milliseconds, a timescale that is shorter than typical diffusion times of proteins on liquid–solid interfaces, thus avoiding surface mass transport and change to the assembly state. Finally, the single-step deposition ensures the attachment of the full molecular content of the sample to the substrate, allowing quantitative measurements of different molecular populations within heterogeneous systems, including protein aggregates.
Neurogenetic profiles delineate large-scale connectivity dynamics of the human brain
Authors: Diez Ibai , Sepulcre Jorge 
Published: September 2018

AbstractExperimental and modeling work of neural activity has described recurrent and attractor dynamic patterns in cerebral microcircuits. However, it is still poorly understood whether similar dynamic principles exist or can be generalizable to the large-scale level. Here, we applied dynamic graph theory-based analyses to evaluate the dynamic streams of whole-brain functional connectivity over time across cognitive states. Dynamic connectivity in local networks is located in attentional areas during tasks and primary sensory areas during rest states, and dynamic connectivity in distributed networks converges in the default mode network (DMN) in both task and rest states. Importantly, we find that distinctive dynamic connectivity patterns are spatially associated with Allen Human Brain Atlas genetic transcription levels of synaptic long-term potentiation and long-term depression-related genes. Our findings support the neurobiological basis of large-scale attractor-like dynamics in the heteromodal cortex within the DMN, irrespective of cognitive state.
Griffithsin carrageenan fast dissolving inserts prevent SHIV HSV-2 and HPV infections in vivo
Authors: Derby Nina , Lal Manjari , Aravantinou Meropi , Kizima Larisa , Barnable Patrick , Rodriguez Aixa , Lai Manshun , Wesenberg Asa , Ugaonkar Shweta , Levendosky Keith , Mizenina Olga , Kleinbeck Kyle , Lifson Jeffrey D. , Peet M. Melissa , Lloyd Zachary , Benson Michael , Heneine Walid , O’Keefe Barry R , Robbiani Melissa , Martinelli Elena , Grasperge Brooke , Blanchard James , Gettie Agegnehu , Teleshova Natalia , Fernández-Romero José A. , Zydowsky Thomas M. 
Published: September 2018

AbstractHuman immunodeficiency virus (HIV) pre-exposure prophylaxis (PrEP) strategies with proven in vivo efficacy rely on antiretroviral drugs, creating the potential for drug resistance and complicated treatment options in individuals who become infected. Moreover, on-demand products are currently missing from the PrEP development portfolio. Griffithsin (GRFT) is a non-antiretroviral HIV entry inhibitor derived from red algae with an excellent safety profile and potent activity in vitro. When combined with carrageenan (CG), GRFT has strong activity against herpes simplex virus-2 (HSV-2) and human papillomavirus (HPV) in vitro and in vivo. Here, we report that GRFT/CG in a freeze-dried fast dissolving insert (FDI) formulation for on-demand use protects rhesus macaques from a high dose vaginal SHIV SF162P3 challenge 4 h after FDI insertion. Furthermore, the GRFT/CG FDI also protects mice vaginally against HSV-2 and HPV pseudovirus. As a safe, potent, broad-spectrum, on-demand non-antiretroviral product, the GRFT/CG FDI warrants clinical development.
Regulation of the terminal maturation of iNKT cells by mediator complex subunit 23
Authors: Xu Yu , Sun Yang , Shen Hao , Dai Yuling , Liu Haifeng , Li Ronghong , Zhang Hongdao , Wu Ligang , Zhu Xiaoyan , Liu Xiaolong 
Published: September 2018

AbstractInvariant natural killer T cells (iNKT cells) are a specific subset of T cells that recognize glycolipid antigens and upon activation rapidly exert effector functions. This unique function is established during iNKT cell development; the detailed mechanisms of this process, however, remain to be elucidated. Here the authors show that deletion of the mediator subunit Med23 in CD4+CD8+double positive (DP) thymocytes completely blocks iNKT cell development at stage 2. This dysregulation is accompanied by a bias in the expression of genes related to the regulation of transcription and metabolism, and functional impairment of the cells including the loss of NK cell characteristics, reduced ability to secrete cytokines and attenuated recruitment capacity upon activation. Moreover,Med23-deficient iNKT cells exhibit impaired anti-tumor activity. Our study identifies Med23 as an essential transcriptional regulator that controls iNKT cell differentiation and terminal maturation.
Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements
Authors: Pärnänen Katariina , Karkman Antti , Hultman Jenni , Lyra Christina , Bengtsson-Palme Johan , Larsson D. G. Joakim , Rautava Samuli , Isolauri Erika , Salminen Seppo , Kumar Himanshu , Satokari Reetta , Virta Marko 
Published: September 2018

AbstractThe infant gut microbiota has a high abundance of antibiotic resistance genes (ARGs) compared to adults, even in the absence of antibiotic exposure. Here we study potential sources of infant gut ARGs by performing metagenomic sequencing of breast milk, as well as infant and maternal gut microbiomes. We find that fecal ARG and mobile genetic element (MGE) profiles of infants are more similar to those of their own mothers than to those of unrelated mothers. MGEs in mothers’ breast milk are also shared with their own infants. Termination of breastfeeding and intrapartum antibiotic prophylaxis of mothers, which have the potential to affect microbial community composition, are associated with higher abundances of specific ARGs, the composition of which is largely shaped by bacterial phylogeny in the infant gut. Our results suggest that infants inherit the legacy of past antibiotic consumption of their mothers via transmission of genes, but microbiota composition still strongly impacts the overall resistance load.
Modulating the hierarchical fibrous assembly of Au nanoparticles with atomic precision
Authors: Li Qi , Russell Jake C. , Luo Tian-Yi , Roy Xavier , Rosi Nathaniel L. , Zhu Yan , Jin Rongchao 
Published: September 2018

AbstractThe ability to modulate nanoparticle (NP) assemblies with atomic precision is still lacking, which hinders us from creating hierarchical NP organizations with desired properties. In this work, a hierarchical fibrous (1D to 3D) assembly of Au NPs (21-gold atom, Au21) is realized and further modulated with atomic precision via site-specific tailoring of the surface hook (composed of four phenyl-containing ligands with a counteranion). Interestingly, tailoring of the associated counterion significantly changes the electrical transport properties of the NP-assembled solids by two orders of magnitude due to the altered configuration of the interacting π–π pairs of the surface hooks. Overall, our success in atomic-level modulation of the hierarchical NP assembly directly evidences how the NP ligands and associated counterions can function to guide the 1D, 2D, and 3D hierarchical self-assembly of NPs in a delicate manner. This work expands nanochemists’ skills in rationally programming the hierarchical NP assemblies with controllable structures and properties.
Atom-hybridization for synthesis of polymetallic clusters
Authors: Tsukamoto Takamasa , Kambe Tetsuya , Nakao Aiko , Imaoka Takane , Yamamoto Kimihisa 
Published: September 2018

AbstractThe chemistry of metal clusters on the sub-nanometer scale is not yet well understood because metal clusters, especially multimetallic clusters, are difficult to synthesize with control over size and composition. The template synthesis of multimetallic sub-nanoclusters is achieved using a phenylazomethine dendrimer as a macromolecular template. Its intramolecular potential gradient allows the precise uptake of metal precursor complexes containing up to eight elements on the template. The usefulness of this method is demonstrated by synthesizing multimetallic sub-nanoclusters composed of five elements (Ga1In1Au3Bi2Sn6). The size and composition of this cluster can be precisely controlled and the metals involved are alloyed with each other. This approach provides the ability to easily blend different metals in various combinations to create new materials on the sub-nanometer scale, which will lead to the development of a new area in the field of chemistry.
Identification of Quantitative Trait Loci and Candidate Genes for Maize Starch Granule Size through Association Mapping
Authors: Liu Na , Zhang Zhanhui , Xue Yadong , Meng Shujun , Huang Yubi , Li Weihua , Huang Jihong , Tang Jihua 
Published: September 2018

AbstractStarch is an important nutrient component of maize kernels, and starch granule size largely determines kernel waxiness, viscosity, and other physiochemical and processing properties. To explore the genetic basis of maize starch granule size, 266 tropical, subtropical, and temperate inbred lines were subjected to genome-wide association analyses with an array of 56,110 random single nucleotide polymorphisms (SNPs). In the present panel, the kernel starch granule size ranged from 7–15.8 µm long and 6.8–14.3 µm wide. Fourteen significant SNPs were identified as being associated with the length of starch granules and 9 with their width. One linkage disequilibrium block flanking both sides of a significant SNP was defined as a quantitative trait locus (QTL) interval, and seven QTLs were mapped for both granule length and width. A total of 79 and 88 candidate genes associated with starch length and width, respectively, were identified as being distributed on QTL genomic regions. Among these candidate genes, six with high scores were predicted to be associated with maize starch granule size. A candidate gene association analysis identified significant SNPs within genes GRMZM2G419655 and GRMZM2G511067, which could be used as functional markers in screening starch granule size for different commercial uses.
Dot-Matrix Hologram Rendering Algorithm and its Validation through Direct Laser Interference Patterning
Authors: Tamulevičius Tomas , Juodėnas Mindaugas , Klinavičius Tomas , Paulauskas Andrius , Jankauskas Kęstutis , Ostreika Armantas , Žutautas Andrius , Tamulevičius Sigitas 
Published: September 2018

AbstractThe fight against forgery of valuable items demands efficient and reasonably priced solutions. A security tag featuring holographic elements for anti-counterfeiting is one of them. However, the content and colours of a diffraction image that would be seen by an observer are often counterintuitive in the design stage. Here, we propose an original algorithm based on the conical diffraction formalism, which can be used to describe the variations of a diffraction image with respect to all aspects of observation. We validate the output of the algorithm by comparing it to test holograms, which we have produced by employing direct laser interference patterning (DLIP) in electrochemically grown nickel foil. We have employed a motorized femtosecond laser system to micro-machine arrays of 65 µm × 65 µm sized diffraction gratings with a defined orientation and pitch on the order of 1 µm. Based on completed diffraction efficiency measurements, we determined optimal ablation parameters, i.e. 57.4 mJ/cm2 fluence per pulse and 1100 pulses/pixel. Furthermore, we show how accurate the proposed algorithm is through measured diffraction spectra as well as captured diffraction images of test holograms produced using the obtained parameters. Finally, we showcase anti-counterfeiting tag prototypes with complex holographic effects, i.e. colour reconstruction, animation effects, and image multiplexing. The proposed algorithm can severely shorten the time between design and production of a holographic tag, especially when realizing it via a competitive origination technology—DLIP.