bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vibrio sp. dhg as a platform for the biorefinery of brown macroalgae
Authors: Lim Hyun Gyu , Kwak Dong Hun , Park Sungwoo , Woo Sunghwa , Yang Jae-Seong , Kang Chae Won , Kim Beomhee , Noh Myung Hyun , Seo Sang Woo , Jung Gyoo Yeol 
Published: June 2019

AbstractAlthough brown macroalgae holds potential as an alternative feedstock, its utilization by conventional microbial platforms has been limited due to the inability to metabolize one of the principal sugars, alginate. Here, we isolate Vibrio sp. dhg, a fast-growing bacterium that can efficiently assimilate alginate. Based on systematic characterization of the genomic information of Vibrio sp. dhg, we establish a genetic toolbox for its engineering. We also demonstrate its ability to rapidly produce ethanol, 2,3-butanediol, and lycopene from brown macroalgae sugar mixture with high productivities and yields. Collectively, Vibrio sp. dhg can be used as a platform for the efficient conversion of brown macroalgae sugars into diverse value-added biochemicals.
Theory of the field-revealed Kitaev spin liquid
Authors: Gordon Jacob S. , Catuneanu Andrei , Sørensen Erik S. , Kee Hae-Young 
Published: June 2019

AbstractElementary excitations in entangled states such as quantum spin liquids may exhibit exotic statistics different from those obeyed by fundamental bosons and fermions. Non-Abelian anyons exist in a Kitaev spin liquid—the ground state of an exactly solvable model. A smoking-gun signature of these excitations, namely a half-integer quantized thermal Hall conductivity, was recently reported in α-RuCl3. While fascinating, a microscopic theory for this phenomenon remains elusive because the pure Kitaev model cannot display this effect in an intermediate magnetic field. Here we present a microscopic theory of the Kitaev spin liquid emerging between the low- and high-field states. Essential to this result is an antiferromagnetic off-diagonal symmetric interaction which allows the Kitaev spin liquid to protrude from the ferromagnetic Kitaev limit under a magnetic field. This generic model displays a strong field anisotropy, and we predict a wide spin liquid regime when the field is perpendicular to the honeycomb plane.
Factors other than hTau overexpression that contribute to tauopathy-like phenotype in rTg4510 mice
Authors: Gamache Julia , Benzow Kellie , Forster Colleen , Kemper Lisa , Hlynialuk Chris , Furrow Eva , Ashe Karen H. , Koob Michael D. 
Published: June 2019

AbstractThe tauopathy-like phenotype observed in the rTg4510 mouse line, in which human tauP301L expression specifically within the forebrain can be temporally controlled, has largely been attributed to high overexpression of mutant human tau in the forebrain region. Unexpectedly, we found that in a different mouse line with a targeted-insertion of the same transgene driven by the same tetracycline-TransActivator (tTA) allele, but with even higher overexpression of tauP301L than rTg4510, atrophy and tau histopathology are delayed, and a different behavioral profile is observed. This suggests that it is not overexpression of mutant human tau alone that contributes to the phenotype in rTg4510 mice. Furthermore we show that the tauopathy-like phenotype seen in rTg4510 requires a ~70-copy tau-transgene insertion in a 244 kb deletion in Fgf14, a ~7-copy tTA-transgene insertion in a 508 kb deletion that disrupts another five genes, in addition to high transgene overexpression. We propose that these additional effects need to be accounted for in any studies using rTg4510.
Simplicial models of social contagion
Authors: Iacopini Iacopo , Petri Giovanni , Barrat Alain , Latora Vito 
Published: June 2019

AbstractComplex networks have been successfully used to describe the spread of diseases in populations of interacting individuals. Conversely, pairwise interactions are often not enough to characterize social contagion processes such as opinion formation or the adoption of novelties, where complex mechanisms of influence and reinforcement are at work. Here we introduce a higher-order model of social contagion in which a social system is represented by a simplicial complex and contagion can occur through interactions in groups of different sizes. Numerical simulations of the model on both empirical and synthetic simplicial complexes highlight the emergence of novel phenomena such as a discontinuous transition induced by higher-order interactions. We show analytically that the transition is discontinuous and that a bistable region appears where healthy and endemic states co-exist. Our results help explain why critical masses are required to initiate social changes and contribute to the understanding of higher-order interactions in complex systems.
Introducing risk inequality metrics in tuberculosis policy development
Authors: Gomes M. Gabriela M. , Oliveira Juliane F. , Bertolde Adelmo , Ayabina Diepreye , Nguyen Tuan Anh , Maciel Ethel L. , Duarte Raquel , Nguyen Binh Hoa , Shete Priya B. , Lienhardt Christian 
Published: June 2019

AbstractGlobal stakeholders including the World Health Organization rely on predictive models for developing strategies and setting targets for tuberculosis care and control programs. Failure to account for variation in individual risk leads to substantial biases that impair data interpretation and policy decisions. Anticipated impediments to estimating heterogeneity for each parameter are discouraging despite considerable technical progress in recent years. Here we identify acquisition of infection as the single process where heterogeneity most fundamentally impacts model outputs, due to selection imposed by dynamic forces of infection. We introduce concrete metrics of risk inequality, demonstrate their utility in mathematical models, and pack the information into a risk inequality coefficient (RIC) which can be calculated and reported by national tuberculosis programs for use in policy development and modeling.
Cellular advective-diffusion drives the emergence of bacterial surface colonization patterns and heterogeneity
Authors: Rossy Tamara , Nadell Carey D. , Persat Alexandre 
Published: June 2019

AbstractMicroorganisms navigate and divide on surfaces to form multicellular structures called biofilms, the most widespread survival strategy found in the bacterial world. One common assumption is that cellular components guide the spatial architecture and arrangement of multiple species in a biofilm. However, bacteria must contend with mechanical forces generated through contact with surfaces and under fluid flow, whose contributions to colonization patterns are poorly understood. Here, we show how the balance between motility and flow promotes the emergence of morphological patterns in Caulobacter crescentus biofilms. By modeling transport of single cells by flow and Brownian-like swimming, we show that the emergence of these patterns is guided by an effective Péclet number. By analogy with transport phenomena we show that, counter-intuitively, fluid flow represses mixing of distinct clonal lineages, thereby affecting the interaction landscapes between biofilm-dwelling bacteria. This demonstrates that hydrodynamics influence species interaction and evolution within surface-associated communities.
High-throughput prediction of the ground-state collinear magnetic order of inorganic materials using Density Functional Theory
Authors: Horton Matthew Kristofer , Montoya Joseph Harold , Liu Miao , Persson Kristin Aslaug 
Published: June 2019

AbstractWe present a robust, automatic high-throughput workflow for the calculation of magnetic ground state of solid-state inorganic crystals, whether ferromagnetic, antiferromagnetic or ferrimagnetic, and their associated magnetic moments within the framework of collinear spin-polarized Density Functional Theory. This is done through a computationally efficient scheme whereby plausible magnetic orderings are first enumerated and prioritized based on symmetry, and then relaxed and their energies determined through conventional DFT + U calculations. This automated workflow is formalized using the atomate code for reliable, systematic use at a scale appropriate for thousands of materials and is fully customizable. The performance of the workflow is evaluated against a benchmark of 64 experimentally known mostly ionic magnetic materials of non-trivial magnetic order and by the calculation of over 500 distinct magnetic orderings. A non-ferromagnetic ground state is correctly predicted in 95% of the benchmark materials, with the experimentally determined ground state ordering found exactly in over 60% of cases. Knowledge of the ground state magnetic order at scale opens up the possibility of high-throughput screening studies based on magnetic properties, thereby accelerating discovery and understanding of new functional materials.
Model of a Support Vector Machine to Assess the Functional Cure for Surgery of Intermittent Exotropia
Authors: Liu Yanli , Liu Chungao , Zhang Wei , Chen Xia , Zhao Kanxing 
Published: June 2019

AbstractIn this paper the optimum timing for the postoperative functional cure of basic intermittent exotropia is explored based on support vector machine (SVM). One hundred and thirty-two patients were recruited in this prospective cross-sectional study with 6 months of follow-up. Examinations included angle of deviation, central and peripheral fusion, controllability, and near and distance stereopsis. Influencing factors of postoperative alignment and stereopsis were analyzed with a chi-squared test and univariate and multivariate logistic regression analyses. At 6 months post-operation, there were 84 successful procedures for the angle of deviation, with 4 overcorrections and 44 undercorrections. The success rate was 63.6%. The angle of deviation on postoperative day 1 was the only significant associated factor. One hundred and thirty patients had normal near stereoacuity, 60 had normal distance stereoacuity according to a Functional Visual Analyzer assessment, and 108 had normal stereoacuity as assessed by the Frisby Davis Distance (FD2) stereotest. The age of onset and preoperative distance stereoacuity with FD2 were the influencing factors of postoperative distance stereopsis restoration. The accuracy of this method of SVM was 82.1%. The angle of deviation for distance on postoperative day 1 was the only significant factor that correlated with alignment at 6 months post-operation, and the model of SVM was useful to determine the optimal time of the postoperative functional cure.
Human osteogenic differentiation in Space: proteomic and epigenetic clues to better understand osteoporosis
Authors: Gambacurta Alessandra , Merlini Giulia , Ruggiero Cristina , Diedenhofen Giacomo , Battista Natalia , Bari Monica , Balsamo Michele , Piccirillo Sara , Valentini Giovanni , Mascetti Gabriele , Maccarrone Mauro 
Published: June 2019

AbstractIn the frame of the VITA mission of the Italian Space Agency (ASI), we addressed the problem of Space osteoporosis by using human blood-derived stem cells (BDSCs) as a suitable osteogenic differentiation model. In particular, we investigated proteomic and epigenetic changes in BDSCs during osteoblastic differentiation induced by rapamycin under microgravity conditions. A decrease in the expression of 4 embryonic markers (Sox2, Oct3/4, Nanog and E-cadherin) was found to occur to a larger extent on board the ISS than on Earth, along with an earlier activation of the differentiation process towards the osteogenic lineage. The changes in the expression of 4 transcription factors (Otx2, Snail, GATA4 and Sox17) engaged in osteogenesis supported these findings. We then ascertained whether osteogenic differentiation of BDSCs could depend on epigenetic regulation, and interrogated changes of histone H3 that is crucial in this type of gene control. Indeed, we found that H3K4me3, H3K27me2/3, H3K79me2/3 and H3K9me2/3 residues are engaged in cellular reprogramming that drives gene expression. Overall, we suggest that rapamycin induces transcriptional activation of BDSCs towards osteogenic differentiation, through increased GATA4 and Sox17 that modulate downstream transcription factors (like Runx2), critical for bone formation. Additional studies are warranted to ascertain the possible exploitation of these data to identify new biomarkers and therapeutic targets to treat osteoporosis, not only in Space but also on Earth.
Morphological organization of point-to-point transport in complex networks
Authors: Kang Min-Yeong , Berthelot Geoffroy , Tupikina Liubov , Nicolaides Christos , Colonna Jean-Francois , Sapoval Bernard , Grebenkov Denis S. 
Published: June 2019

AbstractWe investigate the structural organization of the point-to-point electric, diffusive or hydraulic transport in complex scale-free networks. The random choice of two nodes, a source and a drain, to which a potential difference is applied, selects two tree-like structures, one emerging from the source and the other converging to the drain. These trees merge into a large cluster of the remaining nodes that is found to be quasi-equipotential and thus presents almost no resistance to transport. Such a global “tree-cluster-tree” structure is universal and leads to a power law decay of the currents distribution. Its exponent, −2, is determined by the multiplicative decrease of currents at successive branching points of a tree and is found to be independent of the network connectivity degree and resistance distribution.
Humans Use Predictive Gaze Strategies to Target Waypoints for Steering
Authors: Tuhkanen Samuel , Pekkanen Jami , Rinkkala Paavo , Mole Callum , Wilkie Richard M. , Lappi Otto 
Published: June 2019

AbstractA major unresolved question in understanding visually guided locomotion in humans is whether actions are driven solely by the immediately available optical information (model-free online control mechanisms), or whether internal models have a role in anticipating the future path. We designed two experiments to investigate this issue, measuring spontaneous gaze behaviour while steering, and predictive gaze behaviour when future path information was withheld. In Experiment 1 participants (N = 15) steered along a winding path with rich optic flow: gaze patterns were consistent with tracking waypoints on the future path 1–3 s ahead. In Experiment 2, participants (N = 12) followed a path presented only in the form of visual waypoints located on an otherwise featureless ground plane. New waypoints appeared periodically every 0.75 s and predictably 2 s ahead, except in 25% of the cases the waypoint at the expected location was not displayed. In these cases, there were always other visible waypoints for the participant to fixate, yet participants continued to make saccades to the empty, but predictable, waypoint locations (in line with internal models of the future path guiding gaze fixations). This would not be expected based upon existing model-free online steering control models, and strongly points to a need for models of steering control to include mechanisms for predictive gaze control that support anticipatory path following behaviours.
Modeling the Effect of the Metastatic Microenvironment on Phenotypes Conferred by Estrogen Receptor Mutations Using a Human Liver Microphysiological System
Authors: Miedel Mark T. , Gavlock Dillon C. , Jia Shanhang , Gough Albert , Taylor D. Lansing , Stern Andrew M. 
Published: June 2019

AbstractReciprocal coevolution of tumors and their microenvironments underlies disease progression, yet intrinsic limitations of patient-derived xenografts and simpler cell-based models present challenges towards a deeper understanding of these intercellular communication networks. To help overcome these barriers and complement existing models, we have developed a human microphysiological system (MPS) model of the human liver acinus, a common metastatic site, and have applied this system to estrogen receptor (ER)+ breast cancer. In addition to their hallmark constitutive (but ER-dependent) growth phenotype, different ESR1 missense mutations, prominently observed during estrogen deprivation therapy, confer distinct estrogen-enhanced growth and drug resistant phenotypes not evident under cell autonomous conditions. Under low molecular oxygen within the physiological range (~5–20%) of the normal liver acinus, the estrogen-enhanced growth phenotypes are lost, a dependency not observed in monoculture. In contrast, the constitutive growth phenotypes are invariant within this range of molecular oxygen suggesting that ESR1 mutations confer a growth advantage not only during estrogen deprivation but also at lower oxygen levels. We discuss the prospects and limitations of implementing human MPS, especially in conjunction with in situ single cell hyperplexed computational pathology platforms, to identify biomarkers mechanistically linked to disease progression that inform optimal therapeutic strategies for patients.
Comparative genomics provides new insights into the remarkable adaptations of the African wild dog (Lycaon pictus)
Authors: Chavez Daniel E. , Gronau Ilan , Hains Taylor , Kliver Sergei , Koepfli Klaus-Peter , Wayne Robert K. 
Published: June 2019

AbstractWithin the Canidae, the African wild dog (Lycaon pictus) is the most specialized with regards to cursorial adaptations (specialized for running), having only four digits on their forefeet. In addition, this species is one of the few canids considered to be an obligate meat-eater, possessing a robust dentition for taking down large prey, and displays one of the most variable coat colorations amongst mammals. Here, we used comparative genomic analysis to investigate the evolutionary history and genetic basis for adaptations associated with cursoriality, hypercanivory, and coat color variation in African wild dogs. Genome-wide scans revealed unique amino acid deletions that suggest a mode of evolutionary digit loss through expanded apoptosis in the developing first digit. African wild dog-specific signals of positive selection also uncovered a putative mechanism of molar cusp modification through changes in genes associated with the sonic hedgehog (SHH) signaling pathway, required for spatial patterning of teeth, and three genes associated with pigmentation. Divergence time analyses suggest the suite of genomic changes we identified evolved ~1.7 Mya, coinciding with the diversification of large-bodied ungulates. Our results show that comparative genomics is a powerful tool for identifying the genetic basis of evolutionary changes in Canidae.
Ligand induced switching of the band alignment in aqueous synthesized CdTe/CdS core/shell nanocrystals
Authors: Vale Brener R. C. , Mourão Rafael S. , Bettini Jefferson , Sousa José C. L. , Ferrari Jefferson L. , Reiss Peter , Aldakov Dmitry , Schiavon Marco A. 
Published: June 2019

AbstractCdTe/CdS core/shell quantum dots (QDs) are formed in aqueous synthesis via the partial decomposition of hydrophilic thiols, used as surface ligands. In this work, we investigate the influence of the chemical nature (functional group and chain length) of the used surface ligands on the shell formation. Four different surface ligands are compared: 3-mercaptopropionic acid, MPA, thioglycolic acid, TGA, sodium 3-mercaptopropanesulfonate, MPS, and sodium 2-mercaptoethanesulfonate, MES. The QD growth rate increases when the ligand aliphatic chain length decreases due to steric reasons. At the same time, the QDs stabilized with carboxylate ligands grow faster and achieve higher photoluminescence quantum yields compared to those containing sulfonate ligands. The average PL lifetime of TGA and MPA capped QDs is similar (≈20 ns) while in the case of MPS shorter (≈15 ns) and for MES significantly longer (≈30 ns) values are measured. A detailed structural analysis combining powder X-ray diffraction, and X-ray photoelectron spectroscopy (XPS) indicates the existence of two novel regimes of band alignment: in the case of the mercaptocarboxylate ligands the classic type I band alignment between the core and shell materials is predominant, while the mercaptosulfonate ligands induce a quasi-type II alignment (MES) or an inverted type I alignment (MPS). Finally, the effect of the pH value on the optical properties was evaluated: using a ligand excess in solution allows achieving better stability of the QDs while maintaining high photoluminescence intensity at low pH.
Efficient preparation of kaolinite/methanol intercalation composite by using a Soxhlet extractor
Authors: Qu Hao , He Sihui , Su Haiquan 
Published: June 2019

AbstractKaolinite/methanol intercalation composite (KMe) is a key precursor for preparing clay-based inorganic/organic hybrid materials and kaolinite nanoscrolls. However, synthesis of KMe is a time and methanol dissipative process and the complexity of this process also limits its further applications. In this study, Soxhlet extractor was introduced to synthesize an intercalation composite and KMe was efficiently synthesized in a Soxhlet extractor through a continuous displacement process by using kaolinite/DMSO intercalation composite (KD) as a precursor. The formation process of kaolinite/methanol intercalation composite was studied by X-ray diffraction (XRD) and infrared spectroscopy (IR). The results showed that the DMSO in kaolinite could be completely displaced by methanol in this process and the preparation of KMe could be completed in 8 hours, which was far faster than the reported methods. Moreover, methanol used in this process could be recycled. Furthermore, the resulting material could be successfully used to prepare kaolinite nanoscrolls in high yield.
Amide Proton Transfer-weighted MRI in the Diagnosis of Major Salivary Gland Tumors
Authors: Bae Yun Jung , Choi Byung Se , Jeong Woo-Jin , Jung Young Ho , Park Jung Hyun , Sunwoo Leonard , Jung Cheolkyu , Kim Jae Hyoung 
Published: June 2019

AbstractAmide proton transfer-weighted magnetic resonance imaging (APTw-MRI), which is effective in tumor characterization, has expanded its role in the head and neck. We aimed to evaluate the diagnostic ability of APTw-MRI in differentiating malignant from benign major salivary gland tumors compared with diffusion-weighted imaging (DWI) and dynamic contrast-enhanced (DCE)-MRI. Between December 2017 and November 2018, 38 subjects, who were diagnosed with major salivary gland tumors and who underwent preoperative 3 T MRI, including APTw-MRI, DWI, and DCE-MRI, were included in this retrospective study. Twenty-three subjects had benign tumors, and fifteen had malignancies. APTw-signals of the tumors were measured and compared according to the histopathological diagnosis. Using receiver operating characteristic curve analysis, diagnostic performance of APTw-MRI was evaluated and compared with DWI and DCE-MRI using DeLong test. The maximum, mean, and median APTw-signals were significantly higher in malignant than in benign tumors (P < 0.001). The mean and maximum APTw-signals showed excellent area under the curve for predicting malignant tumors (0.948 and 0.939), which were significantly higher than the combining use of DWI and DCE-MRI (0.780) (P = 0.021 and 0.028). Therefore, APTw-MRI could be a useful tool for differentiating malignant from benign major salivary gland tumors, and can be applicable in the clinical setting.