bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics-dependent density distribution in active suspensions
Authors: Arlt Jochen , Martinez Vincent A. , Dawson Angela , Pilizota Teuta , Poon Wilson C. K. 
Published: May 2019

AbstractSelf-propelled colloids constitute an important class of intrinsically non-equilibrium matter. Typically, such a particle moves ballistically at short times, but eventually changes its orientation, and displays random-walk behaviour in the long-time limit. Theory predicts that if the velocity of non-interacting swimmers varies spatially in 1D, v(x), then their density ρ(x) satisfies ρ(x) = ρ(0)v(0)/v(x), where x = 0 is an arbitrary reference point. Such a dependence of steady-state ρ(x) on the particle dynamics, which was the qualitative basis of recent work demonstrating how to ‘paint’ with bacteria, is forbidden in thermal equilibrium. Here we verify this prediction quantitatively by constructing bacteria that swim with an intensity-dependent speed when illuminated and implementing spatially-resolved differential dynamic microscopy (sDDM) for quantitative analysis over millimeter length scales. Applying a spatial light pattern therefore creates a speed profile, along which we find that, indeed, ρ(x)v(x) = constant, provided that steady state is reached.
Contemporaneous 3D characterization of acute and chronic myocardial I/R injury and response
Authors: Merz Simon F. , Korste Sebastian , Bornemann Lea , Michel Lars , Stock Pia , Squire Anthony , Soun Camille , Engel Daniel R. , Detzer Julia , Lörchner Holger , Hermann Dirk M. , Kamler Markus , Klode Joachim , Hendgen-Cotta Ulrike B. , Rassaf Tienush , Gunzer Matthias , Totzeck Matthias 
Published: May 2019

AbstractCardioprotection by salvage of the infarct-affected myocardium is an unmet yet highly desired therapeutic goal. To develop new dedicated therapies, experimental myocardial ischemia/reperfusion (I/R) injury would require methods to simultaneously characterize extent and localization of the damage and the ensuing inflammatory responses in whole hearts over time. Here we present a three-dimensional (3D), simultaneous quantitative investigation of key I/R injury-components by combining bleaching-augmented solvent-based non-toxic clearing (BALANCE) using ethyl cinnamate (ECi) with light sheet fluorescence microscopy. This allows structural analyses of fluorescence-labeled I/R hearts with exceptional detail. We discover and 3D-quantify distinguishable acute and late vascular I/R damage zones. These contain highly localized and spatially structured neutrophil infiltrates that are modulated upon cardiac healing. Our model demonstrates that these characteristic I/R injury patterns can detect the extent of damage even days after the ischemic index event hence allowing the investigation of long-term recovery and remodeling processes.
Non-trivial surface states of samarium hexaboride at the (111) surface
Authors: Ohtsubo Yoshiyuki , Yamashita Yuki , Hagiwara Kenta , Ideta Shin-ichiro , Tanaka Kiyohisa , Yukawa Ryu , Horiba Koji , Kumigashira Hiroshi , Miyamoto Koji , Okuda Taichi , Hirano Wataru , Iga Fumitoshi , Kimura Shin-ichi 
Published: May 2019

AbstractThe peculiar metallic electronic states observed in the Kondo insulator, samarium hexaboride (SmB6), has stimulated considerable attention among those studying non-trivial electronic phenomena. However, experimental studies of these states have led to controversial conclusions mainly due to the difficulty and inhomogeneity of the SmB6 crystal surface. Here, we show the detailed electronic structure of SmB6 with angle-resolved photoelectron spectroscopy measurements of the three-fold (111) surface where only two inequivalent time-reversal-invariant momenta (TRIM) exist. We observe the metallic two-dimensional state was dispersed across the bulk Kondo gap. Its helical in-plane spin polarisation around the surface TRIM indicates that SmB6 is topologically non-trivial, according to the topological classification theory for weakly correlated systems. Based on these results, we propose a simple picture of the controversial topological classification of SmB6.
Homochirality in biomineral suprastructures induced by assembly of single-enantiomer amino acids from a nonracemic mixture
Authors: Jiang Wenge , Athanasiadou Dimitra , Zhang Shaodong , Demichelis Raffaella , Koziara Katarzyna B. , Raiteri Paolo , Nelea Valentin , Mi Wenbo , Ma Jun-An , Gale Julian D. , McKee Marc D. 
Published: May 2019

AbstractSince Pasteur first successfully separated right-handed and left-handed tartrate crystals in 1848, the understanding of how homochirality is achieved from enantiomeric mixtures has long been incomplete. Here, we report on a chirality dominance effect where organized, three-dimensional homochiral suprastructures of the biomineral calcium carbonate (vaterite) can be induced from a mixed nonracemic amino acid system. Right-handed (counterclockwise) homochiral vaterite helicoids are induced when the amino acid l-Asp is in the majority, whereas left-handed (clockwise) homochiral morphology is induced when d-Asp is in the majority. Unexpectedly, the Asp that incorporates into the homochiral vaterite helicoids maintains the same enantiomer ratio as that of the initial growth solution, thus showing chirality transfer without chirality amplification. Changes in the degree of chirality of the vaterite helicoids are postulated to result from the extent of majority enantiomer assembly on the mineral surface. These mechanistic insights potentially have major implications for high-level advanced materials synthesis.
Moisture outgassing from siloxane elastomers containing surface-treated-silica fillers
Authors: Sharma Hom N. , Lenhardt Jeremy M. , Loui Albert , Allen Patrick G. , McLean William , Maxwell Robert S. , Dinh Long N. 
Published: May 2019

AbstractThe outgassing kinetics from siloxane elastomers is dominated by moisture desorption from the reinforcing silica filler and can be detrimental in moisture-sensitive applications. In this study, a custom 3D printable siloxane rubber (LL50) was analyzed in three different states: after a high temperature vacuum heat treatment, limited re-exposure to moisture after vacuum heat treatment, and in the as-received condition. The outgassing kinetics were extracted using isoconversional and iterative regression analyses. Moisture release by physisorbed and chemisorbed water from the samples have activation energies in the range of 50 kJ/mol (physisorbed type) to 220 kJ/mol (chemisorbed type). Overall, moisture outgassing from LL50 was 10 times lower than that from traditionally prepared siloxane rubbers. The vastly diminished moisture content in LL50 is attributed to the existence of a finite low level of silanol groups that remain on the fumed silica surface even after hydrophobic treatment.
Online Stress Measurement During Laser-aided Metallic Additive Manufacturing
Authors: Lu Yi , Sun Guifang , Xiao Xianfeng , Mazumder Jyoti 
Published: May 2019

AbstractIn situ measurement of residual stress is a challenge, and it is a source of many defects during additive manufacturing (AM). Usually, postmortem measurement is too late to save the product once a defect appears. Most of the existing technologies are predictive simulations and postmortem analysis. However, these technologies cannot directly reflect the stress evolution during the fabrication process. This paper introduces a computer vision-based stress monitoring system combined with finite element method (FEM) technology to estimate the stress development inside of the deposition layer. The system uses a CCD camera and a line laser beam to measure the height of the melt pool and solidified layer, forms a real-time FEM model, and uses the surface displacement between the two states to calculate the stress development during the solidification process. The results show that there is no obvious shape change after solidification. The shape of the melt pool and its solid state is similar. The stress distribution obtained through online monitoring is similar to that from the traditional thermal-stress simulation.
Morphological and molecular analysis of cryptic native and invasive freshwater snails in Chile
Authors: Collado Gonzalo A. , Vidal Marcela A. , Aguayo Karina P. , Méndez Marco A. , Valladares Moisés A. , Cabrera Francisco J. , Pastenes Luis , Gutiérrez Gregoric Diego E. , Puillandre Nicolas 
Published: May 2019

AbstractSpecies delimitation in minute freshwater snails is often difficult to perform using solely shell morphology. The problem intensifies when invasive species spread within the distribution range of morphologically similar native species. In Chile, the Truncatelloidean snails are represented by the native genera Heleobia and Potamolithus plus the invasive mudsnail Potamopyrgus antipodarum, which can easily be confused. Using an integrative approach, we performed molecular phylogenetic analysis and studied reproductive and morphological features to identify superficially similar forms inhabiting the central area of the country. Truncatelloidean snails were identified in 40 of 51 localities sampled, 10 containing Potamopyrgus antipodarum, 23 Heleobia and 7 Potamolithus. Based on these results and previously published data, the known distribution of the mudsnail in Chile encompasses 6 hydrological basins, including 18 freshwater ecosystems. The finding of the mudsnails in several type localities of native species/subspecies of “Heleobia” that were not find in situ suggests species replacement or significant extinction of native fauna, a hypothesis supported by the restudy of type material that shows that endemic forms belong to the genus Potamolithus. This study shows the usefulness of integrative taxonomy not only resolving complex taxa with cryptic morphology but also measuring the extent of an ongoing invasion.
Exploratory Gene Ontology Analysis with Interactive Visualization
Authors: Zhu Junjie , Zhao Qian , Katsevich Eugene , Sabatti Chiara 
Published: May 2019

AbstractThe Gene Ontology (GO) is a central resource for functional-genomics research. Scientists rely on the functional annotations in the GO for hypothesis generation and couple it with high-throughput biological data to enhance interpretation of results. At the same time, the sheer number of concepts (>30,000) and relationships (>70,000) presents a challenge: it can be difficult to draw a comprehensive picture of how certain concepts of interest might relate with the rest of the ontology structure. Here we present new visualization strategies to facilitate the exploration and use of the information in the GO. We rely on novel graphical display and software architecture that allow significant interaction. To illustrate the potential of our strategies, we provide examples from high-throughput genomic analyses, including chromatin immunoprecipitation experiments and genome-wide association studies. The scientist can also use our visualizations to identify gene sets that likely experience coordinated changes in their expression and use them to simulate biologically-grounded single cell RNA sequencing data, or conduct power studies for differential gene expression studies using our built-in pipeline. Our software and documentation are available at http://aegis.stanford.edu.
Territory location and quality, together with climate, affect the timing of breeding in the white-throated dipper
Authors: Nilsson A. L. K. , Slagsvold T. , Røstad O. W. , Knudsen E. , Jerstad K. , Cadahía L. , Reitan T. , Helberg M. , Walseng B. , Stenseth N. C. 
Published: May 2019

AbstractRecent climate change has led to advanced spring phenology in many temperate regions. The phenological response to variation in the local environment, such as the habitat characteristics of the territories birds occupy, is less clear. The aim of this study is to understand how ecological conditions affect breeding time, and its consequences for reproduction, in a white-throated dipper Cinclus cinclus population in a river system in Norway during 34 years (1978–2011). Hatching date advanced almost nine days, indicating a response to higher temperatures and the advanced phenology in the area. Earlier breeding was found in warm springs and at lower altitudes. High population density facilitated earlier breeding close to the coast. Furthermore, when population density was low, breeding was early at territories that were rarely occupied, while in years with high density, breeding was early at territories that were frequently occupied. Also, when population density was low, earlier breeding occurred at territories that on average produced more offspring than other territories, while there was no difference in breeding time in high population years. Selection for early breeding was dependent on spring temperatures and high spring temperatures contributed to higher breeding success during the study period. We found that breeding phenology may have strong effects on fitness in the white-throated dipper, and thus that breeding time is an important ecological factor in a species that feeds mainly on aquatic rather than terrestrial prey.
Runx1 contributes to articular cartilage maintenance by enhancement of cartilage matrix production and suppression of hypertrophic differentiation
Authors: Yano Fumiko , Ohba Shinsuke , Murahashi Yasutaka , Tanaka Sakae , Saito Taku , Chung Ung-il 
Published: May 2019

AbstractOsteoarthritis (OA) results from an imbalance of the dynamic equilibrium between the breakdown and repair of joint tissues. Previously, we reported that Runx1 enhanced chondrogenic differentiation through transcriptional induction ofCOL2A1, and suppressed hypertrophic differentiation. Here, we investigated the involvement of Runx1 in OA development as well as its potential underlying molecular mechanism. When we analysed OA development inCol2a1-Cre;Runx1fl/flandRunx1fl/flmice by surgically inducing joint instability, Cartilage degradation and osteophyte formation ofCol2a1-Cre;Runx1fl/fljoints was accelerated compared with joints inRunx1fl/flanimals 8 weeks after surgery. To investigate chondrocyte regulation by Runx1, we analysed interactions with co-factors and downstream molecules. Runx1 enhanced cartilage matrix production in cooperation with Sox5, Sox6, and Sox9, and co-immunoprecipitation assays showed protein–protein binding between Runx1 and each Sox protein. Knockdown of Runx1 increased expression of a hypertrophic marker, Co10a1, in mouse articular cartilage and primary chondrocytes. This expression was accompanied by decreased expression of Bapx1, a potent suppressor of hypertrophic differentiation. Notably, Runx1-induced suppression of hypertrophic differentiation was diminished by siRNA silencing ofBapx1, whereas chondrogenic markers were unaltered. Thus, Runx1 contributes to articular cartilage maintenance by enhancing matrix production in cooperation with Sox proteins, and suppressing hypertrophic differentiation at least partly via Bapx1 induction.
Transcriptional profiling of coaggregation interactions between Streptococcus gordonii and Veillonella parvula by Dual RNA-Seq
Authors: Mutha Naresh V. R. , Mohammed Waleed K. , Krasnogor Natalio , Tan Geok Y. A. , Wee Wei Yee , Li Yongming , Choo Siew Woh , Jakubovics Nicholas S. 
Published: May 2019

AbstractMany oral bacteria form macroscopic clumps known as coaggregates when mixed with a different species. It is thought that these cell-cell interactions are critical for the formation of mixed-species biofilms such as dental plaque. Here, we assessed the impact of coaggregation between two key initial colonizers of dental plaque, Streptococcus gordonii and Veillonella parvula, on gene expression in each partner. These species were shown to coaggregate in buffer or human saliva. To monitor gene regulation, coaggregates were formed in human saliva and, after 30 minutes, whole-transcriptomes were extracted for sequencing and Dual RNA-Seq analysis. In total, 272 genes were regulated in V. parvula, including 39 genes in oxidoreductase processes. In S. gordonii, there was a high degree of inter-sample variation. Nevertheless, 69 genes were identified as potentially regulated by coaggregation, including two phosphotransferase system transporters and several other genes involved in carbohydrate metabolism. Overall, these data indicate that responses of V. parvula to coaggregation with S. gordonii are dominated by oxidative stress-related processes, whereas S. gordonii responses are more focussed on carbohydrate metabolism. We hypothesize that these responses may reflect changes in the local microenvironment in biofilms when S. gordonii or V. parvula immigrate into the system.
Co-overexpression of AVP1 and OsSIZ1 in Arabidopsis substantially enhances plant tolerance to drought, salt, and heat stresses
Authors: Esmaeili Nardana , Yang Xiaojie , Cai Yifan , Sun Li , Zhu Xunlu , Shen Guoxin , Payton Paxton , Fang Weiping , Zhang Hong 
Published: May 2019

AbstractAbiotic stresses such as water deficit, salt, and heat are major environmental factors that negatively affect plant growth, development, and productivity. Previous studies showed that overexpression of the Arabidopsis vacuolar H+-pyrophosphatase gene AVP1 increases salt and water deficit stress tolerance and overexpression of the rice SUMO E3 ligase gene OsSIZ1 improves heat and water deficit stress tolerance in transgenic plants. In this report, the effects of co-overexpression of AVP1 and OsSIZ1 in Arabidopsis on abiotic stress tolerance were studied. It was found that AVP1/OsSIZ1 co-overexpressing plants performed significantly better than AVP1-overexpressing plants and OsSIZ1-overexpressing plants, and produced 100% more seed than wild-type plants under single stress or multiple stress conditions. The increased stress tolerance in AVP1/OsSIZ1 co-overexpressing plants was substantially larger than the increased stress tolerance in AVP1-overexpressing plants and OsSIZ1-overexpressing plants under every abiotic stress condition tested. This research provides the proof-of-concept that crop yields might be substantially improved using this approach.
Visualization of junctional epithelial cell replacement by oral gingival epithelial cells over a life time and after gingivectomy
Authors: Kato Mayu , Tanaka Junichi , Aizawa Ryo , Yajima-Himuro Sara , Seki Tatsuaki , Tanaka Keisuke , Yamada Atsushi , Ogawa Miho , Kamijo Ryutaro , Tsuji Takashi , Mishima Kenji , Yamamoto Matsuo 
Published: May 2019

AbstractJunctional epithelium (JE), which is derived from odontogenic epithelial cells immediately after eruption, is believed to be gradually replaced by oral gingival epithelium (OGE) over a lifetime. However, the detailed process of replacement remains unclear. The aim of the present study was to clarify the process of JE replacement by OGE cells using a green fluorescent protein (GFP)–positive tooth germ transplantation method. GFP-positive JE was partly replaced by OGE cells and completely replaced on day 200 after transplantation, whereas there was no difference in the expression of integrin β4 (Itgb4) and laminin 5 (Lama5) between JE before and after replacement by OGE cells. Next, GFP-positive JE was partially resected. On day 14 after resection, the regenerated JE consisted of GFP-negative cells and also expressed both Itgb4 and Lama5. In addition, the gene expression profile of JE derived from odontogenic epithelium before gingivectomy was partly different from that of JE derived from OGE after gingivectomy. These results suggest that JE derived from the odontogenic epithelium is gradually replaced by OGE cells over time and JE derived from the odontogenic epithelium might have specific characteristics different to those of JE derived from OGE.
Identification and first characterization of DinJ-YafQ toxin-antitoxin systems in Lactobacillus species of biotechnological interest
Authors: Ferrari Alberto , Maggi Stefano , Montanini Barbara , Levante Alessia , Lazzi Camilla , Yamaguchi Yoshihiro , Rivetti Claudio , Folli Claudia 
Published: May 2019

AbstractDinJ-YafQ is a type II TA system comprising the ribosome-dependent RNase YafQ toxin and the DinJ antitoxin protein. Although the module has been extensively characterized in Escherichia coli, little information is available for homologous systems in lactic acid bacteria. In this study, we employed bioinformatics tools to identify DinJ-YafQ systems in Lactobacillus casei, Lactobacillus paracasei and Lactobacillus rhamnosus species, commonly used in biotechnological processes. Among a total of nineteen systems found, two TA modules from Lactobacillus paracasei and two modules from Lactobacillus rhamnosus wild strains were isolated and their activity was verified by growth assays in Escherichia coli either in liquid and solid media. The RNase activity of the YafQ toxins was verified in vivo by probing mRNA dynamics and metabolism with single-cell Thioflavin T fluorescence. Our findings demonstrate that, albeit DinJ-YafQ TA systems are widely distributed in lactic acid bacteria, only few are fully functional, while others have lost toxicity even though they maintain high sequence identity with wild type YafQ and a likely functional antitoxin protein.
Spatially explicit analysis reveals complex human genetic gradients in the Iberian Peninsula
Authors: Pimenta João , Lopes Alexandra M. , Carracedo Angel , Arenas Miguel , Amorim António , Comas David 
Published: May 2019

AbstractThe Iberian Peninsula is a well-delimited geographic region with a rich and complex human history. However, the causes of its genetic structure and past migratory dynamics are not yet fully understood. In order to shed light on them, here we evaluated the gene flow and genetic structure throughout the Iberian Peninsula with spatially explicit modelling applied to a georeferenced genetic dataset composed of genome-wide SNPs from 746 individuals belonging to 17 different regions of the Peninsula. We found contrasting patterns of genetic structure throughout Iberia. In particular, we identified strong patterns of genetic differentiation caused by relevant barriers to gene flow in northern regions and, on the other hand, a large genetic similarity in central and southern regions. In addition, our results showed a preferential north to south migratory dynamics and suggest a sex-biased dispersal in Mediterranean and southern regions. The estimated genetic patterns did not fit with the geographical relief of the Iberian landscape and they rather seem to follow political and linguistic territorial boundaries.
Urinary peptide panel for prognostic assessment of bladder cancer relapse
Authors: Krochmal Magdalena , van Kessel Kim E. M. , Zwarthoff Ellen C. , Belczacka Iwona , Pejchinovski Martin , Vlahou Antonia , Mischak Harald , Frantzi Maria 
Published: May 2019

AbstractNon-invasive tools stratifying bladder cancer (BC) patients according to the risk of relapse are urgently needed to guide clinical intervention. As a follow-up to the previously published study on CE-MS-based urinary biomarkers for BC detection and recurrence monitoring, we expanded the investigation towards BC patients with longitudinal data. Profiling datasets of BC patients with follow-up information regarding the relapse status were investigated. The peptidomics dataset (n = 98) was split into training and test set. Cox regression was utilized for feature selection in the training set. Investigation of the entire training set at the single peptide level revealed 36 peptides being strong independent prognostic markers of disease relapse. Those features were further integrated into a Random Forest-based model evaluating the risk of relapse for BC patients. Performance of the model was assessed in the test cohort, showing high significance in BC relapse prognosis [HR = 5.76, p-value = 0.0001, c-index = 0.64]. Urinary peptide profiles integrated into a prognostic model allow for quantitative risk assessment of BC relapse highlighting the need for its incorporation in prospective studies to establish its value in the clinical management of BC.