bluuebunny/crossref_metadata_2025_split huggingface dataset:
A high-throughput imaging and nuclear segmentation analysis protocol for cleared 3D culture models
Authors: Boutin Molly E. , Voss Ty C. , Titus Steven A. , Cruz-Gutierrez Kennie , Michael Sam , Ferrer Marc 
Published: July 2018

AbstractImaging and subsequent segmentation analysis in three-dimensional (3D) culture models are complicated by the light scattering that occurs when collecting fluorescent signal through multiple cell and extracellular matrix layers. For 3D cell culture models to be usable for drug discovery, effective and efficient imaging and analysis protocols need to be developed that enable high-throughput data acquisition and quantitative analysis of fluorescent signal. Here we report the first high-throughput protocol for optical clearing of spheroids, fluorescent high-content confocal imaging, 3D nuclear segmentation, and post-segmentation analysis. We demonstrate nuclear segmentation in multiple cell types, with accurate identification of fluorescently-labeled subpopulations, and develop a metric to assess the ability of clearing to improve nuclear segmentation deep within the tissue. Ultimately this analysis pipeline allows for previously unattainable segmentation throughput of 3D culture models due to increased sample clarity and optimized batch-processing analysis.
Quad-mode functional and molecular photoacoustic microscopy
Authors: Liu Wei , Shcherbakova Daria M. , Kurupassery Neel , Li Yang , Zhou Qifa , Verkhusha Vladislav V. , Yao Junjie 
Published: July 2018

AbstractA conventional photoacoustic microscopy (PAM) system typically has to make tradeoffs between its spatial resolution and penetration depth, by choosing a fixed configuration of optical excitation and acoustic detection. The single-scale imaging capability of PAM may limit its applications in biomedical studies. Here, we report a quad-mode photoacoustic microscopy (QM-PAM) system with four complementary spatial resolutions and maximum penetration depths. For this we first developed a ring-shaped focused ultrasound transducer that has two independent elements with respective central frequencies at 20 MHz and 40 MHz, providing complementary acoustically-determined spatial resolutions and penetration depths. To accommodate the dual-element ultrasound transducer, we implemented two optical excitation modes to provide tightly- and weakly-focused light illumination. The dual-element acoustic detection combined with the two optical focusing modes can thus provide four imaging scales in a single imaging device, with consistent contrast mechanisms and co-registered field of views. We have demonstrated the multiscale morphological, functional, and molecular imaging capability of QM-PAM in the mouse head, leg and ear in vivo. We expect the high scale flexibility of QM-PAM will enable broad applications in preclinical studies.
Natural and sexual selection drive multivariate phenotypic divergence along climatic gradients in an invasive fish
Authors: Ouyang Xu , Gao Jiancao , Xie Meifeng , Liu Binghua , Zhou Linjun , Chen Bojian , Jourdan Jonas , Riesch Rüdiger , Plath Martin 
Published: July 2018

AbstractInvasive species that rapidly spread throughout novel distribution ranges are prime models to investigate climate-driven phenotypic diversification on a contemporary scale. Previous studies on adaptive diversification along latitudinal gradients in fish have mainly considered body size and reported either increased or decreased body size towards higher latitudes (i.e. Bergmann’s rule). Our study is the first to investigate phenotypic divergence in multiple traits, including sexually selected traits (size and shape of the male copulatory organ, the gonopodium) of invasive Gambusia affinis in China. We studied body size, life history traits and morphological variation across populations spanning 17 degrees of latitude and 16 degrees of longitude. Even though we found phenotypic variation along climatic gradients to be strongest in naturally selected traits, some sexually selected traits also showed systematic gradual divergence. For example, males from southern populations possessed wider gonopodia with increased armament. Generally, males and females diverged in response to different components of climatic gradients (latitudinal or longitudinal variation) and in different trait suites. We discuss that not only temperature regimes, but also indirect effects of increased resource and mate competition (as a function of different extrinsic overwinter mortality rates) alter the selective landscape along climatic gradients.
Quantifying Anharmonic Vibrations in Thermoelectric Layered Cobaltites and Their Role in Suppressing Thermal Conductivity
Authors: Fujii Susumu , Yoshiya Masato , Fisher Craig A. J. 
Published: July 2018

AbstractOptimizing multiple materials properties which are simultaneously in competition with each other is one of the chief challenges in thermoelectric materials research. Introducing greater anharmonicity to vibrational modes is one strategy for suppressing phonon thermal transport in crystalline oxides without detrimentally affecting electronic conductivity, so that the overall thermoelectric efficiency can be improved. Based on perturbed molecular dynamics and associated numerical analyses, we show that CoO2 layers in layered cobaltite thermoelectrics NaxCoO2 and Ca3Co4O9 are responsible for most of the in-plane heat transport in these materials, and that the non-conducting intermediate layers in the two materials exhibit different kinds of anharmonicity. More importantly, thermal conduction is shown to be altered by modifying the structure of the intermediate layers. The simulation methods developed to quantify the effect of anharmonic atomic vibrations on thermal conductivity provide a new tool for the rational design of thermoelectric materials, and the insights gained should hasten the attainment of higher conversion efficiencies so that thermoelectrics can be put to widespread practical use.
Biscrolled Carbon Nanotube Yarn Structured Silver-Zinc Battery
Authors: Lee Jae Myeong , Choi Changsoon , Kim Ji Hwan , de Andrade Mônica Jung , Baughman Ray H. , Kim Seon Jeong 
Published: July 2018

AbstractFlexible yarn- or fiber-based energy storing devices are attractive because of their small dimension, light weight, and suitability for integration into woven or textile application. Some Li-ion based yarn or fiber batteries were developed due to their performance advantages, realizing highly performing and practically safe wearable battery still remains a challenge. Here, high performance and safe yarn-based battery is demonstrated by embedding active materials into inner structure of yarn and using water based electrolyte. Thanks to biscrolling method, loading level of silver and zinc in yarn electrodes increased up to 99 wt%. Our high loaded Silver and Zinc yarn electrodes enables high linear capacity in liquid electrolyte (0.285 mAh/cm) and solid electrolyte (0.276 mAh/cm), which are significantly higher than previously reported fiber batteries. In additions, due to PVA-KOH based aqueous electrolyte, our yarn battery system is inflammable, non-explosive and safe. Consequently, these high-capacities enable our Silver-Zinc aqueous yarn battery to be applicable to the energy source of portable and wearable electronics like an electric watch.
Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model
Authors: Clayton Jonathan B. , Al-Ghalith Gabriel A. , Long Ha Thang , Tuan Bui Van , Cabana Francis , Huang Hu , Vangay Pajau , Ward Tonya , Minh Vo Van , Tam Nguyen Ai , Dat Nguyen Tat , Travis Dominic A. , Murtaugh Michael P. , Covert Herbert , Glander Kenneth E. , Nadler Tilo , Toddes Barbara , Sha John C. M. , Singer Randy , Knights Dan , Johnson Timothy J. 
Published: July 2018

AbstractRed-shanked doucs (Pygathrix nemaeus) are endangered, foregut-fermenting colobine primates which are difficult to maintain in captivity. There are critical gaps in our understanding of their natural lifestyle, including dietary habits such as consumption of leaves, unripe fruit, flowers, seeds, and other plant parts. There is also a lack of understanding of enteric adaptations, including their unique microflora. To address these knowledge gaps, we used the douc as a model to study relationships between gastrointestinal microbial community structure and lifestyle. We analyzed published fecal samples as well as detailed dietary history from doucs with four distinct lifestyles (wild, semi-wild, semi-captive, and captive) and determined gastrointestinal bacterial microbiome composition using 16S rRNA sequencing. A clear gradient of microbiome composition was revealed along an axis of natural lifestyle disruption, including significant associations with diet, biodiversity, and microbial function. We also identified potential microbial biomarkers of douc dysbiosis, including Bacteroides and Prevotella, which may be related to health. Our results suggest a gradient-like shift in captivity causes an attendant shift to severe gut dysbiosis, thereby resulting in gastrointestinal issues.
Cytological analysis and structural quantification of FtsZ1-2 and FtsZ2-1 network characteristics in Physcomitrella patens
Authors: Özdemir Bugra , Asgharzadeh Pouyan , Birkhold Annette I. , Mueller Stefanie J. , Röhrle Oliver , Reski Ralf 
Published: July 2018

AbstractAlthough the concept of the cytoskeleton as a cell-shape-determining scaffold is well established, it remains enigmatic how eukaryotic organelles adopt and maintain a specific morphology. TheFilamentousTemperatureSensitiveZ(FtsZ) protein family, an ancient tubulin, generates complex polymer networks, with striking similarity to the cytoskeleton, in the chloroplasts of the mossPhyscomitrella patens. Certain members of this protein family are essential for structural integrity and shaping of chloroplasts, while others are not, illustrating the functional diversity within the FtsZ protein family. Here, we apply a combination of confocal laser scanning microscopy and a self-developed semi-automatic computational image analysis method for the quantitative characterisation and comparison of network morphologies and connectivity features for two selected, functionally dissimilar FtsZ isoforms, FtsZ1-2 and FtsZ2-1. We show that FtsZ1-2 and FtsZ2-1 networks are significantly different for 8 out of 25 structural descriptors. Therefore, our results demonstrate that different FtsZ isoforms are capable of generating polymer networks with distinctive morphological and connectivity features which might be linked to the functional differences between the two isoforms. To our knowledge, this is the first study to employ computational algorithms in the quantitative comparison of different classes of protein networks in living cells.
Social Closure and the Evolution of Cooperation via Indirect Reciprocity
Authors: Righi Simone , Takács Károly 
Published: July 2018

AbstractDirect and indirect reciprocity are good candidates to explain the fundamental problem of evolution of cooperation. We explore the conditions under which different types of reciprocity gain dominance and their performances in sustaining cooperation in the PD played on simple networks. We confirm that direct reciprocity gains dominance over indirect reciprocity strategies also in larger populations, as long as it has no memory constraints. In the absence of direct reciprocity, or when its memory is flawed, different forms of indirect reciprocity strategies are able to dominate and to support cooperation. We show that indirect reciprocity relying on social capital inherent in closed triads is the best competitor among them, outperforming indirect reciprocity that uses information from any source. Results hold in a wide range of conditions with different evolutionary update rules, extent of evolutionary pressure, initial conditions, population size, and density.
Synergistic antibacterial activity of silver with antibiotics correlating with the upregulation of the ROS production
Authors: Zou Lili , Wang Jun , Gao Yu , Ren Xiaoyuan , Rottenberg Martin E. , Lu Jun , Holmgren Arne 
Published: July 2018

AbstractThiol-dependent enzymes, including the thioredoxin (Trx) and glutathione (GSH) systems, have recently been found as promising bactericidal targets in multidrug-resistant (MDR) bacteria. We previously discovered that silver acted synergistically with ebselen in the inhibition of the Trx system and also resulted in a fast depletion of GSH in Gram-negative bacteria. Silver has been found by others to improve the sensitivity of bacteria to certain conventional antibiotics. Here, we found that the synergistic antibacterial effects of silver with four conventional antibiotics was correlated with the blockage of bacterial Trx system by silver. The synergistic antibacterial effect came along with the production of reactive oxygen species. All these results suggested that silver primarily enhanced the bactericidal activities of conventional antibiotics towards Gram-negative strains through the upregulation of ROS production.
Enhancing coevolution-based contact prediction by imposing structural self-consistency of the contacts
Authors: Kassem Maher M. , Christoffersen Lars B. , Cavalli Andrea , Lindorff-Larsen Kresten 
Published: July 2018

AbstractBased on the development of new algorithms and growth of sequence databases, it has recently become possible to build robust higher-order sequence models based on sets of aligned protein sequences. Such models have proven useful inde novostructure prediction, where the sequence models are used to find pairs of residues that co-vary during evolution, and hence are likely to be in spatial proximity in the native protein. The accuracy of these algorithms, however, drop dramatically when the number of sequences in the alignment is small. We have developed a method that we termed CE-YAPP (CoEvolution-YAPP), that is based on YAPP (Yet Another Peak Processor), which has been shown to solve a similar problem in NMR spectroscopy. By simultaneously performing structure prediction and contact assignment, CE-YAPP uses structural self-consistency as a filter to remove false positive contacts. Furthermore, CE-YAPP solves another problem, namely how many contacts to choose from the ordered list of covarying amino acid pairs. We show that CE-YAPP consistently improves contact prediction from multiple sequence alignments, in particular for proteins that are difficult targets. We further show that the structures determined from CE-YAPP are also in better agreement with those determined using traditional methods in structural biology.
Optically reconfigurable polarized emission in Germanium
Authors: De Cesari Sebastiano , Bergamaschini Roberto , Vitiello Elisa , Giorgioni Anna , Pezzoli Fabio 
Published: July 2018

AbstractLight polarization can conveniently encode information. Yet, the ability to tailor polarized optical fields is notably demanding but crucial to develop practical methods for data encryption and to gather fundamental insights into light-matter interactions. Here we demonstrate the dynamic manipulation of the chirality of light at telecom wavelengths. This unique possibility is enrooted in the multivalley nature of the conduction band of a conventional semiconductor, namely Ge. In particular, we demonstrate that optical pumping suffices to govern the kinetics of spin-polarized carriers and eventually the chirality of the radiative recombination. We found that the polarized component of the emission can be remarkably swept through orthogonal eigenstates without magnetic field control or phase shifter coupling. Our results provide insights into spin-dependent phenomena and offer guiding information for the future selection and design of spin-enhanced photonic functionalities of group IV semiconductors.
Evolutionary cell biology traces the rise of the exomer complex in Fungi from an ancient eukaryotic component
Authors: Ramirez-Macias Inmaculada , Barlow Lael D. , Anton Carlos , Spang Anne , Roncero Cesar , Dacks Joel B. 
Published: July 2018

AbstractCargo is transported from the trans-Golgi Network to the plasma membrane by adaptor complexes, which are pan-eukaryotic components. However, in yeast, cargo can also be exported by the exomer complex, a heterotetrameric protein complex consisting of two copies of Chs5, and any two members of four paralogous proteins (ChAPs). To understand the larger relevance of exomer, its phylogenetic distribution and function outside of yeast need to be explored. We find that the four ChAP proteins are derived from gene duplications after the divergence of Yarrowia from the remaining Saccharomycotina, with BC8 paralogues (Bch2 and Chs6) being more diverged relative to the BB8 paralogues (Bch1 and Bud7), suggesting neofunctionalization. Outside Ascomycota, a single preduplicate ChAP is present in nearly all Fungi and in diverse eukaryotes, but has been repeatedly lost. Chs5, however, is a fungal specific feature, appearing coincidentally with the loss of AP-4. In contrast, the ChAP protein is a wide-spread, yet uncharacterized, membrane-trafficking component, adding one more piece to the increasingly complex machinery deduced as being present in our ancient eukaryotic ancestor.
Chloroquine exposure triggers distinct cellular responses in sensitive versus resistant Plasmodium falciparum parasites
Authors: Reiling Sarah J. , Krohne Georg , Friedrich Oliver , Geary Timothy G. , Rohrbach Petra 
Published: July 2018

AbstractChloroquine (CQ) treatment failure in Plasmodium falciparum parasites has been documented for decades, but the pharmacological explanation of this phenotype is not fully understood. Current concepts attribute CQ resistance to reduced accumulation of the drug at a given external CQ concentration ([CQ]ex) in resistant compared to sensitive parasites. The implication of this explanation is that the mechanisms of CQ-induced toxicity in resistant and sensitive strains are similar once lethal internal concentrations have been reached. To test this hypothesis, we investigated the mechanism of CQ-induced toxicity in CQ-sensitive (CQS) versus CQ-resistant (CQR) parasites by analyzing the time-course of cellular responses in these strains after exposure to varying [CQ]ex as determined in 72 h toxicity assays. Parasite killing was delayed in CQR parasites for up to 10 h compared to CQS parasites when exposed to equipotent [CQ]ex. In striking contrast, brief exposure (1 h) to lethal [CQ]ex in CQS but not CQR parasites caused the appearance of hitherto undescribed hemozoin (Hz)-containing compartments in the parasite cytosol. Hz-containing compartments were very rarely observed in CQR parasites even after CQ exposures sufficient to cause irreversible cell death. These findings challenge current concepts that CQ killing of malaria parasites is solely concentration-dependent, and instead suggest that CQS and CQR strains fundamentally differ in the consequences of CQ exposure.
In vivo delineation of glioblastoma by targeting tumor-associated macrophages with near-infrared fluorescent silica coated iron oxide nanoparticles in orthotopic xenografts for surgical guidance
Authors: Lee Chaedong , Kim Ga Ram , Yoon Juhwan , Kim Sang Eun , Yoo Jung Sun , Piao Yuanzhe 
Published: July 2018

AbstractGlioblastoma multiforme (GBM) is the most aggressive and lethal type of human brain cancer. Surgery is a current gold standard for GBM treatment but the complete surgical resection of GBM is almost impossible due to their diffusive characteristics into surrounded normal brain tissues. There is an urgent need to develop a sensitive imaging tool for accurate delineation of GBM in the operating room to guide surgeons. Here we illustrate the feasibility of using near-infrared fluorescent silica coated iron oxide nanoparticles (NF-SIONs) with high water dispersion capacity and strong fluorescence stability for intraoperative imaging of GBM by targeting tumor-associated macrophages. Abundant macrophage infiltration is a key feature of GBM margins and it is well associated with poor prognosis. We synthesized NF-SIONs of about 37 nm to maximize endocytosis activity for macrophage uptake. The NF-SIONs selectively visualized tumor-associated macrophage populations by in vitro live-cell imaging and in vivo fluorescence imaging. In the orthotopic GBM xenograft models, the NF-SIONs could successfully penetrate blood-brain barrier and delineated tumor burden specifically. Taken together, this study showcased the potential applications in GBM treatment for improved intraoperative staging and more radical surgery as well as dual modality benefit in order to circumvent previous clinical failure.
Faunal activity rhythms influencing early community succession of an implanted whale carcass offshore Sagami Bay, Japan
Authors: Aguzzi J. , Fanelli E. , Ciuffardi T. , Schirone A. , De Leo F. C. , Doya C. , Kawato M. , Miyazaki M. , Furushima Y. , Costa C. , Fujiwara Y. 
Published: July 2018

AbstractBenthic community succession patterns at whale falls have been previously established by means of punctual submersible and ROV observations. The contribution of faunal activity rhythms in response to internal tides and photoperiod cues to that community succession dynamism has never been evaluated. Here, we present results from a high-frequency monitoring experiment of an implanted sperm whale carcass in the continental slope (500 m depth) offshore Sagami Bay, Japan. The benthic community succession was monitored at a high frequency in a prolonged fashion (i.e. 2-h intervals for 2.5 months) with a seafloor lander equipped with a time-lapse video camera and an acoustic Doppler profiler to concomitantly study current flow dynamics. We reported here for the first time, to the best of our knowledge, the occurrence of strong 24-h day-night driven behavioral rhythms of the most abundant species (Simenchelys parasitica; Macrocheira kaempferi, and Pterothrissus gissu). Those rhythms were detected in detriment of tidally-controlled ones. Evidence of a diel temporal niche portioning between scavengers and predators avoiding co-occurrence at the carcass, is also provided. The high-frequency photographic and oceanographic data acquisition also helped to precisely discriminate the transition timing between the successional stages previously described for whale falls’ attendant communities.
Using Multi-Scale Genetic, Neuroimaging and Clinical Data for Predicting Alzheimer’s Disease and Reconstruction of Relevant Biological Mechanisms
Authors: Khanna Shashank , Domingo-Fernández Daniel , Iyappan Anandhi , Emon Mohammad Asif , Hofmann-Apitius Martin , Fröhlich Holger 
Published: July 2018

AbstractAlzheimer’s Disease (AD) is among the most frequent neuro-degenerative diseases. Early diagnosis is essential for successful disease management and chance to attenuate symptoms by disease modifying drugs. In the past, a number of cerebrospinal fluid (CSF), plasma and neuro-imaging based biomarkers have been proposed. Still, in current clinical practice, AD diagnosis cannot be made until the patient shows clear signs of cognitive decline, which can partially be attributed to the multi-factorial nature of AD. In this work, we integrated genotype information, neuro-imaging as well as clinical data (including neuro-psychological measures) from ~900 normal and mild cognitively impaired (MCI) individuals and developed a highly accurate machine learning model to predict the time until AD is diagnosed. We performed an in-depth investigation of the relevant baseline characteristics that contributed to the AD risk prediction. More specifically, we used Bayesian Networks to uncover the interplay across biological scales between neuro-psychological assessment scores, single genetic variants, pathways and neuro-imaging related features. Together with information extracted from the literature, this allowed us to partially reconstruct biological mechanisms that could play a role in the conversion of normal/MCI into AD pathology. This in turn may open the door to novel therapeutic options in the future.