bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adaptive particle representation of fluorescence microscopy images
Authors: Cheeseman Bevan L. , Günther Ulrik , Gonciarz Krzysztof , Susik Mateusz , Sbalzarini Ivo F. 
Published: November 2018

AbstractModern microscopes create a data deluge with gigabytes of data generated each second, and terabytes per day. Storing and processing this data is a severe bottleneck, not fully alleviated by data compression. We argue that this is because images are processed as grids of pixels. To address this, we propose a content-adaptive representation of fluorescence microscopy images, the Adaptive Particle Representation (APR). The APR replaces pixels with particles positioned according to image content. The APR overcomes storage bottlenecks, as data compression does, but additionally overcomes memory and processing bottlenecks. Using noisy 3D images, we show that the APR adaptively represents the content of an image while maintaining image quality and that it enables orders of magnitude benefits across a range of image processing tasks. The APR provides a simple and efficient content-aware representation of fluosrescence microscopy images.
Stress-induced formation of cell wall-deficient cells in filamentous actinomycetes
Authors: Ramijan Karina , Ultee Eveline , Willemse Joost , Zhang Zheren , Wondergem Joeri A. J. , van der Meij Anne , Heinrich Doris , Briegel Ariane , van Wezel Gilles P. , Claessen Dennis 
Published: November 2018

AbstractThe cell wall is a shape-defining structure that envelopes almost all bacteria and protects them from environmental stresses. Bacteria can be forced to grow without a cell wall under certain conditions that interfere with cell wall synthesis, but the relevance of these wall-less cells (known as L-forms) is unclear. Here, we show that several species of filamentous actinomycetes have a natural ability to generate wall-deficient cells in response to hyperosmotic stress, which we call S-cells. This wall-deficient state is transient, as S-cells are able to switch to the normal mycelial mode of growth. However, prolonged exposure of S-cells to hyperosmotic stress yields variants that are able to proliferate indefinitely without their cell wall, similarly to L-forms. We propose that formation of wall-deficient cells in actinomycetes may serve as an adaptation to osmotic stress.
Spatially and functionally distinct subclasses of breast cancer-associated fibroblasts revealed by single cell RNA sequencing
Authors: Bartoschek Michael , Oskolkov Nikolay , Bocci Matteo , Lövrot John , Larsson Christer , Sommarin Mikael , Madsen Chris D. , Lindgren David , Pekar Gyula , Karlsson Göran , Ringnér Markus , Bergh Jonas , Björklund Åsa , Pietras Kristian 
Published: November 2018

AbstractCancer-associated fibroblasts (CAFs) are a major constituent of the tumor microenvironment, although their origin and roles in shaping disease initiation, progression and treatment response remain unclear due to significant heterogeneity. Here, following a negative selection strategy combined with single-cell RNA sequencing of 768 transcriptomes of mesenchymal cells from a genetically engineered mouse model of breast cancer, we define three distinct subpopulations of CAFs. Validation at the transcriptional and protein level in several experimental models of cancer and human tumors reveal spatial separation of the CAF subclasses attributable to different origins, including the peri-vascular niche, the mammary fat pad and the transformed epithelium. Gene profiles for each CAF subtype correlate to distinctive functional programs and hold independent prognostic capability in clinical cohorts by association to metastatic disease. In conclusion, the improved resolution of the widely defined CAF population opens the possibility for biomarker-driven development of drugs for precision targeting of CAFs.
The origins of malaria artemisinin resistance defined by a genetic and transcriptomic background
Authors: Zhu Lei , Tripathi Jaishree , Rocamora Frances Maureen , Miotto Olivo , van der Pluijm Rob , Voss Till S. , Mok Sachel , Kwiatkowski Dominic P. , Nosten François , Day Nicholas P. J. , White Nicholas J. , Dondorp Arjen M. , Bozdech Zbynek ,   Tracking Resistance to Artemisinin Collaboration I, Phyo Aung Pyae , Ashley Elizabeth A. , Smithuis Frank , Lin Khin , Tun Kyaw Myo , Faiz M Abul , Mayxay Mayfong , Dhorda Mehul , Thuy-Nhien Nguyen Thanh , Newton Paul N. , Pukrittayakamee Sasithon , Hlaing Tin M. , Hien Tran Tinh , Htut Ye 
Published: November 2018

AbstractThe predisposition of parasites acquiring artemisinin resistance still remains unclear beyond the mutations in Pfk13 gene and modulation of the unfolded protein response pathway. To explore the chain of casualty underlying artemisinin resistance, we reanalyze 773 P. falciparum isolates from TRACI-study integrating TWAS, GWAS, and eQTL analyses. We find the majority of P. falciparum parasites are transcriptomically converged within each geographic site with two broader physiological profiles across the Greater Mekong Subregion (GMS). We report 8720 SNP-expression linkages in the eastern GMS parasites and 4537 in the western. The minimal overlap between them suggests differential gene regulatory networks facilitating parasite adaptations to their unique host environments. Finally, we identify two genetic and physiological backgrounds associating with artemisinin resistance in the GMS, together with a farnesyltransferase protein and a thioredoxin-like protein which may act as vital intermediators linking the Pfk13 C580Y mutation to the prolonged parasite clearance time.
Transcriptomic landscape of the blastema niche in regenerating adult axolotl limbs at single-cell resolution
Authors: Leigh Nicholas D. , Dunlap Garrett S. , Johnson Kimberly , Mariano Rachelle , Oshiro Rachel , Wong Alan Y. , Bryant Donald M. , Miller Bess M. , Ratner Alex , Chen Andy , Ye William W. , Haas Brian J. , Whited Jessica L. 
Published: November 2018

AbstractRegeneration of complex multi-tissue structures, such as limbs, requires the coordinated effort of multiple cell types. In axolotl limb regeneration, the wound epidermis and blastema have been extensively studied via histology, grafting, and bulk-tissue RNA-sequencing. However, defining the contributions of these tissues is hindered due to limited information regarding the molecular identity of the cell types in regenerating limbs. Here we report unbiased single-cell RNA-sequencing on over 25,000 cells from axolotl limbs and identify a plethora of cellular diversity within epidermal, mesenchymal, and hematopoietic lineages in homeostatic and regenerating limbs. We identify regeneration-induced genes, develop putative trajectories for blastema cell differentiation, and propose the molecular identity of fibroblast-like blastema progenitor cells. This work will enable application of molecular techniques to assess the contribution of these populations to limb regeneration. Overall, these data allow for establishment of a putative framework for adult axolotl limb regeneration.
Aqueous thermogalvanic cells with a high Seebeck coefficient for low-grade heat harvest
Authors: Duan Jiangjiang , Feng Guang , Yu Boyang , Li Jia , Chen Ming , Yang Peihua , Feng Jiamao , Liu Kang , Zhou Jun 
Published: November 2018

AbstractThermogalvanic cells offer a cheap, flexible and scalable route for directly converting heat into electricity. However, achieving a high output voltage and power performance simultaneously from low-grade thermal energy remains challenging. Here, we introduce strong chaotropic cations (guanidinium) and highly soluble amide derivatives (urea) into aqueous ferri/ferrocyanide ([Fe(CN)6]4−/[Fe(CN)6]3−) electrolytes to significantly boost their thermopowers. The corresponding Seebeck coefficient and temperature-insensitive power density simultaneously increase from 1.4 to 4.2 mV K−1 and from 0.4 to 1.1 mW K−2 m−2, respectively. The results reveal that guanidinium and urea synergistically enlarge the entropy difference of the redox couple and significantly increase the Seebeck effect. As a demonstration, we design a prototype module that generates a high open-circuit voltage of 3.4 V at a small temperature difference of 18 K. This thermogalvanic cell system, which features high Seebeck coefficient and low cost, holds promise for the efficient harvest of low-grade thermal energy.
Single-cell mutation identification via phylogenetic inference
Authors: Singer Jochen , Kuipers Jack , Jahn Katharina , Beerenwinkel Niko 
Published: November 2018

AbstractReconstructing the evolution of tumors is a key aspect towards the identification of appropriate cancer therapies. The task is challenging because tumors evolve as heterogeneous cell populations. Single-cell sequencing holds the promise of resolving the heterogeneity of tumors; however, it has its own challenges including elevated error rates, allelic drop-out, and uneven coverage. Here, we develop a new approach to mutation detection in individual tumor cells by leveraging the evolutionary relationship among cells. Our method, called SCIΦ, jointly calls mutations in individual cells and estimates the tumor phylogeny among these cells. Employing a Markov Chain Monte Carlo scheme enables us to reliably call mutations in each single cell even in experiments with high drop-out rates and missing data. We show that SCIΦ outperforms existing methods on simulated data and applied it to different real-world datasets, namely a whole exome breast cancer as well as a panel acute lymphoblastic leukemia dataset.
Genome wide association analysis in a mouse advanced intercross line
Authors: Gonzales Natalia M. , Seo Jungkyun , Hernandez Cordero Ana I. , St. Pierre Celine L. , Gregory Jennifer S. , Distler Margaret G. , Abney Mark , Canzar Stefan , Lionikas Arimantas , Palmer Abraham A. 
Published: November 2018

AbstractThe LG/J x SM/J advanced intercross line of mice (LG x SM AIL) is a multigenerational outbred population. High minor allele frequencies, a simple genetic background, and the fully sequenced LG and SM genomes make it a powerful population for genome-wide association studies. Here we use 1,063 AIL mice to identify 126 significant associations for 50 traits relevant to human health and disease. We also identify thousands of cis- and trans-eQTLs in the hippocampus, striatum, and prefrontal cortex of ~200 mice. We replicate an association between locomotor activity and Csmd1, which we identified in an earlier generation of this AIL, and show that Csmd1 mutant mice recapitulate the locomotor phenotype. Our results demonstrate the utility of the LG x SM AIL as a mapping population, identify numerous novel associations, and shed light on the genetic architecture of mammalian behavior.
Unifying host-associated diversification processes using butterfly–plant networks
Authors: Braga Mariana P. , Guimarães Paulo R. , Wheat Christopher W. , Nylin Sören , Janz Niklas 
Published: November 2018

AbstractExplaining the exceptional diversity of herbivorous insects is an old problem in evolutionary ecology. Here we focus on the two prominent hypothesised drivers of their diversification, radiations after major host switch or variability in host use due to continuous probing of new hosts. Unfortunately, current methods cannot distinguish between these hypotheses, causing controversy in the literature. Here we present an approach combining network and phylogenetic analyses, which directly quantifies support for these opposing hypotheses. After demonstrating that each hypothesis produces divergent network structures, we then investigate the contribution of each to diversification in two butterfly families: Pieridae and Nymphalidae. Overall, we find that variability in host use is essential for butterfly diversification, while radiations following colonisation of a new host are rare but can produce high diversity. Beyond providing an important reconciliation of alternative hypotheses for butterfly diversification, our approach has potential to test many other hypotheses in evolutionary biology.
The proton and metal binding sites responsible for the pH-dependent green-red bioluminescence color tuning in firefly luciferases
Authors: Viviani Vadim R. , Gabriel Gabriele V. M. , Bevilaqua Vanessa R. , Simões A. F. , Hirano T. , Lopes-de-Oliveira P. S. 
Published: November 2018

AbstractFirefly luciferases produce yellow-green light under physiological and alkaline conditions, however at acidic pH, higher temperatures or in the presence of heavy metals the color changes to red, a property called pH-sensitivity. Despite many decades of studies, the proton and metal binding sites responsible for pH-sensitivity remain enigmatic. Previously we suggested that the salt bridge E311/R337 keeps a closed conformation of the luciferin phenolate binding site. Here we further investigated the effect of this salt bridge and mutations of the neighbor residues H310 and E/N354, on metal and pH-sensitivity of firefly luciferases emitting distinct bioluminescence colors (Cratomorphus distinctus: 548 nm;Macrolampissp2: 569 nm). The substitutions of H310 and E/N354 modulate metal sensitivity, whereas the carboxylate of E311 may work as the catalytic base essential for green bioluminescence and pH-sensitivity. Modeling studies showed that H310, E311 and E354 side-chains coordinate Zinc, constituting the metal binding site and the pH-sensor. Electrostatic potential and pKa calculations suggest that the external couple H310/E354 is affected by pH, whereas E311/R337 make a stabilized internal pair which retains excited oxyluciferin ejected proton near its phenolate group into a high energy state, promoting yellow-green bioluminescence. Protonation or metal binding weaken these electrostatic gates and their ability to retain the excited oxyluciferin released proton near its phenolate, promoting red light emission.
Reconstructing the evolutionary history of F420-dependent dehydrogenases
Authors: Mascotti M. Laura , Kumar Hemant , Nguyen Quoc-Thai , Ayub Maximiliano Juri , Fraaije Marco W. 
Published: November 2018

AbstractDuring the last decade the number of characterized F420-dependent enzymes has significantly increased. Many of these deazaflavoproteins share a TIM-barrel fold and are structurally related to FMN-dependent luciferases and monooxygenases. In this work, we traced the origin and evolutionary history of the F420-dependent enzymes within the luciferase-like superfamily. By a thorough phylogenetic analysis we inferred that the F420-dependent enzymes emerged from a FMN-dependent common ancestor. Furthermore, the data show that during evolution, the family of deazaflavoproteins split into two well-defined groups of enzymes: the F420-dependent dehydrogenases and the F420-dependent reductases. By such event, the dehydrogenases specialized in generating the reduced deazaflavin cofactor, while the reductases employ the reduced F420 for catalysis. Particularly, we focused on investigating the dehydrogenase subfamily and demonstrated that this group diversified into three types of dehydrogenases: the already known F420-dependent glucose-6-phosphate dehydrogenases, the F420-dependent alcohol dehydrogenases, and the sugar-6-phosphate dehydrogenases that were identified in this study. By reconstructing and experimentally characterizing ancestral and extant representatives of F420-dependent dehydrogenases, their biochemical properties were investigated and compared. We propose an evolutionary path for the emergence and diversification of the TIM-barrel fold F420-dependent dehydrogenases subfamily.
Antimicrobial resistance prediction and phylogenetic analysis of Neisseria gonorrhoeae isolates using the Oxford Nanopore MinION sequencer
Authors: Golparian Daniel , Donà Valentina , Sánchez-Busó Leonor , Foerster Sunniva , Harris Simon , Endimiani Andrea , Low Nicola , Unemo Magnus 
Published: November 2018

AbstractAntimicrobial resistance (AMR) in Neisseria gonorrhoeae is common, compromising gonorrhoea treatment internationally. Rapid characterisation of AMR strains could ensure appropriate and personalised treatment, and support identification and investigation of gonorrhoea outbreaks in nearly real-time. Whole-genome sequencing is ideal for investigation of emergence and dissemination of AMR determinants, predicting AMR, in the gonococcal population and spread of AMR strains in the human population. The novel, rapid and revolutionary long-read sequencer MinION is a small hand-held device that generates bacterial genomes within one day. However, accuracy of MinION reads has been suboptimal for many objectives and the MinION has not been evaluated for gonococci. In this first MinION study for gonococci, we show that MinION-derived sequences analysed with existing open-access, web-based sequence analysis tools are not sufficiently accurate to identify key gonococcal AMR determinants. Nevertheless, using an in house-developed CLC Genomics Workbench including de novo assembly and optimised BLAST algorithms, we show that 2D ONT-derived sequences can be used for accurate prediction of decreased susceptibility or resistance to recommended antimicrobials in gonococcal isolates. We also show that the 2D ONT-derived sequences are useful for rapid phylogenomic-based molecular epidemiological investigations, and, in hybrid assemblies with Illumina sequences, for producing contiguous assemblies and finished reference genomes.
Facial expression as a potential measure of both intent and emotion
Authors: Camerlink Irene , Coulange Estelle , Farish Marianne , Baxter Emma M. , Turner Simon P. 
Published: November 2018

AbstractFacial expressions convey information on emotion, physical sensations, and intent. The much debated theories that facial expressions can be emotions or signals of intent have largely remained separated in animal studies. Here we integrate these approaches with the aim to 1) investigate whether pigs may use facial expressions as a signal of intent and; 2) quantify differences in facial metrics between different contexts of potentially negative emotional state. Facial metrics of 38 pigs were recorded prior to aggression, during aggression and during retreat from being attacked in a dyadic contest. Ear angle, snout ratio (length/height) and eye ratio from 572 images were measured. Prior to the occurrence of aggression, eventual initiators of the first bite had a smaller snout ratio and eventual winners showed a non-significant tendency to have their ears forward more than eventual losers. During aggression, pigs’ ears were more forward orientated and their snout ratio was smaller. During retreat, pigs’ ears were backwards and their eyes open less. The results suggest that facial expressions can communicate aggressive intent related to fight success, and that facial metrics can convey information about emotional responses to contexts involving aggression and fear.
Seasonal Deposition and Lifting of Dust on Mars as Observed by the Curiosity Rover
Authors: Vicente-Retortillo Á. , Martínez G. M. , Renno N. , Newman C. E. , Ordonez-Etxeberria I. , Lemmon M. T. , Richardson M. I. , Hueso R. , Sánchez-Lavega A. 
Published: November 2018

AbstractIn situ measurements by the Curiosity rover provide a unique opportunity for studying the effects of dust on assets placed at the surface of Mars. Here we use in situ measurements of solar UV radiation to quantify the seasonal and interannual variability of dust accumulation on the sensor on the rover deck. We show that the amount of dust accumulated on the sensor follows a seasonal cycle, with net dust removal during the perihelion season until Ls ~ 300°, and net dust deposition until the end of the aphelion season (Ls ~ 300°–180°). We use independent in situ measurements of atmospheric opacity and pressure perturbations in combination with numerical modeling, showing that daytime convective vortices and nighttime winds are likely responsible for the seasonal dust cleaning, with the role of nighttime wind being more important in Martian Year (MY) 32 than in MY 33 and that of daytime convective vortices being more important in MY 33 than in MY 32. The fact that the UV sensor is cleaner in MY 33 than in MY 32 indicates that natural cleaning events make solar energy an excellent candidate to power extended (multiannual) Mars missions at similar latitudes as the Curiosity rover.
Left Ventricular Diastolic Dysfunction in a Rat Model of Diabetic Cardiomyopathy using ECG-gated 18F-FDG PET
Authors: Werner Rudolf A. , Eissler Christoph , Hayakawa Nobuyuki , Arias-Loza Paula , Wakabayashi Hiroshi , Javadi Mehrbod S. , Chen Xinyu , Shinaji Tetsuya , Lapa Constantin , Pelzer Theo , Higuchi Takahiro 
Published: November 2018

AbstractIn diabetic cardiomyopathy, left ventricular (LV) diastolic dysfunction is one of the earliest signs of cardiac involvement prior to the definitive development of heart failure (HF). We aimed to explore the LV diastolic function using electrocardiography (ECG)-gated18F-fluorodeoxyglucose positron emission tomography (18F-FDG PET) imaging beyond the assessment of cardiac glucose utilization in a diabetic rat model. ECG-gated18F-FDG PET imaging was performed in a rat model of type 2 diabetes (ZDF fa/fa) and ZL control rats at age of 13 weeks (n = 6, respectively). Under hyperinsulinemic-euglycemic clamp to enhance cardiac activity,18F-FDG was administered and subsequently, list-mode imaging using a dedicated small animal PET system with ECG signal recording was performed. List-mode data were sorted and reconstructed into tomographic images of 16 frames per cardiac cycle. Left ventricular functional parameters (systolic: LV ejection fraction (EF), heart rate (HR) vs. diastolic: peak filling rate (PFR)) were obtained using an automatic ventricular edge detection software. No significant difference in systolic function could be obtained (ZL controls vs. ZDF rats: LVEF, 62.5 ± 4.2 vs. 59.4 ± 4.5%; HR: 331 ± 35 vs. 309 ± 24 bpm; n.s., respectively). On the contrary, ECG-gated PET imaging showed a mild but significant decrease of PFR in the diabetic rats (ZL controls vs. ZDF rats: 12.1 ± 0.8 vs. 10.2 ± 1 Enddiastolic Volume/sec, P < 0.01). Investigating a diabetic rat model, ECG-gated18F-FDG PET imaging detected LV diastolic dysfunction while systolic function was still preserved. This might open avenues for an early detection of HF onset in high-risk type 2 diabetes before cardiac symptoms become apparent.
Inactivation of Pseudomonas aeruginosa and Methicillin-resistant Staphylococcus aureus in an open water system with ozone generated by a compact, atmospheric DBD plasma reactor
Authors: Choudhury Bhaswati , Portugal Sherlie , Mastanaiah Navya , Johnson Judith A. , Roy Subrata 
Published: November 2018

AbstractOzone is a well-known disinfecting agent that is used as an alternative for chlorine in many applications, including water decontamination. However, the utility of ozone in water decontamination is limited by high electrical power consumption and expensive, bulky equipment associated with ozone generation. This study investigates the effectiveness of a lightweight, compact surface dielectric barrier discharge (SDBD) reactor as an ozone generator to inactivatePseudomonas aeruginosaand methicillin-resistantStaphylococcus aureus(MRSA) in an open water system. Experimental details are provided for ozone generation technique, mixing method, ozone concentrations in air and water, and input energy required to produce adequate ozone concentrations for bacterial inactivation in a contaminated, open water system. Specifically, an active plasma module (APM) reactor system of size 48 cubic centimeters, weighing 55 grams, with a maximum ozone yield of 68.6 g/KWh was used in atmospheric conditions as the source of ozone along with an air pump and a diffusion stone for mixing the ozone in water. Over 4-log reduction inP. aeruginosaconcentration was achieved in 4 minutes with 0.1 mg/L ozone concentration in an open water system using 8.8 ± 1.48 J input energy. Also, over 5-log reduction in MRSA concentration was achieved in 2 minutes with 0.04 mg/L ozone concentration in an open water system using 4.4 ± 0.74 J input energy.