bluuebunny/crossref_metadata_2025_split huggingface dataset:
Observation of an acoustic octupole topological insulator
Authors: Xue Haoran , Ge Yong , Sun Hong-Xiang , Wang Qiang , Jia Ding , Guan Yi-Jun , Yuan Shou-Qi , Chong Yidong , Zhang Baile 
Published: May 2020

AbstractBerry phase associated with energy bands in crystals can lead to quantised observables like quantised dipole polarizations in one-dimensional topological insulators. Recent theories have generalised the concept of quantised dipoles to multipoles, resulting in the discovery of multipole topological insulators which exhibit a hierarchy of multipole topology: a quantised octupole moment in a three-dimensional bulk induces quantised quadrupole moments on its two-dimensional surfaces, which in turn induce quantised dipole moments on one-dimensional hinges. Here, we report on the realisation of an octupole topological insulator in a three-dimensional acoustic metamaterial. We observe zero-dimensional topological corner states, one-dimensional gapped hinge states, two-dimensional gapped surface states, and three-dimensional gapped bulk states, representing the hierarchy of octupole, quadrupole and dipole moments. Conditions for forming a nontrivial octupole moment are demonstrated by comparisons with two different lattice configurations having trivial octupole moments. Our work establishes the multipole topology and its full hierarchy in three-dimensional geometries.
The route to transcription initiation determines the mode of transcriptional bursting in E. coli
Authors: Engl Christoph , Jovanovic Goran , Brackston Rowan D. , Kotta-Loizou Ioly , Buck Martin 
Published: May 2020

Abstract
Transcription is fundamentally noisy, leading to significant heterogeneity across bacterial populations. Noise is often attributed to burstiness, but the underlying mechanisms and their dependence on the mode of promotor regulation remain unclear. Here, we measure E. coli single cell mRNA levels for two stress responses that depend on bacterial sigma factors with different mode of transcription initiation (σ70 and σ54). By fitting a stochastic model to the observed mRNA distributions, we show that the transition from low to high expression of the σ70-controlled stress response is regulated via the burst size, while that of the σ54-controlled stress response is regulated via the burst frequency. Therefore, transcription initiation involving σ54 differs from other bacterial systems, and yields bursting kinetics characteristic of eukaryotic systems.
Vulnerable window of yield strength for swelling-driven fracture of phase-transforming battery materials
Authors: Mesgarnejad Ataollah , Karma Alain 
Published: May 2020

AbstractDespite numerous experimental and theoretical investigations of the mechanical behavior of high-capacity Si and Ge Li-ion battery anodes, our basic understanding of swelling-driven fracture in these materials remains limited. Existing theoretical studies have provided insights into elasto-plastic deformations caused by large volume change phase transformations, but have not modeled fracture explicitly beyond Griffith’s criterion. Here, we use a multi-physics phase-field approach to model self-consistently anisotropic phase transformation, elasto-plastic deformation, and crack initiation and propagation during lithiation of Si nanopillars. Our computational results reveal that fracture occurs within a “vulnerable window” inside the two-dimensional parameter space of yield strength and fracture energy and highlight the importance of taking into account the surface localization of plastic deformation to accurately predict the magnitude of tensile stresses at the onset of fracture. They further demonstrate how the increased robustness of hollow nanopillars can be understood as a direct effect of anode geometry on the size of this vulnerable window. Those insights provide an improved theoretical basis for designing next-generation mechanically stable phase-transforming battery materials undergoing large volume changes.
The SIRS criteria have better performance for predicting infection than qSOFA scores in the emergency department
Authors: Gando Satoshi , Shiraishi Atsushi , Abe Toshikazu , Kushimoto Shigeki , Mayumi Toshihiko , Fujishima Seitaro , Hagiwara Akiyoshi , Shiino Yasukazu , Shiraishi Shin-ichiro , Hifumi Toru , Otomo Yasuhiro , Okamoto Kohji , Sasaki Junichi , Takuma Kiyotsugu , Yamakawa Kazuma ,   The Japanese Association for Acute Medicine (JAAM) Sepsis Prognostication in Intensive Care Unit and Emergency Room (SPICE) (JAAM SPICE) Study Group, Hoshino Atsumi , Shiraishi Atsushi , Abe Toshiaki , Sugita Manabu , Hanaki Yoshihiro , Hagiwara Akiyoshi , Shiraishi Shin-ichiro , Shiino Yasukazu , Harada Masahiro , Yoshihara Hideaki , Takuma Kiyotsugu , Otomo Yasuhiro , Morino Kazuma , Shimizu Yoshihiro , Ishikura Hiroyasu , Hifumi Toru , Deguchi Yoshizumi , Nachi Sho , Gando Satoshi , Okamoto Kohji , Kawakami Masato , Fujishima Seitaro , Sasaki Junichi , Maehara Junichi , Okada Kunihiko , Yamakawa Kazuma , Kiyota Kazuya , Miki Yasuo , Koike Kaoru , Muroya Takashi , Yamashita Hisashi , Mayumi Toshihiko , Anan Hideaki , Kaneko Tadashi , Kittaka Hirotada , Yamaguchi Hiroyuki 
Published: May 2020

AbstractSystemic inflammatory response syndrome (SIRS) reportedly has a low performance for distinguishing infection from non-infection. We explored the distribution of the patients diagnosed by SIRS (SIRS patients) or a quick sequential organ failure assessment (qSOFA) (qSOFA patients) and confirmed the performance of the both for predicting ultimate infection after hospital admission. We retrospectively analyzed the data from a multicenter prospective study. When emergency physicians suspected infection, SIRS or the qSOFA were applied. The area under the receiver operating characteristic curves (AUC) was used to assess the performance of the SIRS and qSOFA for predicting established infection. A total of 1,045 patients were eligible for this study. The SIRS patients accounted for 91.6% of qSOFA patients and they showed a higher rate of final infection than that of non-SIRS patients irrespective of the qSOFA diagnosis. The AUCs for predicting infection with SIRS and a qSOFA were 0.647 and 0.582, respectively. The SIRS significantly predicted an ultimate infection (AUC, 0.675; p = 0.018) in patients who met the SIRS and qSOFA simultaneously. In conclusion, the SIRS patients included almost all qSOFA patients. SIRS showed a better performance for predicting infection for qSOFA in those who met both definitions.
Salivary proteome signatures in the early and middle stages of human pregnancy with term birth outcome
Authors: Dey Amit Kumar , Kumar Bhoj , Singh Abhishek Kumar , Ranjan Prakash , Thiruvengadam Ramachandran , Desiraju Bapu Koundinya , Kshetrapal Pallavi , Wadhwa Nitya , Bhatnagar Shinjini , Rashid Faraz , Malakar Dipankar , Salunke Dinakar M. , Maiti Tushar Kanti ,   GARBH-Ini Study Group*, Das Bhabatosh , Misra Sumit , Nair Balakrish G. , Natchu Uma Chandra Mouli , Rath Satyajit , Sachdeva Kanika , Sopory Shailaja , Singh Amanpreet , Sharma Dharmendra , Bal Vineeta , Maitra Arindam , Majumder Partha P. , Bahl Monika , Sharma Sunita , Mehta Umesh , Sindhu Brahmdeep , Arya Sugandha , Bharti Rekha , Chellani Harish , Mittal Pratima , Ramji Siddarth , Tripathi Reva , Garg Anju , Khurana Ashok , Hari Smriti , Gupta Yashdeep , Tandon Nikhil , Gupta Rakesh 
Published: May 2020

AbstractThe establishment and maintenance of pregnancy in humans proceed through a continuous change of biochemical and biophysical processes. It requires a constant interaction between the fetus and the maternal system. The present prospective study aims to elucidate changes in salivary proteome from the early to middle stages of term pregnancy, and establishing an expressional trajectory for modulated proteins. To date, a comprehensive characterization of the longitudinal salivary proteome in pregnancy has not been performed and it is our immediate interest. In the discovery phase, maternal saliva (N = 20) at 6–13, 18–21, and 26–29 weeks of gestation was analyzed using level-free proteomics (SWATH-MS) approach. The expression levels of 65 proteins were found to change significantly with gestational age and distributed into two distinct clusters with a unique expression trajectory. The results revealed that altered proteins are involved in maternal immune modulation, metabolism, and host defense mechanism. Further, verification of 12 proteins was employed using targeted mass spectrometry (MRM-MS) in a separate subset of saliva (N = 14). The MRM results of 12 selected proteins confirmed a similar expression pattern as in SWATH-MS analysis. Overall, the results not only demonstrate the longitudinal maternal saliva proteome for the first time but also set the groundwork for comparative analysis between term birth and adverse pregnancy outcomes.
The Role of European Starlings (Sturnus vulgaris) in the Dissemination of Multidrug-Resistant Escherichia coli among Concentrated Animal Feeding Operations
Authors: Chandler Jeffrey C. , Anders Jennifer E. , Blouin Nicolas A. , Carlson James C. , LeJeune Jeffrey T. , Goodridge Lawrence D. , Wang Baolin , Day Leslie A. , Mangan Anna M. , Reid Dustin A. , Coleman Shannon M. , Hopken Matthew W. , Bisha Bledar 
Published: May 2020

AbstractAntimicrobial use in livestock production is a driver for the development and proliferation of antimicrobial resistance (AMR). Wildlife interactions with livestock, acquiring associated AMR bacteria and genes, and wildlife’s subsequent dispersal across the landscape are hypothesized to play an important role in the ecology of AMR. Here, we examined priority AMR phenotypes and genotypes of Escherichia coli isolated from the gastrointestinal tracts of European starlings (Sturnus vulgaris) found on concentrated animal feeding operations (CAFOs). European starlings may be present in high numbers on CAFOs (>100,000 birds), interact with urban environments, and can migrate distances exceeding 1,500 km in North America. In this study, 1,477 European starlings from 31 feedlots in five U.S. states were sampled for E. coli resistant to third generation cephalosporins (3G-C) and fluoroquinolones. The prevalence of 3G-C and fluoroquinolone-resistant E. coli was 4% and 10%, respectively. Multidrug resistance in the E. coli isolates collected (n = 236) was common, with the majority of isolates displaying resistance to six or more classes of antibiotics. Genetic analyses of a subset of these isolates identified 94 genes putatively contributing to AMR, including seven class A and C β-lactamases as well as mutations in gyrA and parC recognized to confer resistance to quinolones. Phylogenetic and subtyping assessments showed that highly similar isolates (≥99.4% shared core genome, ≥99.6% shared coding sequence) with priority AMR were found in birds on feedlots separated by distances exceeding 150 km, suggesting that European starlings could be involved in the interstate dissemination of priority AMR bacteria.
Structure evolution during deposition and thermal annealing of amorphous carbon ultrathin films investigated by molecular dynamics simulations
Authors: Wang Shengxi , Komvopoulos Kyriakos 
Published: May 2020

AbstractThe evolution of the structure of amorphous carbon (a-C) films during deposition and thermal annealing is of significant interest from both the materials science and application perspectives. However, despite the voluminous literature of studies dealing with the deposition and physical properties of a-C films, basic understanding of the structure evolution due to phase change during film growth and heating is fairly sparse and empirical, presumably due to the lack of high-resolution instruments that can probe structural changes at the atomic and molecular levels in real time. Molecular dynamics (MD) is a powerful computational method for studying atomic/molecular-scale movement and interactions. Thus, the objective of this study was to perform MD simulations that provide insight into changes in the structure of ultrathin a-C films during deposition and annealing. Simulation results reveal a multi-layer film structure, even for a-C films as thin as ~20 Å, the existence of a deposition energy that yields a-C films with the highest sp3 content, the transient and steady-state stages of the structure evolution during annealing at different temperatures, and the changes in the hybridization state (mainly in the bulk layer) encountered during annealing at elevated temperatures. The MD results of this study are of particular importance to applications where the deposition conditions and operation temperature affect the structure and, in turn, the physical properties of ultrathin a-C films used as protective overcoats.
Dyspnea perception during the inspiratory resistive loads test in obese subjects waiting bariatric surgery
Authors: Tomasini Karina , Ziegler Bruna , Sanches Paulo Roberto Stefani , da Silva Junior Danton Pereira , Thomé Paulo Ricardo , Dalcin Paulo de Tarso Roth 
Published: May 2020

AbstractIdentification of low dyspnea perception is relevant, since this condition is significantly associated with worse outcomes. We investigated dyspnea perception during the inspiratory resistive loads test on obese subjects waiting bariatric surgery in comparison with normal subjects. Secondarily, we analysed the proportion of obese subjects with low, moderate and high dyspnea perception. This observational study included subjects with body mass index (BMI) ≥ 35 kg/m2, compared to healthy subjects with BMI ≥ 18 and <25 kg/m2. Subject underwent clinical evaluation, inspiratory test with progressive resistive loads and spirometry. We studied 23 obese subjects (mean BMI = 51.9 ± 9.3 kg/m2) and 25 normal subjects (mean BMI = 24.3 ± 2.3 kg/m2). With the increase magnitude of resistive loads there was a significant increase in dyspnea score (p < 0.001) and progressive increase of the generated inspiratory pressure (p < 0.001), but there was no difference between the groups in terms of dyspnea score (p = 0.191) and no interaction effect (p = 0.372). Among the obese subjects, 4 individuals were classified as low perception, 11 as moderate and 8 as high. In conclusion, the degree of dyspnea perception during the inspiratory progressive resistive loads test did not differ between obese and normal subjects. Among obese subjects, only 17% were classified as low dyspnea perception.
Distinguishing the taphonomic signature of wolves from humans and other predators on small prey assemblages
Authors: Lloveras Lluís , Nadal Jordi , Fullola Josep Maria 
Published: May 2020

AbstractThe study of human subsistence strategies in prehistoric hunter-gatherer communities is essential to understanding the evolution of human behaviour. An important topic of interest is the expansion of dietary breadth, resulting in the procurement of a larger number of small game species. However, to make accurate interpretations of human subsistence, the correct identification of the agents responsible for archaeofaunal assemblages is crucial, and actualistic studies that establish the taphonomic signature of the different predators are indispensable. Despite being one of the most ubiquitous carnivores in prehistoric archaeological sites, the role of wolves (Canis lupus) as agents responsible for small-prey accumulations has never been examined. The aims of this study are to analyse the taphonomic patterns left by wolves on rabbit remains and to put forward a series of criteria that can help distinguish assemblages produced by this carnivore from those accumulated by people or by other predators. Our results reveal that wolves ingest and consume the whole rabbit carcass, with the consequence that all rabbit remains accumulated by wolves come from the scats. The referential framework provided in this study will make it possible to discriminate wolves as agents of fossil rabbit accumulations.
Digital Proxy of a Bio-Reactor (DIYBOT) combines sensor data and data analytics to improve greywater treatment and wastewater management systems
Authors: McLamore Eric S. , Huffaker Ray , Shupler Matthew , Ward Katelyn , Datta Shoumen Palit Austin , Katherine Banks M. , Casaburi Giorgio , Babilonia Joany , Foster Jamie S. 
Published: May 2020

AbstractTechnologies to treat wastewater in decentralized systems are critical for sustainable development. Bioreactors are suitable for low-energy removal of inorganic and organic compounds, particularly for non-potable applications where a small footprint is required. One of the main problems associated with bioreactor use is sporadic spikes of chemical toxins, including nanoparticles. Here, we describe the development of DIYBOT (Digital Proxy of a Bio-Reactor), which enables remote monitoring of bioreactors and uses the data to inform decisions related to systems management. To test DIYBOT, a household-scale membrane aerated bioreactor with real-time water quality sensors was used to treat household greywater simulant. After reaching steady-state, silver nanoparticles (AgNP) representative of the mixture found in laundry wastewater were injected into the system to represent a chemical contamination. Measurements of carbon metabolism, effluent water quality, biofilm sloughing rate, and microbial diversity were characterized after nanoparticle exposure. Real-time sensor data were analyzed to reconstruct phase-space dynamics and extrapolate a phenomenological digital proxy to evaluate system performance. The management implication of the stable-focus dynamics, reconstructed from observed data, is that the bioreactor self-corrects in response to contamination spikes at AgNP levels below 2.0 mg/L. DIYBOT may help reduce the frequency of human-in-the-loop corrective management actions for wastewater processing.
Performance of four platforms for KRAS mutation detection in plasma cell-free DNA: ddPCR, Idylla, COBAS z480 and BEAMing
Authors: Vessies D. C. L. , Greuter M. J. E. , van Rooijen K. L. , Linders T. C. , Lanfermeijer M. , Ramkisoensing K. L. , Meijer G. A. , Koopman M. , Coupé V. M. H. , Vink G. R. , Fijneman R. J. A. , van den Broek D. 
Published: May 2020

AbstractMultiple platforms are commercially available for the detection of circulating cell-free tumour DNA (ctDNA) from liquid biopsies. Since platforms have different input and output variables, deciding what platform to use for a given clinical or research question can be daunting. This study aimed to provide insight in platform selection criteria by comparing four commercial platforms that detect KRAS ctDNA hotspot mutations: Bio-Rad droplet digital PCR (ddPCR), BioCartis Idylla, Roche COBAS z480 and Sysmex BEAMing. Platform sensitivities were determined using plasma samples from metastatic colorectal cancer (mCRC) patients and synthetic reference samples, thereby eliminating variability in amount of plasma analysed and ctDNA isolation methods. The prevalence of KRAS nucleotide alterations was set against platform-specific breadth of target. Platform comparisons revealed that ddPCR and BEAMing detect more KRAS mutations amongst mCRC patients than Idylla and COBAS z480. Maximum sample throughput was highest for ddPCR and COBAS z480. Total annual costs were highest for BEAMing and lowest for Idylla and ddPCR. In conclusion, when selecting a platform for detection of ctDNA hotspot mutations the desired test sensitivity, breadth of target, maximum sample throughput, and total annual costs are critical factors that should be taken into consideration. Based on the results of this study, laboratories will be able to select the optimal platform for their needs.
Homoplastic single nucleotide polymorphisms contributed to phenotypic diversity in Mycobacterium tuberculosis
Authors: Tantivitayakul Pornpen , Ruangchai Wuthiwat , Juthayothin Tada , Smittipat Nat , Disratthakit Areeya , Mahasirimongkol Surakameth , Viratyosin Wasna , Tokunaga Katsushi , Palittapongarnpim Prasit 
Published: May 2020

AbstractHomoplastic mutations are mutations independently occurring in different clades of an organism. The homoplastic changes may be a result of convergence evolution due to selective pressures. Reports on the analysis of homoplastic mutations in Mycobacterium tuberculosis have been limited. Here we characterized the distribution of homoplastic single nucleotide polymorphisms (SNPs) among genomes of 1,170 clinical M. tuberculosis isolates. They were present in all functional categories of genes, with pe/ppe gene family having the highest ratio of homoplastic SNPs compared to the total SNPs identified in the same functional category. Among the pe/ppe genes, the homoplastic SNPs were common in a relatively small number of homologous genes, including ppe18, the protein of which is a component of a promising candidate vaccine, M72/AS01E. The homoplastic SNPs in ppe18 were particularly common among M. tuberculosis Lineage 1 isolates, suggesting the need for caution in extrapolating the results of the vaccine trial to the population where L1 is endemic in Asia. As expected, homoplastic SNPs strongly associated with drug resistance. Most of these mutations are already well known. However, a number of novel mutations associated with streptomycin resistance were identified, which warrants further investigation. A SNP in the intergenic region upstream of Rv0079 (DATIN) was experimentally shown to increase transcriptional activity of the downstream gene, suggesting that intergenic homoplastic SNPs should have effects on the physiology of the bacterial cells. Our study highlights the potential of homoplastic mutations to produce phenotypic changes. Under selective pressure and during interaction with the host, homoplastic mutations may confer advantages to M. tuberculosis and deserve further characterization.
Composite Hydrogel Model of Cartilage Predicts Its Load-Bearing Ability
Authors: Horkay Ferenc , Basser Peter J. 
Published: May 2020

AbstractArticular cartilage is a load-bearing tissue found in animal and human joints. It is a composite gel-like material in which a fibrous collagen network encapsulates large proteoglycan assemblies that imbibe fluid and “inflate” the network. Here we describe a composite hydrogel consisting of a cross-linked polyvinyl alcohol matrix filled with poly(acrylic acid) microparticles that mimics functional properties and biomechanical behavior of cartilage. The swelling and mechanical behaviors of this biomimetic model system are strikingly similar to that of human cartilage. The development of synthetic composite gel-based articular cartilage analog suggests new avenues to explore material properties, and their change in disease and degeneration, as well as novel strategies for developing composite tissue-engineered cartilage constructs for regenerative medicine applications.
Behavioural effects of the common brain-infecting parasite Pseudoloma neurophilia in laboratory zebrafish (Danio rerio)
Authors: Midttun Helene L. E. , Vindas Marco A. , Nadler Lauren E. , Øverli Øyvind , Johansen Ida B. 
Published: May 2020

AbstractResearch conducted on model organisms may be biased due to undetected pathogen infections. Recently, screening studies discovered high prevalence of the microsporidiumPseudoloma neurophiliain zebrafish (Danio rerio) facilities. This spore-forming unicellular parasite aggregates in brain regions associated with motor function and anxiety, and despite its high occurrence little is known about how sub-clinical infection affects behaviour. Here, we assessed howP. neurophiliainfection alters the zebrafish´s response to four commonly used neurobehavioral tests, namely: mirror biting, open field, light/dark preference and social preference, used to quantify aggression, exploration, anxiety, and sociability. Although sociability and aggression remained unaltered, infected hosts exhibited reduced activity, elevated rates of freezing behaviour, and sex-specific effects on exploration. These results indicate that caution is warranted in the interpretation of zebrafish behaviour, particularly since in most cases infection status is unknown. This highlights the importance of comprehensive monitoring procedures to detect sub-clinical infections in laboratory animals.