bluuebunny/crossref_metadata_2025_split huggingface dataset:
Formation of stable and responsive collective states in suspensions of active colloids
Authors: Bäuerle Tobias , Löffler Robert C. , Bechinger Clemens 
Published: May 2020

AbstractMany animal species organise into disordered swarms, polarised flocks or swirls to protect from predators or optimise foraging. Previous studies suggest that such collective states are related to a critical point, which could explain their balance between robustness to noise and high responsiveness regarding external perturbations. Here we provide experimental evidence for this idea by investigating the stability of swirls formed by light-responsive active colloids which adjust their individual motion to positions and orientations of neighbours. Because their behaviour can be precisely tuned, controlled changes between different collective states can be achieved. During the transition between stable swirls and swarms we observe a maximum of the group’s susceptibility indicating the vicinity of a critical point. Our results support the idea of system-independent organisation principles of collective states and provide useful strategies for the realisation of responsive yet stable ensembles in microrobotic systems.
Epithelial plasticity can generate multi-lineage phenotypes in human and murine bladder cancers
Authors: Sfakianos John P. , Daza Jorge , Hu Yang , Anastos Harry , Bryant Geoffrey , Bareja Rohan , Badani Ketan K. , Galsky Matthew D. , Elemento Olivier , Faltas Bishoy M. , Mulholland David J. 
Published: May 2020

AbstractTumor heterogeneity is common in cancer, however recent studies have applied single gene expression signatures to classify bladder cancers into distinct subtypes. Such stratification assumes that a predominant transcriptomic signature is sufficient to predict progression kinetics, patient survival and treatment response. We hypothesize that such static classification ignores intra-tumoral heterogeneity and the potential for cellular plasticity occurring during disease development. We have conducted single cell transcriptome analyses of mouse and human model systems of bladder cancer and show that tumor cells with multiple lineage subtypes not only cluster closely together at the transcriptional level but can maintain concomitant gene expression of at least one mRNA subtype. Functional studies reveal that tumor initiation and cellular plasticity can initiate from multiple lineage subtypes. Collectively, these data suggest that lineage plasticity may contribute to innate tumor heterogeneity, which in turn carry clinical implications regarding the classification and treatment of bladder cancer.
Constructing chiral bicyclo[3.2.1]octanes via palladium-catalyzed asymmetric tandem Heck/carbonylation desymmetrization of cyclopentenes
Authors: Yuan Zhenbo , Zeng Yuye , Feng Ziwen , Guan Zhe , Lin Aijun , Yao Hequan 
Published: May 2020

AbstractTransition-metal-catalyzed tandem Heck/carbonylation reaction has emerged as a powerful tool for the synthesis of structurally diverse carbonyl molecules, as well as natural products and pharmaceuticals. However, the asymmetric version was rarely reported, and remains a challenging topic. Herein, we describe a palladium-catalyzed asymmetric tandem Heck/carbonylation desymmetrization of cyclopentenes. Alcohols, phenols and amines are employed as versatile coupling reagents for the construction of multifunctional chiral bicyclo[3.2.1]octanes with one all-carbon quaternary and two tertiary carbon stereogenic centers in high diastereo- and enantioselectivities. This study represents an important progress in both the asymmetric tandem Heck/carbonylation reactions and enantioselective difunctionalization of internal alkenes.
Density-dependence tips the change of plant–plant interactions under environmental stress
Authors: Zhang Ruichang , Tielbörger Katja 
Published: May 2020

AbstractFacilitation studies typically compare plants under differential stress levels with and without neighbors, while the density of neighbors has rarely been addressed. However, recent empirical studies indicate that facilitation may be density-dependent too and peak at intermediate neighbor densities. Here, we propose a conceptual model to incorporate density-dependence into theory about changes of plant–plant interactions under stress. To test our predictions, we combine an individual-based model incorporating both facilitative response and effect, with an experiment using salt stress andArabidopsis thaliana. Theoretical and experimental results are strikingly consistent: (1) the intensity of facilitation peaks at intermediate density, and this peak shifts to higher densities with increasing stress; (2) this shift further modifies the balance between facilitation and competition such that the stress-gradient hypothesis applies only at high densities. Our model suggests that density-dependence must be considered for predicting plant–plant interactions under environmental change.
Glycopeptide epitope facilitates HIV-1 envelope specific humoral immune responses by eliciting T cell help
Authors: Sun Lina , Paschall Amy V. , Middleton Dustin R. , Ishihara Mayumi , Ozdilek Ahmet , Wantuch Paeton L. , Aceil Javid , Duke Jeremy A. , LaBranche Celia C. , Tiemeyer Michael , Avci Fikri Y. 
Published: May 2020

AbstractThe inherent molecular complexity of human pathogens requires that mammals evolved an adaptive immune system equipped to handle presentation of non-conventional MHC ligands derived from disease-causing agents, such as HIV-1 envelope (Env) glycoprotein. Here, we report that a CD4+ T cell repertoire recognizes a glycopeptide epitope on gp120 presented by MHCII pathway. This glycopeptide is strongly immunogenic in eliciting glycan-dependent cellular and humoral immune responses. The glycopeptide specific CD4+ T cells display a prominent feature of Th2 and Th17 differentiation and exert high efficacy and potency to help Env trimer humoral immune responses. Glycopeptide-induced CD4+ T cell response prior to Env trimer immunization elicits neutralizing antibody development and production of antibodies facilitating uptake of immunogens by antigen-presenting cells. Our identification of gp120 glycopeptide–induced, T cell–specific immune responses offers a foundation for developing future knowledge-based vaccines that elicit strong and long-lasting protective immune responses against HIV-1 infection.
Long-term alterations in brain and behavior after postnatal Zika virus infection in infant macaques
Authors: Raper Jessica , Kovacs-Balint Zsofia , Mavigner Maud , Gumber Sanjeev , Burke Mark W. , Habib Jakob , Mattingly Cameron , Fair Damien , Earl Eric , Feczko Eric , Styner Martin , Jean Sherrie M. , Cohen Joyce K. , Suthar Mehul S. , Sanchez Mar M. , Alvarado Maria C. , Chahroudi Ann 
Published: May 2020

AbstractZika virus (ZIKV) infection has a profound impact on the fetal nervous system. The postnatal period is also a time of rapid brain growth, and it is important to understand the potential neurobehavioral consequences of ZIKV infection during infancy. Here we show that postnatal ZIKV infection in a rhesus macaque model resulted in long-term behavioral, motor, and cognitive changes, including increased emotional reactivity, decreased social contact, loss of balance, and deficits in visual recognition memory at one year of age. Structural and functional MRI showed that ZIKV-infected infant rhesus macaques had persistent enlargement of lateral ventricles, smaller volumes and altered functional connectivity between brain areas important for socioemotional behavior, cognitive, and motor function (e.g. amygdala, hippocampus, cerebellum). Neuropathological changes corresponded with neuroimaging results and were consistent with the behavioral and memory deficits. Overall, this study demonstrates that postnatal ZIKV infection in this model may have long-lasting neurodevelopmental consequences.
Peripheral nerve resident macrophages share tissue-specific programming and features of activated microglia
Authors: Wang Peter L. , Yim Aldrin K. Y. , Kim Ki-Wook , Avey Denis , Czepielewski Rafael S. , Colonna Marco , Milbrandt Jeffrey , Randolph Gwendalyn J. 
Published: May 2020

AbstractWhereas microglia are recognized as fundamental players in central nervous system (CNS) development and function, much less is known about macrophages of the peripheral nervous system (PNS). Here, by comparing gene expression across neural and conventional tissue-resident macrophages, we identified transcripts that were shared among neural resident macrophages as well as selectively enriched in PNS macrophages. Remarkably, PNS macrophages constitutively expressed genes previously identified to be upregulated by activated microglia during aging, neurodegeneration, or loss of Sall1. Several microglial activation-associated and PNS macrophage-enriched genes were also expressed in spinal cord microglia at steady state. We further show that PNS macrophages rely on IL-34 for maintenance and arise from both embryonic and hematopoietic precursors, while their expression of activation-associated genes did not differ by ontogeny. Collectively, these data uncover shared and unique features between neural resident macrophages and emphasize the role of nerve environment for shaping PNS macrophage identity.
Real-time terahertz imaging with a single-pixel detector
Authors: Stantchev Rayko Ivanov , Yu Xiao , Blu Thierry , Pickwell-MacPherson Emma 
Published: May 2020

AbstractTerahertz (THz) radiation is poised to have an essential role in many imaging applications, from industrial inspections to medical diagnosis. However, commercialization is prevented by impractical and expensive THz instrumentation. Single-pixel cameras have emerged as alternatives to multi-pixel cameras due to reduced costs and superior durability. Here, by optimizing the modulation geometry and post-processing algorithms, we demonstrate the acquisition of a THz-video (32 × 32 pixels at 6 frames-per-second), shown in real-time, using a single-pixel fiber-coupled photoconductive THz detector. A laser diode with a digital micromirror device shining visible light onto silicon acts as the spatial THz modulator. We mathematically account for the temporal response of the system, reduce noise with a lock-in free carrier-wave modulation and realize quick, noise-robust image undersampling. Since our modifications do not impose intricate manufacturing, require long post-processing, nor sacrifice the time-resolving capabilities of THz-spectrometers, their greatest asset, this work has the potential to serve as a foundation for all future single-pixel THz imaging systems.
Insect herbivory dampens Subarctic birch forest C sink response to warming
Authors: Silfver Tarja , Heiskanen Lauri , Aurela Mika , Myller Kristiina , Karhu Kristiina , Meyer Nele , Tuovinen Juha-Pekka , Oksanen Elina , Rousi Matti , Mikola Juha 
Published: May 2020

AbstractClimate warming is anticipated to make high latitude ecosystems stronger C sinks through increasing plant production. This effect might, however, be dampened by insect herbivores whose damage to plants at their background, non-outbreak densities may more than double under climate warming. Here, using an open-air warming experiment among Subarctic birch forest field layer vegetation, supplemented with birch plantlets, we show that a 2.3 °C air and 1.2 °C soil temperature increase can advance the growing season by 1–4 days, enhance soil N availability, leaf chlorophyll concentrations and plant growth up to 400%, 160% and 50% respectively, and lead up to 122% greater ecosystem CO2 uptake potential. However, comparable positive effects are also found when insect herbivory is reduced, and the effect of warming on C sink potential is intensified under reduced herbivory. Our results confirm the expected warming-induced increase in high latitude plant growth and CO2 uptake, but also reveal that herbivorous insects may significantly dampen the strengthening of the CO2 sink under climate warming.
Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection
Authors: Kaul Drishti , Rathnasinghe Raveen , Ferres Marcela , Tan Gene S. , Barrera Aldo , Pickett Brett E. , Methe Barbara A. , Das Suman R. , Budnik Isolda , Halpin Rebecca A. , Wentworth David , Schmolke Mirco , Mena Ignacio , Albrecht Randy A. , Singh Indresh , Nelson Karen E. , García-Sastre Adolfo , Dupont Chris L. , Medina Rafael A. 
Published: May 2020

AbstractInfection with influenza can be aggravated by bacterial co-infections, which often results in disease exacerbation. The effects of influenza infection on the upper respiratory tract (URT) microbiome are largely unknown. Here, we report a longitudinal study to assess the temporal dynamics of the URT microbiomes of uninfected and influenza virus-infected humans and ferrets. Uninfected human patients and ferret URT microbiomes have stable healthy ecostate communities both within and between individuals. In contrast, infected patients and ferrets exhibit large changes in bacterial community composition over time and between individuals. The unhealthy ecostates of infected individuals progress towards the healthy ecostate, coinciding with viral clearance and recovery. Pseudomonadales associate statistically with the disturbed microbiomes of infected individuals. The dynamic and resilient microbiome during influenza virus infection in multiple hosts provides a compelling rationale for the maintenance of the microbiome homeostasis as a potential therapeutic target to prevent IAV associated bacterial co-infections.
High-throughput screening platform for solid electrolytes combining hierarchical ion-transport prediction algorithms
Authors: He Bing , Chi Shuting , Ye Anjiang , Mi Penghui , Zhang Liwen , Pu Bowei , Zou Zheyi , Ran Yunbing , Zhao Qian , Wang Da , Zhang Wenqing , Zhao Jingtai , Adams Stefan , Avdeev Maxim , Shi Siqi 
Published: May 2020

AbstractThe combination of a materials database with high-throughput ion-transport calculations is an effective approach to screen for promising solid electrolytes. However, automating the complicated preprocessing involved in currently widely used ion-transport characterization algorithms, such as the first-principles nudged elastic band (FP-NEB) method, remains challenging. Here, we report on high-throughput screening platform for solid electrolytes (SPSE) that integrates a materials database with hierarchical ion-transport calculations realized by implementing empirical algorithms to assist in FP-NEB completing automatic calculation. We first preliminarily screen candidates and determine the approximate ion-transport paths using empirical both geometric analysis and the bond valence site energy method. A chain of images are then automatically generated along these paths for accurate FP-NEB calculation. In addition, an open web interface is actualized to enable access to the SPSE database, thereby facilitating machine learning. This interactive platform provides a workflow toward high-throughput screening for future discovery and design of promising solid electrolytes and the SPSE database is based on the FAIR principles for the benefit of the broad research community.
Evaluating Nodes of Latent Mediators in Heterogeneous Communities
Authors: Yamano Hiroko , Asatani Kimitaka , Sakata Ichiro 
Published: May 2020

AbstractConventionally, the importance of nodes in a network has been debated from the viewpoint of the amount of information received by the nodes and its neighbors. While node evaluation based on the adjacency relationship mainly uses local proximity information, the community structure that characterizes the network has hardly been considered. In this study, we propose a new node index that contributes to the understanding of the inter-community structure of a network by combining the measures of link distribution and community relevance. The visualization of node rankings and rank correlations with respect to the attack tolerance of networks demonstrated that the proposed index shows the highest performance in comparison with five previously proposed indexes, suggesting a new way to detect latent mediators in heterogeneous networks.
Rapid Detection of Mobilized Colistin Resistance using a Nucleic Acid Based Lab-on-a-Chip Diagnostic System
Authors: Rodriguez-Manzano Jesus , Moser Nicolas , Malpartida-Cardenas Kenny , Moniri Ahmad , Fisarova Lenka , Pennisi Ivana , Boonyasiri Adhiratha , Jauneikaite Elita , Abdolrasouli Alireza , Otter Jonathan A. , Bolt Frances , Davies Frances , Didelot Xavier , Holmes Alison , Georgiou Pantelis 
Published: May 2020

AbstractThe increasing prevalence of antimicrobial resistance is a serious threat to global public health. One of the most concerning trends is the rapid spread of Carbapenemase-Producing Organisms (CPO), where colistin has become the last-resort antibiotic treatment. The emergence of colistin resistance, including the spread of mobilized colistin resistance (mcr) genes, raises the possibility of untreatable bacterial infections and motivates the development of improved diagnostics for the detection of colistin-resistant organisms. This work demonstrates a rapid response for detecting the most recently reported mcr gene, mcr−9, using a portable and affordable lab-on-a-chip (LoC) platform, offering a promising alternative to conventional laboratory-based instruments such as real-time PCR (qPCR). The platform combines semiconductor technology, for non-optical real-time DNA sensing, with a smartphone application for data acquisition, visualization and cloud connectivity. This technology is enabled by using loop-mediated isothermal amplification (LAMP) as the chemistry for targeted DNA detection, by virtue of its high sensitivity, specificity, yield, and manageable temperature requirements. Here, we have developed the first LAMP assay for mcr−9 - showing high sensitivity (down to 100 genomic copies/reaction) and high specificity (no cross-reactivity with other mcr variants). This assay is demonstrated through supporting a hospital investigation where we analyzed nucleic acids extracted from 128 carbapenemase-producing bacteria isolated from clinical and screening samples and found that 41 carried mcr−9 (validated using whole genome sequencing). Average positive detection times were 6.58 ± 0.42 min when performing the experiments on a conventional qPCR instrument (n = 41). For validating the translation of the LAMP assay onto a LoC platform, a subset of the samples were tested (n = 20), showing average detection times of 6.83 ± 0.92 min for positive isolates (n = 14). All experiments detected mcr−9 in under 10 min, and both platforms showed no statistically significant difference (p-value > 0.05). When sample preparation and throughput capabilities are integrated within this LoC platform, the adoption of this technology for the rapid detection and surveillance of antimicrobial resistance genes will decrease the turnaround time for DNA detection and resistotyping, improving diagnostic capabilities, patient outcomes, and the management of infectious diseases.
Multi-classifier prediction of knee osteoarthritis progression from incomplete imbalanced longitudinal data
Authors: Widera Paweł , Welsing Paco M. J. , Ladel Christoph , Loughlin John , Lafeber Floris P. F. J. , Petit Dop Florence , Larkin Jonathan , Weinans Harrie , Mobasheri Ali , Bacardit Jaume 
Published: May 2020

AbstractConventional inclusion criteria used in osteoarthritis clinical trials are not very effective in selecting patients who would benefit from a therapy being tested. Typically majority of selected patients show no or limited disease progression during a trial period. As a consequence, the effect of the tested treatment cannot be observed, and the efforts and resources invested in running the trial are not rewarded. This could be avoided, if selection criteria were more predictive of the future disease progression. In this article, we formulated the patient selection problem as a multi-class classification task, with classes based on clinically relevant measures of progression (over a time scale typical for clinical trials). Using data from two long-term knee osteoarthritis studies OAI and CHECK, we tested multiple algorithms and learning process configurations (including multi-classifier approaches, cost-sensitive learning, and feature selection), to identify the best performing machine learning models. We examined the behaviour of the best models, with respect to prediction errors and the impact of used features, to confirm their clinical relevance. We found that the model-based selection outperforms the conventional inclusion criteria, reducing by 20–25% the number of patients who show no progression. This result might lead to more efficient clinical trials.
Nonlinear Analysis of Visually Normal EEGs to Differentiate Benign Childhood Epilepsy with Centrotemporal Spikes (BECTS)
Authors: Sathyanarayana Aarti , El Atrache Rima , Jackson Michele , Alter Aliza S. , Mandl Kenneth D. , Loddenkemper Tobias , Bosl William J. 
Published: May 2020

AbstractChildhood epilepsy with centrotemporal spikes, previously known as Benign Epilepsy with Centro-temporal Spikes (BECTS) or Rolandic Epilepsy, is one of the most common forms of focal childhood epilepsy. Despite its prevalence, BECTS is often misdiagnosed or missed entirely. This is in part due to the nocturnal and brief nature of the seizures, making it difficult to identify during a routine electroencephalogram (EEG). Detecting brain activity that is highly associated with BECTS on a brief, awake EEG has the potential to improve diagnostic screening for BECTS and predict clinical outcomes. For this study, 31 patients with BECTS were retrospectively selected from the BCH Epilepsy Center database along with a contrast group of 31 patients in the database who had no form of epilepsy and a normal EEG based on a clinical chart review. Nonlinear features, including multiscale entropy and recurrence quantitative analysis, were computed from 30-second segments of awake EEG signals. Differences were found between these multiscale nonlinear measures in the two groups at all sensor locations, while visual EEG inspection by a board-certified child neurologist did not reveal any distinguishing features. Moreover, a quantitative difference in the nonlinear measures (sample entropy, trapping time and the Lyapunov exponents) was found in the centrotemporal region of the brain, the area associated with a greater tendency to have unprovoked seizures, versus the rest of the brain in the BECTS patients. This difference was not present in the contrast group. As a result, the epileptic zone in the BECTS patients appears to exhibit lower complexity, and these nonlinear measures may potentially serve as a clinical screening tool for BECTS, if replicated in a larger study population.