bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Hydrogel Microneedle-assisted Assay Integrating Aptamer Probes and Fluorescence Detection for Reagentless Biomarker Quantification
Authors: Zheng Hanjia , GhavamiNejad Amin , GhavamiNejad Peyman , Samarikhalaj Melisa , Giacca Adria , Poudineh Mahla 
Published: October 2021

AbstractAnalyzing interstitial fluid (ISF) via microneedle (MN) devices enables patient health monitoring in a minimally invasive manner and at point-of-care settings. However, most MN-based diagnostic approaches require complicated fabrication processes or post-processing of the extracted ISF. Here we show in-situ and on-needle measurement of target analytes by integrating hydrogel microneedles (HMN) with aptamer probes as the target recognition elements. Fluorescently tagged aptamer probes are chemically attached to the hydrogel matrix while a crosslinked patch is formed. We use the assay for specific and sensitive quantification of glucose concentrations in an animal model of diabetes to track hypoglycemia, euglycemia, and hyperglycemia conditions. The assay can track the rising and falling concentrations of glucose and the extracted measurements closely match those from the gold standard techniques. The assay enables rapid and reagentless target detection and can be readily modified to measure other target analytes in vivo. Our system has the potential to improve the quality of life of patients who are in need of close monitoring of biomarkers of health and disease.
Interferon-Gamma Signaling Promotes Melanoma Progression and Metastasis
Authors: Zhou Bo , Basu Jayati , Kazmi Hasan R. , Mo Xuan , Preston-Alp Sarah , Cai Kathy Q. , Kappes Dietmar , Zaidi M. Raza 
Published: October 2021

SUMMARYInterferon-gamma (IFNG) has long been regarded as the flag-bearer for the anti-cancer immunosurveillance mechanisms. However, relatively recent studies have suggested a dual role of IFNG, albeit there is no direct experimental evidence for its potential pro-tumor functions. Here we providein vivoevidence that treatment of mouse melanoma cell lines with physiological levels of Ifng enhances their tumorigenicity and metastasis in lung colonization allograft assays performed in immunocompetent syngeneic host mice, but not in immunocompromised host mice. We also show that this enhancement is dependent on downstream signaling via Stat1 but not Stat3, providing evidence of an oncogenic function of Stat1 in melanoma. The experimental results suggest that melanoma cell-specific Ifng signaling modulates the tumor microenvironment and its pro-tumorigenic effects are dependent on the γδ T cells, as Ifng-enhanced tumorigenesis was inhibited in the TCR-δ knockout mice. Overall, these results show that Ifng signaling may have tumor-promoting effects in melanoma by modulating the immune cell composition of the tumor microenvironment.
Polypolish: short-read polishing of long-read bacterial genome assemblies
Authors: Wick Ryan R. , Holt Kathryn E. 
Published: October 2021

AbstractLong-read-only bacterial genome assemblies usually contain residual errors, most commonly homopolymer-length errors. Short-read polishing tools can use short reads to fix these errors, but most rely on short-read alignment which is unreliable in repeat regions. Errors in such regions are therefore challenging to fix and often remain after short-read polishing. Here we introduce Polypolish, a new short-read polisher which uses all-per-read alignments to repair errors in repeat sequences that other polishers cannot. Polypolish performed well in benchmarking tests using both simulated and real reads, and it almost never introduced errors during polishing. The best results were achieved by using Polypolish in combination with other short-read polishers.Author summaryRecent improvements in Oxford Nanopore Technologies sequencing platforms and assembly algorithms have made it easier than ever to generate complete bacterial genome sequences. However, Oxford Nanopore genome sequences suffer from errors that limit their utility in downstream analyses. To fix these errors, one can ‘polish’ the genome with Illumina sequencing, exploiting the fact that Oxford Nanopore and Illumina sequencing have different error profiles. There are several polishing tools which can fix most errors in an Oxford Nanopore genome, but they struggle with errors in repetitive regions of the genome. With this in mind, we have developed a polisher, Polypolish, which uses a novel approach that allows it to fix more errors in genomic repeats. Our results show that Polypolish is both effective at repairing sequence errors and very unlikely to introduce new errors. Polypolish can often fix errors that other polishers cannot and vice versa, so the best results come from using a combination of tools. Polypolish therefore has an important role in bacterial genome assembly methods that aim for the highest possible sequence accuracy.
Single-cell Networks Reorganise to Facilitate Whole-brain Supercritical Dynamics During Epileptic Seizures
Authors: Burrows DRW , Diana G , Pimpel B , Moeller F , Richardson MP , Bassett DS , Meyer MP , Rosch RE 
Published: October 2021

SummaryExcitation-inhibition (EI) balance may be required for the organisation of brain dynamics to a phase transition, criticality, which confers computational benefits. Brain pathology associated with EI imbalance may therefore occur due to a deviation from criticality. However, evidence linking critical dynamics with EI imbalance-induced pathology is lacking. Here, we studied the effect of EI imbalance-induced epileptic seizures on brain dynamics, usingin vivowhole-brain 2-photon imaging of GCaMP6s larval zebrafish at single-neuron resolution. We demonstrate the importance of EI balance for criticality, with EI imbalance causing a loss of whole-brain critical statistics. Using network models we show that a reorganisation of network topology drives this loss of criticality. Seizure dynamics match theoretical predictions for networks driven away from a phase transition into disorder, with the emergence of chaos and a loss of network-mediated separation, dynamic range and metastability. These results demonstrate that EI imbalance drives a pathological deviation from criticality.
Into the range: a latitudinal gradient or a center-margins differentiation of ecological strategies in Arabidopsis thaliana?
Authors: Estarague Aurélien , Vasseur François , Sartori Kevin , Bastias Cristina , Cornet Denis , Rouan Lauriane , Beurier Gregory , Exposito-Alonso Moises , Herbette Stéphane , Bresson Justine , Vile Denis , Violle Cyrille 
Published: October 2021

AbstractBackground and AimsDetermining within-species large-scale variation in phenotypic traits is central to elucidate the drivers of species’ ranges. Intraspecific comparisons offer the opportunity to understand how trade-offs and biogeographical history constrain adaptation to contrasted environmental conditions. Here we test whether functional traits, ecological strategies and phenotypic plasticity in response to abiotic stress vary along a latitudinal or a center-margins gradient within the native range of Arabidopsis thaliana.MethodsThe phenotypic outcomes of plant adaptation at the center and margins of its geographic range were experimentally examined in 30 accessions from southern, central and northern Europe. The variation of traits related to stress tolerance, resource use, colonization ability as well as survival and fecundity was determined in response to high temperature (34°C) or frost (- 6°C), in combination with response to water deficit.Key ResultsBoth evidence for a latitudinal and a center-margins differentiation was found. Traits related to the acquisitive/conservative strategy trade-off varied along a latitudinal gradient. Northern accessions presented a greater survival to stress than central and southern accessions. Traits related to a colonization-competition trade-off followed a center-margin differentiation. Central accessions presented a higher phenotypic plasticity and trait values associated with a higher colonization ability than northern and southern accessions which instead had a higher competition ability.ConclusionsIntraspecific phenotypic variation helps us understand how the distribution range has evolved in Arabidopsis thaliana, which is shaped both by climate and the population migratory history. We advocate to consider intraspecific trait variation in species range studies instead of species means only as classically done in macroecology.
Chemophoresis Engine: Universal Principle of ATPase-driven Cargo Transport
Authors: Sugawara Takeshi , Kaneko Kunihiko 
Published: October 2021

ABSTRACTCell polarity regulates the orientation of the cytoskeleton members that directs intracellular transport for cargo-like organelles, using chemical gradients sustained by ATP or GTP hydrolysis. However, how cargo transports are directly mediated by chemical gradients remains unknown. We previously proposed a physical mechanism that enables directed movement of cargos, referred to as chemophoresis. According to the mechanism, a cargo with reaction sites is subjected to a chemophoresis force in the direction of the increased concentration. Based on this, we introduce an extended model, the chemophoresis engine, as a general mechanism of cargo motion, which transforms chemical free energy into directed motion through the catalytic ATP hydrolysis. We applied the engine to plasmid motion in a parABS system to demonstrate the the self-organization system for directed plasmid movement and pattern dynamics of ParA-ATP concentration, thereby explaining plasmid equi-positioning and pole-to-pole oscillation observed in bacterial cells and in vitro experiments. We mathematically show the existence and stability of the plasmid-surfing pattern, which allows the cargo-directed motion through the symmetry-breaking transition of the ParA-ATP spatiotemporal pattern. Finally, based on its generality, we discuss the chemophoresis engine as a universal principle of hydrolysis-driven intracellular transport.SIGNIFICANCEThe formation of organelle/macromolecule patterns depending on chemical concentration under non-equilibrium conditions, first observed during macroscopic morphogenesis (1), has recently been observed at the intracellular level as well, and its relevance as intracellular morphogen has been demonstrated in the case of bacterial cell division. These studies have discussed how cargos maintain positional information provided by chemical concentration gradients/localization. However, how cargo transports are directly mediated by chemical gradients remains unknown. Based on the previously proposed mechanism of chemotaxis-like behavior of cargos (referred to as chemophoresis, (2, 3)), we introduce a chemophoresis engine as a physicochemical mechanism of cargo motion, which transforms chemical free energy to directed motion. The engine is based on the chemophoresis force to make cargoes move in the direction of the increasing ATPase(-ATP) concentration and an enhanced catalytic ATPase hydrolysis at the positions of the cargoes. Applying the engine to ATPase-driven movement of plasmid-DNAs in bacterial cells, we constructed a mathematical model to demonstrate the self-organization for directed plasmid motion and pattern dynamics of ATPase concentration, as is consistent with in vitro and in vivo experiments. We propose that this chemophoresis engine works as a universal principle of hydrolysis-driven intracellular transport.
Extremely reduced supergroup F Wolbachia: transition to obligate insect symbionts
Authors: Mahmood Sazzad , Nováková Eva , Martinů Jana , Sychra Oldřich , Hypša Václav 
Published: October 2021

AbstractWolbachia are widely distributed symbionts among invertebrates that manifest by a broad spectrum of lifestyles from parasitism to mutualism. Wolbachia Supergroup F is considered a particularly interesting group which gave rise to symbionts of both arthropods and nematodes, and some of its members are obligate mutualists. Further investigations on evolutionary transitions in symbiosis have been hampered by a lack of genomic data for Supergroup F members. In this study, we present genomic data for five new supergroup F Wolbachia strains associated with four chewing lice species. These new strains in different evolutionary stages show genomic characteristics well-illustrating the evolutionary trajectory which symbiotic bacteria experience during their transition to mutualism. Three of the strains have not yet progressed with the transition, the other two show typical signs of ongoing gene deactivation and removal (genome size, coding density, low number of pseudogenes). Particularly, wMeur1, a symbiont fixed in all Menacanthus eurysternus populations across four continents, possesses a highly reduced genome of 733,850 bp with a horizontally acquired capacity for pantothenate synthesis. Comparing with other strains showed wMeur1 genome as the smallest currently known among all Wolbachia and the first example of Wolbachia which has completed genomic streamlining known from the gammaproteobacterial obligate symbionts.
The biological sink of atmospheric H2 is more sensitive to spatial variation of microbial diversity than N2O and CO2 emissions in an agroecosystem
Authors: Baril Xavier , Durand Audrey-Anne , Srei Narin , Lamothe Steve , Provost Caroline , Martineau Christine , Guertin Claude , Dunfield Kari , Constant Philippe 
Published: October 2021

AbstractThe relationship between soil microbial diversity and agroecosystem functioning is controversial due to the elevated diversity level and the functional redundancy of microorganisms. A field trial was established to test the hypothesis that enhanced crop diversity with the integration of winter cover crops (WCC) in a conventional maize-soy rotation promotes microbial diversity and the biological sink of H2 in soil, while reducing N2O emissions to the atmosphere. Vicia villosa (hairy vetch), Avena sativa (oat), and Raphanus sativus (Daikon radish) were cultivated alone or in combinations and flux measurements were performed throughout two subsequent growing seasons. Soil acted as a net sink for H2 and as a net source for CO2 and N2O. CO2 flux was the most sensitive to WCC whereas a significant spatial variation was observed for H2 flux with soil uptake rates observed in the most productive area two-fold greater than the baseline level. Sequencing and quantification of taxonomic and functional genes were integrated to explain variation in trace gas fluxes with compositional changes in soil microbial communities. Fungal communities were the most sensitive to WCC, but neither community abundance nor beta diversity were found to be indicative of fluxes. The alpha diversity of taxonomic and functional genes, expressed as the number of effective species, was integrated into composite variables extracted from multivariate analyses. Only the composite variable computed with the inverse Simpson’s concentration index displayed a reproducible pattern throughout both growing seasons, with functional genes and bacterial 16S rRNA gene defining the two most contrasting gradients. The composite variable was decoupled from WCC treatment and explained 19-20% spatial variation of H2 fluxes. Sensitivity of the trace gas exchange process to soil properties at the local scale was inconsistent among H2, N2O and CO2, with the former being the most related to microbial diversity distribution pattern.
Endogenous recruitment of frontal-sensory circuits during visual discrimination
Authors: Broom Eluned , Imbriotis Vivian , Sengpiel Frank , Connelly William M. , Ranson Adam 
Published: October 2021

SummaryA long-range circuit linking anterior cingulate cortex (ACC) to primary visual cortex (V1) has been previously proposed to mediate visual selective attention in mice during visually guided behaviour. Here we used in vivo two-photon functional imaging to measure endogenous activity of ACC neurons projecting to layer 1 of V1 (ACC-V1axons) in mice either passively viewing stimuli or performing a go/no-go visually guided task. We observed that while ACC-V1axons were recruited under these conditions, this was not linked to enhancement of neural or behavioural measures of sensory coding. Instead, ACC-V1axon activity was observed to be associated with licking behaviour, modulated by reward, and biased towards task relevant sensory cortex.
Comparative reconstruction of the predatory feeding structures of the polyphenic nematode Pristionchus pacificus
Authors: Harry Clayton J. , Messar Sonia M. , Ragsdale Erik J. 
Published: October 2021

AbstractPristionchus pacificus is a nematode model for the developmental genetics of morphological polyphenism, especially at the level of individual cells. Morphological polyphenism in this species includes an evolutionary novelty, moveable teeth, which have enabled predatory feeding in this species and others in its family (Diplogastridae). From transmission electron micrographs of serial thin sections through an adult hermaphrodite of P. pacificus, we three-dimensionally reconstructed all epithelial and myoepithelial cells and syncytia, corresponding to 74 nuclei, of its face, mouth, and pharynx. We found that the epithelia that produce the predatory morphology of P. pacificus are identical to Caenorhabditis elegans in the number of cell classes and nuclei. However, differences in cell form, spatial relationships, and nucleus position correlate with gross morphological differences from C. elegans and outgroups. Moreover, we identified fine-structural features, especially in the anteriormost pharyngeal muscles, that underlie the conspicuous, left-right asymmetry that characterizes the P. pacificus feeding apparatus. Our reconstruction provides an anatomical map for studying the genetics of polyphenism, feeding behavior, and the development of novel form in a satellite model to C. elegans.
Single-Shot Optical Projection tomography for high-speed volumetric imaging
Authors: Darling Connor , Davis Samuel P.X. , Kumar Sunil , French Paul M.W. , McGinty James 
Published: October 2021

AbstractWe present a single-shot adaptation of Optical Projection Tomography (OPT) for high-speed volumetric snapshot imaging of dynamic mesoscopic samples. Conventional OPT has been applied to in vivo imaging of animal models such as D. rerio but the sequential acquisition of projection images required for volumetric reconstruction typically requires samples to be immobilised during the acquisition of an OPT data set. We present a proof-of-principle system capable of single-shot imaging of a 1 mm diameter volume, demonstrating camera-limited rates of up to 62.5 volumes/second, which we have applied to 3D imaging of a freely-swimming zebrafish embryo. This is achieved by recording 8 projection views simultaneously on 4 low-cost CMOS cameras. With no stage required to rotate the sample, this single-shot OPT system can be implemented with a component cost of under £5,000. The system design can be adapted to different sized fields of view and may be applied to a broad range of dynamic samples, including fluid dynamics.
A network information theoretic framework to characterise muscle synergies in space and time
Authors: Reilly David Ó’ , Delis Ioannis 
Published: October 2021

AbstractObjectiveCurrent approaches to muscle synergy extraction rely on linear dimensionality reduction algorithms that make specific assumptions on the underlying signals. However, to capture nonlinear time varying, large-scale but also muscle-specific interactions, a more generalised approach is required.ApproachHere we developed a novel framework for muscle synergy extraction that relaxes model assumptions by using a combination of information- and network theory and dimensionality reduction. We first quantify informational dynamics between muscles, time-samples or muscle-time pairings using a novel mutual information formulation. We then model these pairwise interactions as multiplex networks and identify modules representing the network architecture. We employ this modularity criterion as the input parameter for dimensionality reduction, which verifiably extracts the identified modules, and also to characterise salient structures within each module.Main resultsThis novel framework captures spatial, temporal and spatiotemporal interactions across two benchmark datasets of reaching movements, producing distinct spatial groupings and both tonic and phasic temporal patterns. Readily interpretable muscle synergies spanning multiple spatial and temporal scales were identified, demonstrating significant task dependence, ability to capture trial-to-trial fluctuations and concordance across participants. Furthermore, our framework identifies submodular structures that represent the distributed networks of co-occurring signal interactions across scales.SignificanceThe capabilities of this framework are illustrated through the concomitant continuity with previous research and novelty of the insights gained. Several previous limitations are circumvented including the extraction of functionally meaningful and multiplexed pairwise muscle couplings under relaxed model assumptions. The extracted synergies provide a holistic view of the movement while important details of task performance are readily interpretable. The identified muscle groupings transcend biomechanical constraints and the temporal patterns reveal characteristics of fundamental motor control mechanisms. We conclude that this framework opens new opportunities for muscle synergy research and can constitute a bridge between existing models and recent network-theoretic endeavours.
Bilaterally Reduced Rolandic Beta Band Activity in Minor Stroke Patients
Authors: Kulasingham Joshua P. , Brodbeck Christian , Khan Sheena , Marsh Elisabeth B. , Simon Jonathan Z. 
Published: October 2021

AbstractStroke patients with hemiparesis display decreased beta band (13-25 Hz) rolandic activity, correlating to impaired motor function. However, patients without significant weakness, with small lesions far from sensorimotor cortex, nevertheless exhibit bilateral decreased motor dexterity and slowed reaction times. We investigate whether these minor stroke patients also display abnormal beta band activity.Magnetoencephalographic (MEG) data were collected from nine minor stroke patients (NIHSS < 4) without significant hemiparesis, at ~1 and ~6 months postinfarct, and eight age-similar controls. Rolandic relative beta power during matching tasks and resting state, and Beta Event Related (De)Synchronization (ERD/ERS) during button press responses were analyzed.Regardless of lesion location, patients had significantly reduced relative beta power and ERS compared to controls. Abnormalities persisted over visits, and were present in both ipsi- and contra-lesional hemispheres, consistent with bilateral impairments in motor dexterity and speed.Minor stroke patients without severe weakness display reduced rolandic beta band activity in both hemispheres, which may be linked to bilaterally impaired dexterity and processing speed, implicating global connectivity dysfunction affecting sensorimotor cortex. Rolandic beta band activity may be a potential biomarker and treatment target, even for minor stroke patients with small lesions far from sensorimotor areas.