bluuebunny/crossref_metadata_2025_split huggingface dataset:
The temporal pattern of intracortical microstimulation pulses elicits distinct temporal and spatial recruitment of cortical neuropil and neurons
Authors: Eles James R , Stieger Kevin C , Kozai Takashi D Y 
Published: October 2020

Abstract

Objective. The temporal spacing or distribution of stimulation pulses in therapeutic neurostimulation waveforms—referred to here as the Temporal Pattern (TP)—has emerged as an important parameter for tuning the response to deep-brain stimulation and intracortical microstimulation (ICMS). While it has long been assumed that modulating the TP of ICMS may be effective by altering the rate coding of the neural response, it is unclear how it alters the neural response at the network level. The present study is designed to elucidate the neural response to TP at the network level. Approach. We use in vivo two-photon imaging of mice expressing the calcium sensor Thy1-GCaMP or the glutamate sensor hSyn-iGluSnFr to examine the layer II/III neural response to ICMS with different TPs. We study the neuronal calcium and glutamate response to TPs with the same average frequency (10 Hz) and same total charge injection, but varying degrees of bursting. We also investigate one control pattern with an average frequency of 100 Hz and 10X the charge injection. Main Results. Stimulation trains with the same average frequency and same total charge injection but distinct TPs recruit distinct sets of neurons. More than half (60% of 309 cells) of neurons prefer one TP over the other. Despite their distinct spatial recruitment patterns, cells exhibit similar ability to follow 30 s trains of both TPs without failing, and they exhibit similar levels of glutamate release during stimulation. Both neuronal calcium and glutamate release entrain to the bursting TP pattern, with a ∼21-fold increase in relative power at the frequency of bursting. Bursting also results in a statistically significant elevation in the correlation between somatic calcium activity and neuropil activity, which we explore as a metric for inhibitory-excitatory tone. Interestingly, soma-neuropil correlation during the bursting pattern is a statistically significant predictor of cell preference for TP, which exposes a key link between TP and inhibitory-excitatory tone. Finally, using mesoscale imaging, we show that both TPs result in distal inhibition during stimulation, which reveals complex spatial and temporal interactions between TP and inhibitory-excitatory tone in ICMS. Significance. Our results may ultimately suggest that TP is a valuable parameter space to modulate inhibitory-excitatory tone and to recruit distinct network activity in ICMS. This presents a broader mechanism of action than rate coding, as previously thought. By implicating these additional mechanisms, TP may have broader utility in the clinic and should be pursued to expand the efficacy of ICMS therapies.
Design optimization and experimental study of a novel mechanism for a hover-able bionic flapping-wing micro air vehicle
Authors: Deng Huichao , Xiao Shengjie , Huang Binxiao , Yang Lili , Xiang Xinyi , Ding Xilun 
Published: October 2020

Abstract

Allomyrina dichotoma has a natural ultra-high flying ability and maneuverability. Especially its ability to fly flexibly in the air, makes it more adaptable to the harsh ecological environment. In this study, a bionic flapping-wing micro air vehicle (FMAV) is designed and fabricated by mimicking the flight mode of A. dichotoma. Parametric design was employed for combining the airframe structure and flight characteristics analysis. To improve the transmission efficiency and compactness of the FMAV mechanisms, this study first analyses the body structure of A. dichotoma, and then proposes a novel mechanism of FMAV based on its biological motion characteristics, the flight motion characteristics, and its musculoskeletal system. By optimizing the flapping-wing mechanism and mimicking the flying mechanism of A. dichotoma, the large angle amplitude and the high-frequency flapping motion can be achieved to generate more aerodynamic force. Meanwhile, to improve the bionic effect and the wing performance of FMAV, the flexible deformation of A. dichotoma wings for each flapping period was observed by a high-speed camera. Furthermore, the bionic design of wings the prototype was carried out, therefore the wings can generate a high lift force in the flapping process. The experiment demonstrated that the aircraft can achieve a flapping angle of 160 degrees and 30 Hz flapping frequency. The attitude change of FMAV is realized by mimicking the movement for the change of attitude of the A. dichotoma, by changing the angle of attack of the wing, and executing the flight action of multiple degrees of freedom including pitch, roll and yaw. Finally, the aerodynamic experiment demonstrated that the prototype can offer 27.8 g lift and enough torque for altitude adjustment.
Effect of wing–wing interaction coupled with morphology and kinematic features of damselflies
Authors: Lai Yu-Hsiang , Lin You-Jun , Chang Sheng-Kai , Yang Jing-Tang 
Published: October 2020

Abstract
We investigated the effect of the wing–wing interaction, which is one key aspect of flight control, of damselflies (Matrona cyanoptera and Euphaea formosa) in forward flight that relates closely to their body morphologies and wing kinematics. We used two high-speed cameras aligned orthogonally to measure the flight motions and adopted 3D numerical simulation to analyze the flow structures and aerodynamic efficiencies. The results clarify the effects of wing–wing interactions, which are complicated combinations of biological morphology, wing kinematics and fluid dynamics. As the amplitude of the hindwing of M. cyanoptera is larger than that of E. formosa, the effect of the wing–wing interaction is more constructive. Restricted by the body morphology of E. formosa, the flapping range of the hindwing is below the body. With the forewing in the lead, the hindwing is farther from the forewing, which is not susceptible to the wake of the forewing, and enables superior lift and thrust. Because of the varied rotational motions, the different shed direction of the wakes of the forewings causes the optimal thrust to occur in different wing phases. Because of its biological limitations, a damselfly can use an appropriate phase to fulfill the desired flight mode. The wing–wing interaction is a compromise between lift efficiency and thrust efficiency. The results reveal that a damselfly with the forewing in the lead can have an effective aerodynamic performance in flight. As an application, in the design concept of a micro-aircraft, increasing the amplitude of the hindwing might enhance the wing–wing interaction, thus controlling the flight modes.
Modal decompositions of the kinematics of Crevalle jack and the fluid–caudal fin interaction
Authors: Ullah Khalid Muhammad Saif , Wang Junshi , Akhtar Imran , Dong Haibo , Liu Moubin 
Published: October 2020

Abstract
To understand the governing mechanisms of bio-inspired swimming has always been challenging due to intense interactions between flexible bodies of natural aquatic species and water around them. Advanced modal decomposition techniques provide us with tools to develop more in-depth understating about these complex dynamical systems. In this paper, we employ proper orthogonal decomposition (POD) and dynamic mode decomposition (DMD) techniques to extract energetically strongest spatio-temporal orthonormal components of complex kinematics of a Crevalle jack (Caranx hippos) fish. Then, we present a computational framework for handling fluid–structure interaction related problems in order to investigate their contributions towards the overall dynamics of highly nonlinear systems. We find that the undulating motion of this fish can be described by only two standing-wave like spatially orthonormal modes. Constructing the data set from our numerical simulations for flows over the membranous caudal fin of the jack fish, our modal analyses reveal that only the first few modes receive energy from both the fluid and structure, but the contribution of the structure in the remaining modes is minimal. For the viscous and transitional flow conditions considered here, both spatially and temporally orthonormal modes show strikingly similar coherent flow structures. Our investigations are expected to assist in developing data-driven reduced-order mathematical models to examine the dynamics of bio-inspired swimming robots and develop new and effective control strategies to bring their performance closer to real fish species.
Bone marrow mesenchymal stem cells preconditioned with nitric-oxide-releasing chitosan/PVA hydrogel accelerate diabetic wound healing in rabbits
Authors: Ahmed Rashid , Afreen Afshan , Tariq Muhammad , Zahid Alap Ali , Masoud Muhammad Shareef , Ahmed Maqsood , Ali Imran , Akram Zeeshan , Hasan Anwarul 
Published: October 2020

AbstractImpaired diabetic wounds are one of the major pathophysiological complications caused by persistent microbial infections, prolonged inflammation, and insufficient angiogenic responses. Here, we report the development of nitric-oxide (NO) -releasing S-nitroso-N-acetyl-penicillamine (SNAP) -loaded chitosan/polyvinyl–alcohol hydrogel and its efficacy in enhancing the wound-healing potential of bone marrow mesenchymal stem cells in diabetic wounds. NO-releasing hydrogels significantly increased the cell viability and cell proliferation of hydrogen-peroxide (H2O2) -pretreated bone marrow stem cells (BMSCs), demonstrating their cytoprotective activity, which was further confirmed by gene expression of many times as much B-cell lymphoma 2 (Bcl-2), stromal cell-derived factor-1alpha (SDF-1α), proliferating cell nuclear antigen (PCNA) and vascular endothelial growth factor (VEGF). Furthermore, the SNAP-loaded hydrogel showed continuous cell-proliferating activity for six days, due to the slow release of NO from the hydrogel. Wound-healing studies of rabbits with induced diabetes showed that the application of SNAP-preconditioned BMSCs and NO-releasing hydrogels significantly sped up the healing process, compared to the control group. The wound-healing potential of BMSCs plus NO-releasing hydrogel was further validated by improved collagen deposition and epithelial layer formation, as confirmed by histopathological examination, as well as upregulation of VEGF and SDF-1α biomarkers, as evidenced by gene-expression analysis. These results demonstrated that the application of BMSCs with NO-releasing hydrogel can promote faster regeneration of damaged tissues. Therefore, BMSCs plus NO-releasing hydrogels can be very useful for the treatment of diabetic wounds.
Paper-supported co-culture system for dynamic investigations of the lung-tropic migration of breast cancer cells
Authors: Lin Dongguo , Chen Xiao , Lin Zhun , Lin Jinqiong , Liu Yang , Liu Dayu 
Published: October 2020

Abstract
Tumor tropism metastasis is a multi-step process that involves interactions between tumor cells and the microenvironment. Due to the limitations of experimental techniques, current studies are not able to gain insight into the dynamic process of such tropism migration. To overcome this issue, we developed a paper-supported co-culture system for dynamic investigations of the lung-tropic migration of breast cancer cells. This co-culture system contains a tumor layer, a recruitment layer, and several invasion layers between these two parts. The tumor and recruitment layers are impregnated with breast cancer cells and lung cells, respectively. Stacking these layers forms a co-culture device that comprises interactions between breast cancer and lung, destacking such a device represents cancer cells at different stages of the migration process. Thus, the paper-supported co-culture system offers the possibility of investigating migration from temporal and spatial aspects. Invasion assays using the co-culture system showed that breast cancer cells induced lung fibroblasts to convert to cancer-associated fibroblasts (CAFs), and the CAFs, in turn, recruited breast cancer cells. During migration, the local invasion of the cancer cells is a collective behavior, while the long-distance migration comes from individual cell behaviors. Breast cancer cells experienced repetitive processes of migration and propagation, accompanied by epithelial–mesenchymal and mesenchymal–epithelial transitions, and changes in stemness and drug resistance. Based on these results, the lung-tropic migration of breast cancer is interpreted as a process of bilateral interaction with the local and host-organ microenvironment. The developed paper-supported co-culture system offers the possibility of dynamically investigating tropism migration under the pre-metastatic niche, thus providing an advantageous tool for studying tumor metastasis.
Single crystal flake parameters of MoS2 and MoSe2 exfoliated using anodic bonding technique and its potential in rapid prototyping
Authors: Malavika C , Roshini R Anu , Surya Kanthi R S , Kannan E S 
Published: October 2020

Abstract
Rapid prototyping of devices using exfoliated Molybednum di-Sulphide (MoS2) and Molybdenum di-Selenide (MoSe2) requires an experimental protocol for maximizing the probability of realizing flakes with desired physical dimension and properties. In this work, we analyzed the size and thickness distribution of MoS2 and MoSe2 single crystalline flakes exfoliated using anodic bonding technique and established a correlation between physical dimension of the flakes and the bonding parameters. Anodic bonding was carried out by applying a fixed voltage of 200 V with a set temperature of 150 °C for four different bonding time intervals. On analyzing the flake parameters from the four anodic bonded substrates using the optical and atomic force microscopy, it is found that the probability of getting flakes with large lateral size (>200 μm) increases as the bonding time interval is increased. Most of these large sized flakes have thickness of more than one hundred mono-layers and a tiny fraction of them have thickness of the order of few monolayers. A similar trend was also observed for MoSe2 single crystals. To demonstrate the feasibility of this technique in rapid prototyping, ultra thin MoS2 flakes was directly bridged between two ITO electrodes and their transport properties was investigated. Micro-Raman and photoluminescence studies were taken on selected regions of the thicker and thinner exfoliated flakes and their physical properties are compared.
Post-Concussion Acute Signs and Reliable Cognitive Decline in a Finnish Youth Ice Hockey Sample
Authors: Kati Peltonen , Matti Vartiainen , Sanna Koskinen , Jon Pertab , Tiina Laitala , Laura Hokkanen 
Published: October 2020

AbstractObjectiveIn sports concussion research, the importance of an individualized approach incorporating neuropsychological assessment data has been emphasized. This study examined the impact of acute signs of concussion on post-injury cognitive functioning using reliable change methodology in a sample of Finnish, elite-level, youth ice hockey players.MethodsFrom a sample of 1,823 players (all male, 14–20 years old) who completed preseason baseline testing with the Immediate Post-Concussion Assessment and Cognitive Testing (ImPACT®) battery, two subgroups were identified. First, in total, 312 uninjured athletes, who completed baseline testing twice—1 year apart. The scores were contrasted to calculate reliable change indices (RCIs). Second, from a subsample of 570 athletes participating in an intensive follow-up arm of the project, the analysis included 32 concussed athletes. The RCIs were determined for the five ImPACT composite scores and used in identifying athletes with declined performance 3 days post-injury.ResultsTest-retest reliability ranged from .39 to .71. Athletes who had experienced an acute loss of consciousness, amnesia, or postural instability had increased odds for declines in two or more areas assessed by ImPACT (odds ratio = 7.67–8.00, p &lt; .05). In contrast, acute disorientation or vacant look did not lead to cognitive change that met the reliable change threshold.ConclusionsThe reliability coefficients and RCIs differed from those published earlier emphasizing the importance of national reference values. The presence of acute loss of consciousness, amnesia, or postural instability may indicate a more severe injury and predict the need for more intensive cognitive follow-up.
Kinship does not predict the structure of a shark social network
Authors: Mourier Johann , Planes Serge 
Published: October 2020

AbstractGenetic relatedness in animal societies is often a factor that drives the structure of social groups. In the marine world, most studies which have investigated this question have focused on marine mammals such as whales and dolphins. For sharks, recent studies have demonstrated preferential associations among individuals from which social communities emerge. Assortment patterns have been found according to phenotypic or behavioral traits, but the role of genetic relatedness in shaping the social structure of adult shark populations has, to the best of our knowledge, never been investigated. Here, we used a social network analysis crossed with DNA microsatellite genotyping to investigate the role of the genetic relatedness in the social structure of a blacktip reef shark (Carcharhinus melanopterus) population. Based on the data from 156 groups of sharks, we used generalized affiliation indices to isolate social preferences from nonsocial associations, controlling for the contribution of sex, size, gregariousness, spatial, and temporal overlap on social associations, to test for the influence of genetic relatedness on social structure. A double-permutation procedure was employed to confirm our results and account for issues arising from potentially elevated type I and type II error rates. Kinship was not a predictor of associations and affiliations among sharks at the dyad or community levels as individuals tended to associate independently of the genetic relatedness among them. The lack of parental care in this species may contribute to the breakdown of family links in the population early in life, thereby preventing the formation of kin-based social networks.
GP4: an integrated Gram-Positive Protein Prediction Pipeline for subcellular localization mimicking bacterial sorting
Authors: Grasso Stefano , van Rij Tjeerd , van Dijl Jan Maarten 
Published: October 2020

AbstractSubcellular localization is a critical aspect of protein function and the potential application of proteins either as drugs or drug targets, or in industrial and domestic applications. However, the experimental determination of protein localization is time consuming and expensive. Therefore, various localization predictors have been developed for particular groups of species. Intriguingly, despite their major representation amongst biotechnological cell factories and pathogens, a meta-predictor based on sorting signals and specific for Gram-positive bacteria was still lacking. Here we present GP4, a protein subcellular localization meta-predictor mainly for Firmicutes, but also Actinobacteria, based on the combination of multiple tools, each specific for different sorting signals and compartments. Novelty elements include improved cell-wall protein prediction, including differentiation of the type of interaction, prediction of non-canonical secretion pathway target proteins, separate prediction of lipoproteins and better user experience in terms of parsability and interpretability of the results. GP4 aims at mimicking protein sorting as it would happen in a bacterial cell. As GP4 is not homology based, it has a broad applicability and does not depend on annotated databases with homologous proteins. Non-canonical usage may include little studied or novel species, synthetic and engineered organisms, and even re-use of the prediction data to develop custom prediction algorithms. Our benchmark analysis highlights the improved performance of GP4 compared to other widely used subcellular protein localization predictors. A webserver running GP4 is available at http://gp4.hpc.rug.nl/
scGMAI: a Gaussian mixture model for clustering single-cell RNA-Seq data based on deep autoencoder
Authors: Yu Bin , Chen Chen , Qi Ren , Zheng Ruiqing , Skillman-Lawrence Patrick J , Wang Xiaolin , Ma Anjun , Gu Haiming 
Published: October 2020

Abstract
The rapid development of single-cell RNA sequencing (scRNA-Seq) technology provides strong technical support for accurate and efficient analyzing single-cell gene expression data. However, the analysis of scRNA-Seq is accompanied by many obstacles, including dropout events and the curse of dimensionality. Here, we propose the scGMAI, which is a new single-cell Gaussian mixture clustering method based on autoencoder networks and the fast independent component analysis (FastICA). Specifically, scGMAI utilizes autoencoder networks to reconstruct gene expression values from scRNA-Seq data and FastICA is used to reduce the dimensions of reconstructed data. The integration of these computational techniques in scGMAI leads to outperforming results compared to existing tools, including Seurat, in clustering cells from 17 public scRNA-Seq datasets. In summary, scGMAI is an effective tool for accurately clustering and identifying cell types from scRNA-Seq data and shows the great potential of its applicative power in scRNA-Seq data analysis. The source code is available at https://github.com/QUST-AIBBDRC/scGMAI/.
Cell-based Culture Informs Infectivity and Safe De-Isolation Assessments in Patients with Coronavirus Disease 2019
Authors: Basile Kerri , McPhie Kenneth , Carter Ian , Alderson Susan , Rahman Hossinur , Donovan Linda , Kumar Shanil , Tran Tyna , Ko Danny , Sivaruban Tharshini , Ngo Christine , Toi Cheryl , O’Sullivan Matthew V , Sintchenko Vitali , Chen Sharon C-A , Maddocks Susan , Dwyer Dominic E , Kok Jen 
Published: October 2020

Abstract

Background
The detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA by reverse-transcription polymerase chain reaction (PCR) does not necessarily indicate shedding of infective virions. There are limited data on the correlation between the isolation of SARS-CoV-2, which likely indicates infectivity, and PCR.

Methods
A total of 195 patients with Coronavirus disease 2019 were tested (outpatients, n = 178; inpatients, n = 12; and critically unwell patients admitted to the intensive care unit [ICU] patients, n = 5). SARS-CoV-2 PCR-positive samples were cultured in Vero C1008 cells and inspected daily for cytopathic effect (CPE). SARS-CoV-2–induced CPE was confirmed by PCR of culture supernatant. Where no CPE was observed, PCR was performed on day 4 to confirm absence of virus replication. The cycle thresholds (Cts) of the day 4 PCR (Ctculture) and the PCR of the original clinical sample (Ctsample) were compared, and positive cultures were defined where Ctsample − Ctculture was ≥3.

Results
Of 234 samples collected, 228 (97%) were from the upper respiratory tract. SARS-CoV-2 was isolated from 56 (24%), including in 28 of 181 (15%), 19 of 42 (45%), and 9 of 11 samples (82%) collected from outpatients, inpatients, and ICU patients, respectively. All 56 samples had Ctsample ≤32; CPE was observed in 46 (20%). The mean duration from symptom onset to culture positivity was 4.5 days (range, 0–18). SARS-CoV-2 was significantly more likely to be isolated from samples collected from inpatients (P &lt; .001) and ICU patients (P &lt; .0001) compared with outpatients, and in samples with lower Ctsample.

Conclusions
SARS-CoV-2 culture may be used as a surrogate marker for infectivity and inform de-isolation protocols.