Miracle-dz/UniFAR-FTUs huggingface dataset:
Stepwise construction of dynamic microscale concentration gradients around hydrogel-encapsulated cells in a microfluidic perfusion culture device

Inside living organisms, concentration gradients dynamically change over time as biological processes progress. Therefore, methods to construct dynamic microscale concentration gradients in a spatially controlled manner are needed to provide more realistic research environments. Here, we report a novel method for the construction of dynamic microscale concentration gradients in a stepwise manner around cells in micropatterned hydrogel. In our method, cells are encapsulated in a photodegradable hydrogel formed inside a microfluidic perfusion culture device, and perfusion microchannels are then fabricated in the hydrogel by micropatterned photodegradation. The cells in the micropatterned hydrogel can then be cultured by perfusing culture medium through the fabricated microchannels. By using this method, we demonstrate the simultaneous construction of two dynamic concentration gradients, which allowed us to expose the cells encapsulated in the hydrogel to a dynamic microenvironment.
A Novel Prediction Tool Based on Large Cohorts to Determine the Cancer-Specific Survival Probability of Patients With Locally Advanced Pancreatic Cancer After Irreversible Electroporation Treatment

Irreversible electroporation (IRE) is a novel method which was especially suitable for the treatment of locally advanced pancreatic cancer (LAPC). The purpose of this study was to evaluate probabilities of overall survival (OS) and cancer-specific survival (CSS) in patients with LAPC after IRE treatment and to construct nomograms to predict survival for these patients. Data of patients were retrospectively collected from the Surveillance, Epidemiology, and End Results (SEER) database and medical records of Sun Yat-sen University Cancer Center (SYSUCC). A total of 312 LAPC patients after IRE treatment were included into this study. The 3-year cumulative incidence of cancer-specific mortality for patients with LAPC after IRE treatment was 74.3%. Nomograms for predicting probabilities of OS, CSS, and non-cancer-specific survival (NCSS) were built and calibrated with the concordance index (C-index) and the area under receiver operating characteristic (ROC) curve (AUC). The established nomograms were well-calibrated, with C-indexes of 0.782 for OS prediction, 0.729 for CSS prediction, and 0.730 for NCSS prediction. Compared with the TNM stage system, the established nomograms displayed higher values of AUC and showed better discriminatory power for predicting OS, CSS, and NCSS. These nomograms were well-calibrated and could serve to guide management of LAPC patients after IRE treatment.
Semisupervised graph convolutional network for hyperspectral image classification

Abstract. Deep learning has been widely used in hyperspectral image (HSI) classification. However, a deep learning model is a data-driven machine learning method, and collecting labeled data is quite time-consuming for an HSI classification task, which means that a deep learning model needs a lot of labeled data and cannot deal with the small sample problem. We explore the small sample classification problem of HSI with graph convolutional network (GCN). First, HSI with a small number of labeled samples are treated as a graph. Then, the GCN (an efficient variant of convolutional neural networks) operates directly on the graph constructed from the HSI. GCN utilizes the adjacency nodes in graph to approximate the convolution. In other words, graph convolution can use both labeled and unlabeled nodes. Therefore, our method is a semisupervised method. Three HSI are used to assess the performance of the proposed method. The experimental results show that the proposed method outperforms the traditional semisupervised methods and advanced deep learning methods.
Semisupervised hyperspectral imagery classification based on a three-dimensional convolutional adversarial autoencoder model with low sample requirements

Abstract. Although there are many state-of-the-art methods for hyperspectral classification, data deficiency is a problem that should be addressed before popularizing hyperspectral technology. To solve this problem, it is worth exploring methods based on small datasets. Inspired by the advanced deep learning classification methods and the autoencoder structure, we propose a structure named three-dimensional convolutional adversarial autoencoder that combines the two processes for semisupervised hyperspectral classification. Our experiments show its utility in data-deficient situations, and our study analyzes its advantages and disadvantages, and points out a probable direction toward optimization.
Chemogenetic Suppression of the Subthalamic Nucleus Induces Attentional Deficits and Impulsive Action in a Five-Choice Serial Reaction Time Task in Mice

The subthalamic nucleus (STN), a key component of the basal ganglia circuitry, receives inputs from broad cerebral cortical areas and relays cortical activity to subcortical structures. Recent human and animal studies have suggested that executive function, which is assumed to consist of a set of different cognitive processes for controlling behavior, depends on precise information processing between the cerebral cortex and subcortical structures, leading to the idea that the STN contains neurons that transmit the information required for cognitive processing through their activity, and is involved in such cognitive control directly and dynamically. On the other hand, the STN activity also affects intracellular signal transduction and gene expression profiles influencing plasticity in other basal ganglia components. The STN may also indirectly contribute to information processing for cognitive control in other brain areas by regulating slower signaling mechanisms. However, the precise correspondence and causal relationship between the STN activity and cognitive processes are not fully understood. To address how the STN activity is involved in cognitive processes for controlling behavior, we applied Designer Receptors Exclusively Activated by Designer Drugs (DREADD)-based chemogenetic manipulation of neural activity to behavioral analysis using a touchscreen operant platform. We subjected mice selectively expressing DREADD receptors in the STN neurons to a five-choice serial reaction time task, which has been developed to quantitatively measure executive function. Chemogenetic suppression of the STN activity reversibly impaired attention, especially required under highly demanding conditions, and increased impulsivity but not compulsivity. These findings, taken together with the results of previous lesion studies, suggest that the STN activity, directly and indirectly, participates in cognitive processing for controlling behavior, and dynamically regulates specific types of subprocesses in cognitive control probably through fast synaptic transmission.
VAE-Sim: A Novel Molecular Similarity Measure Based on a Variational Autoencoder

Molecular similarity is an elusive but core ‘unsupervised’ cheminformatics concept, yet different ‘fingerprint’ encodings of molecular structures return very different similarity values even when using the same similarity metric. Each encoding may be of value when applied to other problems with objective or target functions, implying that a priori none is ‘better’ than the others, nor than encoding-free metrics such as maximum common substructure (MCSS). We here introduce a novel approach to molecular similarity, in the form of a variational autoencoder (VAE). This learns the joint distribution p(z|x) where z is a latent vector and x are the (same) input/output data. It takes the form of a ‘bowtie’-shaped artificial neural network. In the middle is a ‘bottleneck layer’ or latent vector in which inputs are transformed into, and represented as, a vector of numbers (encoding), with a reverse process (decoding) seeking to return the SMILES string that was the input. We train a VAE on over 6 million druglike molecules and natural products (including over one million in the final holdout set). The VAE vector distances provide a rapid and novel metric for molecular similarity that is both easily and rapidly calculated. We describe the method and its application to a typical similarity problem in cheminformatics.
Historical changes in the phenology of British Odonata are related to climate

Responses of biota to climate change take a number of forms including distributional shifts, behavioural changes and life history changes. This study examined an extensive set of biological records to investigate changes in the timing of life history transitions (specifically emergence) in British Odonata between 1960 and 2004. The results show that there has been a significant, consistent advance in phenology in the taxon as a whole over the period of warming that is mediated by life history traits. British odonates significantly advanced the leading edge (first quartile date) of the flight period by a mean of 1.51 ±0.060 (SEM, n=17) days per decade or 3.08±1.16 (SEM, n=17) days per degree rise in temperature when phylogeny is controlled for. This study represents the first review of changes in odonate phenology in relation to climate change. The results suggest that the damped temperature oscillations experienced by aquatic organisms compared with terrestrial organisms are sufficient to evoke phenological responses similar to those of purely terrestrial taxa.
Direct data domain space-time adaptive processing method based on joint sparse representation with single snapshot for MIMO radar

Abstract. To improve the performance of exiting sparse recovery-based space-time adaptive processing (STAP) methods in nonstationary and heterogeneous environments, a STAP method, called the joint sparse representation (JSR)-based direct data domain STAP method using MIMO subarraying radar, is proposed. First, by exploiting the property of waveforms orthogonal diversity of MIMO subarraying radar, the received single snapshot signal of the range cell under test is expressed as multiple snapshot signals. Second, the JSR model of clutter plus target spatiotemporal spectrum estimation is established and the joint sparsity is proved. The spatiotemporal spectrum of clutter and target is then estimated by the typical JSR algorithm. At last, the clutter covariance clutter matrix and the corresponding weight vector of the STAP processor are calculated based on the clutter space-time distribution extracted by the rough priori knowledge of the target. By utilizing the data of the range cell under test only, the proposed method could achieve accurate spatiotemporal spectrum estimation and great performance of clutter suppression. Experimental simulations demonstrate the validity of the proposed method.
Population Genetics of Konosirus punctatus in Chinese Coastal Waters Inferred From Two mtDNA Genes (COI and Cytb)

Konosirus punctatus inhabits areas of significant commercial importance in Chinese coastal waters. Twelve populations distributed all along the Chinese coast were analyzed using two mtDNA genes. The cytochrome oxidase subunit I (COI) and cytochrome b (Cytb) genes were amplified from 242 and 259 individuals, respectively, and fragments of 999 and 415 bp sequence in length were used for analysis. COI and Cytb denoted a high haplotype diversity and low nucleotide diversity. The COI mtDNA gene revealed a high molecular variance within populations and low variance among populations, whereas Cytb showed a high variance among populations and low within populations. FST values obtained for COI and Cytb showed low genetic differentiation among the populations, except for the Zhongshan population where the Cytb gene showed high FST values. The constructed phylogenetic tree and haplotype network tree showed a single lineage, however, Cytb gene data showed that the Zhongshan population has a greater difference level within a population. The present investigation contributed to existing knowledge of the genetic structure of K. punctatus and can be useful for its future conservation.
Multimodal radiomics and cyst fluid inflammatory markers model to predict preoperative risk in intraductal papillary mucinous neoplasms

Abstract. Purpose: Our paper contributes to the burgeoning field of surgical data science. Specifically, multimodal integration of relevant patient data is used to determine who should undergo a complex pancreatic resection. Intraductal papillary mucinous neoplasms (IPMNs) represent cystic precursor lesions of pancreatic cancer with varying risk for malignancy. We combine previously defined individual models of radiomic analysis of diagnostic computed tomography (CT) with protein markers extracted from the cyst fluid to create a unified prediction model to identify high-risk IPMNs. Patients with high-risk IPMN would be sent for resection, whereas patients with low-risk cystic lesions would be spared an invasive procedure. Approach: Retrospective analysis of prospectively acquired cyst fluid and CT scans was undertaken for this study. A predictive model combining clinical features with a cyst fluid inflammatory marker (CFIM) was applied to patient data. Quantitative imaging (QI) features describing radiomic patterns predictive of risk were extracted from scans. The CFIM model and QI model were combined into a single predictive model. An additional model was created with tumor-associated neutrophils (TANs) assessed by a pathologist at the time of resection. Results: Thirty-three patients were analyzed (7 high risk and 26 low risk). The CFIM model yielded an area under the curve (AUC) of 0.74. Adding the QI model improved performance with an AUC of 0.88. Combining the CFIM, QI, and TAN models further increased performance to an AUC of 0.98. Conclusions: Quantitative analysis of routinely acquired CT scans combined with CFIMs provides accurate prediction of risk of pancreatic cancer progression. Although a larger cohort is needed for validation, this model represents a promising tool for preoperative assessment of IPMN.
G9a/GLP-sensitivity of H3K9me2 Demarcates Two Types of Genomic Compartments

In the nucleus, chromatin is folded into hierarchical architecture that is tightly linked to various nuclear functions. However, the underlying molecular mechanisms that confer these architectures remain incompletely understood. Here, we investigated the functional roles of H3 lysine 9 dimethylation (H3K9me2), one of the abundant histone modifications, in three-dimensional (3D) genome organization. Unlike mouse embryonic stem cells (mESCs), inhibition of methyltransferases G9a and GLP in differentiated cells eliminated H3K9me2 predominantly at A-type (active) genomic compartments, and the level of residual H3K9me2 modification was strongly associated with genomic compartments in differentiated cells. Furthermore, chemical inhibition of G9a/GLP in mouse hepatocytes led to the decreased chromatin-nuclear lamina interactions mainly at G9a/GLP sensitive regions (GSRs), the increased degree of genomic compartmentalization, and the up-regulation of hundreds of genes that were associated with alterations of the 3D chromatin. Collectively, our data demonstrated essential roles of H3K9me2 in 3D genome organization.
Enhanced Nitric Oxide Synthesis Through Nitrate Supply Improves Drought Tolerance of Sugarcane Plants

Nitric oxide (NO) is an important signaling molecule associated with many biochemical and physiological processes in plants under stressful conditions. Nitrate reductase (NR) not only mediates the reduction of NO3− to NO2− but also reduces NO2− to NO, a relevant pathway for NO production in higher plants. Herein, we hypothesized that sugarcane plants supplied with more NO3− as a source of N would produce more NO under water deficit. Such NO would reduce oxidative damage and favor photosynthetic metabolism and growth under water limiting conditions. Sugarcane plants were grown in nutrient solution and received the same amount of nitrogen, with varying nitrate:ammonium ratios (100:0 and 70:30). Plants were then grown under well-watered or water deficit conditions. Under water deficit, plants exhibited higher root [NO3−] and [NO2−] when supplied with 100% NO3−. Accordingly, the same plants also showed higher root NR activity and root NO production. We also found higher photosynthetic rates and stomatal conductance in plants supplied with more NO3−, which was associated with increased root growth. ROS accumulation was reduced due to increases in the activity of catalase in leaves and superoxide dismutase and ascorbate peroxidase in roots of plants supplied with 100% NO3− and facing water deficit. Such positive responses to water deficit were offset when a NO scavenger was supplied to the plants, thus confirming that increases in leaf gas exchange and plant growth were induced by NO. Concluding, NO3− supply is an interesting strategy for alleviating the negative effects of water deficit on sugarcane plants, increasing drought tolerance through enhanced NO production. Our data also provide insights on how plant nutrition could improve crop tolerance against abiotic stresses, such as drought.
Biology of the harpactorine assassin bug, Panthous bimaculatus Distant (Hemiptera: Reduviidae) on three different diets

The biology of the predatory reduviid, Panthous bimaculatus Distant, when maintained at a temperature of 32 (±2) °C, 75±5 % relative humidity and 12 (±1) hour’s photoperiod on three different diets, namely, Corcyra cephalonica, artificial diet and Spodoptera litura was investigated. The incubation period was 21.3 ± 0.86, 21.00 ± 0.00, 23.00 ± 0.00 when fed on Corcyra cephalonica, artificial diet and Spodoptera litura respectively. The duration of development for the first, second, third, fourth and fifth instars fed with C. cephalonica was 13.47 ± 0.44, 11.56 ± 0.34, 16.24 ± 0.77, 15.24 ± 0.96 and 18.57 ± 2.53. With artificial diet, the readings were 15.76 ± 1.36, 17.00 ± 3.27, 24.25 ± 5.08, 15.00 ± 0.00 and 17.20 ± 1.57. The developmental time with regard to the feed S. litura was 13.67 ± 0.55, 11.97 ± 0.60, 15.86 ± 1.04, 15.36 ± 1.47 and 16.25 ± 1.82.
Teneriffia sebahatae sp. nov. (Acari: Trombidiformes: Teneriffiidae), the first teneriffiid mite from Turkey

Abstract A new species of the family Teneriffiidae, Teneriffia sebahatae sp. nov., is described. It was collected on the sea shore of Antalya, Turkey. It is distinguished from other species in this genus by the absence of “clasps” on the venter of the gnathosoma, fewer ventral setae and the number of solenidia on tarsi III and IV. A revised key to all the species of the genus Teneriffia is provided. The new species represents the first report of Teneriffiidae from Turkey.
Deep Ancestral Introgression Shapes Evolutionary History of Dragonflies and Damselflies

Introgression is arguably one of the most important biological processes in the evolution of groups of related species, affecting at least 10% of the extant species in the animal kingdom. Introgression reduces genetic divergence between species, and in some cases can be highly beneficial, facilitating rapid adaptation to ever-changing environmental pressures. Introgression also significantly impacts inference of phylogenetic species relationships where a strictly binary tree model cannot adequately explain reticulate net-like species relationships. Here we use phylogenomic approaches to understand patterns of introgression along the evolutionary history of a unique, non-model, relic insect system: dragonflies and damselflies (Odonata). We demonstrate that introgression is a pervasive evolutionary force across various taxonomic levels within Odonata. In particular, we show that the morphologically “intermediate” species of Anisozygoptera (one of the three primary suborders within Odonata besides Zygoptera and Anisoptera), which retain phenotypic characteristics of the other two suborders, experienced high levels of introgression probably coming from zygopteran genomes. Additionally, we found evidence for multiple cases of deep inter-familial ancestral introgression. However, weaker evidence of introgression was found within more recently diverged focal clades: Aeshnidae, Gomphidae+Petaluridae and Libellulidae.
Mitigation of the Adverse Effects of the El Niño (El Niño, La Niña) Southern Oscillation (ENSO) Phenomenon and the Most Important Diseases in Avocado cv. Hass Crops

Areas cultivated with Hass avocado crops in Colombia have growth rapidly. One of the major limitations is the avocado wilt complex disease (AWC) caused by biotic and abiotic factors which have increased under the El Niño southern oscillation ENSO phenomenon (El Niño, La Niña). The objective of this study was to evaluate different strategies for mitigating the adverse effects associated with the ENSO phenomenon and AWC in avocado crops. We evaluated native materials, mulches, and parameters associated with the production of seedlings and planting practices in the field. The response variables tested were plant development, incidence, severity, mortality, and microbial dynamics, among others. The results indicated that native genotypes of Persea americana had different levels of adaptability to drought and flooding conditions. These genotypes also showed some degree of resistance to Phytophthora cinnamomi and Verticillium sp. infection with several degrees of rootstock-scion incompatibility with the Hass cultivar. In addition, mulch reduced the variability of soil moisture and temperature in the soil profile. Adequate selection of genotypes and new tools for planting have decreased the susceptibility to adverse effects associated with the ENSO phenomenon and the incidence and mortality caused by diseases under drought and flooding conditions. This work presents alternatives to mitigate adverse effects of climate variability in avocado crops under tropical conditions.
Elores : A New Antibiotic Adjuvant Entity Active Against Metallo-β-Lactamases Producing Organisms

The aim of the present study was to investigate the prevalence of New Delhi metallo-β-lactamase (NDM-1) in multi-drug resistant Enterobacteriaceae particularly Escherichia coli and Klebsiella pneumoniae and in nonfermenting gram-negative bacilli (Acinetobacter baumannii and Pseudomonas aeruginosa) in India and compared the antibacterial activity of Elores with other βlactam antibiotics against these NDM-1 producing isolates. Phenotypic characterization of the isolates was done using imipenem and imipenem+EDTA (ethylenediaminetetra acetic acid) disc diffusion method. The prevalence of NDM-1 among these isolates was studied using polymerase chain reaction (PCR). Antibiotic susceptibility study was performed according to the Clinical Laboratory Standards Institute method (CLSI). Out of the five hundred forty one isolates, four hundred sixty four isolates (85.7 %) were found to be carbapenem resistant. Further screening of these isolates revealed approximately 81.7 % (379/464) isolates were found to be NDM-1 positive through PCR method. Elores appeared to be most active antibacterial agents with 95.0% susceptibility to NDM-1 positive K. pneumoniae followed by A. baumannii (94.0 %), E. coli (93.5%) and P. aeruginosa (92.8 %), however, it showed 1 to 2% resistant and 3 to 6 % intermediate response to these isolates. Among the penems (imipenem+cilastatin, doripenem and meropenem), imipenem plus cilastatin showed 100 % resistant to A. baumannii, P. aeruginosa and K. pneumoniae against NDM-1 producing isolates whereas doripenem exhibited 5.5% susceptibility and 79.6% resistant to E. coli followed by A. baumannii (4.5% susceptibility, 86.5% resistance), K. pneumoniae (1.6% susceptibility, 91.6% resistance) and P. aeruginosa (1.2% susceptibility, 95.2 % resistance) while meropenem showed 1 to 2 % susceptibility, 88 to 97% resistance and 1 to 8 % intermediate response against E. coli, K. pneumoniae, A. baumannii and P. aeruginosa. Piperacillin plus tazobactam demonstrated 88 to 93 % resistance, and 6 to 7 % intermediate response and only 1 to 3 % susceptibility response. In conclusion, Elores was the most active which showed 92 to 95 % susceptibility therefore can be a potent antibacterial agent for the treatment of infections caused by carbapenemase producing A. baumannii.