Miracle-dz/UniFAR-FTUs huggingface dataset:
Hyperspectral image classification by optimizing convolutional neural networks based on information theory and 3D-Gabor filters

ABSTRACT Recently, deep learning approaches, especially convolutional neural networks (CNNs), have been employed for feature extraction (FE) and hyperspectral images (HSIs) classification. The CNN, with all its capabilities, suffers from the input data size and the vast number of parameters, particularly the weights of fully connected (FC) layers. These problems become bottlenecks in real-time systems and cause overfitting in many applications. This paper presents two methods for solving these problems: 1) FE from the input data by applying 3D-Gabor filters, and 2) optimizing the weights of the FC layer based on information theory to decrease the complexity of the FC layer. Traditional 3D-Gabor filters include steerable characteristics that are of interest. Furthermore, they can efficiently extract the spatial features including textures and edges. They consequently provide more generalized and optimized features, which reduce the burden of FE and classification in CNNs. On the other hand, by analysing the weights in the FC layer, from a statistical distribution point of view, each column of the weights follows a coloured Gaussian distribution. Based on this analysis, a method is proposed to optimize the FC layer. The optimization criterion is based on singular value decomposition (SVD) and QR decomposition where Q is an orthogonal matrix and R is a right triangular matrix. The spectral and spatial features are extracted by 3D-Gabor filters. Then, they are classified using CNN which is optimized based on SVD-QR in the training process. The proposed method is tested on Indian Pines, Pavia University, and Kennedy Space Center (KSC) datasets and the quantitative and visual results show the superiority of the proposed method compared to conventional approaches.
Aircraft detection in remote sensing images based on deconvolution and position attention

ABSTRACT Motivated by the development of deep convolution neural networks (DCNNs), the aircraft detection from remote sensing images has gained tremendous progress. However, due to complex background and multi-scale characteristics, it remains a challenge in remote sensing detection. In this paper, we propose a two-stage aircraft detection method based on deep neural networks, which integrates Deconvolution operation with Position Attention mechanism (DPANet). Specifically, considering that remote sensing images are taken from the top-down perspective, which leads to significant external structural characteristic, we introduce a deconvolution module to capture the external structural feature representation of aircraft during the feature map generation process. Moreover, aiming at reducing the error detections caused by complex background in remote sensing, we propose a position attention module in the second stage. By calculating the feature similarity between any two pixels of the target feature map, DPANet can extract the complicated internal structure feature representation of aircraft, which improve the ability to distinguish background and aircraft. By integrating the deconvolution and position attention modules, DPANet can provide better representation ability for the structural characteristic of aircraft in remote sensing images. Experimental results show that the proposed method can effectively reduce the error detections and improve the accuracy of the aircraft detection.
Novitates neocaledonicae XI: A new endemic species of Garcinia L. (Clusiaceae), with an emended description of G. virgata Vieill. ex Guillaumin

ABSTRACT A new species, Garcinia urceolata Munzinger, Bruy & M. Pignal, sp. nov. (Clusiaceae), is described from New Caledonia. It is restricted to North Province, from the Tchamba valley in the south to Mandjélia in the north of the main island of Grande-Terre, occurring in dense humid rainforests on non-ultramafic substrate. Material of this small tree species was first collected more than fifty years ago but was confused with G. virgata Vieill. ex Guillaumin as both taxa have small leaves. Garcinia urceolata, sp. nov. differs from G. virgata in a number of features of the leaves, flowers and fruits. Garcinia urceolata, sp. nov. also grows at higher elevation and in wetter conditions than G. virgata. Both species are purported to have dehiscent fruit, along with other New Caledonian members of the genus, a distinctive character that was used to justify the description of the genus Septogarcinia Kosterm. , which is no longer regarded as distinct from Garcinia L. Line drawings and colour photos are provided for both the new species and for G. virgata for comparison, along with a preliminary risk of extinction assessment for each of them, which indicates that G. urceolata, sp. nov. is Vulnerable (VU) while G. virgata is Near Threatened (NT).
Mending a broken heart: In vitro, in vivo and in silico models of congenital heart disease

ABSTRACT Birth defects contribute to ∼0.3% of global infant mortality in the first month of life, and congenital heart disease (CHD) is the most common birth defect among newborns worldwide. Despite the significant impact on human health, most treatments available for this heterogenous group of disorders are palliative at best. For this reason, the complex process of cardiogenesis, governed by multiple interlinked and dose-dependent pathways, is well investigated. Tissue, animal and, more recently, computerized models of the developing heart have facilitated important discoveries that are helping us to understand the genetic, epigenetic and mechanobiological contributors to CHD aetiology. In this Review, we discuss the strengths and limitations of different models of normal and abnormal cardiogenesis, ranging from single-cell systems and 3D cardiac organoids, to small and large animals and organ-level computational models. These investigative tools have revealed a diversity of pathogenic mechanisms that contribute to CHD, including genetic pathways, epigenetic regulators and shear wall stresses, paving the way for new strategies for screening and non-surgical treatment of CHD. As we discuss in this Review, one of the most-valuable advances in recent years has been the creation of highly personalized platforms with which to study individual diseases in clinically relevant settings. Summary: In vitro, in vivo and in silico models of congenital heart disease provide important insights into the causes, evolution and pathological effects of congenital structural heart disease – a group of largely heterogenous disorders with substantial morbidity – and aid in designing effective therapies.
Pure and Ca-doped LaCoO 3 Nanopowders: Sol-Gel Synthesis, Characterization and Magnetic Properties

ABSTRACT This work is focused on the sol-gel synthesis of pure and Ca-doped LaCoO 3 nanopowders. The samples were prepared starting from methanolic solutions of cobalt (II) acetate (Co(CH 3 COO) 2 . 4H 2 O), lanthanum (III) nitrate (La(NO 3 ) 3 . 6H 2 O) and calcium (II) acetate (Ca(CH 3 COO) 2 . H 2 O). After solvent evaporation, the obtained powders were dried under vacuum and subsequently treated in air up to 1273 K. The system evolution under thermal annealing was studied by X-ray Diffraction (XRD) and Transmission Electron Microscopy (TEM), while the chemical composition was analyzed by X-ray Photoelectron (XPS) and X-ray Excited Auger electron (XE-AES) spectroscopies. The temperature and field dependence of the magnetic properties of the Ca-doped samples were investigated, and compared to those of the corresponding pure LaCoO 3 powders. INTRODUCTION Perovskite-type oxides of rare-earth and transition metals (LaMO 3 , M = Co, Mn, Fe…) are being increasingly investigated due to their potential applications in heterogeneous catalysis, oxygen sensing and Solid Oxide Fuel Cells (SOFCs) [1]. Among them, lanthanum cobaltite is particularly promising, thanks to the accessibility for cobalt of the II and III oxidation states. Furthermore, the partial substitution of lanthanum by strontium and calcium improves the material functional properties,
Investigation of Direct Electrooxidation Behavior of NADH at a Chemically Modified Glassy Carbon Electrode

In this study, the composite material that made up polyglycine/3d-4f hybrid-metallic cyano-bridged mixed coordination polymers (CyMCP) was successfully decorated onto a glassy carbon rotating disk electrode (GC RDE) using electrodeposition. The voltammetric behavior of NADH showed typical direct electrooxidation characteristics on the modified GC electrode. Our polyglycine/CyMCP-modified GC RDE was able to measure the apparent heterogeneous electron transfer rate constant of NADH during its direct electrooxidation by preventing fouling effects on the working electrode, which would generally cause a decrease in the oxidative peak current of NADH. In addition, differential pulse voltammetry provided a large linear range between the oxidative peak current and the concentration of NADH from 2‐1500 μM at the polyglycine/CyMCP/GC electrode. Finally, the apparent heterogeneous electron transfer rate constant (ks NADH ) of NADH was determined to be 1.73 × 10 −2 cm ·s −1 using the polyglycine/CyMCP-modified GC RDE.
Spatiotemporal control of actomyosin contractility by MRCKβ signaling drives phagocytosis

Phagocytosis requires myosin-generated contractile force to regulate actin dynamics. However, little is known about the molecular mechanisms that guide this complex morphodynamic process. Here we show that particle binding to Mer Tyrosine Kinase (MerTK), a widely expressed phagocytic receptor, stimulates phosphorylation of the Cdc42 GEF Dbl3 in the retinal pigment epithelium (RPE), triggering activation of MRCKβ and its co-effector N-WASP that cooperate to deform the membrane into cups. Continued MRCKβ activity then drives recruitment of a mechanosensing bridge enabling transmission of the cytoskeletal force required for cup closure and particle internalization. MRCKβ is also required for Fc receptor-mediated phagocytosis by macrophages. In vivo, MRCKβ is essential for RPE phagocytosis of photoreceptor debris and, hence, retinal integrity. MerTK-independent activation of MRCKβ signaling by a phosphomimetic Dbl3 mutant rescues phagocytosis in retinitis pigmentosa RPE cells lacking functional MerTK. Thus, conserved MRCKβ signaling controls spatiotemporal regulation of actomyosin contractility to guide actomyosin dynamics-driven phagocytosis and represents the principle phagocytic effector pathway downstream of MerTK.
Antiviral Antibody Epitope Selection is a Heritable Trait

There is enormous variability in human immune responses to viral infections. However, the genetic factors that underlie this variability are not well characterized. We used VirScan, a high-throughput viral epitope scanning technology, to analyze the antibody binding specificities of twins and SNP-genotyped individuals. These data were used to estimate the heritability and identify genomic loci associated with antibody epitope selection, response breadth, and the control of Epstein-Barr Virus (EBV) viral load. We identified 4 epitopes of EBV that were heritably targeted, and at least two EBNA-2 binding specificities that were associated with variants in the MHC class-II locus. We identified an EBV serosignature that predicted viral load in white blood cells and was associated with genetic variants in the MHC class-I locus. Our study provides a new framework for identifying genes important for pathogen immunity, with specific implications for the genetic architecture of EBV humoral responses and the control of viral load.
The natural sequence of events in larval settlement and metamorphosis of Hydroides elegans (Polychaeta; Serpulidae)

The broadly distributed serpulid worm Hydroides elegans has become a model organism for studies of marine biofouling, development and the processes of larval settlement and metamorphosis induced by surface microbial films. Contrasting descriptions of the initial events of these recruitment processes, whether settlement is induced by (1) natural multi-species biofilms, (2) biofilms composed of single bacterial species known to induce settlement, or (3) a bacterial extract stimulated the research described here. We found that settlement induced by natural biofilms or biofilms formed by the bacterium Pseudoalteromonas luteoviolacea is invariably initiated by attachment and secretion of an adherent and larva-enveloping primary tube, followed by loss of motile cilia and ciliated cells and morphogenesis. The bacterial extract containing complex tailocin arrays derived from an assemblage of phage genes incorporated into the bacterial genome appears to induce settlement events by destruction of larval cilia and ciliated cells, followed by attachment and primary-tube formation. Similar destruction occurred when precompetent larvae and larvae of a nudibranch gastropod were exposed to the extract, neither of which metamorphosed. We further argue that larvae that lose their cilia before attachment would be swept away from the sites that stimulated settlement by the turbulent flow characteristic of most marine habitats.
A Class of Simple Biomolecular Antithetic Proportional-Integral-Derivative Controllers

Proportional-Integral-Derivative (PID) feedback controllers have been the most widely used controllers in the industry for almost a century. This is mainly due to their simplicity and intuitive operation. Recently, motivated by their success in various engineering disciplines, PID controllers found their way into molecular biology. In this paper, we consider the mathematical realization of (nonlinear) PID controllers via biomolecular interactions in both the deterministic and stochastic settings. We propose several simple biomolecular PID control architectures that take into consideration the biological implementation aspect. We verify the underlying PID control structures by performing a linear perturbation analysis and examine their effects on the (deterministic and stochastic) performance and stability. In fact, we demonstrate that different proportional controllers exhibit different capabilities of enhancing the dynamics and reducing variance (cell-to-cell variability). Furthermore, we propose a simple derivative controller that is mathematically realized by cascading the antithetic integral controller with an incoherent feedforward loop without adding any additional species. We demonstrate that the derivative component is capable of enhancing the transient dynamics at the cost of boosting the variance, which agrees with the well known vulnerability of the derivative controller to noise. We also show that this can be mitigated by carefully designing the inhibition pathway of the incoherent feedforward loop. Throughout the paper, the stochastic analysis is carried out based on a tailored moment-closure technique and is also backed up by simulations.
A beta-glucosidase of an insect herbivore determines both toxicity and deterrence of a dandelion defense metabolite

Gut enzymes can metabolize plant defense metabolites and thereby affect the growth and fitness of insect herbivores. Whether these enzymes also influence herbivore behavior and feeding preference is largely unknown. We studied the metabolization of taraxinic acid β-D-glucopyranosyl ester (TA-G), a sesquiterpene lactone of the common dandelion (Taraxacum officinale) that deters its major root herbivore, the common cockchafer larva (Melolontha melolontha). We demonstrate that TA-G is rapidly deglycosylated and conjugated to glutathione in the insect gut. A broad-spectrum M. melolontha β-glucosidase, Mm_bGlc17, is sufficient and necessary for TA-G deglycosylation. Using plants and insect RNA interference, we show that Mm_bGlc17 reduces TA-G toxicity. Furthermore, Mm_bGlc17 is required for the preference of M. melolontha larvae for TA-G deficient plants. Thus, herbivore metabolism modulates both the toxicity and deterrence of a plant defense metabolite. Our work illustrates the multifacteted roles of insect digestive enzymes as mediators of plant-herbivore interactions.
minicore: Fast scRNA-seq clustering with various distances

Single-cell RNA-sequencing (scRNA-seq) analyses typically begin by clustering a gene-by-cell expression matrix to empirically define groups of cells with similar expression profiles. We describe new methods and a new open source library, minicore, for efficient k-means++ center finding and k-means clustering of scRNA-seq data. Minicore works with sparse count data, as it emerges from typical scRNA-seq experiments, as well as with dense data from after dimensionality reduction. Minicore’s novel vectorized weighted reservoir sampling algorithm allows it to find initial k-means++ centers for a 4-million cell dataset in 1.5 minutes using 20 threads. Minicore can cluster using Euclidean distance, but also supports a wider class of measures like Jensen-Shannon Divergence, Kullback-Leibler Divergence, and the Bhattacharyya distance, which can be directly applied to count data and probability distributions. Further, minicore produces lower-cost centerings more efficiently than scikit-learn for scRNA-seq datasets with millions of cells. With careful handling of priors, minicore implements these distance measures with only minor (<2-fold) speed differences among all distances. We show that a minicore pipeline consisting of k-means++, localsearch++ and minibatch k-means can cluster a 4-million cell dataset in minutes, using less than 10GiB of RAM. This memory-efficiency enables atlas-scale clustering on laptops and other commodity hardware. Finally, we report findings on which distance measures give clusterings that are most consistent with known cell type labels. Availability The open source library is at https://github.com/dnbaker/minicore. Code used for experiments is at https://github.com/dnbaker/minicore-experiments.
Divergent epigenetic profiles from two differentially impacted wild populations of estuarine cordgrass (Sporobolus alterniflorus)

The effects of urbanization on watershed ecosystems present critical challenges to modern survival. Organisms in urbanized areas experience high rates of evolutionary change, but genetic adaptation alone cannot mitigate the rapid and severe effects of urbanization on biodiversity. Highly resilient, foundation species are key to maintaining an ecosystem’s integrity in the face of urban stressors. However, the rapid collapse and disappearance of watershed ecosystems calls into question the extent to which we can rely on such species for their services. Our research investigates the molecular mechanisms by which the foundation ecosystems provider, Sporobolus alterniflorus, adapts to life in an urbanized environment. To elucidate these mechanisms, we quantified changes in global DNA methylation (% 5-mC) as a result of acute heat stress. Specimens from two differentially impacted populations across an urban to suburban geographical transect formed the basis of this study. These two populations of Sporobolus alterniflora exhibit inverse global DNA methylation patterns when exposed to the same acute heat stress. Our findings suggest that epigenetic mechanisms, such as DNA methylation, control rapid and transient adaptation, in the form of differential stress responses, to distinct environment challenges. Highlights for manuscript submission ▪ estuarine grasses native to the Bronx River, NY face stresses associated with low dissolved oxygen and urbanization ▪ differentially impacted populations of estuarine grasses exhibit inverse global DNA methylation profiles in response to acute heat stress ▪ DNA methylation may represent a mechanism by which plants transiently respond to environmental stressors, and this may represent a form of rapid adaptive evolution ▪ stress priming by transgenerational epigenetic modification may enhance fitness in grasses native to the heavily impacted Bronx River estuary
Comparative genome analysis using sample-specific string detection in accurate long reads

Motivation Comparative genome analysis of two or more whole-genome sequenced (WGS) samples is at the core of most applications in genomics. These include discovery of genomic differences segregating in population, case-control analysis in common diseases, and rare disorders. With the current progress of accurate long-read sequencing technologies (e.g., circular consensus sequencing from PacBio sequencers) we can dive into studying repeat regions of genome (e.g., segmental duplications) and hard-to-detect variants (e.g., complex structural variants). Results We propose a novel framework for addressing the comparative genome analysis by discovery of strings that are specific to one genome (“samples-specific” strings). We have developed an accurate and efficient novel method for discovery of samples-specific strings between two groups of WGS samples. The proposed approach will give us the ability to perform comparative genome analysis without the need to map the reads and is not hindered by shortcomings of the reference genome. We show that the proposed approach is capable of accurately finding samples-specific strings representing nearly all variation (> 98%) reported across pairs or trios of WGS samples using accurate long reads (e.g., PacBio HiFi data). Availability The proposed tool is publicly available at https://github.com/Parsoa/PingPong.
The Marburg Collection: A Golden Gate DNA Assembly Framework for Synthetic Biology Applications in Vibrio natriegens

Vibrio natriegens is known as the world’s fastest growing organism with a doubling time of less than 10 minutes. This incredible growth speed empowers V. natriegens as a chassis for synthetic and molecular biology, potentially replacing E. coli in many applications. While first genetic parts have been built and tested for V. natriegens, a comprehensive toolkit containing well-characterized and standardized parts did not exist. To close this gap, we created the Marburg Collection – a highly flexible Golden Gate Assembly-based cloning toolbox optimized for the emerging chassis organism V. natriegens. The Marburg Collection overcomes the paradigm of plasmid construction – integrating inserts into a backbone – by enabling the de novo assembly of plasmids from basic genetic parts. This allows users to select the plasmid replication origin and resistance part independently, which is highly advantageous when limited knowledge about the behavior of those parts in the target organism is available. Additional design highlights of the Marburg Collection are novel connector parts, which facilitate modular circuit assembly and, optionally, the inversion of individual transcription units to reduce transcriptional crosstalk in multigene constructs. To quantitatively characterize the genetic parts contained in the Marburg Collection in V. natriegens, we developed a reliable microplate reader measurement workflow for reporter experiments and overcame organismspecific challenges. We think the Marburg Collection with its thoroughly characterized parts will provide a valuable resource for the growing V. natriegens community.