Miracle-dz/UniFAR-FTUs huggingface dataset:
Ship Identification Based on Improved SSD

Aiming at the low accuracy of ship recognition at sea and the fact that traditional target detection algorithms are greatly affected by the environment, this paper proposes a marine ship recognition method based on an improved SSD (Single shot multibox detector). On the basis of the original SSD algorithm, the original backbone network VGG16 was first replaced with resnet50, and the convolution in the last 5 layers of the Resnet50 Conv4_x structure was replaced by a hole convolution, followed by the removal of Conv5_x, followed by the subsequent prediction feature layer. A multiscale receptive field module was introduced to improve the feature extraction capabilities of the model. Finally, the high-level semantic information is enhanced by introducing a CBAM attention mechanism to improve the detection ability of the model. The experimental results show that the map of the algorithm is 94.5%, which is 17.7% higher than the original SSD algorithm, and the improved SSD algorithm has a better recognition effect of ships at sea.
Substation work ticket identification and extraction algorithm based on multi-task model

With the large-scale construction of new substations and the intelligent upgrading of existing substations, higher requirements have been put forward for efficient and intelligent maintenance of substations. In practical applications, the substation work ticket forms are complex and diverse, and the current mainstream work ticket key information extraction algorithms cannot meet the work needs. This paper proposed an intelligent recognition system for extracting safety measures from a work ticket in a substation. Based on the traditional text detection algorithm, a Multi-task network for text detection, frame extraction and form classification structure was proposed. The text recognition network used CRNN+CTC to train and tested the multi-model text recognition network on the work ticket interface text image data set. Advanced functions such as automatic generation, automatic execution, calibration and restoration of operation steps from a work ticket to safety measures in the substation were realized. In order to prove the effectiveness of the algorithm, an experimental study was carried out, and a comparative experiment was carried out in text detection and text recognition. The module has been tested in Yangzhou Power Supply Company of State Grid, and the results show that the scheme has good feasibility and effectively improves the work efficiency of operation and maintenance personnel.
Reconstruction From Limited-Angle Projections Based on a Transformation

ABSTRACT Limited angle computed tomography (CT) is common in medical and industrial applications where incomplete projection data can cause artifacts in the reconstructed image. we propose a new algorithm for reconstructing a density function , (an image), in the plane from a limited number of Radon projections on a range of angles for some acute angle Assuming that is subjected to a linear transformation to produce a new image ; the new image is then recovered. In fact, the well-known relation between the desired image and the transformed image, in the transform domain, is used. This relation allows us to map a uniformly distributed view angles over to some range of view angles that are available for the original image. It is known that uniformizing the view angles of projections improves the performance of some algorithms such as the filter back projection algorithm. In this way, the transformed image is reconstructed from the uniformly distributed angles that correspond to a limited number of projections. The effectiveness of the proposed approach is validated by simulation and by applications to synthetic images.
Morphometric analysis of the terminal ductal lobular unit architecture in human breast

The major lactiferous ducts of the human breast branch out and ultimately end at terminal ductal lobular units (TDLUs). These glandular structures are the source of milk upon lactation, and also the most common origin of breast cancer. Despite their functional and clinical importance, the three dimensional (3D) architecture of TDLUs has remained undetermined, largely due to their absence in rodent animal models. By utilizing recent technological advances in optical tissue clearing and microscopy, we imaged the 3D structure of healthy human breast tissue to determine whether general branching patterns or cell type specific niches exist in the TDLU. Our data demonstrate that TDLUs have a consistent shape and their branch parameters are largely comparable between different TDLUs and individuals irrespective of age or parity. Simulation of TDLU branching morphogenesis in 3D by mathematical modelling suggests that evolutionarily conserved mechanisms regulate mammary gland branching in humans and mice, despite their anatomical differences. The data also demonstrate a new level of organization within the TDLU structure identifying a main branch that dominates in bifurcation events and exhibits a more duct-like keratin expression pattern. In all, our data provide the first structural insights into 3D human breast anatomy and branching, and exemplify the power of volumetric imaging in deeper understanding of human breast biology. Graphical Abstract
Pathology of natural infection with highly pathogenic avian influenza virus (H5N1) clade 2.3.4.4b in wild terrestrial mammals in the United States in 2022

This article describes the first detections of disease due to natural infection with highly pathogenic avian influenza virus (HPAIv) H5N1 of the Eurasian lineage goose/Guangdong clade 2.3. 4.4b in wild terrestrial mammals throughout the United States during 2021-2022. Affected mammalian species include 50 red foxes (Vulpes vulpes), 6 striped skunks (Mephitis mephitis), 4 raccoons (Procyon lotor), 2 bobcats (Lynx rufus), 2 Virginia opossums (Didelphis virginiana), 1 coyote (Canis latrans), 1 fisher (Pekania pennanti), and 1 gray fox (Urocyon cinereoargenteus). Infected mammals primarily exhibited neurological signs. Necrotizing meningoencephalitis, interstitial pneumonia, and myocardial necrosis were the most common lesions; however, species variations in lesion distribution were observed. Genotype analysis of sequences from 48 animals indicates that these cases represent spillover infections from wild birds.
Improving the sensitivity of fluorescence-based immunoassays by time-resolved and spatial-resolved measurements

Detection of target molecules, such as proteins, antibodies, or specific DNA sequences, is critical in medical laboratory science. Commonly used assays rely on tagging the target molecules with fluorescent probes. These are then fed to high-sensitivity detection systems. Such systems typically consist of a photodetector or camera and use time-resolved measurements that require sophisticated and expensive optics. Magnetic modulation biosensing (MMB) is a novel, fast, and sensitive detection technology that has been used successfully to detect viruses such as Zika and SARS-CoV-2. While this powerful tool is known for its high analytical and clinical sensitivity, the current signal-processing method for detecting the target molecule and estimating its dose is based on time-resolved measurements only. To improve the MMB-system performance, we propose here a novel signal processing algorithm that uses both temporally and spatially resolved measurements. We show that this combination significantly improves the sensitivity of the MMB-based assay. To evaluate the new method statistically, we performed multiple dose responses of Human Interleukin 9 (IL −8) on different days. Compared to standard time-resolved methods, the new algorithm provides a 2-3 fold improvement in detection limit and a 25% improvement in quantitative resolution.
Loss of daylength sensitivity by splice site mutation in Cannabis

Adaptations to high latitude photoperiods have been under positive selection during the domestication of many short-day (SD) flowering crops. Photoperiod insensitivity (auto-flowering) in drug-type Cannabis sativa circumvents the need for SD flowering requirements making outdoor cultivation in high latitudes possible. However, the benefits of photoperiod insensitivity are counterbalanced by low cannabinoid contents and poor flower quality in auto-flowering genotypes. Despite recent legalization in some countries, a mechanistic understanding of photoperiod insensitivity in cannabis is still lacking. Herein, we identify a splice site mutation within PSEUDO-RESPONSE REGULATOR 37 (CsPRR37) in auto-flowering cannabis that causes photoperiod insensitivity. Using a combination of GWAS, fine mapping, and gene expression analyses, our results strongly indicate CsPRR37 as the most likely candidate for causing photoperiod insensitivity. Research into the pervasiveness of this mutation and others effecting flowering time will help elucidate its domestication history and advance cannabis breeding towards a more sustainable outdoor cultivation system.
Modulating Nucleic Acid Phase Transitions as a Mechanism of Action for Cell-Penetrating Antimicrobial Peptides

Antimicrobial peptides (AMPs) are a vital part of the immune system that helps combat bacterial infections by disrupting the bacterial cell membrane or interacting with intracellular targets. However, the mechanisms by which AMPs act on intracellular targets are not well understood. Using machine learning-based sequence analysis, we have discovered that a significant number of AMPs have a strong tendency to form liquid-like condensates in the presence of nucleic acids, a process known as phase separation. We have demonstrated that this phase separation propensity is linked to the effectiveness of the AMPs in inhibiting transcription and translation in vitro, as well as their ability to compact nucleic acids and form clusters with bacterial nucleic acids in bacterial cells. We propose that the AMP-driven compaction of nucleic acids and modulation of their phase transitions constitute a previously unrecognised mechanism by which AMPs exert their antibacterial effects. These findings open up exciting possibilities for the development of antimicrobials that target nucleic acid phase transitions.
Disequilibrium between BRCA1 and BRCA2 Circular and Messenger RNAs Plays a Role in Breast Cancer

Breast cancer is a frequent disease for which the discovery of markers for early detection or prognostic assessment remains challenging. Circular RNAs (circRNAs) are single-stranded structures in closed loops, produced by backsplicing. CircRNA and messenger RNA (mRNA) are generated cotranscriptionally and backsplicing and linear splicing compete against each other. As mRNAs are key players in tumorigenesis, we hypothesize that a balance disruption between circRNAs and mRNAs could promote breast cancer. Hence, we developed an assay for a simultaneous study of circRNAs and mRNAs, called Splice and Expression Analyses by exon Ligation and High Throughput Sequencing (SEALigTHS). Following SEALigHTS validation for BRCA1 and BRCA2, our hypothesis was tested using an independent research set of 95 pairs of tumour and adjacent normal breast tissues. On this research set, ratios of BRCA1 and BRCA2 circRNAs/mRNAs were significantly lower in tumour breast tissue compared to normal tissue (p=1.6e-09 and p=4.4e-05 for BRCA1 and BRCA2, respectively). Overall, we developed an innovative method to study linear and backsplicing, described the repertoire of BRCA1 and BRCA2 circRNAs, including 10 novel ones, and showed for the first time that a disequilibrium between BRCA1 and BRCA2 circRNAs and mRNAs plays a role in breast cancer.
Efficient computation of Sommerfeld integral tails – methods and algorithms

A review is presented of the most effective methods for the computation of Sommerfeld integral tails. Such integrals, which are often oscillatory, singular and divergent, commonly arise in layered media Green functions. The mathematical foundations of various pertinent methods are discussed in detail and their performance is illustrated by relevant numerical examples. The associated algorithms are given in pseudocode for their easy computer implementation.
Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch

Molecular dynamics simulations reveal site-specific mechanisms of Mg2+ ions in conformational transitions of the SAM/SAH riboswitch for ligand and ribosome binding. The SAM/SAH riboswitch binds S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) with similar affinities. Mg^2+ is generally known to stabilize RNA structures by neutralizing phosphates, but how it contributes to ligand binding and conformational transition is understudied. Here, extensive molecular dynamics simulations (totaling 120 μs) predicted over 10 inner-shell Mg^2+ ions in the SAM/SAH riboswitch. Six of them line the two sides of a groove to widen it and thereby pre-organize the riboswitch for ligand entry. They also form outer-shell coordination with the ligands and stabilize an RNA-ligand hydrogen bond, which effectively diminishes the selectivity between SAM and SAH. One Mg^2+ ion unique to the apo form maintains the Shine–Dalgarno sequence in an autonomous mode and thereby facilitates its release for ribosome binding. Mg^2+ thus plays vital roles in SAM/SAH riboswitch function.
Homozygous haplotype deficiency in Manech Tête Rousse dairy sheep revealed a nonsense variant in MMUT gene affecting newborn lamb viability

Recessive deleterious variants are known to segregate in livestock populations as in human, and some may cause lethality when homozygous. By scanning the genome of 6,845 Manech Tête Rousse dairy sheep using phased 50k SNP genotypes and pedigree data, we searched for deficiency in homozygous haplotype (DHH). Five Manech Tête Rousse deficient homozygous haplotypes (MTRDHH1 to 5) were identified with a homozygous deficiency ranging from 84% to 100%. These haplotypes are located on OAR1 (MTRDHH2 and 3), OAR10 (MTRDHH4), OAR13 (MTRDHH5) and OAR20 (MTRDHH1), and have frequencies ranging from 7.8% to 16.6%. When comparing at-risk mating between DHH carriers to safe mating between non-carriers, two DHH (MTRDHH1 and 2) showed significant effects on decreasing artificial insemination success and/or increasing stillbirth rate. We particularly investigated the MTRDHH1 haplotype highly increasing stillbirth rate, and we identified a single nucleotide variant (SNV) inducing a premature stop codon (p.Gln409*) in the MMUT gene (methylmalonyl-CoA mutase) by using a whole genome sequencing (WGS) approach. We generated homozygous lambs for the MMUT mutation by oriented mating, and most of them died within the first 24h after birth without any obvious clinical defect. RT-qPCR and western blotting performed on post-mortem liver and kidney biological samples showed a decreased expression of MMUT mRNA in the liver and absence of a full-length MMUT protein in mutated homozygous lambs. In parallel, MTRDHH4 and MTRDHH5 showed partial association with variants in RXFP2 and ASIP genes, respectively, already known to control horned/polled and coat color phenotypes in sheep, two morphological traits accounting in the MTR breed standard. Further investigations are needed to identified the supposed recessive deleterious variant hosted by MTRDHH2 and MTRDHH3. Anyway, an appropriate management of these haplotypes/variants in the MTR dairy sheep selection program should increase the overall fertility and lamb survival. Author Summary In this article, we used reverse genetics screen in ovine using large genotype data available in the framework of genomic selection program in Manech Tête Rousse dairy sheep. We identified five genomic regions with a highly significant deficit in homozygous animal. These regions are thus supposed to host recessive deleterious mutations. In one of these genomic regions, we identified a nonsense mutation in MMUT that alters the functioning of this essential gene of cell metabolism, causing perinatal mortality of homozygous lambs. In this work, we also identified other regions possibly associated with morphological appearance part of the breed standard such as polledness and coat color. Increasing knowledge in these genomic regions will help the future genetic management of the Manech Tête Rousse breed, particularly to reduce lamb mortality.
Analyticity and metric transitivity on the torus

Suppose we are given an analytic divergence free vector field $(X,Y)$ on the standard torus. We can find constants $a$ and $b$ and a function $F(x,y)$ of period one in both $x$ and $y$ such that $(X,Y)=(a-F_y,b+F_x)$. For a given $F$, let $P$ be the map sending $(x,y)$ into $(F_y(x,y),-F_x(x,y))$. Let $A$ be the image of the torus under this map and let $B$ be the image under this map of the set of points $(x,y)$ at which $F_{xx}F_{yy}-(F_{xy})^2$ vanishes. For any point $(a,b)$ in the complement of the interior of $A$, the flow on the torus arising from the differential equations $dx/dt=a-F_y(x,y)$, $dy/dt=b+F_x(x,y)$ is metrically transitive if and only if $a/b$ is irrational. For any point in $A$ but not in $B$ the flow is not metrically transitive. Moreover, if $a/b$ is irrational but the flow on the torus is not metrically transitive and we use our differential equations to define a flow in the entire plane (rather than on the torus), this flow has a nonstationary periodic orbit. It is an open question whether a point $(a,b)$ in the interior of $A$ can give rise to a metrically transitive flow.
Deep audio embeddings for vocalisation clustering

The study of non-human animals’ communication systems generally relies on the transcription of vocal sequences using a finite set of discrete units. This set is referred to as a vocal repertoire, which is specific to a species or a sub-group of a species. When conducted by human experts, the formal description of vocal repertoires can be laborious and/or biased. This motivates computerised assistance for this procedure, for which machine learning algorithms represent a good opportunity. Unsupervised clustering algorithms are suited for grouping close points together, provided a relevant representation. This paper therefore studies a new method for encoding vocalisations, allowing for automatic clustering to alleviate vocal repertoire characterisation. Borrowing from deep representation learning, we use a convolutional auto-encoder network to learn an abstract representation of vocalisations. We report on the quality of the learnt representation, as well as of state of the art methods, by quantifying their agreement with expert labelled vocalisation types from 7 datasets of other studies across 6 species (birds and marine mammals). With this benchmark, we demonstrate that using auto-encoders improves the relevance of vocalisation representation which serves repertoire characterisation using a very limited number of settings. We also publish a Python package for the bioacoustic community to train their own vocalisation auto-encoders or use a pretrained encoder to browse vocal repertoires and ease unit wise annotation.
The CRL plastid outer envelope protein supports TOC75-V / OEP80 complex formation in Arabidopsis

Embedded β-barrel proteins in the outer envelope membrane mediate most cellular traffic between the cytoplasm and the plastids. Although TOC75-V/OEP80 has been implicated in the insertion and assembly of β-barrel proteins in the outer envelope membrane of Arabidopsis thaliana, relatively little is known about this process. CRUMPLED LEAF (CRL) encodes a protein localizing in the outer envelope membrane, and its loss of function results in pleiotropic defects, including altered plant morphogenesis, growth retardation, suppression of plastid division, and spontaneous light intensity-dependent localized cell death. A suppressor screen conducted on mutagenized crl mutants with ethyl methanesulfonate revealed that a missense mutation in OEP80 suppresses crl’s pleiotropic defects. Furthermore, we found that the complex formation of OEP80 was compromised in crl. Furthermore, we demonstrated that CRL interacts with OEP80 in vivo and that a portion of CRL is present in protein complexes with the same molecular weight as the OEP80-associated complex. Our results suggest that CRL interacts with OEP80 to regulate its complex formation. CRL has been shown to be involved in plastid protein import; therefore, pleiotropic defects in crl are likely due to the combined effects of decreased plastid protein import and altered membrane integration of β-barrel proteins in the outer envelope membrane. This study sheds light on the mechanisms that allow the integration of β-barrel proteins into the outer envelope membrane of plastids and the significance of this finding for plant cellular processes.
An Empirical Analysis of Similarity Matrix for Spectral Clustering

Constructing the similarity matrix is the key step for spectral clustering, and its goal is to model the local neighborhood relationships between the data points. In order to evaluate the influence of similarity matrix on performance of the different spectral clustering algorithms and find the rules on how to construct an appropriate similarity matrix, a system empirical study was carried out. In the study, six recently proposed spectral clustering algorithms were selected as evaluation object, and normalized mutual information, F-measures and Rand Index were used as evaluation metrics. Then experiments were carried out on eight synthetic datasets and eleven real word datasets respectively. The experimental results show that with multiple metrics the results are more comprehensive and confident, and the comprehensive performance of locality spectral clustering algorithm is better than other five algorithms on synthetic datasets and real word datasets.
Complex rays for radio waves in an absorbing ionosphere

Ray techniques are used to construct an approximate solution for radio waves propagating in the ionosphere when the loss of energy due to collisions is not negligible. For the time-harmonic problem, the solution is in the form of an asymptotic expansion in a large parameter scaling the operating frequency and the natural frequencies characterizing the ionospheric properties. Complex rays are introduced as the characteristics of the resulting eikonal equation, analytically extended to complex space points. The rapidly varying exponential factor and a series for the wave amplitude are both determined by integrating along the rays. The propagation of narrow-band modulation is also determined by integrating along the same complex rays. It is shown that the nature of the initial disturbance plays a vital role in determining the character of the rays required for the solution of a particular problem.
Direct discretization of planar div-curl problems

A control volume method is proposed for planar div-curl systems. The method is independent of potential and least squares formulations, and works directly with the div-curl system. The novelty of the technique lies in its use of a single local vector field component and two control volumes rather than the other way round. A discrete vector field theory comes quite naturally from this idea and is developed in the paper. Error estimates are proved for the method, and other ramifications investigated.
Implicit Normal Mode Initialization for an Operational Regional Model

Abstract In a previous study based on the shallow-water equations, it was shown that nonlinear normal mode initialization (NMI) can be implemented without knowing the normal modes of a model; this implicit form of nonlinear NMI is particularly useful in models for which computing the horizontal normal modes is impracticable. The present paper extends the technique to the multilevel Canadian Operational Finite-Element Regional Model. This paper shows that the method yields well-balanced initial conditions and consistent vertical velocity fields. Forecasts from these initial conditions using a semi-Lagrangian time-integration scheme with relatively large time steps are free from unrealistic high-frequency oscillations.