Miracle-dz/UniFAR-FTUs huggingface dataset:
A conserved N protein nano‐vaccine of COVID‐19 exerts potent and cross‐reactive humoral and cellular immune responses in mice

As severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) mutates continually, the current vaccines are unable to provide sufficient protection. It is important to develop a broad‐spectrum vaccine with conserved antigens to prevent variant infection. Here we fused the SARS‐CoV‐2 N protein with Helicobacter pylori nonheme ferritin to construct a SARS‐CoV‐2 N‐Ferritin nanoparticle vaccine. Compared with the monomer N protein, the N‐Ferritin nanoparticles induced more lymph node dendritic cells in mice to trigger adoptive immunity. Following this, the N‐Ferritin elicited more robust and long‐lasting antibody responses, which had better cross‐reactivity with the SARS‐CoV N protein. It is also worth noting that higher levels of N‐specific IgG and IgA were distributed in the lungs of N‐Ferritin‐immunized mice. Furthermore, the N‐Ferritin nanoparticles also resulted higher proportion of interferon‐γ+ CD8+ T cells, CD8+ Tcm cells, and T cells with cross‐reactivity in SARS‐CoV‐2, SARS‐CoV, and Middle East respiratory syndrome‐related coronavirus. The conserved N‐based nanoparticles could provide a promising vaccine developing strategy against SARS‐CoV‐2 variants and other coronaviruses.
USO, MANEJO Y CONSERVACIÓN DE “yosú”, Stenocereus griseus (CACTACEAE), EN LA ALTA GUAJIRA COLOMBIANA

The present paper characterizes the usage and handling system, demand and potential offer of Stenocereus griseus, a columnar cactus widely used by the "Wayuu", an indigenous community in the Colombian Caribbean region of "La Guajira". The current use of S. griseus is restricted to the collection of dry timber wood ("yotojoro") for house building; of the fruit, which is used for human consumption; and of the young stems, used as goat fodder, and as living fences. An evaluation of the factors that affect the populations allowed the detection of five different harm categories: those caused by cuttings with cutlass (type I); by insects (type II); goats (type III); birds (type IV); and wind (type V). The annual "yotojoro" demand is subject to the building needs of the people in the area, which is defined as occasional. The current cropping and extraction method was not found to be causing any local disequilibrium in the species population maintenance. There is a steady cardon demand for fodder and living fences all year long; one which is causing the highest harm impact. Finally, the main conservation problems of the species are discussed, together with the suggestion of management alternatives for grazing activities.
DeepHistoNet: A robust deep‐learning model for the classification of hepatocellular, lung, and colon carcinoma

In recent days, non‐communicable diseases (NCDs) require more attention since they require specialized infrastructure for treatment. As per the cancer population registry estimate, nearly 800,000 new cancer cases will be detected yearly. The statistics alarm the need for early cancer detection and diagnosis. Cancer identification can be made either through manual efforts or by computer‐aided algorithms. Manual efforts‐based cancer detection is labor intensive and also offers more time complexity. In contrast, computer‐aided algorithms offer feasibility in reducing time and manual efforts. With the motivation to develop a computer‐aided diagnosis system for NCD, we developed a cancer detection methodology. In the present article, a deep learning (DL)‐based cancer identification model is developed. In DL‐based architectures, the features are generally extracted using convolutional neural networks. The proposed attention‐guided, densely connected residual, and dilated convolution deep neural network called DeepHistoNet acquire precise patterns for classification. Experimentation has been carried out on Kasturba Medical College (KMC), TCGA‐LIHC, and LC25000 datasets to prove the robustness of the model. Performance evaluation metrics like F1‐score, sensitivity, specificity, recall, and accuracy validate the experimentation. Experimental results demonstrate that the proposed DeepHistoNet model outperforms the other state‐of‐the‐art methods. The proposed model has been able to classify the KMC liver dataset with 97.1% accuracy and 0.9867 value of area under the curve–receiver operating characteristic curve (AUC‐ROC), which is the best result obtained compared to the state‐of‐the‐art techniques. The performance of the DeepHistoNet has been even better on the LC25000 dataset. On the LC25000 dataset, the proposed model achieved 99.8% classification accuracy. To our knowledge, DeepHistoNet is a novel approach for multiple histopathological image classification.
PDB‐BRE: A ligand–protein interaction binding residue extractor based on Protein Data Bank

Proteins typically exert their biological functions by interacting with other biomolecules or ligands. The study of ligand–protein interactions is crucial in elucidating the biological mechanisms of proteins. Most existing studies have focused on analyzing ligand–protein interactions, and they ignore the additional situational of inserted and modified residues. Besides, the resources often support only a single ligand type and cannot obtain satisfied results in analyzing novel complexes. Therefore, it is important to develop a general analytical tool to extract the binding residues of ligand–protein interactions in complexes fully. In this study, we propose a ligand–protein interaction binding residue extractor (PDB‐BRE), which can be used to automatically extract interacting ligand or protein‐binding residues from complex three‐dimensional (3D) structures based on the RCSB Protein Data Bank (RCSB PDB). PDB‐BRE offers a notable advantage in its comprehensive support for analyzing six distinct types of ligands, including proteins, peptides, DNA, RNA, mixed DNA and RNA entities, and non‐polymeric entities. Moreover, it takes into account the consideration of inserted and modified residues within complexes. Compared to other state‐of‐the‐art methods, PDB‐BRE is more suitable for massively parallel batch analysis, and can be directly applied for downstream tasks, such as predicting binding residues of novel complexes. PDB‐BRE is freely available at http://bliulab.net/PDB-BRE.
Dysfunction of CD169+ macrophages and blockage of erythrocyte maturation as a mechanism of anemia in Plasmodium yoelii infection

Significance Malaria parasites infect hundreds of millions of people and kill over half a million annually. Severe malarial anemia (SMA) is one of the most common severe complications in malaria patients. Although the destruction of infected and noninfected red blood cells (RBCs) and inhibition of RBC production are reported to contribute to SMA, the mechanism of SMA is not completely understood. Here, we show that macrophages from Plasmodium yoelii yoelii 17XNL parasite-infected mice are defective in supporting erythroblast/RBC maturation in vitro and in vivo. Reduced expression of macrophage surface molecule CD169 may provide a marker for the erythropoiesis defect and anemia in malaria. Restoration of the functions of erythroblastic island macrophages may provide a strategy for the treatment of SMA.
Advances in Amyloid-β Clearance in the Brain and Periphery: Implications for Neurodegenerative Diseases

This review examines the role of impaired amyloid-β clearance in the accumulation of amyloid-β in the brain and the periphery, which is closely associated with Alzheimer's disease (AD) and cerebral amyloid angiopathy (CAA). The molecular mechanism underlying amyloid-β accumulation is largely unknown, but recent evidence suggests that impaired amyloid-β clearance plays a critical role in its accumulation. The review provides an overview of recent research and proposes strategies for efficient amyloid-β clearance in both the brain and periphery. The clearance of amyloid-β can occur through enzymatic or non-enzymatic pathways in the brain, including neuronal and glial cells, blood-brain barrier, interstitial fluid bulk flow, perivascular drainage, and cerebrospinal fluid absorption-mediated pathways. In the periphery, various mechanisms, including peripheral organs, immunomodulation/immune cells, enzymes, amyloid-β-binding proteins, and amyloid-β-binding cells, are involved in amyloid-β clearance. Although recent findings have shed light on amyloid-β clearance in both regions, opportunities remain in areas where limited data is available. Therefore, future strategies that enhance amyloid-β clearance in the brain and/or periphery, either through central or peripheral clearance approaches or in combination, are highly encouraged. These strategies will provide new insight into the disease pathogenesis at the molecular level and explore new targets for inhibiting amyloid-β deposition, which is central to the pathogenesis of sporadic AD (amyloid-β in parenchyma) and CAA (amyloid-β in blood vessels).
Genomic insights into pediatric intestinal inflammatory and eosinophilic disorders using single-cell RNA-sequencing

Chronic inflammation of the gastrointestinal (GI) tissues underlies GI inflammatory disorders, leading to tissue damage and a constellation of painful and debilitating symptoms. These GI disorders include inflammatory bowel diseases (Crohn's disease (CD) and ulcerative colitis (UC)), and esinophilic disorders (eosinophilic esophagitis (EoE) and eosinophilic duodenitis (EoD)). GI inflammatory disorders can often present with overlapping symptoms necessitating the use of invasive procedures to give a proper diagnosis. This study aims to use peripheral blood mononuclear cells (PBMCs) from individuals with CD, UC, EoE, and EoD to better understand the alterations to the transcriptome of individuals with these diseases and identify potential markers of active inflammation within the peripheral blood of patients that may be useful in diagnosis. Single-cell RNA-sequencing (scRNA-seq) was performed on PBMCs isolated from the blood samples of pediatric patients diagnosed with a GI disorder, including CD, UC, EoE, EoD, and controls with histologically healthy gastrointestinal tracts. We identified 1,185 (FDR < 0.05) differentially expressed genes (DEGs) between individuals with GI disorders and controls across six distinct immune cell populations. Few patterns of gene dysregulation were common among all GI disorders, including the downregulation of ESR2 in CD4+ T cells compared to controls. Many DEGs showed distinct patterns of dysregulation among individuals with CD, UC, EoE, and EoD compared to controls, such as dysregulation of genes associated with oxidative stress in monocytes of individuals CD and the upregulation of SCGB3A1 in CD4+ T cells in individuals with EoD. These findings indicate both overlapping and distinct alterations to the transcriptome of individuals with CD, UC, EoD, and EoE compared to controls, which provide insight as to which genes may be useful as markers for disease in the peripheral blood of patients.
MFD-Net: Modality Fusion Diffractive Network for Segmentation of Multimodal Brain Tumor Image

Automatic brain tumor segmentation using multi-parametric magnetic resonance imaging (mpMRI) holds substantial importance for brain diagnosis, monitoring, and therapeutic strategy planning. Given the constraints inherent to manual segmentation, adopting deep learning networks for accomplishing accurate and automated segmentation emerges as an essential advancement. In this article, we propose a modality fusion diffractive network (MFD-Net) composed of diffractive blocks and modality feature extractors for the automatic and accurate segmentation of brain tumors. The diffractive block, designed based on Fraunhofer's single-slit diffraction principle, emphasizes neighboring high-confidence feature points and suppresses low-quality or isolated feature points, enhancing the interrelation of features. Adopting a global passive reception mode overcomes the issue of fixed receptive fields. Through a self-supervised approach, the modality feature extractor effectively utilizes the inherent generalization information of each modality, enabling the main segmentation branch to focus more on multimodal fusion feature information. We apply the diffractive block on nn-UNet in the MICCAI BraTS 2022 challenge, ranked first in the pediatric population data and third in the BraTS continuous evaluation data, proving the superior generalizability of our network. We also train separately on the BraTS 2018, 2019, and 2021 datasets. Experiments demonstrate that the proposed network outperforms state-of-the-art methods.
Using Historic Weather Data to Automatically Determine Length of Time for Crop Coefficient Growth Periods

A computer irrigation scheduling program is no more accurate then the crop coefficient (Kc) values and corresponding coefficient curve being employed. The Kc values proffered by the widely accepted FAO-56 procedure were developed for regions with mild climates. In the cases where local weather conditions differ from these, FAO-56 provides straightforward methodologies to adjust those values.
EVALUATING THE OCCURRENCE AND SPATIAL DISTRIBUTION OF THE RADIOACTIVE ISOTOPES 226Ra, 228Ra, 222Rn AND 238U IN THE GROUNDWATERS OF REGIÃO DOS LAGOS - RJ BRAZIL

Um levantamento da concentracao de isotopos radioativos naturais nas aguas subterrâneas da Regiao dos Lagos, estado do Rio de Janeiro-Brasil, foi realizado com a finalidade de verificar os niveis naturais de radioisotopos nas aguas subterrâneas, identificar os principais fatores que influenciam as suas concentracoes e, numa avaliacao preliminar, estimar os niveis de ingestao destes isotopos pela populacao adulta da regiao. Os valores de concentracao dos ions maiores nas aguas variaram substancialmente, mostrando a influencia da agua do mar na composicao das aguas subterrâneas. Valores muito baixos de pH foram encontrados em uma especifica area da regiao de estudo e a analise estatistica enfatizou a forte influencia das altas concentracoes de ion hidrogenio nas altas concentracoes de radio encontradas. Baixas concentracoes de radonio foram verificadas e sao imputadas ao escape do gas diretamente dos pocos de abastecimento. As concentracoes de urânio em todas as amostras analisadas foram inferiores aos valores permissiveis. Das setenta e cinco amostras de agua coletadas na regiao, dezessete tinham niveis de isotopos de radio (Ra-226 e Ra- 228) superiores aos niveis de radioatividade estabelecidos pelo Ministerio Brasileiro de Saude para agua potavel (0,1 Bq/l para alfa e 1 Bq/l para beta), sendo necessario avaliar o risco potencial para a saude da populacao em decorrencia da exposicao a estes radioisotopos nas aguas de abastecimento. ABSTRACT A survey of radionuclide concentrations in ground waters of Regiao dos Lagos, the Lake's Region - Rio de Janeiro State-Brazil, was performed in order to verify the natural levels of radionuclides in the groundwater, to identify main factors influencing the radioisotope concentration and in a first approach to estimate natural radionuclide ingestion levels by the adult inhabitants. The concentration values of the major ion concentrations varied widely, showing the seawater influence over the groundwaters. Unusual low pH values were found in a specific region and the statistical analysis stressed its strong influence on the high radium concentrations. Probably the high Ra concentrations in the waters are due to Ra leaching from rock matrix, which is incited by the low pH. Generally low concentrations of radon found even in samples with high radium concentrations were a consequence of radon de-gassing. The concentrations of uranium were lower than maximum allowable limit for all samples. Seventeen of the eighty-eight water samples collected in the region had levels of naturally occurring radium that exceeded the maximum allowable values recommended by Brazilian Health Minister for drinking water, being necessary to assess the potential risks for the population from the exposure to these radionuclides in the waters.
Clinical determinants for State–Trait Anxiety Inventory of the parents of children with respiratory problems

Understanding factors associated with anxiety of parents/carers of children with respiratory problems is clinically important yet there is relative paucity of data. In 106 children seen in the respiratory clinic of a pediatric hospital, we evaluated (a) the determinants for parental anxiety and (b) whether the anxiety scores correlate with quality‐of‐life (QoL) scores in the subset with chronic cough.
Early development and adaptive functioning in children with Bardet‐Biedl syndrome

This study had two aims. Aim one investigated achievement of 10 developmental milestones in children with Bardet‐Biedl syndrome (BBS). Aim one data were derived from retrospective responses by caregivers of individuals with BBS who are enrolled in the Clinical Registry Investigating Bardet‐Biedl syndrome (CRIBBS). CRIBBS is a natural history registry acquiring serial observations. Aim two investigated early adaptive skills using the Adaptive Behavior Assessment System (ABAS‐II 0–5) completed by caregivers of children with BBS aged from 0 to 5. There were 652 individuals with milestone information (with some variability based on availability of information for specific milestones), and 101 individuals (including 95 among the 652) with ABAS‐II information. Results revealed wide‐ranging delays in adaptive skills, particularly in the domain of Self‐Care. Expressive language appears to be the most frequently delayed developmental milestone. We found a difference by BBS genotype wherein individuals with BBS1 had higher adaptive/developmental scores than individuals with BBS10. Age also carried a significant association with adaptive skills diverging farther from a normative trajectory as children with BBS progress through early childhood.
Tumor regression grade combined with post‐therapy lymph node status: A novel independent prognostic factor for patients treated with neoadjuvant therapy followed by surgery in locally advanced gastroesophageal junction and gastric carcinoma

Tumor regression grade (TRG) is a measure of histopathological response to neoadjuvant therapy (NAT). Post‐therapy lymph node (ypN) metastasis was reported as a prognostic factor. However, the evaluation of the treatment effectiveness of NAT has not been well studied. Here, we explored whether TRG combined with ypN status could be a prognostic factor for gastroesophageal junction (GEJ) and gastric cancer (GC). Besides, we aimed at making clear the association of different neoadjuvant regimens with different TRG and ypN status.
Vertical profiles of HDO/H 2 O in the troposphere

[1] This paper reanalyzes the measurements of the D content in tropospheric water vapor by Ehhalt (1974) correcting for the isotopic contamination by wall water in the sampling tubes. The resulting corrections decrease the original D content. They are small for the data from the flights through 1967, which extended from the surface to 9 km altitude, but are large for the flights beginning 1971, which ranged from 6 to 13 km altitude and collected smaller amounts of water vapor. No correction therefore was attempted for the latter. The corrected data of the earlier flights are presented in the form of seasonally averaged profiles over Scotts Bluff, Nebraska; Death Valley, California; and the Pacific offshore of San Luis Obispo, California. As to be expected, the vertical profiles from the earlier flights show a decrease in the D content with altitude and a seasonal variation at all altitudes. However, when plotted against the water vapor mixing ratio, the D data from all seasons collapse on a line which closely follows that given by Rayleigh condensation with a fractionation factor α = 1.1, constant with altitude. These data can be explained by a simple one-dimensional convection model and the assumption that condensed water is lofted along with the water vapor.
Évaluation de la concurrence généralisée intergroupes: un outil matriciel

[eng] Input-output matrices and structural analysis are applied to the analysis and forecast of consequences of offensive actions in the case of multiproduct multimarket large firms. [fre] Les matrices entrees-sorties et l'analyse structurale sont appliquees a l'analyse et a la prevision des consequences des actions offensives dans le cas de groupes industriels multiproduits et multimarches.
Pattern detection in the TGFβ cascade controls the induction of long-term synaptic plasticity

Significance Stimulus repetition in the environment leads to effective long-term memory (LTM) formation in the brain, but the cellular and molecular mechanisms underlying this phenomenon are not well understood. We find that temporal patterning within the transforming growth factor β (TGFβ) signaling system provides a unique sensor for stimulus repetition, via proteolytic activation of the growth factor proligand, that enables the induction of long-term synaptic plasticity critical for LTM. We propose that the timing of TGFβ signaling during learning enables interaction between two separate training events, ultimately resulting in LTM.
New insights into the generation of the 2013 Lushan Earthquake (Ms 7.0), China

Global seismic waveform inversion can provide information on where the 2013 Ms 7.0 Lushan earthquake occurred in Sichuan Province, China, and how its aftershock sequence expanded. To investigate the generation mechanism of the Lushan earthquake and its relation to the 2008 Wenchuan earthquake (Ms 8.0), 50 temporary seismic stations were installed in the source area following the Lushan earthquake. Crustal stress data were also collected along the Longmen‐Shan Fault zone (LMFZ) to reveal its influence on the generation of the Lushan earthquake. Seismic imaging and crustal stress analysis have revealed that the Lushan earthquake occurred in a distinct area with high velocity (Vp, Vs), low Poisson's ratio (σ), and high crustal stress. The high‐velocity zone at the Lushan source may reflect Precambrian metasedimentary or igneous rock in the seismogenic layer, which enables the accumulation of high crustal stress to generate large earthquakes. However, a sharply contrasting gap zone with low‐velocity, high‐σ anomalies is clearly imaged in the upper crust under the concatenated area between the Lushan and Wenchuan earthquakes. Seismic images indicate that the low‐velocity gap zone is associated with fluid‐bearing ductile flow from the lower crustal materials of Tibet being pushed into a weakened segment of the LMFZ. This study suggests that the 2013 Lushan earthquake may have been triggered by high crustal stress accumulation together with high coseismic stress further increased by the Wenchuan earthquake in the metamafic seismogenic layer. Contrasting rheological variations in the crust and crustal stress changes along the LMFZ control the rupture processes that generated the Lushan and Wenchuan earthquakes, as well as the generation of new earthquakes in the future.