Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptome analysis of the response of Hypomyces chrysospermus to cadmium stress

Hypomyces chrysospermus is a fungal parasite that grows on Boletus species. One isolated strain of H. chrysospermus from B. griseus was obtained and proved of strong ability to tolerate and absorb cadmium (Cd) by previous research. However, the molecular mechanisms of underlying the resistance of H. chrysospermus to Cd stress have not been investigated. This study aimed to assess the effect of Cd stress on the global transcriptional regulation of H. chrysospermus. A total of 1,839 differentially expressed genes (DEGs) were identified under 120 mg/l Cd stress. Gene ontology (GO) enrichment analysis revealed that large amounts of DEGs were associated with cell membrane components, oxidoreductase activity, and transport activity. KEGG enrichment analysis revealed that these DEGs were mainly involved in the translation, amino acid metabolism, transport and catabolism, carbohydrate metabolism, and folding/sorting and degradation pathways under Cd stress. Moreover, the expression of DEGs encoding transporter proteins, antioxidant enzymes, nonenzymatic antioxidant proteins, detoxification enzymes, and transcription factors was associated with the Cd stress response. These results provide insights into the molecular mechanisms underlying Cd tolerance in H. chrysospermus and serve as a valuable reference for further studies on the detoxification mechanisms of heavy metal-tolerant fungi. Our findings may also facilitate the development of new and improved fungal bioremediation strategies.
Kynurenine serves as useful biomarker in acute, Long- and Post-COVID-19 diagnostics

Introduction In patients with SARS-CoV-2, innate immunity is playing a central role, depicted by hyperinflammation and longer lasting inflammatory response. Reliable inflammatory markers that cover both acute and long-lasting COVID-19 monitoring are still lacking. Thus, we investigated one specific inflammatory marker involved as one key player of the immune system, kynurenine (Kyn), and its use for diagnosis/detection of the Long-/Post-COVID syndrome in comparison to currently used markers in both serum and saliva samples. Material and methods The study compromised in total 151 inpatients with a SARS-CoV-2 infection hospitalized between 03/2020 and 09/2021. The group NC (normal controls) included blood bank donors (n=302, 144f/158m, mean age 47.1 ± 18.3 years (range 18-75)). Two further groups were generated based on Group A (n=85, 27f/58m, mean age 63.1 ± 18.3 years (range 19-90), acute admission to the hospital) and Group B (n=66, 22f/44m, mean age 66.6 ± 17.6 years (range 17-90), admitted either for weaning or for rehabilitation period due to Long-COVID symptoms/syndrome). Plasma concentrations of Kyn, C-Reactive Protein (CRP) and interleukin-6 (IL-6) were measured on admission. In Group B we determined Kyn 4 weeks after the negative PCR-test. In a subset of patients (n=11) concentrations of Kyn and CRP were measured in sera and saliva two, three and four months after dismission. We identified 12 patients with Post-COVID symptoms >20 weeks with still significant elevated Kyn-levels. Results Mean values for NC used as reference were 2.79 ± 0.61 µM, range 1.2-4.1 µM. On admission, patients showed significantly higher concentrations of Kyn compared to NC (p-values < 0.001). Kyn significantly correlated with IL-6 peak-values (r=0.411; p-values <0.001) and CRP (r=0.488, p-values<0.001). Kyn values in Group B (Long-/Post-COVID) showed still significant higher values (8.77 ± 1.72 µM, range 5.5-16.6 µM), whereas CRP values in Group B were in the normal range. Conclusion Serum and saliva Kyn are reflecting the acute and long-term pathophysiology of the SARS-CoV-2 disease concerning the innate immune response and thus may serve a useful biomarker for diagnosis and monitoring both Long- and Post-COVID syndrome and its therapy.
Identification and characterization of long noncoding RNAs involved in the aluminum stress response in Medicago truncatula via genome-wide analysis

Numerous studies have shown that plant long noncoding RNAs (lncRNAs) play an important regulatory role in the plant response to environmental stress. However, there are no reports on lncRNAs regulating and enhancing aluminum (Al) stress tolerance in legumes. This study analyzed the role of lncRNAs in response to Al stress in the legume model plant Medicago truncatula. A total of 219.49 Gb clean data were generated: 3,284 lncRNA genes were identified, of which 515 were differentially expressed, and 1,254 new genes were functionally annotated through database alignment. We further predicted and classified putative targets of these lncRNAs and found that they were enriched in biological processes and metabolic pathways such as plant hormone signal transduction, cell wall modification and the tricarboxylic acid (TCA) cycle. Finally, we characterized the functions of 2 Al-activated-malate-transporter-related lncRNAs in yeast. The recombinant plasmids of MSTRG.12506. 5 and MSTRG.34338. 20 were transformed into yeast, and these yeast exhibited better growth than those carrying empty vectors on medium supplemented with 10 μM AlCl3 and showed that they have biological functions affording Al stress tolerance. These findings suggest that lncRNAs are involved in regulating plant responses to Al stress. Our findings help to understand the role of lncRNAs in the response to Al stress in legumes and provide candidate lncRNAs for further studies.
Altered distribution and function of NK-cell subsets lead to impaired tumor surveillance in JAK2V617F myeloproliferative neoplasms

In cancer, tumor cells and their neoplastic microenvironment can sculpt the immunogenic phenotype of a developing tumor. In this context, natural killer (NK) cells are subtypes of lymphocytes of the innate immune system recognized for their potential to eliminate neoplastic cells, not only through direct cytolytic activity but also by favoring the development of an adaptive antitumor immune response. Even though the protective effect against leukemia due to NK-cell alloreactivity mediated by the absence of the KIR-ligand has already been shown, and some data on the role of NK cells in myeloproliferative neoplasms (MPN) has been explored, their mechanisms of immune escape have not been fully investigated. It is still unclear whether NK cells can affect the biology of BCR-ABL1-negative MPN and which mechanisms are involved in the control of leukemic stem cell expansion. Aiming to investigate the potential contribution of NK cells to the pathogenesis of MPN, we characterized the frequency, receptor expression, maturation profile, and function of NK cells from a conditional Jak2V617F murine transgenic model, which faithfully resembles the main clinical and laboratory characteristics of human polycythemia vera, and MPN patients. Immunophenotypic analysis was performed to characterize NK frequency, their subtypes, and receptor expression in both mutated and wild-type samples. We observed a higher frequency of total NK cells in JAK2V617F mutated MPN and a maturation arrest that resulted in low-numbered mature CD11b+ NK cells and increased immature secretory CD27+ cells in both human and murine mutated samples. In agreement, inhibitory receptors were more expressed in MPN. NK cells from Jak2V617F mice presented a lower potential for proliferation and activation than wild-type NK cells. Colonies generated by murine hematopoietic stem cells (HSC) after mutated or wild-type NK co-culture exposure demonstrated that NK cells from Jak2V617F mice were deficient in regulating differentiation and clonogenic capacity. In conclusion, our findings suggest that NK cells have an immature profile with deficient cytotoxicity that may lead to impaired tumor surveillance in MPN. These data provide a new perspective on the behavior of NK cells in the context of myeloid malignancies and can contribute to the development of new therapeutic strategies, targeting onco-inflammatory pathways that can potentially control transformed HSCs.
Full-length transcriptional analysis reveals the complex relationship of leaves and roots in responses to cold-drought combined stress in common vetch

Plant responses to single or combined abiotic stresses between aboveground and underground parts are complex and require crosstalk signaling pathways. In this study, we explored the transcriptome data of common vetch (Vicia sativa L.) subjected to cold and drought stress between leaves and roots via meta-analysis to identify the hub abiotic stress-responsive genes. A total of 4,836 and 3,103 differentially expressed genes (DEGs) were identified in the leaves and roots, respectively. Transcriptome analysis results showed that the set of stress-responsive DEGs to concurrent stress is distinct from single stress, indicating a specialized and unique response to combined stresses in common vetch. Gene Ontology (GO) enrichment analyses identified that “Photosystem II,” “Defence response,” and “Sucrose synthase/metabolic activity” were the most significantly enriched categories in leaves, roots, and both tissues, respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis results indicated that “ABC transporters” are the most enriched pathway and that all of the genes were upregulated in roots. Furthermore, 29 co-induced DEGs were identified as hub genes based on the consensus expression profile module of single and co-occurrence stress analysis. In transgenic yeast, the overexpression of three cross-stress tolerance candidate genes increased yeast tolerance to cold-drought combined stress. The elucidation of the combined stress-responsive network in common vetch to better parse the complex regulation of abiotic responses in plants facilitates more adequate legume forage breeding for combined stress tolerance.
Fast identification and quantification of c-Fos protein using you-only-look-once-v5

In neuroscience, protein activity characterizes neuronal excitability in response to a diverse array of external stimuli and represents the cell state throughout the development of brain diseases. Importantly, it is necessary to characterize the proteins involved in disease progression, nuclear function determination, stimulation method effect, and other aspects. Therefore, the quantification of protein activity is indispensable in neuroscience. Currently, ImageJ software and manual counting are two of the most commonly used methods to quantify proteins. To improve the efficiency of quantitative protein statistics, the you-only-look-once-v5 (YOLOv5) model was proposed. In this study, c-Fos immunofluorescence images data set as an example to verify the efficacy of the system using protein quantitative statistics. The results indicate that YOLOv5 was less time-consuming or obtained higher accuracy than other methods (time: ImageJ software: 80.12 ± 1.67 s, manual counting: 3.41 ± 0.25 s, YOLOv5: 0.0251 ± 0.0003 s, p < 0.0001, n = 83; simple linear regression equation: ImageJ software: Y = 1.013 × X + 0.776, R2 = 0.837; manual counting: Y = 1.0*X + 0, R2 = 1; YOLOv5: Y = 0.9730*X + 0.3821, R2 = 0.933, n = 130). The findings suggest that the YOLOv5 algorithm provides feasible methods for quantitative statistical analysis of proteins and has good potential for application in detecting target proteins in neuroscience.
Isolation and characterization of avian leukosis virus subgroup J associated with hemangioma and myelocytoma in layer chickens in China

A strain of avian leukosis virus (ALV) belonging to a new envelope subgroup J (ALV-J) emerged in 1988 as a new subgroup of ALV and spread rapidly throughout the world. Due to the infection and spread of ALV-J, the global poultry industry experienced a significant loss. Although the disease had been prevented and controlled effectively by culling domestic chickens in the infected zone, a few field cases of ALV-J infection were reported in China in recent years. This study was conducted to characterize the genome and analyze the lesions and histopathology of the ALV-J strain named HB2020, which was isolated from layer chickens in Hubei Province, China. The full-length proviral genome sequence analysis of ALV-J HB2020 revealed that it was a recombinant strain of ev-1 and HPRS-103 in the gag gene in comparison to ALV-J prototype HPRS-103. In the 3′-untranslated region (3'UTR) of the nucleotide sequence, there were found 205-base pairs (bp) deletion, of which 175 were detected in the redundant transmembrane (rTM) region. Besides, the surface glycoprotein gene gp85 had five mutations in a conservative site, whereas the transmembrane protein gene gp37 was relatively conserved. The animal experiments conducted later on this strain have shown that HB2020 can cause various neoplastic lesions in chickens, including enlarged livers with hemangiomas and spleens with white nodules. Additionally, as the exposure time increased, the number of tumor cells that resembled myelocytes in the blood smears of infected chickens gradually increased. These results indicated that HB2020 on recombination with ALV subgroup E (ALV-E) and ALV-J could induce severe hemangiomas and myelocytomas. This inference might provide a molecular basis for further research about the pathogenicity of ALV and emphasize the need for control and prevention of avian leukosis.
Functional analysis of the BEige and Chediak-Higashi domain gene MpSPIRRIG in Marchantia polymorpha

BEige and Chediak–Higashi domain containing proteins (BDCPs) have been described to function in membrane-dependent processes in eukaryotes. This role was also observed for the BDCP SPIRRIG (SPI) in the model plant Arabidopsis thaliana in the context of cell morphogenesis. Additionally, AtSPI was found to control salt stress resistance by mediating mRNA stability and salt stress-dependent processing body formation. In this work, we utilize an evolutionarily comparative approach to unravel conserved, basal BDCP functions in the liverwort Marchantia polymorpha. Our phenotypic and physiological analyses show that MpSPI is involved in cell morphogenesis and salt resistance regulation, indicating that both functions are evolutionarily conserved between the two species. Co-localization was found with endosomal and P-body markers, suggesting links to membrane-dependent processes and mRNA metabolism. Finally, we present transcriptomics data showing that AtSPI and MpSPI regulate orthologous genes in A. thaliana and M. polymorpha.
Identification of tree species based on the fusion of UAV hyperspectral image and LiDAR data in a coniferous and broad-leaved mixed forest in Northeast China

Rapid and accurate identification of tree species via remote sensing technology has become one of the important means for forest inventory. This paper is to develop an accurate tree species identification framework that integrates unmanned airborne vehicle (UAV)-based hyperspectral image and light detection and ranging (LiDAR) data under the complex condition of natural coniferous and broad-leaved mixed forests. First, the UAV-based hyperspectral image and LiDAR data were obtained from a natural coniferous and broad-leaved mixed forest in the Maoer Mountain area of Northeast China. The preprocessed LiDAR data was segmented using a distance-based point cloud clustering algorithm to obtain the point cloud of individual trees; the hyperspectral image was segmented using the projection outlines of individual tree point clouds to obtain the hyperspectral data of individual trees. Then, different hyperspectral and LiDAR features were extracted, respectively, and the importance of the features was analyzed by a random forest (RF) algorithm in order to select appropriate features for the single-source and multi-source data. Finally, tree species identification in the study area were conducted by using a support vector machine (SVM) algorithm together with hyperspectral features, LiDAR features and fused features, respectively. Results showed that the total accuracy for individual tree segmentation was 84.62%, and the fused features achieved the best accuracy for identification of the tree species (total accuracy = 89.20%), followed by the hyperspectral features (total accuracy = 86.08%) and LiDAR features (total accuracy = 76.42%). The optimal features for tree species identification based on fusion of the hyperspectral and LiDAR data included the vegetation indices that were sensitive to the chlorophyll, anthocyanin and carotene contents in the leaves, the partial components of the transformed independent component analysis (ICA), minimum noise fraction (MNF) and principal component analysis (PCA), and the intensity features of the LiDAR echo, respectively. It was concluded that the framework developed in this study was effective in tree species identification under the complex conditions of natural coniferous and broad-leaved mixed forest and the fusion of UAV-based hyperspectral image and LiDAR data can achieve enhanced accuracy compared the single-source UAV-based remote sensing data.
Influence of perceived equity, job enrichment, and burnout among educators in Indian private universities on job satisfaction and the desire to quit

The desire to quit converts into actual attrition if left unaddressed. Additionally, employees’ job satisfaction strongly influences their desire to stay or leave. Several individual and organizational factors affect job satisfaction levels, all of which must be thoroughly analyzed to curb both the desire to quit and attrition. The current study tests a model associating perceived equity, job enrichment, and burnout with job satisfaction and the desire to quit of educators employed in private universities in India. Data were collected from 272 university faculty members using five scales, namely, job enrichment, perceived equity, employee burnout, job satisfaction, and intention to leave, and were analyzed using AMOS 17. The initial fitness results failed to support the hypothesized framework, but a revised framework yielded a good fit for the data. Results show that perceived equity has a positive influence on job satisfaction (Hypothesis 2), job enrichment positively affects job satisfaction (Hypothesis 3), burnout negatively influences job satisfaction (Hypothesis 4), and job satisfaction negatively affects the desire to leave (Hypothesis 1). Perceived equity, burnout, and job satisfaction were found to mediate the association between job enrichment and the desire to leave. The results indicate that private universities must focus on job satisfaction to reduce employees’ desire to quit, thereby reducing the attrition level, which is currently a severe problem with both financial and non-financial consequences to universities. From the results, it can be seen that job enrichment has acted as a mediator to influence employees’ job satisfaction. Future research can explore HR practices contributing to high job enrichment, and this study would have considerable practical implications.
Topographic organization of the human caudate functional connectivity and age-related changes with resting-state fMRI

The striatum is postulated to play a central role in gating cortical processing during goal-oriented behavior. While many human neuroimaging studies have treated the striatum as an undivided whole or several homogeneous compartments, some recent studies showed that its circuitry is topographically organized and has more complex relations with the cortical networks than previously assumed. Here, we took a gradient functional connectivity mapping approach that utilizes the entire anatomical space of the caudate nucleus to examine the organization of its functional relationship with the rest of the brain and how its topographic mapping changes with age. We defined the topography of the caudate functional connectivity using three publicly available resting-state fMRI datasets. We replicated and extended previous findings. First, we found two stable gradients of caudate connectivity patterns along its medial-lateral (M-L) and anterior-posterior (A-P) axes, supporting findings from previous tract-tracing studies of non-human primates that there are at least two main organizational principles within the caudate nucleus. Second, unlike previous emphasis of the A-P topology, we showed that the differential connectivity patterns along the M-L gradient of caudate are more clearly organized with the large-scale neural networks; such that brain networks associated with internal vs. external orienting behavior are respectively more closely linked to the medial vs. lateral extent of the caudate. Third, the caudate's M-L organization showed greater age-related reduction in integrity, which was further associated with age-related changes in behavioral measures of executive functions. In sum, our analysis confirmed a sometimes overlooked M-L functional connectivity gradient within the caudate nucleus, with its lateral longitudinal zone more closely linked to the frontoparietal cortical circuits and age-related changes in cognitive control. These findings provide a more precise mapping of the human caudate functional connectivity, both in terms of the gradient organization with cortical networks and age-related changes in such organization.
Successes and failures of angiogenesis blockade in gastric and gastro-esophageal junction adenocarcinoma

Gastric and gastro-esophageal junction adenocarcinoma (GEA) remains a considerable major public health problem worldwide, being the fifth most common cancer with a fatality-to-case ratio that stands still at 70%. Angiogenesis, which is a well-established cancer hallmark, exerts a fundamental role in cancer initiation and progression and its targeting has been actively pursued as a promising therapeutic strategy in GEA. A wealth of clinical trials has been conducted, investigating anti-angiogenic agents including VEGF-directed monoclonal antibodies, small molecules tyrosine kinase inhibitors and VEGF-Trap agents both in the resectable and advanced setting, reporting controversial results. While phase III randomized trials testing the anti-VEGFR-2 antibody Ramucirumab and the selective VEGFR-2 tyrosine kinase inhibitor Apatinib demonstrated a significant survival benefit in later lines, the shift of angiogenesis inhibitors in the perioperative and first-line setting failed to improve patients’ outcome in GEAs. The molecular landscape of disease, together with novel combinatorial strategies and biomarker-selected approaches are under investigation as key elements to the success of angiogenesis blockade in GEA. In this article, we critically review the existing literature on the biological rationale and clinical development of antiangiogenic agents in GEA, discussing major achievements, limitations and future developments, aiming at fully realizing the potential of this therapeutic approach.