Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessment of cognitive impairment after acute cerebral infarction with T1 relaxation time measured by MP2RAGE sequence and cerebral hemodynamic by transcranial Doppler

Objective This study aimed to investigate early brain microstructural changes discovered using magnetization-prepared two rapid acquisition gradient echo (MP2RAGE) sequence and cerebral hemodynamic using TCD for cognitive impairment after acute cerebral infarction. Methods We enrolled 43 patients with acute cerebral infarction and 21 healthy people in the study, who were subjected to cognitive assessments, the MP2RAGE sequence, and a cerebral hemodynamic examination. A total of 26 brain regions of interest were investigated. Furthermore, we used cerebral hemodynamics to explain brain microstructural changes, which helped us better understand the pathophysiology of cognitive impairment after acute cerebral infarction and guide treatment. Results T1 relaxation times in the left frontal lobe, right frontal lobe, right temporal lobe, left precuneus, left thalamus, right hippocampus, right head of caudate nucleus, and splenium of corpus callosum were substantially different across the three groups, which were significantly correlated with neuropsychological test scores. CI group patients had significantly lower cerebral blood flow velocity than those in the N-CI and Normal groups. The receiver operating curve analysis revealed that most T1 relaxation times had high sensitivity and specificity, especially on the right temporal lobe and right frontal lobe. There was a potential correlation between T1 relaxation times and MMSE scores through TCD parameters. Conclusion The MP2RAGE sequence can detect alterations in whole brain microstructure in patients with cognitive impairment after acute cerebral infarction. Brain microstructural changes could influence cognitive function through cerebral hemodynamics. T1 relaxation times on the right temporal lobe and the right frontal lobe are expected to be a prospective biomarker of cognitive impairment after acute cerebral infarction.
Development of Numberline and Measurement Concepts

In a two-part study, children in Grades 1 through 3 were given a set of numberline estimation problems and a set of similar numberline estimation problems that were to be solved using specially designed rulers. The estimation tasks showed a complex pattern of change in accuracy and strategies over the three grade levels. This pattern indicated that children progressively altered their estimation strategies from strictly sequential ones to ones that incorporate elements of proportional reasoning. This shift was gradual and implemented school-learned numerical relationships in the solution of these novel tasks. There was no indication that, in the Piagetian sense, stage changes contributed to strategy development. However, the use of rulers with different spacings between the numbers indicated that children's acquisition of a principled concept of equal intervals required both the learned convention of equal intervals and the achievement of conservation of length.
Deletion of classical transient receptor potential 1, 3 and 6 alters pulmonary vasoconstriction in chronic hypoxia-induced pulmonary hypertension in mice

Chronic hypoxia-induced pulmonary hypertension (CHPH) is a severe disease that is characterized by increased proliferation and migration of pulmonary arterial smooth muscle cells (PASMCs) leading to pulmonary vascular remodeling. The resulting increase in pulmonary vascular resistance (PVR) causes right ventricular hypertrophy and ultimately right heart failure. In addition, increased PVR can also be a consequence of hypoxic pulmonary vasoconstriction (HPV) under generalized hypoxia. Increased proliferation and migration of PASMCs are often associated with high intracellular Ca2+ concentration. Recent publications suggest that Ca2+-permeable nonselective classical transient receptor potential (TRPC) proteins—especially TRPC1 and 6—are crucially involved in acute and sustained hypoxic responses and the pathogenesis of CHPH. The aim of our study was to investigate whether the simultaneous deletion of TRPC proteins 1, 3 and 6 protects against CHPH-development and affects HPV in mice. We used a mouse model of chronic hypoxia as well as isolated, ventilated and perfused mouse lungs and PASMC cell cultures. Although right ventricular systolic pressure as well as echocardiographically assessed PVR and right ventricular wall thickness (RVWT) were lower in TRPC1, 3, 6-deficient mice, these changes were not related to a decreased degree of pulmonary vascular muscularization and a reduced proliferation of PASMCs. However, both acute and sustained HPV were almost absent in the TRPC1, 3, 6-deficient mice and their vasoconstrictor response upon KCl application was reduced. This was further validated by myographical experiments. Our data revealed that 1) TRPC1, 3, 6-deficient mice are partially protected against development of CHPH, 2) these changes may be caused by diminished HPV and not an altered pulmonary vascular remodeling.
Characteristics of piRNAs and their comparative profiling in testes of sheep with different fertility

As a novel class of small RNAs, piRNAs are highly expressed in the animal gonads and their main known role is to inhibit transposon activity for ensuring the correctness and integrity of genome. In order to explore the characteristics of piRNAs in sheep testis and their possible regulatory roles on male reproduction, deep sequencing technology was used to sequence small RNAs and identify piRNAs in testes of sheep. The length of piRNAs in sheep testes showed a unimodal distribution between 26 and 31 nt, with a peak at 29 nt. These piRNAs exhibited obvious ping-pong signature and strand specificity. In the genome, they were mainly aligned to CDS, intron, repetitive sequence regions and unannotated regions. Furthermore, in transposon analysis, piRNAs were aligned predominantly to LINE, SINE, and LTR types of retrotransposon in sheep testes, and the piRNAs derived from each type showed obvious ping-pong signature. The piRNA clusters identified in sheep testes were mainly distributed on chromosomes 3, 7, 15, 17, 18 and 20. The results combining semen determination with pathway enrichment analysis implied that differentially expressed piRNAs between the testes of rams with different fertility might participate in spermatogenesis by regulating multiple pathways closely related to stabilization of blood-testis barrier and renewal and differentiation of spermatogonial stem cell. Taken together, the study provided new insights into the characteristics, origin and expression patterns of piRNAs in sheep testes tissue, which would help us better understand the role of piRNAs in sheep reproduction.
Mixtures of autoregressive-autoregressive conditionally heteroscedastic models: semi-parametric approach

We propose data generating structures which can be represented as a mixture of autoregressive-autoregressive conditionally heteroscedastic models. The switching between the states is governed by a hidden Markov chain. We investigate semi-parametric estimators for estimating the functions based on the quasi-maximum likelihood approach and provide sufficient conditions for geometric ergodicity of the process. We also present an expectation–maximization algorithm for calculating the estimates numerically.
Micro-Fourier transform infrared spectroscopy of degradation-resistant organic microfossils; Influence of preservation environment and phylogeny

To gain more insight into the effect of early diagenetic processes in different redox environments on the molecular characteristics of degradation resistant particulate organic matter, the molecular cyst wall characteristics of the closely related dinoflagellates Impagidinium aculeatum and I. patulum from oxic and anoxic sedimentary environments in the Madeira Abyssal Plain F-turbidite and in the surface sediments of the eastern Mediterranean Sea have been analysed with micro-FTIR spectroscopy. Both species have cysts that are representatives of particulate organic matter being extremely resistant against degradation in natural environments. Their walls primarily consist of a carbohydrate-based polymer. Spectral differences could not be observed between cysts from oxic and anoxic environments, neither from different areas nor from different geological times. However, we identify consistent compositional differences between both species. Compared to I. patulum, cyst walls of I. aculeatum contain more C-O probably of secondary alcohols that might imply a slightly higher resistance to decay of I. patulum. Comparison with cyst species that represent particular organic matter being extremely sensitive and slightly resistant against aerobic degradation in natural settings reveals that cysts walls of the most vulnerable species show C=N, N-H, N-O, C-N bending/stretching, as well as the presence of C=O and C-O bounds. Cyst species that are somewhat less sensitive have a strong indication of the presence of nitrogen in their macromolecules. More resistant species lack nitrogen whereas the most resistant cyst species I. aculeatum and I. patulum show low amounts of C=O.
The collaborative mode by PmSVPs and PmDAMs reveals neofunctionalization in the switch of the flower bud development and dormancy for Prunus mume

Prunus mume (Rosaceae, Prunoideae) serves as an excellent ornamental woody plant with a large-temperature-range cultivation scope. Its flower buds require a certain low temperature to achieve flowering circulation. Thus, it is important to delve into the processes of flower bud differentiation and dormancy, which affected its continuous flowering. These processes are generally considered as regulation by the MADS-box homologs, SHORT VEGETATIVE PHASE (SVP), and DORMANCY-ASSOCIATED MADS-BOX (DAM). However, a precise model on their interdependence and specific function, when acting as a complex in the flower development of P. mume, is needed. Therefore, this study highlighted the integral roles of PmDAMs and PmSVPs in flower organ development and dormancy cycle. The segregation of PmDAMs and PmSVPs in a different cluster suggested distinct functions and neofunctionalization. The expression pattern and yeast two-hybrid assays jointly revealed that eight genes were involved in the floral organ development stages, with PmDAM1 and PmDAM5 specifically related to prolificated flower formation. PmSVP1–2 mingled in the protein complex in bud dormancy stages with PmDAMs. Finally, we proposed the hypothesis that PmSVP1 and PmSVP2 could combine with PmDAM1 to have an effect on flower organogenesis and interact with PmDAM5 and PmDAM6 to regulate flower bud dormancy. These findings could help expand the current molecular mechanism based on MADS-box genes during flower bud development and dormancy.
A mucosal recovery software tool for endoscopic submucosal dissection in early gastric cancer

Background Due to the limited diagnostic ability, the low detection rate of early gastric cancer (EGC) is a serious health threat. The establishment of the mapping between endoscopic images and pathological images can rapidly improve the diagnostic ability to detect EGC. To expedite the learning process of EGC diagnosis, a mucosal recovery map for the mapping between ESD mucosa specimen and pathological images should be performed in collaboration with endoscopists and pathologists, which is a time-consuming and laborious work. Methods 20 patients at the Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital of Hangzhou Medical College from March 2020 to July 2020 were enrolled in this study. We proposed the improved U-Net to obtain WSI-level segmentation results, and the WSI-level results can be mapped to the macroscopic image of the specimen. For the convenient use, a software pipeline named as “Pathology Helper” for integration the workflow of the construction of mucosal recovery maps was developed. Results The MIoU and Dice of our model can achieve 0.955 ± 0.0936 and 0.961 ± 0.0874 for WSI-level segmentation, respectively. With the help of “Pathology Helper”, we can construct the high-quality mucosal recovery maps to reduce the workload of endoscopists and pathologists. Conclusion “Pathology Helper” will accelerate the learning of endoscopists and pathologists, and rapidly improve their abilities to detect EGC. Our work can also improve the detection rate of early gastric cancer, so that more patients with gastric cancer will be treated in a timely manner.
Case Report: Peripheral blood T cells and inflammatory molecules in lung cancer patients with immune checkpoint inhibitor-induced thyroid dysfunction: Case studies and literature review

Immunotherapy has changed the paradigm of cancer treatment, yet immune checkpoint inhibitors (ICIs) such as PD-1/PD-L1 monoclonal antibodies may cause immune-related adverse events (irAEs) in some patients. In this report, two non-small cell lung cancer (NSCLC) patients treated with nivolumab presented with checkpoint inhibitor-induced thyroid dysfunction (CITD), followed by a second irAE of pneumonitis and intestinal perforation, respectively. Increases in peripheral CD8+ T cells correlated with the onset of CITD in the patients. Intriguingly, common inflammatory biomarkers, including C-reactive protein (CRP) and neutrophil/lymphocyte ratio (NLR), were not consistently increased during the onset of CITD but were substantially increased during the onset of pneumonitis and intestinal perforation irAEs. The observations suggest that unlike other irAEs such as pneumonitis, CRP levels and NLR were non-contributory in diagnosing CITD, whereas T cell expansion may be associated with immunotherapy-induced thyroiditis.
Diagnostic performance of 99mTc-HYNIC-PSMA SPECT/CT for biochemically recurrent prostate cancer after radical prostatectomy

Objectives 99mTc-HYNIC-PSMA is a novel technetium-99m-labeled small-molecule inhibitor of prostate-specific membrane antigen (PSMA) for detection of prostate cancer. The present study investigated the diagnostic yield of 99mTc-HYNIC-PSMA Single photon emission computed tomography (SPECT)/CT in 147 patients with biochemically recurrent prostate cancer after radical prostatectomy. Methods 147 patients with biochemical relapse after radical prostatectomy were finally eligible for this retrospective analysis. The median prostate-specific antigen (PSA) level was 8.26 ng/mL (range, 0.22-187.40 ng/mL). Of the 147 patients, 72 patients received androgen deprivation therapy (ADT) at least 6 months before the 99mTc-HYNIC-PSMA SPECT/CT. All patients underwent planar whole-body scans and subsequent SPECT/CT of the thoracic and abdominal regions after intravenous injection of 705 ± 70 MBq of 99mTc-HYNIC-PSMA. Images were evaluated for the presence and location of PSMA-positive lesions, in which SUVmax were also measured. Detection rates were stratified according to PSA levels, ADT and Gleason scores. The relationships between SUVmax and clinical characteristics were analyzed using univariate and multivariable linear regression models for patients with positive findings. Results Of the 147 patients, 99mTc-HYNIC-PSMA SPECT/CT revealed at least one positive lesion in 118 patients with a high detection rate (80.3%). The detection rates were 48.6% (17/35), 85.1% (40/47), 92.1% (35/38), and 96.3% (26/27) at PSA levels of greater than 0.2 to 2, greater than 2 to 5, greater than 5 to 10, and greater than 10 ng/mL, respectively. PSMA SPECT/CT indicated local recurrence, lymph node metastases, bone metastases, and visceral metastases in 14 (9.5%), 73 (49.7%), 48 (32.7%) and 3 (2.0%) patients. The detection rates of local recurrence and metastasis increased with increasing PSA levels. The detection rate was higher in patients treated with ADT than those without (90.3% vs. 70.7%; P =0.0029). In patients with Gleason scores ≥8, detection rate was slightly higher than those with ≤7 (81.7% vs. 78.5%), but not statistically significant (P = 0.6265). Multivariable linear regression analysis showed a significant correlation of PSA levels and ADT with SUVmax (P=0.0005 and P=0.0397). Conclusions 99mTc-HYNIC-PSMA SPECT/CT offers high detection rates for biochemically recurrent prostate cancer after radical prostatectomy. The detection rate and SUVmax were positively correlated with PSA levels and ADT.
Rapid hydrogel-based phage susceptibility test for pathogenic bacteria

Phage therapy is one alternative to cure infections caused by antibiotic resistant bacteria. Due to the narrow host range of phages, hundreds to thousands of phages are required to cover the diversity of bacterial pathogens. In personalized phage therapy, fast selection of the phages for individual patients is essential for successful therapy. The aims of this study were to set up a rapid hydrogel-based liquid phage susceptibility assay (PST) for the selection of phages for therapeutic use and to establish a “ready-to-screen” plate concept, where phages are readily stored in hydrogel as small droplets in microtiter plate wells. We first tested four commercially available hydrogels (GrowDex, Askina, Purilon, and Intrasite) for their suitability as phage matrices in PSTs with four phages, two of which infecting Escherichia coli and two Staphylococcus aureus. Of these four hydrogels, GrowDex was the best matrix for PST, as it did not inhibit bacterial growth, released phages quickly when mixed with bacterial culture, and maintained phage viability well. We then optimized the assay for both optical density and microscopy readers using GrowDex as matrix with 23 bacterial strains representing 10 different species and 23 phages possessing different morphologies and genome sizes. When the bacterial growth was monitored by microscopy reader, the PST was executed in just 3 hours, and there was no need for overnight culturing bacterial cells prior to the assay, whereas using optical density reader, bacteria had to be pre-cultured overnight, and the assay time was five hours. Finally, we evaluated the effect of three different chemical stabilizers (trehalose, hyaluronic acid, and gelatin) in a six-month stability assay with six model phages. These phages assay behaved very differently in respect to the chemical stabilizers, and there was not a single stabilizer suitable for all phages. However, when gelatin (0.01%) or hyaluronic acid (0.2 mg/ml) was used as stabilizer, all tested phages were still considered as positives in PST after a six-month storage in 1 ml volume. In “ready-to-screen” plates, the differences in phage stabilities were even more profound, varying from two to six months for the most and least stable phages, respectively.
Research progress on the role of hormones in ischemic stroke

Ischemic stroke is a major cause of death and disability around the world. However, ischemic stroke treatment is currently limited, with a narrow therapeutic window and unsatisfactory post-treatment outcomes. Therefore, it is critical to investigate the pathophysiological mechanisms following ischemic stroke brain injury. Changes in the immunometabolism and endocrine system after ischemic stroke are important in understanding the pathophysiological mechanisms of cerebral ischemic injury. Hormones are biologically active substances produced by endocrine glands or endocrine cells that play an important role in the organism’s growth, development, metabolism, reproduction, and aging. Hormone research in ischemic stroke has made very promising progress. Hormone levels fluctuate during an ischemic stroke. Hormones regulate neuronal plasticity, promote neurotrophic factor formation, reduce cell death, apoptosis, inflammation, excitotoxicity, oxidative and nitrative stress, and brain edema in ischemic stroke. In recent years, many studies have been done on the role of thyroid hormone, growth hormone, testosterone, prolactin, oxytocin, glucocorticoid, parathyroid hormone, and dopamine in ischemic stroke, but comprehensive reviews are scarce. This review focuses on the role of hormones in the pathophysiology of ischemic stroke and discusses the mechanisms involved, intending to provide a reference value for ischemic stroke treatment and prevention.
Opposite roles of MAPKKK17 and MAPKKK21 against Tetranychus urticae in Arabidopsis

After recognizing a biotic stress, plants activate signalling pathways to fight against the attack. Typically, these signalling pathways involve the activation of phosphorylation cascades mediated by Mitogen-Activated Protein Kinases (MAPKs). In the Arabidopsis thaliana-Tetranychus urticae plant-herbivore model, several Arabidopsis MAP kinases are induced by the mite attack. In this study, we demonstrate the participation of the MEKK-like kinases MAPKKK17 and MAPKKK21. Leaf damage caused by the mite was assessed using T-DNA insertion lines. Differential levels of damage were found when the expression of MAPKKK17 was increased or reduced. In contrast, reduced expression of MAPKKK21 resulted in less damage caused by the mite. Whereas the expression of several genes associated with hormonal responses did not suffer significant variations in the T-DNA insertion lines, the expression of one of these kinases depends on the expression of the other one. In addition, MAPKKK17 and MAPKKK21 are coexpressed with different sets of genes and encode proteins with low similarity in the C-terminal region. Overall, our results demonstrate that MAPKKK17 and MAPKKK21 have opposite roles. MAPKKK17 and MAPKKK21 act as positive and negative regulators, respectively, on the plant response. The induction of MAPKKK17 and MAPKKK21 after mite infestation would be integrated into the bulk of signalling pathways activated to balance the response of the plant to a biotic stress.
Academic motivation at early ages: Spanish validation of the Elementary School Motivation Scale (ESMS-E)

The Elementary School Motivation Scale (ESMS) is the only validated and adapted instrument to assess motivation in early ages and in specific domains using the Self-Determination Theory. The present study aims to validate the ESMS in Spanish population (ESMS-E). To this end, 1,190 students from the first half of Elementary education (6–10 years old) filled in the ESMS-E. To translate the instrument the back translation method was used. Internal consistency was assessed through composite reliability (CR), correlations among the dimensions and Confirmatory Factor Analysis (CFA) were used to analyze the theoretical structure proposed by the original instrument. Results showed optimal internal consistency in the different dimensions (CR = 0.701–0.901) and showed a great fit for the model (RMSEA = 0.064, CFI = 0.929, TLI = 0.913), confirming the original model with nine dimensions and the self-determination continuum. The ESMS-E is valid and reliable in the Spanish version. This validation offers a tool for researchers interested in exploring the motives that drive students in early stages in relation to specific learning domains (i.e., reading, writing and mathematics).