Miracle-dz/UniFAR-FTUs huggingface dataset:
MeCP2 Deficiency Disrupts Kainate-Induced Presynaptic Plasticity in the Mossy Fiber Projections in the Hippocampus

Methyl cytosine binding protein 2 (MeCP2) is a structural chromosomal protein involved in the regulation of gene expression. Mutations in the gene encoding MeCP2 result in Rett Syndrome (RTT), a pervasive neurodevelopmental disorder. RTT is one of few autism spectrum disorders whose cause was identified as a single gene mutation. Remarkably, abnormal levels of MeCP2 have been associated to other neurodevelopmental disorders, as well as neuropsychiatric disorders. Therefore, many studies have been oriented to investigate the role of MeCP2 in the nervous system. In the present work, we explore cellular and molecular mechanisms affecting synaptic plasticity events in vivo in the hippocampus of MeCP2 mutant mice. While most studies addressed postsynaptic defects in the absence of MeCP2, we took advantage of an in vivo activity-paradigm (seizures), two models of MeCP2 deficiency, and neurobiological assays to reveal novel defects in presynaptic structural plasticity in the hippocampus in RTT rodent models. These approaches allowed us to determine that MeCP2 mutations alter presynaptic components, i.e., disrupts the plastic response of mossy fibers to synaptic activity and results in reduced axonal growth which is correlated with imbalanced trophic and guidance support, associated with aberrant expression of brain-derived neurotrophic factor and semaphorin 3F. Our results also revealed that adult-born granule cells recapitulate maturational defects that have been only shown at early postnatal ages. As these cells do not mature timely, they may not integrate properly into the adult hippocampal circuitry. Finally, we performed a hippocampal-dependent test that revealed defective spatial memory in these mice. Altogether, our studies establish a model that allows us to evaluate the effect of the manipulation of specific pathways involved in axonal guidance, synaptogenesis, or maturation in specific circuits and correlate it with changes in behavior. Understanding the mechanisms underlying the neuronal compromise caused by mutations in MeCP2 could provide information on the pathogenic mechanism of autistic spectrum disorders and improve our understanding of brain development and molecular basis of behavior.
Global Transcriptome Profiling of Multiple Porcine Organs Reveals Toxoplasma gondii-Induced Transcriptional Landscapes

We characterized the porcine tissue transcriptional landscapes that follow Toxoplasma gondii infection. RNAs were isolated from liver, spleen, cerebral cortex, lung, and mesenteric lymph nodes (MLNs) of T. gondii-infected and uninfected (control) pigs at days 6 and 18 postinfection, and were analyzed using next-generation sequencing (RNA-seq). T. gondii altered the expression of 178, 476, 199, 201, and 362 transcripts at 6 dpi and 217, 223, 347, 119, and 161 at 18 dpi in the infected brain, liver, lung, MLNs and spleen, respectively. The differentially expressed transcripts (DETs) were grouped into five expression patterns and 10 sub-clusters. Gene Ontology enrichment and pathway analysis revealed that immune-related genes dominated the overall transcriptomic signature and that metabolic processes, such as steroid biosynthesis, and metabolism of lipid and carboxylic acid, were downregulated in infected tissues. Co-expression network analysis identified transcriptional modules associated with host immune response to infection. These findings not only show how T. gondii infection alters porcine transcriptome in a tissue-specific manner, but also offer a gateway for testing new hypotheses regarding human response to T. gondii infection.
Cerebral Hemodynamic Evaluation After Cerebral Recanalization Therapy for Acute Ischemic Stroke

Cerebral recanalization therapy, either intravenous thrombolysis or mechanical thrombectomy, improves the outcomes in patients with acute ischemic stroke (AIS) by restoring the cerebral perfusion of the ischemic penumbra. Cerebral hemodynamic evaluation after recanalization therapy, can help identify patients with high risks of reperfusion-associated complications. Among the various hemodynamic modalities, magnetic resonance imaging (MRI), computed tomography perfusion, and transcranial Doppler sonography (TCD) are the most commonly used. Poststroke hypoperfusion is associated with infarct expansion, while hyperperfusion, which once was considered the hallmark of successful recanalization, is associated with hemorrhagic transformation. Either the hypo- or the hyperperfusion may result in poor clinical outcomes. Individual blood pressure target based on cerebral hemodynamic evaluation was crucial to improve the prognosis. This review summarizes literature on cerebral hemodynamic evaluation and management after recanalization therapy to guide clinical decision making.
sRNA Profiling Combined With Gene Function Analysis Reveals a Lack of Evidence for Cross-Kingdom RNAi in the Wheat – Zymoseptoria tritici Pathosystem

Cross-kingdom small RNA (sRNA) silencing has recently emerged as a mechanism facilitating fungal colonization and disease development. Here we characterized RNAi pathways in Zymoseptoria tritici, a major fungal pathogen of wheat, and assessed their contribution to pathogenesis. Computational analysis of fungal sRNA and host mRNA sequencing datasets was used to define the global sRNA populations in Z. tritici and predict their mRNA targets in wheat. 389 in planta-induced sRNA loci were identified. sRNAs generated from some of these loci were predicted to target wheat mRNAs including those potentially involved in pathogen defense. However, molecular approaches failed to validate targeting of selected wheat mRNAs by fungal sRNAs. Mutant strains of Z. tritici carrying deletions of genes encoding key components of RNAi such as Dicer-like (DCL) and Argonaute (AGO) proteins were generated, and virulence bioassays suggested that these are dispensable for full infection of wheat. Nonetheless, our results did suggest the existence of non-canonical DCL-independent pathway(s) for sRNA biogenesis in Z. tritici. dsRNA targeting essential fungal genes applied in vitro or generated from an RNA virus vector in planta in a procedure known as HIGS (Host-Induced Gene Silencing) was ineffective in preventing Z. tritici growth or disease. We also demonstrated that Z. tritici is incapable of dsRNA uptake. Collectively, our data suggest that RNAi approaches for gene function analyses in this fungal species and potentially also as a control measure may not be as effective as has been demonstrated for some other plant pathogenic fungi.
Synthesis and Supramolecular Assembly of a Terrylene Diimide Derivative Decorated With Long Branched Alkyl Chains

Terrylene diimide derivatives are pigments for dyes and optoelectric devices. A terrylene diimide derivative N,N'-di(1-undecyldodecyl)terrylene-3,4:11,12-tetracarboxdiimide (DUO-TDI) decorated with long branched alkyl chains on both imide nitrogen atoms was designed and synthesized. The supramolecular assembly behaviors of DUO-TDI in solution and at the liquid-solid interface were both investigated. The assembled nanostructures and photophysical properties of TDI in solution were explored by varying solvent polarity with spectral methods (UV-Vis, FL and FT-IR) and morphological characterization (AFM). Depending on the solution polarities, fibers, disk structures and wires could be observed and they showed diverse photophysical properties. In addition, the interfacial assembly of DUO-TDI was further investigated at the liquid-Highly Oriented Pyrolytic Graphite (HOPG) interface probed by scanning tunneling microscope (STM). Long range ordered monolayers composed of lamellar structures were obtained. The assembly mechanisms were studied for DUO-TDI both in solution and at the interface. Our investigation provides alternative strategy for designing and manipulation of supramolecular nanostructures and corresponding properties of TDI based materials.
The Commensal Microbiota and Viral Infection: A Comprehensive Review

The human body is inhabited by a diverse microbial community that is collectively coined as commensal microbiota. Recent research has greatly advanced our understanding of how the commensal microbiota affects host health. Among the various kinds of pathogenic infections of the host, viral infections constitute one of the most serious public health problems worldwide. During the infection process, viruses may have substantial and intimate interactions with the commensal microbiota. A plethora of evidence suggests that the commensal microbiota regulates and is in turn regulated by invading viruses through diverse mechanisms, thereby having stimulatory or suppressive roles in viral infections. Furthermore, the integrity of the commensal microbiota can be disturbed by invading viruses, causing dysbiosis in the host and further influencing virus infectivity. In the present article, we discuss current insights into the regulation of viral infection by the commensal microbiota. We also draw attention to the disruption of microbiota homeostasis by several viruses.
Fecal Microbiome Data Distinguish Liver Recipients With Normal and Abnormal Liver Function From Healthy Controls

Emerging evidence suggests that altered intestinal microbiota plays an important role in the pathogenesis of many liver diseases, mainly by promoting inflammation via the “intestinal microbiota-immunity-liver” axis. We aimed to investigate the fecal microbiome of liver recipients with abnormal/normal liver function using 16S rRNA gene sequencing. Fecal samples were collected from 90 liver recipients [42 with abnormal liver function (Group LT_A) and 48 with normal liver function (Group LT_N)] and 61 age- and gender-matched healthy controls (HCs). Fecal microbiomes were analyzed for comparative composition, diversity, and richness of microbial communities. Principal coordinates analysis successfully distinguished the fecal microbiomes of recipients in Group LT_A from healthy subjects, with the significant decrease of fecal microbiome diversity in recipients in Group LT_A. Other than a higher relative abundance of opportunistic pathogens such as Klebsiella and Escherichia/Shigella in all liver recipients, the main difference in gut microbiome composition between liver recipients and HC was the lower relative abundance of beneficial butyrate-producing bacteria in the recipients. Importantly, we established a fecal microbiome index (specific alterations in Staphylococcus and Prevotella) that could be used to distinguish Group LT_A from Group LT_N, with an area under the receiver operating characteristic curve value of 0.801 and sensitivity and specificity values of 0.771 and 0.786, respectively. These findings revealed unique gut microbial characteristics of liver recipients with abnormal and normal liver functions, and identified fecal microbial risk indicators of abnormal liver function in liver recipients.
Nrf2 Plays a Protective Role Against Intravascular Hemolysis-Mediated Acute Kidney Injury

Massive intravascular hemolysis is associated with acute kidney injury (AKI). Nuclear factor erythroid-2-related factor 2 (Nrf2) plays a central role in the defense against oxidative stress by activating the expression of antioxidant proteins. We investigated the role of Nrf2 in intravascular hemolysis and whether Nrf2 activation protected against hemoglobin (Hb)/heme-mediated renal damage in vivo and in vitro. We observed renal Nrf2 activation in human hemolysis and in an experimental model of intravascular hemolysis promoted by phenylhydrazine intraperitoneal injection. In wild-type mice, Hb/heme released from intravascular hemolysis promoted AKI, resulting in decreased renal function, enhanced expression of tubular injury markers (KIM-1 and NGAL), oxidative and endoplasmic reticulum stress (ER), and cell death. These features were more severe in Nrf2-deficient mice, which showed decreased expression of Nrf2-related antioxidant enzymes, including heme oxygenase 1 (HO-1) and ferritin. Nrf2 activation with sulforaphane protected against Hb toxicity in mice and cultured tubular epithelial cells, ameliorating renal function and kidney injury and reducing cell stress and death. Nrf2 genotype or sulforaphane treatment did not influence the severity of hemolysis. In conclusion, our study identifies Nrf2 as a key molecule involved in protection against renal damage associated with hemolysis and opens novel therapeutic approaches to prevent renal damage in patients with severe hemolytic crisis. These findings provide new insights into novel aspects of Hb-mediated renal toxicity and may have important therapeutic implications for intravascular hemolysis-related diseases.
Associations Between Anxiety, Body Mass Index, and Sex Hormones in Women

Background: Several studies have shown a positive association between anxiety and obesity, particularly in women. We aimed to study whether sex hormone alterations related to obesity might play a role in this association. Patients and methods: Data for this study were obtained from a population-based cohort study (the LIFE-Adult-Study). A total of 3,124 adult women (970 premenopausal and 2,154 postmenopausal) were included into the analyses. The anxiety symptomatology was assessed using the GAD-7 questionnaire (cut-off ≥ 10 points). Sex hormones were measured from fasting serum samples. Results: We did not find significant differences in anxiety prevalence in premenopausal obese women compared with normal-weight controls (4.8% vs. 5.5%). Both obesity and anxiety symptomatology were separately associated with the same sex hormone alteration in premenopausal women: higher total testosterone level (0.97 ± 0.50 in obese vs. 0.86 ± 0.49 nmol/L in normal-weight women, p = 0.026 and 1.04 ± 0.59 in women with vs. 0.88 ± 0.49 nmol/L in women without anxiety symptomatology, p = 0.023). However, women with anxiety symptomatology had non-significantly higher estradiol levels than women without anxiety symptomatology (548.0 ± 507.6 vs. 426.2 ± 474.0 pmol/L), whereas obesity was associated with lower estradiol levels compared with those in normal-weight group (332.7 ± 386.5 vs. 470.8 ± 616.0 pmol/L). Women with anxiety symptomatology had also significantly higher testosterone and estradiol composition (p = 0.006). No associations of sex hormone levels and BMI with anxiety symptomatology in postmenopausal women were found. Conclusions: Although both obesity and anxiety symptomatology were separately associated with higher testosterone level, there was an opposite impact of anxiety and obesity on estradiol levels in premenopausal women. We did not find an evidence that the sex hormone alterations related to obesity are playing a significant role in anxiety symptomatology in premenopausal women. This could be the explanation why we did not find an association between obesity and anxiety. In postmenopausal women, other mechanisms seem to work than in the premenopausal group.
Plant Host-Associated Mechanisms for Microbial Selection

Plants serve as host to numerous microorganisms. The members of these microbial communities interact among each other and with the plant, and there is increasing evidence to suggest that the microbial community may promote plant growth, improve drought tolerance, facilitate pathogen defense and even assist in environmental remediation. Therefore, it is important to better understand the mechanisms that influence the composition and structure of microbial communities, and what role the host may play in the recruitment and control of its microbiome. In particular, there is a growing body of research to suggest that plant defense systems not only provide a layer of protection against pathogens but may also actively manage the composition of the overall microbiome. In this review, we provide an overview of the current research into mechanisms employed by the plant host to select for and control its microbiome. We specifically review recent research that expands upon the role of keystone microbial species, phytohormones, and abiotic stress, and in how they relate to plant driven dynamic microbial structuring.
Influenza passaging annotations: what they tell us and why we should listen

Abstract Influenza databases now contain over 100,000 worldwide sequence records for strains influenza A(H3N2) and A(H1N1). Although these data facilitate global research efforts and vaccine development practices, they also represent a stumbling block for researchers because of their confusing and heterogeneous annotation. Unclear passaging annotations are particularly concerning given the recent work highlighting the presence and risk of false adaptation signals introduced by cell passaging of viral isolates. With this in mind, we aim to provide a concise outline of why viruses are passaged, a clear overview of passaging annotation nomenclature currently in use, and suggestions for a standardized nomenclature going forward. Our hope is that this summary will empower researchers and clinicians alike to more easily understand a virus sample’s passage history when analyzing influenza sequences.
Characterization of gene promoters in pig: conservative elements, regulatory motifs and evolutionary trend

It is vital to understand the conservation and evolution of gene promoter sequences in order to understand environmental adaptation. The level of promoter conservation varies greatly between housekeeping (HK) and tissue-specific (TS) genes, denoting differences in the strength of the evolutionary constraints. Here, we analyzed promoter conservation and evolution to exploit differential regulation between HK and TS genes. The analysis of conserved elements showed CpG islands, short tandem repeats and G-quadruplex sequences are highly enriched in HK promoters relative to TS promoters. In addition, the type and density of regulatory motifs in TS promoters are much higher than HK promoters, indicating that TS genes show more complex regulatory patterns than HK genes. Moreover, the evolutionary dynamics of promoters showed similar evolutionary trend to coding sequences. HK promoters suffer more stringent selective pressure in the long-term evolutionary process. HK genes tend to show increased upstream sequence conservation due to stringent selection pressures acting on the promoter regions. The specificity of TS gene expression may be due to complex regulatory motifs acting in different tissues or conditions. The results from this study can be used to deepen our understanding of adaptive evolution.
Crosstalk in guided-wave electro-optic tunable filters

The crosstalk performance of a four-port electrooptic tunable filter in lithium niobate is analyzed, based on the transient response of the filter to an input optical pulse. Crosstalk is calculated for Blackman apodizing functions for input pulse widths representative of high-data-rate systems. It is concluded that crosstalk level below -30 dB for 20 Gb/s data rates and 100 GHz channel spacing is achievable with presently available substrate dimensions.
Two new Erythrophylloporus species (Boletaceae) from Thailand, with two new combinations of American species

Abstract Erythrophylloporus is a lamellate genus in the family Boletaceae that has been recently described from China based on E.cinnabarinus, the only known species. Typical characters of Erythrophylloporus are reddish-orange to yellowish-red basidiomata, including lamellae, bright yellow basal mycelium and smooth, broadly ellipsoid, ellipsoid to nearly ovoid basidiospores. During our survey on diversity of Boletaceae in Thailand, several yellowish-orange to reddish- or brownish-orange lamellate boletes were collected. Based on both morphological evidence and molecular analyses of a four-gene dataset (atp6, tef1, rpb2 and cox3), they were recognised as belonging in Erythrophylloporus and different from the already known species. Two new species, E.paucicarpus and E.suthepensis are therefore introduced from Thailand with detailed descriptions and illustrations. Moreover, two previously described Phylloporus species, P.aurantiacus and P.fagicola, were also revised and recombined in Erythrophylloporus. A key to all known Erythrophylloporus species is provided.
Subgingival microbiome of experimental gingivitis: shifts associated with the use of chlorhexidine and N-acetyl cysteine mouthwashes

ABSTRACT This study aimed to demonstrate subgingival microbial changes associated with development, prevention, and treatment of experimental gingivitis using chlorhexidine (CHX) and N-acetylcysteine (NAC) mouthwashes. This randomized clinical trial comprised two parts: a 3-week prevention sub-study in which 30 study subjects were equally assigned to either mouthwash or placebo while developing experimental gingivitis; followed by a 2-week treatment sub-study in which 20 subjects with experimental gingivitis were assigned to either mouthwash. Subgingival samples were collected at the beginning and end of each sub-study for microbial profiling with 16S rRNA gene sequencing. As expected, CHX was effective in both preventing and reversing experimental gingivitis; NAC had a modest effect. Gingivitis was associated with enrichment of TM7 HOT-346/349, Tannerella HOT-286, Cardiobacterium valvarum, Campylobacter gracilis, Porphyromonas catoniae, Leptotrichia HOT-219, and Selenomonas spp. At the phylum/genus level, TM7 showed the strongest association. Gingival health was associated with increased abundance of Haemophilus parainfluenzae, Lautropia mirabilis, Rothia spp. , Streptococcus spp. , and Kingella oralis. CHX demonstrated largely indiscriminate antimicrobial action, resulting in significant drop in biomass and diversity. Our results substantiate the role of specific oral bacterial species in the development of gingivitis. They also indicate that NAC is not a promising mouthwash at the concentration tested.
Face Recognition with Triangular Fuzzy Set-Based Local Cross Patterns in Wavelet Domain

In this study, a new face recognition architecture is proposed using fuzzy-based Discrete Wavelet Transform (DWT) and fuzzy with two novel local graph descriptors. These graph descriptors are called Local Cross Pattern (LCP). The proposed fuzzy wavelet-based face recognition architecture consists of DWT, Triangular fuzzy set transformation, and textural feature extraction with local descriptors and classification phases. Firstly, the LL (Low-Low) sub-band is obtained by applying the 2 Dimensions Discrete Wavelet Transform (2D DWT) to face images. After that, the triangular fuzzy transformation is applied to this band in order to obtain A, B, and C images. The proposed LCP is then applied to the B image. LCP consists of two types of descriptors: Vertical Local Cross Pattern (VLCP) and Horizontal Local Cross Pattern (HLCP). Linear discriminant analysis, quadratic discriminant, analysis, quadratic kernel-based support vector machine (QKSVM), and K-nearest neighbors (KNN) were ultimately used to classify the extracted features. Ten widely used descriptors in the literature are applied to the fuzzy wavelet architecture. AT&T, CIE, Face94, and FERET databases are used for performance evaluation of the proposed methods. Experimental results show that the LCP descriptors have high face recognition performance, and the fuzzy wavelet-based model significantly improves the performances of the textural descriptors-based face recognition methods. Moreover, the proposed fuzzy-based domain and LCP method achieved classification accuracy rates of 97.3%, 100.0%, 100.0%, and 96.3% for AT&T, CIE, Face94, and FERET datasets, respectively.