Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Analysis of Virulence Mechanisms of Trypanosomatids Pathogenic to Humans

Trypanosoma brucei, Leishmania spp. , and T. cruzi are flagellate protozoans of the family Trypanosomatidae and the causative agents of human African trypanosomiasis, leishmaniasis, and Chagas disease, respectively. These diseases affect humans worldwide and exert a significant impact on public health. Over the course of evolution, the parasites associated with these pathologies have developed mechanisms to circumvent the immune response system throughout the infection cycle. In cases of human infection, this function is undertaken by a group of proteins and processes that allow the parasites to propagate and survive during host invasion. In T. brucei, antigenic variation is promoted by variant surface glycoproteins and other proteins involved in evasion from the humoral immune response, which helps the parasite sustain itself in the extracellular milieu during infection. Conversely, Leishmania spp. and T. cruzi possess a more complex infection cycle, with specific intracellular stages. In addition to mechanisms for evading humoral immunity, the pathogens have also developed mechanisms for facilitating their adhesion and incorporation into host cells. In this review, the different immune evasion strategies at cellular and molecular levels developed by these human-pathogenic trypanosomatids have been discussed, with a focus on the key molecules responsible for mediating the invasion and evasion mechanisms and the effects of these molecules on virulence.
An Epigenetically Distinct Subset of Children With Autism Spectrum Disorder Resulting From Differences in Blood Cell Composition

Background: Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder that often involves impaired cognition, communication difficulties and restrictive, repetitive behaviors. ASD is extremely heterogeneous both clinically and etiologically, which represents one of the greatest challenges in studying the molecular underpinnings of ASD. While hundreds of ASD-associated genes have been identified that confer varying degrees of risk, no single gene variant accounts for >1% of ASD cases. Notably, a large number of ASD-risk genes function as epigenetic regulators, indicating potential epigenetic dysregulation in ASD. As such, we compared genome-wide DNA methylation (DNAm) in the blood of children with ASD (n = 265) to samples from age- and sex-matched, neurotypical controls (n = 122) using the Illumina Infinium HumanMethylation450 arrays. Results: While DNAm patterns did not distinctly separate ASD cases from controls, our analysis identified an epigenetically unique subset of ASD cases (n = 32); these individuals exhibited significant differential methylation from both controls than the remaining ASD cases. The CpG sites at which this subset was differentially methylated mapped to known ASD risk genes that encode proteins of the nervous and immune systems. Moreover, the observed DNAm differences were attributable to altered blood cell composition, i.e., lower granulocyte proportion and granulocyte-to-lymphocyte ratio in the ASD subset, as compared to the remaining ASD cases and controls. This ASD subset did not differ from the rest of the ASD cases in the frequency or type of high-risk genomic variants. Conclusion: Within our ASD cohort, we identified a subset of individuals that exhibit differential methylation from both controls and the remaining ASD group tightly associated with shifts in immune cell type proportions. This is an important feature that should be assessed in all epigenetic studies of blood cells in ASD. This finding also builds on past reports of changes in the immune systems of children with ASD, supporting the potential role of altered immunological mechanisms in the complex pathophysiology of ASD. The discovery of significant molecular and immunological features in subgroups of individuals with ASD may allow clinicians to better stratify patients, facilitating personalized interventions and improved outcomes.
Modulation of endometrial E-Cadherin and N-Cadherin by ovarian steroids and embryonic stimuli

The endometrium is a dynamic tissue that undergoes extensive remodelling to attain a receptive state which is further modulated in presence of an embryo for successful initiation of pregnancy. Cadherins are the proteins of junctional complex of which E-cadherin (E-Cad) is crucial for maintaining epithelial cell state and integrity of the epithelial barrier; gain of N-cadherin (N-Cad) in epithelial cells leads to epithelial to mesenchymal transition (EMT). In the present study, we aimed to investigate the expression of E-Cad and N-Cad in the mouse endometrial luminal epithelium and its modulation by estrogen, progesterone and embryonic stimuli. We observed that E-Cad is diffusely expressed in the luminal epithelium of mouse endometrium during the estrus stage and upon estrogen treatment. It is apico-laterally and basolaterally sorted at the diestrus stage and in response to combined treatment of estrogen and progesterone. In 3D spheroids of human endometrial epithelial cells, combined treatment with estrogen and progesterone led to lateral sorting of E-Cad. In the mouse endometrium at the time of embryo implantation, there is loss of E-Cad which was associated with the gain of N-Cad suggestive of EMT in the luminal epithelium. This EMT is possibly driven by embryonic stimuli as treatment with estrogen and progesterone did not lead to gain of N-Cad expression. In conclusion, the present study demonstrates that steroid hormones directly affect E-Cad sorting in the endometrial epithelium.
White Matter Hyperintensities, Grey Matter Atrophy, and Cognitive Decline in Neurodegenerative Diseases

Introduction White matter hyperintensities (WMHs) as seen on T2w and FLAIR scans represent small-vessel disease related changes in the brain. WMHs are associated with cognitive decline in the normal aging population in general and more specifically in patients with neurodegenerative diseases. In this study, we assessed the different spatial patterns and relationships between WMHs and grey matter (GM) atrophy in normal aging, individuals with mild cognitive impairment (MCI), Alzheimer’s dementia (AD), fronto-temporal dementia (FTD), and de novo Parkinson’s disease (PD). Methods Imaging and clinical data were obtained from 3 large multi-center databases: The Alzheimer’s Disease Neuroimaging Initiative (ADNI), the frontotemporal lobar degeneration neuroimaging initiative (NIFD), and the Parkinson’s Progression Markers Initiative (PPMI). WMHs and GM atrophy maps were measured in normal controls (N= 571), MCI (N= 577), AD (N= 222), FTD (N= 144), and PD (N= 363). WMHs were segmented using T1w and T2w/PD or FLAIR images and mapped onto 45 white matter tracts using the Yeh WM atlas. GM volume was estimated from the Jacobian determinant of the nonlinear deformation field required to map the subject’s MRI to a standard template. The CerebrA atlas was used to obtain volume estimates in 84 GM regions. Mixed effects models were used to compare WMH in different WM tracts and volume of multiple GM structures between patients and controls, assess the relationship between regional WMHs and GM loss for each disease, and investigate their impact on cognition. Results MCI, AD, and FTD patients had significantly higher WMH loads than the matched controls. There was no significant difference in WMHs between PD and controls. For each cohort, significant interactions between WMH load and GM atrophy were found for several regions and tracts, reflecting additional contribution of WMH burden to GM atrophy. While these associations were more relevant for insular and parieto-occipital regions in MCI and AD cohorts, WMH burden in FTD subjects had greater impact on frontal and basal ganglia atrophy. Finally, we found additional contribution of WMH burden to cognitive deficits in AD and FTD subjects compared with matched controls, whereas their impact on cognitive performance in MCI and PD were not significantly different from controls. Conclusions WMHs occur more extensively in MCI, AD, and FTD patients than age-matched normal controls. WMH burden on WM tracts also correlates with regional GM atrophy in regions anatomically and functionally related to those tracts, suggesting a potential involvement of WMHs in the neurodegenerative process.
Comparison of Scalp ERP to Faces in Macaques and Humans

Face recognition is an essential activity of social living, common to many primate species. Underlying processes in the brain have been investigated using various techniques and compared between species. Functional imaging studies have shown face-selective cortical regions and their degree of correspondence across species. However, the temporal dynamics of face processing, particularly processing speed, are likely different between them. Across sensory modalities activation of primary sensory cortices in macaque monkeys occurs at about 3/5 the latency of corresponding activation in humans, though this human simian difference may diminish or disappear in higher cortical regions. We recorded scalp event-related potentials (ERPs) to presentation of faces in macaques and estimated the peak latency of ERP components. Comparisons of latencies between macaques and humans indicated that the 3:5 ratio is preserved in higher cognitive regions of face processing between those species.
Atorvastatin Upregulates microRNA-186 and Inhibits the TLR4-Mediated MAPKs/NF-κB Pathway to Relieve Steroid-Induced Avascular Necrosis of the Femoral Head

Steroid-induced avascular necrosis of the femoral head (SANFH) is caused by the death of active components of the femoral head owing to hormone overdoses. The use of lipid-lowering drugs to prevent SANFH in animals inspired us to identify the mechanisms involving Atorvastatin (Ato) in SANFH. However, it is still not well understood how and to what extent Ato affects SANFH. This study aimed to figure out the efficacy of Ato in SANFH and the underlying molecular mechanisms. After establishment of the SANFH model, histological evaluation, lipid metabolism, inflammatory cytokines, oxidative stress, apoptosis, and autophagy of the femoral head were evaluated. The differentially expressed microRNAs (miRs) after Ato treatment were screened out using microarray analysis. The downstream gene and pathway of miR-186 were predicted and their involvement in SANFH rats was analyzed. OB-6 cells were selected to simulate SANFH in vitro. Cell viability, cell damage, inflammation responses, apoptosis, and autophagy were assessed. Ato alleviated SANFH, inhibited apoptosis, and promoted autophagy. miR-186 was significantly upregulated after Ato treatment. miR-186 targeted TLR4 and inactivated the MAPKs/NF-κB pathway. Inhibition of miR-186 reversed the protection of Ato on SANFH rats, while inhibition of TLR4 restored the protective effect of Ato. Ato reduced apoptosis and promoted autophagy of OB-6 cells by upregulating miR-186 and inhibiting the TLR4/MAPKs/NF-κB pathway. In conclusion, Ato reduced apoptosis and promoted autophagy, thus alleviating SANFH via miR-186 and the TLR4-mediated MAPKs/NF-κB pathway.
The Charming World of the Extracellular Matrix: A Dynamic and Protective Network of the Intestinal Wall

The intestinal extracellular matrix (ECM) represents a complex network of proteins that not only forms a support structure for resident cells but also interacts closely with them by modulating their phenotypes and functions. More than 300 molecules have been identified, each of them with unique biochemical properties and exclusive biological functions. ECM components not only provide a scaffold for the tissue but also afford tensile strength and limit overstretch of the organ. The ECM holds water, ensures suitable hydration of the tissue, and participates in a selective barrier to the external environment. ECM-to-cells interaction is crucial for morphogenesis and cell differentiation, proliferation, and apoptosis. The ECM is a dynamic and multifunctional structure. The ECM is constantly renewed and remodeled by coordinated action among ECM-producing cells, degrading enzymes, and their specific inhibitors. During this process, several growth factors are released in the ECM, and they, in turn, modulate the deposition of new ECM. In this review, we describe the main components and functions of intestinal ECM and we discuss their role in maintaining the structure and function of the intestinal barrier. Achieving complete knowledge of the ECM world is an important goal to understand the mechanisms leading to the onset and the progression of several intestinal diseases related to alterations in ECM remodeling.
Genetic Manipulation of Sirtuin 3 Causes Alterations of Key Metabolic Regulators in Melanoma

The mitochondrial sirtuin SIRT3 plays key roles in cellular metabolism and energy production, which makes it an obvious target for the management of cancer, including melanoma. Previously, we have demonstrated that SIRT3 was constitutively upregulated in human melanoma and its inhibition resulted in anti-proliferative effects in vitro in human melanoma cells and in vivo in human melanoma xenografts. In this study, we expanded our data employing knockdown and overexpression strategies in cell culture and mouse xenografts to further validate and establish the pro-proliferative function of SIRT3 in melanocytic cells, and its associated potential mechanisms, especially focusing on the metabolic regulation. We found that short-hairpin RNA (shRNA) mediated SIRT3 knockdown in G361 melanoma cells showed diminished tumorigenesis in immunodeficient Nu/Nu mice. Conversely, SIRT3 overexpressing Hs294T melanoma cells showed increased tumor growth. These effects were consistent with changes in markers of proliferation (PCNA), survival (Survivin) and angiogenesis (VEGF) in xenografted tissues. Further, in in vitro culture system, we determined the effect of SIRT3 knockdown on glucose metabolism in SK-MEL-2 cells, using a PCR array. SIRT3 knockdown caused alterations in a total of 37 genes involved in the regulation and enzymatic pathways of glucose (32 genes) and glycogen (5 genes) metabolism. Functions annotation of these identified genes, using the ingenuity pathway analysis (IPA), predicted cumulative actions of decreased cell viability/proliferation, tumor growth and reactive oxygen species (ROS), and increased apoptosis in response to SIRT3 knockdown. Further, IPA gene network analysis of SIRT3 modulated genes revealed the interactions among these genes in addition to several melanoma-associated genes. Sirtuin pathway was identified as one of the top canonical pathways showing the interaction of SIRT3 with metabolic regulatory genes along with other sirtuins. IPA analysis also predicted the inhibition of HIF1α, PKM, KDM8, PPARGC1A, mTOR, and activation of P53 and CLPP; the genes involved in major cancer/melanoma-associated signaling events. Collectively, these results suggest that SIRT3 inhibition affects cellular metabolism, to impart an anti-proliferative response against melanoma.
A Positive Regulatory Feedback Loop between EKLF/KLF1 and TAL1/SCL Sustaining the Erythropoiesis

The erythroid Krüppel-like factor EKLF/KLF1 is a hematopoietic transcription factor binding to CACCC DNA motif and participating in the regulation of erythroid differentiation. With combined use of microarray-based gene expression profiling and promoter-based ChIP-chip assay of E14.5 fetal liver cells from wild type (WT) and EKLF-knockout (Eklf−/−) mouse embryos, we have identified the pathways and direct target genes activated or repressed by EKLF. This genome-wide study together with molecular/cellular analysis of mouse erythroleukemic cells (MEL) indicate that among the downstream direct target genes of EKLF is Tal1/Scl. Tal1/Scl encodes another DNA-binding hematopoietic transcription factor TAL1/SCL known to be an Eklf activator and essential for definitive erythroid differentiation. Further identification of the authentic Tall gene promoter in combination with in vivo genomic footprinting approach and DNA reporter assay demonstrate that EKLF activates Tall gene through binding to a specific CACCC motif located in its promoter. These data establish the existence of a previously unknow positive regulatory feedback loop between two DNA-binding hematopoietic transcription factors that sustains the mammalian erythropoiesis.
Traveling waves in the prefrontal cortex during working memory

Neural oscillations are evident across cortex but their spatial structure is not well-explored. Are oscillations stationary or do they form “traveling waves”, i.e., spatially organized patterns whose peaks and troughs move sequentially across cortex? Here, we show that oscillations in the prefrontal cortex (PFC) organized as traveling waves in the theta (4-8Hz), alpha (8-12Hz) and beta (12-30Hz) bands. Some traveling waves were planar but most rotated. The waves were modulated during performance of a working memory task. During baseline conditions, waves flowed bidirectionally along a specific axis of orientation. Waves in different frequency bands could travel in different directions. During task performance, there was an increase in waves in one direction over the other, especially in the beta band. Author Summary We found that oscillations in the prefrontal cortex form “traveling waves”. Traveling waves are spatially extended patterns in which aligned peaks of activity move sequentially across the cortical surface. Some traveling waves were planar but most rotated. The prefrontal cortex is important for working memory. The traveling waves changed when monkeys performed a working memory task. There was an increase in waves in one direction over the other, especially in the beta band. Traveling waves can serve specific functions. For example, they help maintain network status and help control timing relationships between spikes. Given their functional advantages, a greater understanding of traveling waves should lead to a greater understanding of cortical function.
Klebsiella pneumoniae BolA contributes to cell morphology, siderophore production, stresses challenge, cell adhesion and virulence

Klebsiella pneumoniae infection is one of the important reasons for the increased of morbidity and mortality. The main virulence factors of K. pneumoniae include capsule polysaccharide, lipopolysaccharide, fimbriae, outer membrane proteins and siderophores. BolA homologues form a broadly conserved family of proteins in prokaryotes and eukaryotes. In Escherichia coli, bolA expression is quickly induced in response to different stresses or stationary phase that rapidly adapt to changing environments. In this report, we confirmed that bolA mutant strain exhibited increased sensitivity to bile and oxidative stresses. In addition, gene deletion showed that bolA has an important role for the adherence of K. pneumoniae to host cell and establishment in mice, including liver, spleen, kidney and lung tissues, and induce the formation of liver abscess in mice. Our results also demonstrated that K. pneumoniae bolA increases the production of siderophore and virulence in Galleria mellonella larvae. Collectively, our results demonstrated that K. pneumoniae BolA is a new virulence factor which contributes to survival in different stresses and overcome host defense. These findings are helpful for the research of new treatment strategies for K. pneumoniae infection. IMPORTANCE Klebsiella pneumoniae is an important conditional pathogen causing nosocomial infections and community-acquired infections. It can resistant to multiple antibiotics, causing refractory infections and public health threat. Therefore, new treatments are required to fight the pathogen, and a better understanding of its virulence factors are needed to develop new drugs. Here, we unraveled the role of BolA in survival under different stresses and overcome host defense. Our results suggested that bolA actively contributes to cell morphology, stresses challenge, cell adhesion and siderophore production that are tightly related to bacterial virulence. Therefore, bolA mutant strain reduces the virulence of K. pneumoniae in G. mellonella larvae and its colonization ability in mice. These results reported bolA is a key virulence factor in K. pneumoniae, and they are helpful for research of new therapies to treat this increasingly problematic pathogen.
Total Knee Replacement: Subject-Specific Modeling, Finite Element Analysis, and Evaluation of Dynamic Activities

This study presents a semi-automatic framework to create subject-specific total knee replacement finite element models, which can be used to analyze locomotion patterns and evaluate knee dynamics. In recent years, much scientific attention was attracted to pre-clinical optimization of customized total knee replacement operations through computational modeling to minimize post-operational adverse effects. However, the time-consuming and laborious process of developing a subject-specific finite element model poses an obstacle to the latter. One of this work's main goals is to automate the finite element model development process, which speeds up the proposed framework and makes it viable for practical applications. This pipeline's reliability was ratified by developing and validating a subject-specific total knee replacement model based on the 6th SimTK Grand Challenge data set. The model was validated by analyzing contact pressures on the tibial insert in relation to the patient's gait and analysis of tibial contact forces, which were found to be in accordance with the ones provided by the Grand Challenge data set. Subsequently, a sensitivity analysis was carried out to assess the influence of modeling choices on tibial insert's contact pressures and determine possible uncertainties on the models produced by the framework. Parameters, such as the position of ligament origin points, ligament stiffness, reference strain, and implant-bone alignment were used for the sensitivity study. Notably, it was found that changes in the alignment of the femoral component in reference to the knee bones significantly affect the load distribution at the tibiofemoral joint, with an increase of 206.48% to be observed at contact pressures during 5° internal rotation. Overall, the models produced by this pipeline can be further used to optimize and personalize surgery by evaluating the best surgical parameters in a simulated manner before the actual surgery.
Fluorescence-Based Sensing of Pesticides Using Supramolecular Chemistry

The detection of pesticides in real-world environments is a high priority for a broad range of applications, including in areas of public health, environmental remediation, and agricultural sustainability. While many methods for pesticide detection currently exist, the use of supramolecular fluorescence-based methods has significant practical advantages. Herein, we will review the use of fluorescence-based pesticide detection methods, with a particular focus on supramolecular chemistry-based methods. Illustrative examples that show how such methods have achieved success in real-world environments are also included, as are areas highlighted for future research and development.
The Role of Liquid Biopsy in Early Diagnosis of Lung Cancer

Liquid biopsy is an emerging technology with a potential role in the screening and early detection of lung cancer. Several liquid biopsy-derived biomarkers have been identified and are currently under ongoing investigation. In this article, we review the available data on the use of circulating biomarkers for the early detection of lung cancer, focusing on the circulating tumor cells, circulating cell-free DNA, circulating micro-RNAs, tumor-derived exosomes, and tumor-educated platelets, providing an overview of future potential applicability in the clinical practice. While several biomarkers have shown exciting results, diagnostic performance and clinical applicability is still limited. The combination of different biomarkers, as well as their combination with other diagnostic tools show great promise, although further research is still required to define and validate the role of liquid biopsies in clinical practice.