Miracle-dz/UniFAR-FTUs huggingface dataset:
Can fMRI reveal the representation of syntactic structure in the brain?

While studying semantics in the brain, neuroscientists use two approaches. One is to identify areas that are correlated with semantic processing load. Another is to find areas that are predicted by the semantic representation of the stimulus words. However, in the domain of syntax, most studies have focused only on identifying areas correlated with syntactic processing load. One possible reason for this discrepancy is that representing syntactic structure in an embedding space such that it can be used to model brain activity is a non-trivial computational problem. Another possible reason is that it is unclear if the low signal-to-noise ratio of neuroimaging tools such as functional Magnetic Resonance Imaging (fMRI) can allow us to reveal correlates of complex (and perhaps subtle) syntactic representations. In this study, we propose novel multi-dimensional features that encode information about the syntactic structure of sentences. Using these features and fMRI recordings of participants reading a natural text, we model the brain representation of syntax. First, we find that our syntactic structure-based features explain additional variance in the brain activity of various parts of the language system, even after controlling for complexity metrics that capture processing load. At the same time, we see that regions well-predicted by syntactic features are distributed in the language system and are not distinguishable from those processing semantics.
The modifying enzyme Tsr3 establishes the hierarchy of Rio kinase activity in 40S ribosome assembly

Ribosome assembly is an intricate process, which in eukaryotes is promoted by a large machinery comprised of over 200 assembly factors (AF) that enable the modification, folding, and processing of the ribosomal RNA (rRNA) and the binding of the 79 ribosomal proteins. While some early assembly steps occur via parallel pathways, the process overall is highly hierarchical, which allows for the integration of maturation steps with quality control processes that ensure only fully and correctly assembled subunits are released into the translating pool. How exactly this hierarchy is established, in particular given that there are many instances of RNA substrate “handover” from one highly related AF to another remains to be determined. Here we have investigated the role of Tsr3, which installs a universally conserved modification in the P-site of the small ribosomal subunit late in assembly. Our data demonstrate that Tsr3 separates the activities of the Rio kinases, Rio2 and Rio1, with whom it shares a binding site. By binding after Rio2 dissociation, Tsr3 prevents rebinding of Rio2, promoting forward assembly. After rRNA modification is complete, Tsr3 dissociates, thereby allowing for recruitment of Rio1. Inactive Tsr3 blocks Rio1, which can be rescued using mutants that bypass the requirement for Rio1 activity. Finally, yeast strains lacking Tsr3 randomize the binding of the two kinases, leading to the release of immature ribosomes into the translating pool. These data demonstrate a role for Tsr3 and its modification activity in establishing a hierarchy for the function of the Rio kinases.
Leukocyte adhesion is governed by endolysosomal two pore channel 2 (TPC2)

In response to pro-inflammatory challenges including pathogenic attack and tissue damage, the endothelial cell surface is rearranged to present leukocyte-engaging cell surface receptors. The initial contact needed for leukocyte tethering and rolling is mediated via adhesion demand-driven exocytosis of Weibel-Palade bodies (WPB) that contain the leukocyte receptor P-selectin together with the stabilizing co-factor CD63. We found that diminished expression of the endolysosomal non-selective cation channel TPC2 or inhibition of TPC2-mediated Ca2+-release via trans-Ned 19 led to reduced endolysosomal Ca2+ efflux, and blocked transfer of CD63 from late endosomes/lysosomes (LEL) to WPB, and a concomitant loss of P-selectin on the endothelial cell surface. Accordingly, P-selectin-mediated leukocyte recruitment to trans-Ned 19-treated HUVEC under flow was significantly reduced without disturbing VWF exocytosis. Our findings establish the endolysosome-related TPC2 Ca2+ channel as a key element in the maintenance of proper endothelial functions and a potential pharmacological target in the control of inflammatory leukocyte recruitment.
Involvement of non-LTR retrotransposons in mammal cancer incidence and ageing

The presence in nature of closely related species showing drastic differences in lifespan and cancer incidence has recently increased the interest of the scientific community on these topics. In particular, the adaptations and genomic characteristics underlying the evolution of cancer-resistant and long-lived species have recently focused on the presence of alterations in the number of non-coding RNAs, on epigenetic regulation and, finally, on the activity of transposable elements (TEs). In this study, we compared the content and dynamics of TE activity in the genomes of four rodent and six bat species exhibiting different lifespans and cancer susceptibility. Mouse, rat and guinea pig (short-lived and cancer-prone organisms) were compared with the naked mole rat (Heterocephalus glaber) which is the rodent with the longest lifespan. The long-lived and cancer-resistant bats of the genera Myotis, Rhinolophus, Pteropus and Rousettus were instead compared with the Molossus, which is instead a short-lived and cancer-resistant organism. Analyzing the patterns of recent accumulations of TEs in the genome in these species, we found a strong suppression or negative selection to accumulation, of non-LTR retrotransposons in long-lived and cancer-resistant organisms. On the other hand, all short-lived and cancer-prone species have shown recent accumulation of this class of TEs. Among bats, the Molossus molossus turned out to be a very particular species and, at the same time, an important model because, despite being susceptible to rapid ageing, it is resistant to cancer. In particular, we found that its genome has the highest density of SINE (non-LTR retrotransposons), but, on the other hand, a total lack of active LINE retrotransposons. Our hypothesis is that the lack of LINEs presumably makes the Molossus cancer resistant due to lack of retrotransposition but, at the same time, the high presence of SINE, may be related to their short life span due to “sterile inflammation” and high mutation load. We suggest that research on ageing and cancer evolution should put particular attention to the involvement of non-LTR retrotransposons in these phenomena.
Oscillations in PP1 activity are essential for accurate progression through mammalian oocyte meiosis

ABSTRACT Tightly controlled fluctuations in kinase and phosphatase activity play important roles in regulating M-phase transitions. Protein Phosphatase 1 (PP1) is one of these phosphatases, with oscillations in PP1 activity driving mitotic M-phase. Evidence from a variety of experimental systems also points to roles in meiosis. Here, we report that PP1 is important for M-phase transitions through mouse oocyte meiosis. We employed a unique small-molecule approach to inhibit or activate PP1 at distinct phases of mouse oocyte meiosis. These studies show that temporal control of PP1 activity is essential for the G2/M transition, metaphase I/anaphase I transition, and the formation of a normal metaphase II oocyte. Our data also reveal that inappropriate activation of PP1 is more deleterious at the G2/M transition than at prometaphase I-to-metaphase I, and that an active pool of PP1 during prometaphase is vital for metaphase I/anaphase I transition and metaphase II chromosome alignment. Taken together, these results establish that loss of oscillations in PP1 activity causes a range of severe meiotic defects, pointing to essential roles for PP1 in female fertility, and more broadly, M-phase regulation.
The cytokine receptor DR3 identifies and activates thymic NKT17 cells

Invariant natural killer T (iNKT) cells are thymus-generated T cells with innate-like characteristics and effector function. Several functionally distinct iNKT subsets have been identified, but NKT17 is the only iNKT subset that produces the proinflammatory cytokine IL-17. NKT17 cells are generated in the thymus and then exported into the periphery to populate lymphoid organs and barrier tissues, such as the lung, to provide critical support in host defense. However, the molecular mechanisms that drive the thymic development and subset-specific activation of NKT17 cells remain mostly unknown. Here, we identify the cytokine receptor DR3, a member of the TNF receptor superfamily, being selectively expressed on NKT17 cells but absent on all other thymic iNKT subsets. We further demonstrate that DR3 ligation leads to the in vivo activation of thymic NKT17 cells and provides in vitro costimulatory effects upon α-GalCer-stimulation. Thus, our study reports the identification of a specific surface marker for thymic NKT17 cells that selectively triggers their activation both in vivo and in vitro. These findings provide new insights for deciphering the role and function of IL-17-producing NKT17 cells and for understanding the development and activation mechanisms of iNKT cells in general.
Fast and cost-effective age estimation in Bengal tiger and Asiatic lion: applicability of cementum analysis method

Age estimation methods, through cementum analysis, for wild animals are rarely developed in Southeast Asian Countries. In the present study, we describe the applicability of the cementum analysis technique for developing a fast (±19 hours) and cost-effective age estimation method for Bengal tiger (Panthera tigris tigris) and Asiatic lion (Panthera leo persica) using incisor tooth. The I2 and I3 incisor teeth from the right mandible of a tiger and I2 and I3 from the left maxilla of a lion were used in the study. The longitudinal sections of the tooth were made using a low cost hand grinding technique on sand papers followed by decalcification and staining with hematoxylin. The cementum layers were counted under the microscope at 100X or 200X magnifications. Two cementum layers were observed in each of the I2 and I3 incisor tooth of tiger and six cementum layers were observed in each of the I2 and I3 incisor teeth of lion. The permanent incisors in tiger and lion erupt between 12-14 months; hence, we added 1 year to the counted number of cementum layers to estimate the final age of tiger and lion incisors. The absolute age of tiger and lion incisors was estimated to be of 2+1 years and 6+1 years, respectively. The same number of cementum layers in both incisors respective to the tiger and lion were observed. Therefore, we suggest (i) undertake the blind test and (ii) collect incisor teeth from naturally died or killed individuals for strengthening the database on the age of the wild population. This optimized method may be suitable for many carnivore species, applicable in wildlife forensic studies and can be used by researchers with minimum expertise, time, and funds requirements throughout the world.
Global Metabolome Analysis of Dunaliella tertiolecta, Phaeobacter italicus R11 Co-cultures using Thermal Desoprtion - Comprehensive Two-dimensional Gas Chromatography - Time-of-Flight Mass Spectrometry (TD-GC×GC-TOFMS)

Dunaliella tertiolecta is a marine microalgae that has been studied extensively as a potential carbon-neutral biofuel source [1]. Microalgae oil contains high quantities of energy-rich fatty acids and lipids, but is not yet commercially viable as an alternative fuel. Carefully optimised growth conditions, and more recently, algal-bacterial co-cultures have been explored as a way of improving the yield of Dunaliella tertiolecta microalgae oils. The relationship between the host microalgae and bacterial co-cultures is currently poorly understood. Here, a complete workflow is proposed to analyse the global metabolomic profile of co-cultured Dunaliella tertiolectra and Phaeobacter italicus R11, which will enable researchers to explore the chemical nature of this relationship in more detail. Graphical Abstract Highlights A method for direct microalgae sample introduction is proposed. Advanced chemometric tools can extract, useful and discriminating metabolomic features even from very noisy complex datasets.
Expression of Ferroptosis-Related Genes Shapes Tumor Microenvironment and Pharmacological Profile in Gastric Cancer

Background: Ferroptosis is a form of regulated cell death that occurs as a consequence of lethal lipid peroxidation. A wealth of studies has demonstrated that ferroptosis profoundly modulated numerous biological behaviors of tumor. However, its natural functions in gastric cancer (GC) remain to be explored. Methods: Firstly, a total of over 1,000 GC patients from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) database were included in our study. Secondly, 32 ferroptosis-related genes were extracted from the ferrDb website. Then, unsupervised clustering was performed to classify patients into three distinct ferroptosis-related clusters. Subsequently, we systematically and comprehensively explored the biological characteristics of each cluster. Finally, we constructed a scoring system, named ferroptosis score, to quantify each cluster and also investigated the predictive therapeutic value of the ferroptosis score for chemotherapy and immunotherapy. Results: Based on the expressions of 32 ferroptosis-related genes, three distinct ferroptosis-related subtypes with various biological characteristics were determined. Integrated analysis showed that cluster 1 is a microsatellite instability (MSI)-like subtype, cluster 2 is an epithelial–mesenchymal transition (EMT)-like subtype, while cluster 3 tends to be a metabolic-like subtype. Prognostic analysis revealed that patients in cluster 2 had a worse overall survival and relapse-free survival. The distribution of the ferroptosis score was significantly different in clusters and gene clusters. The ferroptosis score could predict the biological characteristics of each cluster, the stromal activity, and progression of tumor. The low ferroptosis score group was characterized by the activation of antigen processing and presentation, DNA damage repair pathways, and metabolic pathways, while the high ferroptosis score group was characterized by stromal activation. In response to anticancer drugs, the ferroptosis score was highly negatively associated with drugs targeting MAPK signaling and PI3K/mTOR signaling, while it was positively correlated with drugs targeting the cell cycle, mitosis, and metabolism. Finally, we also proved that the ferroptosis score could serve as a reliable biomarker to predict response to immunotherapy. Conclusion: This work revealed that tumor cells and their surrounding microenvironment could be shaped by varying the activation degrees of ferroptosis. Establishing ferroptosis-related subtypes would guide in predicting the biological features of individual tumors and selecting appropriate treatment protocols for patients.
Ultrashort Peptides and Gold Nanoparticles: Influence of Constrained Amino Acids on Colloidal Stability

Poor colloidal stability of gold nanoparticles (AuNPs) in physiological environments remains one of the major limitations that contribute to their difficult translation from bench to clinic. For this reason, an active research field is the development of molecules able to hamper AuNPs aggregation tendency in physiological environments. In this context, synthetic peptides are gaining an increased interest as an alternative to the use of biomacromolecules and polymers, due to their easiness of synthesis and their profitable pharmacokinetic profile. In this work, we reported on the use of ultrashort peptides containing conformationally constrained amino acids (AAs) for the stabilization of AuNPs. A small library of non-natural self-assembled oligopeptides were synthesized and used to functionalize spherical AuNPs of 20 nm diameter, via the ligand exchange method. The aim was to investigate the role of the constrained AA, the anchor point (at C- or N-terminus) and the peptide length on their potential use as gold binding motif. Ultrashort Aib containing peptides were identified as effective tools for AuNPs colloidal stabilization. Furthermore, peptide coated AuNPs were found to be storable as powders without losing the stabilization properties once re-dispersed in water. Finally, the possibility to exploit the developed systems for binding proteins via molecular recognition was also evaluated using biotin as model.
Multilevel Resilience of Fishing Communities of Coastal Bangladesh Against Covid-19 Pandemic and 65-Day Fishing Ban

The unusual situation that arose due to the COVID-19 pandemic and the 65-day fishing ban (national policy to boost depleted fish stocks) affected the lower-income fishing communities in coastal Bangladesh. Shocks and stresses were posed, and community people adopted strategies to adapt to the changes. In the process of adaptation, social-ecological systems resilience at different levels plays a crucial role. Though resilience is acknowledged as multilevel feature, studies on the interaction between the levels while understanding communities’ responses to shock and stress are limited. Thus, in this study, we explored the shocks and stresses the fishing community faced and their views on the resilience feature at different levels (i.e., individual, household, and community level) in coastal Bangladesh during the COVID-19 pandemic and 65-day fishing ban period. The study found that the most resilience promoting features (e.g., diversified livelihood, friendship, and network of supports) were adopted at the individual and household levels. However, positive and negative interactions were explored between resilience features at all levels. Low community-level resilience was not translated into a lack of household-level resilience, and strong individual-level resilience did not mean high household-level resilience. It was noted that the increased resilience of a particular individual or household could negatively affect community resilience. Resilience features showed inconsistent interactions within or among the three levels’ resilience features. The study also revealed that multilevel resilience features stressed the importance of combining persistence (i.e., keeping fishing as the main livelihood) and adaptation process (e.g., livelihood diversification). The study showcases the importance of considering multilevel resilience that offers insight into crucial resilience factors which would not be evident if only one level were studied. The overall finding of this study will contribute to framing governance strategies to ensure sustainable coastal management even in the time of any abrupt or expected changes, such as the COVID-19 pandemic and the fishing ban policy.
Structural and Catalytic Characterization of TsBGL, a β-Glucosidase From Thermofilum sp. ex4484_79

Beta-glucosidase is an enzyme that catalyzes the hydrolysis of the glycosidic bonds of cellobiose, resulting in the production of glucose, which is an important step for the effective utilization of cellulose. In the present study, a thermostable β-glucosidase was isolated and purified from the Thermoprotei Thermofilum sp. ex4484_79 and subjected to enzymatic and structural characterization. The purified β-glucosidase (TsBGL) exhibited maximum activity at 90°C and pH 5.0 and displayed maximum specific activity of 139. 2μmol/min/mgzne against p-nitrophenyl β-D-glucopyranoside (pNPGlc) and 24. 3μmol/min/mgzen against cellobiose. Furthermore, TsBGL exhibited a relatively high thermostability, retaining 84 and 47% of its activity after incubation at 85°C for 1.5h and 90°C for 1.5h, respectively. The crystal structure of TsBGL was resolved at a resolution of 2. 14Å, which revealed a classical (α/β)8-barrel catalytic domain. A structural comparison of TsBGL with other homologous proteins revealed that its catalytic sites included Glu210 and Glu414. We provide the molecular structure of TsBGL and the possibility of improving its characteristics for potential applications in industries.
A Novel Three-Dimensional Culture Device Favors a Myelinating Morphology of Neural Stem Cell-Derived Oligodendrocytes

The complexity of the central nervous system (CNS) requires researchers to consider all the variables linked to the interaction between the different cell inhabitants. On this basis, any in vitro study of the physiological and pathological processes regarding the CNS should consider the balance between the standardization of the assay and the complexity of the cellular system which mimics the in vivo microenvironment. One of the main structural and functional components of the CNS is the oligodendrocyte precursor cell (OPC), responsible for developmental myelination and myelin turnover and repair during adulthood following differentiation into mature oligodendrocytes. In the present brief research report, we describe a 3D culture tool (VITVO) based on an inert and biocompatible synthetic polymer material scaffold, functionalized with laminin coating, and tested as a new culture microenvironment for neural stem/precursor cell (NSPC) differentiation compared to standard 2D cultures. NSPCs spontaneously differentiate in the three neural lineages (neurons, astrocytes and OPCs), identified by specific markers, along the fibers in the 3D structure. Analysis of the mRNA levels for lineage differentiation markers reveals a higher expression compared to those seeded on a 2D surface, suggesting an acceleration of the differentiation process. We then focused on the oligodendroglial lineage, showing that in VITVO, mature oligodendrocytes exhibit a myelinating morphology, proven by 3D image elaboration, linked to a higher expression of mature oligodendrocyte markers. This preliminary study on an innovative 3D culture system is the first robust step in producing new microenvironment-based strategies to investigate in vitro OPC and oligodendrocyte biology.
Dietary Intake of Total Carbohydrates, Sugar and Sugar-Sweetened Beverages, and Risk of Inflammatory Bowel Disease: A Systematic Review and Meta-Analysis of Prospective Cohort Studies

Objectives: No earlier study has summarized findings from prospective cohort studies on the association of dietary carbohydrates, sugar, and sugar-sweetened beverages (SSBs) consumption and risk of inflammatory bowel disease (IBD). The current study was done to quantitatively summarize earlier information from prospective cohort studies on the link between dietary carbohydrates, sugar, and SSBs intake with risk of IBD. Methods: Relevant studies published up to June 2021 were searched through PubMed, Medline, SCOPUS, EMBASE, and Google Scholar with the use of relevant keywords. All prospective cohort studies investigating the association of dietary carbohydrates, sugar, and SSBs consumption with risk of IBD were included. Results: Combining 5 effect sizes from 4 cohort studies, no significant association was found between dietary intake of carbohydrates and risk of ulcerative colitis (UC) (RR: 1.22; 95% CI: 0.70–2.14). The same findings were obtained for risk of Crohn's disease (CD) (RR: 1.06; 95% CI: 0.64–1.75) based on 4 studies with 5 effect sizes. A significant positive association was observed between sugar intake and risk of UC (RR: 1.59; 95% CI: 1.15–2.20), as well as CD (RR: 1.90; 95% CI: 1.06–3.41) when 5 effect sizes from 4 cohort studies were combined. The overall effect size, based on 4 estimates, revealed no significant association between SSBs consumption and risk of UC (RR: 1.02; 95% CI: 0.92–1.12) and CD (RR: 1.22; 95% CI: 0.91–1.64). Conclusions: Summarizing earlier studies, sugar intake was found to be associated with increased risk of IBD and its subtypes. Any significant association between dietary intake of carbohydrates and SSBs and risk of IBD and its subtypes was not found.