Miracle-dz/UniFAR-FTUs huggingface dataset:
Calculating the cost: place, mobility and price in higher education decision-making for students on small islands around the UK

ABSTRACT The decision of whether and where to attend higher education is an inherently geographical decision. Amongst the structural inequalities that determine how decisions about higher education are made are a number of complex socio-spatial factors ranging from proximity of higher education institution to place of residence and availability of transport options, to national and locally-specific expectations of undergraduate mobility and personal relationships of belonging to place. This article situates these multi-layered factors in the particular geographical context of the United Kingdom (UK), and more specifically in the small islands that surround the UK, presenting findings from a multi-sited case study of three island colleges. The article adapts the language of cost and price, commonly used in discussions of social mobility, arguing for the importance of considering place and geographical mobility for higher education as part of the balancing of financial and social risks, benefits and investments that structure higher education decisions. Focusing on three aspects of cost and higher education, – costs of tuition, living expenses and travel expenses – the article asks how place and mobility shape higher education decision-making in the often-ignored context of the small island, and what might be learned from these contexts about the workings of geographies in places with more familiar and therefore more naturalised relationships to higher education.
Timecourse and source localization of abstract and concrete semantic representations

Dual coding theories of knowledge suggest that meaning is represented in the brain by a double code, which comprises language-derived representations in the Anterior Temporal Lobe and sensory-derived representations in perceptual and motor regions. This approach predicts that concrete semantic features should activate both codes, whereas abstract features rely exclusively on the linguistic code. Using magnetoencephalography (MEG), we adopted a temporally resolved multiple regression approach to identify the contribution of abstract and concrete semantic predictors to the underlying brain signal. Results evidenced early involvement of anterior-temporal and inferior-frontal brain areas in both abstract and concrete semantic information encoding. At later stages, occipito-temporal regions showed greater responses to concrete compared to abstract features. The present findings shed new light on the temporal dynamics of abstract and concrete semantic representations in the brain and suggest that the concreteness of words processed first with a transmodal/linguistic code, housed in frontotemporal brain systems, and only after with an imagistic/sensorimotor code in perceptual and motor regions.
Catching a wave: on the suitability of traveling-wave solutions in epidemiological modeling

Ordinary differential equation models such as the classical SIR model are widely used in epidemiology to study and predict infectious disease dynamics. However, these models typically assume that populations are homogeneously mixed, disregarding possible variations in disease prevalence due to spatial heterogeneity. To address this issue, reaction-diffusion models have been proposed as an alternative approach for modeling spatially continuous populations in which individuals move in a diffusive manner. In this study, we explore the conditions under which such spatial structure must be explicitly considered to accurately predict disease spread, and when the assumption of homogeneous mixing remains adequate. In particular, we derive a critical threshold for the diffusion coefficient below which disease transmission dynamics display spatial heterogeneity. We validate our analytical results with individual-based simulations of disease transmission across a two-dimensional continuous landscape. Using this framework, we further explore how key epidemiological parameters such as the establishment probability of a disease, its maximal incidence, and its final epidemic size are affected by incorporating spatial structure in SI, SIS, and SIR models. We discuss the implications of our findings for epidemiological modeling and identify design considerations and limitations for spatial simulation models of disease dynamics.
Prolonged Kaposi's Sarcoma-associated Herpesvirus vIL-6 Exposure 1 Enhances Inflammatory Responses by Epigenetic Reprogramming 2 3

Prolonged Kaposi's Sarcoma-associated Herpesvirus vIL-6 Exposure 1 Enhances Inflammatory Responses by Epigenetic Reprogramming 2 3 Tomoki Inagaki, Kang-Hsin Wang, Ashish Kumar, Chie Izumiya, Hiroki Miura, 4 Somayeh Komaki, Ryan R. Davis, Clifford G. Tepper, Harutaka Katano, 5 Michiko Shimoda, & Yoshihiro Izumiya 3, * 6 7 1 Department of Dermatology, School of Medicine, the University of California Davis (UC Davis), 8
Identification and Characterization of CtUGT3 as the Key Player of Astragalin Biosynthesis in Safflower

Safflower (Carthamus tinctorius L.) flowers are used as a traditional Chinese medicine for a long history. Flavonoids are the main bioactive components in safflower flowers, and most of them exist in the form of flavonoid glycosides. Only few glycosyltransferases have been identified in safflower. To reveal the uridine diphosphate glycosyltransferase (UGT) involved in flavonoid glycosides biosynthesis in safflower, a metabolomics and transcriptome analysis was performed by using the flowers under different light qualities treatments. Three differentially expressed UGT genes were screened, and their expressions were significantly related with concentrations of 9 flavonoid O-glycosides. Safflower corolla protoplasts were further used to confirm flavonoid O-glycosylation ability of UGT candidates. The astragalin (kaempferol 3-O-glucoside) content was only significantly increased when CtUGT3 was overexpressed in protoplasts. The biochemical properties and kinetic parameters of CtUGT3 were determined. CtUGT3 also showed flavonoid 3-OH and 7-OH glycosylation activities in vitro. Molecular modeling and site-directed mutagenesis revealed that E384 and S276 were critical catalytic residues for the 3-OH glycosylation of CtUGT3. These results demonstrate that CtUGT3 has a flavonoid 3-OH glycosylation function and is involved in the biosynthesis of astragalin in safflower. This study provides insights into the catalytic mechanisms of flavonoid O-glycosyltransferases, and makes a reference for flavonoid biosynthesis genes research in medicinal plants.
A New Highly Efficient Molecule for Both Optogenetic and Chemogenetic Control Driven by FRET Amplification of BioLuminescence

Significance Bioluminescent optogenetics (BL-OG) offers a unique and powerful approach to manipulate neural activity both opto- and chemogenetically using a single actuator molecule (a LuMinOpsin, LMO). Aim To further enhance the utility of BL-OG by improving the efficacy of chemogenetic (bioluminescence- driven) LMO activation. Approach We developed novel luciferases optimized for Förster resonance energy transfer (FRET) when fused to the fluorescent protein mNeonGreen, generating bright bioluminescent (BL) emitters spectrally tuned to Volvox Channelrhodopsin 1 (VChR1). Results A new LMO generated from this approach (LMO7) showed significantly stronger BL-driven opsin activation compared to previous and other new variants. We extensively benchmarked LMO7 against LMO3 (current standard), and found significantly stronger neuronal activity modulation ex vivo and in vivo, and efficient modulation of behavior. Conclusions We report a robust new option for achieving multiple modes of control in a single actuator, and a promising engineering strategy for continued improvement of BL-OG.
Deletion of a conserved genomic region associated with adolescent idiopathic scoliosis leads to vertebral rotation in mice

Adolescent idiopathic scoliosis (AIS) is the most common form of scoliosis, in which spinal curvature develops in adolescence, and 90% of patients are female. Scoliosis is a debilitating disease that often requires bracing or surgery in severe cases. AIS affects 2-5.2 percent of the population; however, the biological origin of the disease remains poorly understood. In this study, we aimed to determine the function of a highly conserved genomic region previously linked to AIS using a mouse model generated by CRISPR-CAS9 gene editing to knockout this area of the genome to better understand the biological cause of AIS, which we named AIS_CRMΛ. We also investigated the upstream factors that regulate the activity of this enhancer in vivo, whether the spatial expression of the LBX1 protein would change with the loss of AIS-CRM function, and whether any phenotype would arise after deletion of this region. We found a significant increase in mRNA expression in the developing neural tube at E10.5, and E12.5, for not only Lbx1 but also other neighboring genes. Adult knockout mice showed vertebral rotation and proprioceptive deficits, also observed in human AIS patients. In conclusion, our study sheds light on the elusive biological origins of AIS, by targeting and investigating a highly conserved genomic region linked to AIS in humans. These findings provide valuable insights into the function of the investigated region and contribute to our understanding of the underlying causes of this debilitating disease.
Vocabulary Matters: An Annotation Pipeline and Two Deep Learning Algorithms for Enzyme Named Entity Recognition

Enzymes are indispensable substances in many biological processes. With biomedical literature growing exponentially, it becomes more difficult to review the literature effectively. Hence, text-mining techniques are needed to facilitate and speed up literature review. The aims of this study are to create a corpus with annotated enzymes to train and evaluate enzyme named-entity recognition (NER) models. A novel pipeline was built using a combination of dictionary matching and rulebased keyword searching to automatically annotate enzyme entities in over 4,800 biomedical full texts. Two Bidirectional Long Short-Term Memory (BiLSTM) networks using BioBERT and SciBERT as tokeniser and word embedding layers were trained on this corpus and evaluated on a manually annotated test set of 526 full-text publications. The dictionary- and rule-based annotation pipeline achieved an F1-score of 0.863 (precision 0.996, recall 0.762). The SciBERT-BiLSTM model (F1-score 0.965, precision 0.981, recall 0.954) largely out-performed the BioBERT-BiLSTM model (F1-score 0.955, precision 0.981, recall 0.937). This study contributed a novel dictionary- and rule-based automatic pipeline with almost perfect precision which runs in a matter of seconds on a standard laptop. Both deep learning (DL) models achieved state-of-the-art performance (F1>0.95) for enzyme NER, with the SciBERT-based model outperforming the BioBERT-based model in terms of recall, demonstrating the vocabulary used by models matters. The proposed pipeline with the DL models can facilitate more effective enzyme text-mining and information extraction research for literature review and are the first algorithms specifically for enzyme NER. Availability All codes are available for automatic annotation and model training (including data), with instructions on how to deploy the model on new text, from https://github.com/omicsNLP/enzymeNER.
Experience replay facilitates the rapid formation of multi-scale hexagonal patterns of grid cells

Reverse neuronal replay, characterized by the sequential reactivation of hippocampal place cells to represent past experiences, is proposed to organize learned knowledge into a cognitive map. Here we utilized the continuous attractor model to simulate the formation of multi-scale hexagonal patterns of entorhinal grid cells, which serve as the metric for the cognitive map, during experience replay of hippocampal place cells. We found a significant increase in grid periodicity with reverse replay compared to that without replay. This effect was exclusive to reverse replay, as neither forward nor shuffled-experience replay produced a similar enhancement. Further analysis revealed that the effect of the replay was modulated by the interaction between grid scales and the length of experience replay. That is, the replay was particularly effective for small grid scales, which helped in maintaining the excitation of formed grid bumps during pattern translation. In summary, our study illustrates a causative link between experience replay and the rapid formation of multi-scale hexagonal patterns from computational perspective, providing insights into how the experience replay by hippocampal place cells influences the formation of hexagonal patterns of entorhinal grid cells.
wTSA-CRAFT: an open-access web server for rapid analysis of thermal shift assay experiments

The automated data processing provided by the TSA-CRAFT tool enables now to reach high throughput speed analysis of thermal shift assays. While the software is powerful and freely available, it still requires installation process and command line efforts that could be discouraging. To simplify the procedure, we decided to make it available and easy to use by implementing it with a graphical interface via a web server, enabling a cross-platform usage from any web browsers. We developed a web server embedded version of the TSA-CRAFT tool, enabling a user-friendly graphical interface for formatting and submission of the input file and visualization of the selected thermal denaturation profiles. We describe a typical case study of buffer condition optimization of the biologically relevant APH(3’)-IIb bacterial protein in a 96 deep-well thermal shift analysis screening. wTSA-CRAFT is freely accessible for non-commercial usage at https://bioserv.cbs. cnrs.fr/TSA_CRAFT.
Metabolic engineering of Corynebacterium glutamicum for the production of anthranilate from glucose and xylose

Anthranilate and its derivative aniline are important basic chemicals for the synthesis of polyurethanes as well as various dyes and food additives. Today, aniline is mainly chemically produced from petroleum-derived benzene, but it could be also obtained more sustainably by decarboxylation of the microbially produced shikimate pathway intermediate anthranilate. In this study, Corynebacterium glutamicum was engineered for the microbial production of anthranilate from a carbon source mixture of glucose and xylose. First, a feedback-resistant 3-deoxy- arabinoheptulosonate-7-phosphate synthase from E. coli, catalyzing the first step of the shikimate pathway, was functionally introduced into C. glutamicum to enable anthranilate production. Modulation of the translation efficiency of the genes for the shikimate kinase (aroK) and the anthranilate phosphoribosyltransferase (trpD) improved product formation. Deletion of two genes, one for a putative phosphatase (nagD) and one for a quinate/shikimate dehydrogenase (qsuD), abolished by-product formation of glycerol and quinate. However, the introduction of an engineered anthranilate synthase (TrpEG) unresponsive to feedback inhibition by tryptophan had the most pronounced effect on anthranilate production. Component I of this enzyme (TrpE) was engineered using a biosensor-based in vivo screening strategy for identifying variants with increased feedback-resistance in a semi-rational library of TrpE muteins. The final strain accumulated up to 5.9 g/L (43 mM) anthranilate in defined CGXII medium from a mixture of glucose and xylose in bioreactor cultivations. We believe that the constructed C. glutamicum variants are not only limited to anthranilate production, but could also be suitable for the synthesis of other biotechnologically interesting shikimate pathway intermediates, or any other aromatic compound derived thereof.
Analysis of online user discussions on Reddit associated with the transition of use between HIV PrEP therapy

In 2019, the U.S. Food and Drug Administration (FDA) approved emtricitabine and tenofovir alafenamide (Descovy) as another option for HIV pre-exposure prophylaxis (PrEP) prevention for high-risk adults and adolescents. With the introduction of this new PrEP, millions of current users on emtricitabine and tenofovir disoproxil fumarate (Truvada), another PrEP medication currently used to prevent HIV transmission, have options of whether to continue their current treatment regime or transition to new treatment options. The objective of this study was to conduct a descriptive analysis to characterize user-generated social media conversations on Reddit associated with FDA-approved PrEP prevention treatment options. Key themes identified were associated with perceptions, knowledge, and attitudes associated with the transition of use of different PrEP medications. Data were collected retrospectively and prospectively from the Reddit platform for posts with keywords filtered for HIV, PrEP, and FDA-approved PrEP prevention treatment from October 2020 to December 2020. We chose the Reddit platform based on prior studies that have identified PrEP user conversations and insights on access challenges for specific AIDS communities, such as gays and men who have sex with men (MSM). Reddit posts were then manually annotated using an inductive content coding approach for key themes regarding the transition of use and other emergent themes from user-generated content. Formal coding of text data was conducted with refined codes, and sub-codes created. A total of 3,120 posts were analyzed from Reddit resulting in 315 posts that were coded for PrEP and 105 posts (33.33%) specific to user discussions regarding the transition of PrEP prevention. Overall, users expressed interest in drug switching to Descovy, particularly in the context of poorer adherence or concerns about existing side effects associated with Truvada. Other major themes included discussions about the cost of Descovy, apprehension about side effects in comparison to Truvada, insurance coverage changes, and discussions about the donation of Truvada to other users after transitioning. Among these discussions, topics related to sexual minorities, including MSM, reported concerns when considering a switch in their HIV prevention regime. Understanding the changing public perception associated with the introduction of new HIV prevention is important in the context of market access, patient safety, pharmacovigilance, and health equity, particularly among high-risk populations such as MSM. Results support the use of social media from a digital pharmacovigilance perspective to better understand emerging HIV prevention, treatment, and adherence challenges experienced by patients.
Regional contributions of D-serine to Alzheimer’s disease pathology in male AppNL–G–F/NL–G–F mice

Background Neurodegenerative processes in Alzheimer’s disease (AD) are associated with excitotoxicity mediated by the N-methyl-D-aspartate receptor (NMDAR). D-Serine is an endogenous co-agonist necessary for NMDAR-mediated excitotoxicity. In the mammalian brain, it is produced by serine racemase (SRR) from L-serine, suggesting that dysregulation of L-serine, D-serine, or SRR may contribute to AD pathogenesis. Objective and methods We examined the contributions of D-serine to AD pathology in the AppNL–G–F/NL–G–F gene knock-in (APPKI) mouse model of AD. We first examined brain SRR expression levels and neuropathology in APPKI mice and then assessed the effects of long-term D-serine supplementation in drinking water on neurodegeneration. To further confirm the involvement of endogenous D-serine in AD progression, we generated Srr gene-deleted APPKI (APPKI-SRRKO) mice. Finally, to examine the levels of brain amino acids, we conducted liquid chromatography–tandem mass spectrometry. Results Expression of SRR was markedly reduced in the retrosplenial cortex (RSC) of APPKI mice at 12 months of age compared with age-matched wild-type mice. Neuronal density was decreased in the hippocampal CA1 region but not altered significantly in the RSC. D-Serine supplementation exacerbated neuronal loss in the hippocampal CA1 of APPKI mice, while APPKI-SRRKO mice exhibited attenuated astrogliosis and reduced neuronal death in the hippocampal CA1 compared with APPKI mice. Furthermore, APPKI mice demonstrated marked abnormalities in the cortical amino acid levels that were partially reversed in APPKI-SRRKO mice. Conclusion These findings suggest that D-serine participates in the regional neurodegenerative process in the hippocampal CA1 during the amyloid pathology of AD and that reducing brain D-serine can partially attenuate neuronal loss and reactive astrogliosis. Therefore, regulating SRR could be an effective strategy to mitigate NMDAR-dependent neurodegeneration during AD progression.
Gut microbiota influences feeding behavior via changes in olfactory receptor gene expression in Colorado potato beetles

The Colorado potato beetle (CPB) is an internationally recognized plant quarantine pest that causes serious losses to potato agricultural production. The gut microbiota plays an important role in its growth and development, and the olfactory system plays an important role in insect feeding behavior. The gut microbiota is known to be capable of inducing changes in the olfactory systems of insects. However, the way these associated gut microbes influence the feeding-related behaviors of CPBs remains unclear. To explore the relationship between them, fresh potato leaves immersed in a mixture of five antibiotics (tetracycline, penicillin, ofloxacin, ciprofloxacin, and ampicillin) at specific concentrations for 1 h were fed to adult CPBs to reduce the abundance of gut microbes. We found that the feeding behavior of CPBs was significantly affected by the gut microbiota and that Pseudomonas was significantly higher in abundance in the control group than in the antibiotic group. We then used transcriptome sequencing to explore the differences in olfactory receptor genes in the heads of non-treatment and antibiotic-fed CPBs. Through Illumina Hiseq™ sequencing and screening of differential genes, we found that the olfactory receptor gene LdecOR9 was significantly upregulated and LdecOR17 was significantly downregulated after antibiotic feeding. A real-time polymerase chain reaction was used to verify the changes in olfactory receptor gene expression in the non-treatment groups and antibiotic-treated groups. The feeding behavior was partially rescued after CPBs were re-fed with intestinal bacteria. These results indicate that a certain amount of gut microbiota can result in the loss of the olfactory discrimination ability of CPBs to host plants. In summary, this study investigated the relationship between gut microbiota and olfactory genes, providing a reference for research on microbial control.