Miracle-dz/UniFAR-FTUs huggingface dataset:
Promoterless Gene Targeting Approach Combined to CRISPR/Cas9 Efficiently Corrects Hemophilia B Phenotype in Neonatal Mice

Many inborn errors of metabolism require life-long treatments and, in severe conditions involving the liver, organ transplantation remains the only curative treatment. Non-integrative AAV-mediated gene therapy has shown efficacy in adult patients. However, treatment in pediatric or juvenile settings, or in conditions associated with hepatocyte proliferation, may result in rapid loss of episomal viral DNA and thus therapeutic efficacy. Re-administration of the therapeutic vector later in time may not be possible due to the presence of anti-AAV neutralizing antibodies. We have previously shown the permanent rescue of the neonatal lethality of a Crigler-Najjar mouse model by applying an integrative gene-therapy based approach. Here, we targeted the human coagulation factor IX (hFIX) cDNA into a hemophilia B mouse model. Two AAV8 vectors were used: a promoterless vector with two arms of homology for the albumin locus, and a vector carrying the CRISPR/SaCas9 and the sgRNA. Treatment of neonatal P2 wild-type mice resulted in supraphysiological levels of hFIX being stable 10 months after dosing. A single injection of the AAV vectors into neonatal FIX KO mice also resulted in the stable expression of above-normal levels of hFIX, reaching up to 150% of the human levels. Mice subjected to tail clip analysis showed a clotting capacity comparable to wild-type animals, thus demonstrating the rescue of the disease phenotype. Immunohistological analysis revealed clusters of hFIX-positive hepatocytes. When we tested the approach in adult FIX KO mice, we detected hFIX in plasma by ELISA and in the liver by western blot. However, the hFIX levels were not sufficient to significantly ameliorate the bleeding phenotype upon tail clip assay. Experiments conducted using a AAV donor vectors containing the eGFP or the hFIX cDNAs showed a higher recombination rate in P2 mice compared to adult animals. With this study, we demonstrate an alternative gene targeting strategy exploiting the use of the CRISPR/SaCas9 platform that can be potentially applied in the treatment of pediatric patients suffering from hemophilia, also supporting its application to other liver monogenic diseases. For the treatment of adult patients, further studies for the improvement of targeting efficiency are still required.
Porphyromonas gingivalis Induces Increases in Branched-Chain Amino Acid Levels and Exacerbates Liver Injury Through livh/livk

Porphyromonas gingivalis, a keystone periodontal pathogen, has emerged as a risk factor for systemic chronic diseases, including non-alcoholic fatty liver disease (NAFLD). To clarify the mechanism by which this pathogen induces such diseases, we simultaneously analyzed the transcriptome of intracellular P. gingivalis and infected host cells via dual RNA sequencing. Pathway analysis was also performed to determine the differentially expressed genes in the infected cells. Further, the infection-induced notable expression of P. gingivalis livk and livh genes, which participate in branched-chain amino acid (BCAA) transfer, was also analyzed. Furthermore, given that the results of recent studies have associated NAFLD progression with elevated serum BCAA levels, which reportedly, are upregulated by P. gingivalis, we hypothesized that this pathogen may induce increases in serum BCAA levels and exacerbate liver injury via livh/livk. To verify this hypothesis, we constructed P. gingivalis livh/livk-deficient strains (Δlivk, Δlivh) and established a high-fat diet (HFD)-fed murine model infected with P. gingivalis. Thereafter, the kinetic growth and exopolysaccharide (EPS) production rates as well as the invasion efficiency and in vivo colonization of the mutant strains were compared with those of the parental strain. The serum BCAA and fasting glucose levels of the mice infected with either the wild-type or mutant strains, as well as their liver function were also further investigated. It was observed that P. gingivalis infection enhanced serum BCAA levels and aggravated liver injury in the HFD-fed mice. Additionally, livh deletion had no effect on bacterial growth, EPS production, invasion efficiency, and in vivo colonization, whereas the Δlivk strain showed a slight decrease in invasion efficiency and in vivo colonization. More importantly, however, both the Δlivk and Δlivh strains showed impaired ability to upregulate serum BCAA levels or exacerbate liver injury in HFD-fed mice. Overall, these results suggested that P. gingivalis possibly aggravates NAFLD progression in HFD-fed mice by increasing serum BCAA levels, and this effect showed dependency on the bacterial BCAA transport system.
The Role of the Ventromedial Prefrontal Cortex in Preferential Decisions for Own- and Other-Age Faces

Own-age bias is a well-known bias reflecting the effects of age, and its role has been demonstrated, particularly, in face recognition. However, it remains unclear whether an own-age bias exists in facial impression formation. In the present study, we used three datasets from two published and one unpublished functional magnetic resonance imaging (fMRI) study that employed the same pleasantness rating task with fMRI scanning and preferential choice task after the fMRI to investigate whether healthy young and older participants showed own-age effects in face preference. Specifically, we employed a drift-diffusion model to elaborate the existence of own-age bias in the processes of preferential choice. The behavioral results showed higher rating scores and higher drift rate for young faces than for older faces, regardless of the ages of participants. We identified a young-age effect, but not an own-age effect. Neuroimaging results from aggregation analysis of the three datasets suggest a possibility that the ventromedial prefrontal cortex (vmPFC) was associated with evidence accumulation of own-age faces; however, no clear evidence was provided. Importantly, we found no age-related decline in the responsiveness of the vmPFC to subjective pleasantness of faces, and both young and older participants showed a contribution of the vmPFC to the parametric representation of the subjective value of face and functional coupling between the vmPFC and ventral visual area, which reflects face preference. These results suggest that the preferential choice of face is less susceptible to the own-age bias across the lifespan of individuals.
Insights Into Genome-Wide Association Study for Diabetes: A Bibliometric and Visual Analysis From 2001 to 2021

Hundreds of research and review articles concerning genome-wide association study (GWAS) in diabetes have been published in the last two decades. We aimed to evaluate the hotspots and future trends in GWAS in diabetes research through bibliometric analysis. Accordingly, 567 research and review articles published between 2001 and 2021 were included. A rising trend was noted in the annual number of publications and citations on GWAS in diabetes during this period. Harvard University and Harvard Medical School have played leading roles in genome research. Hotspot analyses indicated that DNA methylation and genetic variation, especially in type 2 diabetes mellitus, are likely to remain the research hotspots. Moreover, the identification of genetic phenotypes associated with adiposity, metabolic memory, pancreatic islet, and inflammation is the leading trend in this research field. Through this review, we provide predictions on the main research trends in the future so as to shed light on new directions and ideas for further investigations on the genetic etiology of diabetes for its prevention and treatment.
Digital Transformation of Concrete Technology—A Review

Digital transformation of concrete technology is one of the current “hot topics” tackled by both academia and industry. The final goal is to fully integrate the already existing advanced concrete technologies with novel sensors, virtual reality, or Internet of things to create self-learning and highly automated platforms controlling design, production, and long-term usage and maintenance of concrete and concrete structures. The digital transformation should ultimately enhance sustainability, elongate service life, and increase technological and cost efficiencies. This review article focuses on up-to-date developments. It explores current pathways and directions seen in research and industrial practices. It indicates benefits, challenges, and possible opportunities related to the digital transformation of concrete technology.
Parental Sex and Not Kinship Determines Egg Cannibalism in Arma custos Fallou (Hemiptera: Pentatomidae: Asopinae)

Background Arma custos Fallou (Hemiptera: Asopinae) is an important predatory insect native to China, South Korea, and Mongolia. It is important to understand the evolution of egg cannibalism in A. custos to evaluate the biocontrol potential of this species. However, few reports have suggested egg cannibalism in A. custos, and whether hungry adult A. custos males and females prey on their eggs remains unknown. Here, we investigated the effects of the parental sex of A. custos adults on egg cannibalism of parental and non-parental eggs (kinship) under no-choice and free-choice conditions, along with the effects of predator and egg density on egg cannibalism under starvation conditions. Results Females frequently visited and cannibalized a higher proportion of eggs, whereas males almost did not participate in egg cannibalism (less than 17% males showed egg cannibalism behavior). Moreover, regardless of their relationship with the egg, neither male nor female adults consumed all available eggs even in the absence of an alternative food source, and >70% of eggs remained unconsumed. In contrast, cannibalistic males and females did not discriminate between parental and non-parental egg types. Meanwhile, cannibalism rates were similar when adults were offered 30 eggs or more. However, when offered fewer than 30 eggs, cannibalism rates declined disproportionally, suggesting that limited egg availability reduced cannibalism. Additionally, the lifespan of A. custos adult females increased significantly with increasing number of consumed eggs (p < 0.05). Conclusion Arma custos females exhibit a higher tendency for egg cannibalism than males. Neither male or female A. custos discriminated between parental and non-parental egg types. Cannibalism enhances survival in that a starved individual who predates on eggs survives similarly to a well-fed individual. These findings provide a model to study the evolution and biological significance of egg cannibalism in A. custos and also contribute to the efficient mass rearing and realization of A. custos for biological control.
Automated Synapse Detection Method for Cerebellar Connectomics

The connectomic analyses of large-scale volumetric electron microscope (EM) images enable the discovery of hidden neural connectivity. While the technologies for neuronal reconstruction of EM images are under rapid progress, the technologies for synapse detection are lagging behind. Here, we propose a method that automatically detects the synapses in the 3D EM images, specifically for the mouse cerebellar molecular layer (CML). The method aims to accurately detect the synapses between the reconstructed neuronal fragments whose types can be identified. It extracts the contacts between the reconstructed neuronal fragments and classifies them as synaptic or non-synaptic with the help of type information and two deep learning artificial intelligences (AIs). The method can also assign the pre- and postsynaptic sides of a synapse and determine excitatory and inhibitory synapse types. The accuracy of this method is estimated to be 0.955 in F1-score for a test volume of CML containing 508 synapses. To demonstrate the usability, we measured the size and number of the synapses in the volume and investigated the subcellular connectivity between the CML neuronal fragments. The basic idea of the method to exploit tissue-specific properties can be extended to other brain regions.
Integration of an Independent Monitor Unit Check for High-Magnetic-Field MR-Guided Radiation Therapy System

Purpose Commercial independent monitor unit (IMU) check systems for high-magnetic-field MR-guided radiation therapy (RT) systems are lacking. We investigated the feasibility of adopting an existing treatment planning system (TPS) as an IMU check for online adaptive radiotherapy using 1.5-Tesla MR-Linac. Methods The 7-MV flattening filter free (FFF) beam and multi-leaf collimator (MLC) models of a 1.5-T Elekta Unity MR-Linac within Monte Carlo-based Monaco TPS were used to generate an optimized beam model in Eclipse TPS. The MLC dosimetric leaf gap of the beam in Eclipse was determined by matching the dose distribution of Eclipse-generated intensity-modulated radiation therapy (IMRT) plans using the Analytical Anisotropic Algorithm (AAA) algorithm to Monaco plans. The plans were automatically adjusted for different source-to-axis distances (SADs) between the two systems. For IMU check, the treatment plans developed in Monaco were transferred to Eclipse to recalculate the dose using AAA. A plug-in within Eclipse was created to perform a 2D gamma analysis of the AAA and Monte Carlo dose distribution on a beam’s eye view parallel plane. Monaco dose distribution was shifted laterally by 2 mm during gamma analysis to account for the impact of magnetic field on electron trajectories. Eclipse doses for posterior beams were corrected for both the Unity couch and the posterior MR coil attenuation. Thirteen patients, each with 4–5 fractions for a variety of tumor sites (pancreas, rectum, and prostate), were tested. Results After thorough commissioning, the method was implemented as part of the standard clinical workflow. A total of 62 online plans, each with approximately 15 beams, were evaluated. The average per-beam gamma (3%/3 mm) pass rate for plans was 97.9% (range, 95.9% to 98.8%). The average pass rate per beam for all 932 beams used in these plans was 97.9% ± 1.9%, with the lowest per-beam gamma pass rate at 88.4%. The time for the process was within 3.2 ± 0.9 min. Conclusion The use of a second planning system provides an efficient way to perform IMU checks with clinically acceptable accuracy for online adaptive plans on Unity MR-Linac. This is essential for meeting the safety requirements for second checks as outlined in American Association of Physicists in Medicine Task Group (AAPM TG) reports 114 and 219.
Leaf Polyphenolic Profile as a Determinant of Croatian Native Grapevine Varieties’ Susceptibility to Plasmopara viticola

Since grapevine is highly susceptible to various pathogens, enormous amounts of pesticides are applied each season to achieve profitable production. One of the most destructive grapevine diseases is downy mildew, and their interaction has been in the spotlight for more than a decade. When it comes to a metabolome level, phenolic compounds are relevant to investigate due to their involvement in the plant immune system and known antifungal properties. Croatian grapevine germplasm is highly heterogeneous due to its long history of cultivation in diversified geographical regions. Since it has been found that native varieties react differently to the infection of Plasmopara viticola, the intention of this study is to define if the chemical background of the leaves, i.e., polyphenolic composition, is responsible for these dissimilarities. Therefore, the leaves of 17 genotypes, among which 14 were native and 3 were controls, were analyzed using high-performance liquid chromatography (HPLC) in four terms: before inoculation and 24, 48, and 96 h post inoculation (hpi). During this early phase, significant differences were found neither between the terms nor between the non-inoculated and inoculated samples, except for resveratrol-3-O-glucoside. By applying principal component analysis (PCA) using initial leaf polyphenolic composition, varieties of V. vinifera were clearly separated into three different groups corresponding to their International Organization of Vine and Wine (OIV) classes of susceptibility to P. viticola. Results obtained in this research suggest that the initial constitutive polyphenolic composition of the cultivar leaves has a crucial influence on their susceptibility to P. viticola, and this finding can be used to improve the success of grapevine breeding programs toward downy mildew resistance.
Spatial Assessment of Heterogeneous Tissue Natural Frequency Using Micro-Force Optical Coherence Elastography

Analysis of corneal tissue natural frequency was recently proposed as a biomarker for corneal biomechanics and has been performed using high-resolution optical coherence tomography (OCT)-based elastography (OCE). However, it remains unknown whether natural frequency analysis can resolve local variations in tissue structure. We measured heterogeneous samples to evaluate the correspondence between natural frequency distributions and regional structural variations. Sub-micrometer sample oscillations were induced point-wise by microliter air pulses (60–85 Pa, 3 ms) and detected correspondingly at each point using a 1,300 nm spectral domain common path OCT system with 0.44 nm phase detection sensitivity. The resulting oscillation frequency features were analyzed via fast Fourier transform and natural frequency was characterized using a single degree of freedom (SDOF) model. Oscillation features at each measurement point showed a complex frequency response with multiple frequency components that corresponded with global structural features; while the variation of frequency magnitude at each location reflected the local sample features. Silicone blocks (255.1 ± 11.0 Hz and 249.0 ± 4.6 Hz) embedded in an agar base (355.6 ± 0.8 Hz and 361.3 ± 5.5 Hz) were clearly distinguishable by natural frequency. In a beef shank sample, central fat and connective tissues had lower natural frequencies (91.7 ± 58.2 Hz) than muscle tissue (left side: 252.6 ± 52.3 Hz; right side: 161.5 ± 35.8 Hz). As a first step, we have shown the possibility of natural frequency OCE methods to characterize global and local features of heterogeneous samples. This method can provide additional information on corneal properties, complementary to current clinical biomechanical assessments, and could become a useful tool for clinical detection of ocular disease and evaluation of medical or surgical treatment outcomes.
Bridging the Transient Intraluminal Stroke Preclinical Model to Clinical Practice: From Improved Surgical Procedures to a Workflow of Functional Tests

Acute ischemic stroke (AIS) remains a leading cause of mortality, despite significant advances in therapy (endovascular thrombectomy). Failure in developing novel effective therapies is associated with unsuccessful translation from preclinical studies to clinical practice, associated to inconsistent and highly variable infarct areas and lack of relevant post-stroke functional evaluation in preclinical research. To outreach these limitations, we optimized the intraluminal transient middle cerebral occlusion, a widely used mouse stroke model, in two key parameters, selection of appropriate occlusion filaments and time of occlusion, which show a significant variation in the literature. We demonstrate that commercially available filaments with short coating length (1–2 mm), together with 45-min occlusion, results in a consistent affected brain region, similar to what is observed in most patients with AIS. Importantly, a dedicated post-stroke care protocol, based on clinical practice applied to patients who had stroke, resulted in lower mortality and improved mice welfare. Finally, a battery of tests covering relevant fine motor skills, sensory functions, and learning/memory behaviors revealed a significant effect of tMCAO brain infarction, which is parallel to patient symptomatology as measured by relevant clinical scales (NIH Stroke Scale, NIHSS and modified Rankin Scale, mRS). Thus, in order to enhance translation to clinical practice, future preclinical stroke research must consider the methodology described in this study, which includes improved reproducible surgical procedure, postoperative care, and the battery of functional tests. This will be a major step s closing the gap from bench to bedside, rendering the development of novel effective therapeutic approaches. Graphical Abstract Improving translation of tMCAO mice model. Improvement of the surgical procedure, post-operative care and functional evaluation in the tMCAO mice, gives rise to a model with high parallel and translation into clinical reality. Induction of ischemia for 45-mins using smaller commercial filaments gives rise to uniform lesion volume that together with the improved post-operative care, decreases this model mortality. Furthermore, this allows for intensive long-term functional evaluation of mice. This way, clinical symptoms and ethology, as well as scales used to evaluate stroke, are mimicked in a mouse model.
Pericyte Loss Leads to Capillary Stalling Through Increased Leukocyte-Endothelial Cell Interaction in the Brain

The neurovascular unit is a functional unit composed of neurons, glial cells, pericytes, and endothelial cells which sustain brain activity. While pericyte is a key component of the neurovascular unit, its role in cerebral blood flow regulation remains elusive. Recently, capillary stalling, which means the transient interruption of microcirculation in capillaries, has been shown to have an outsized impact on microcirculatory changes in several neurological diseases. In this study, we investigated capillary stalling and its possible causes, such as the cerebral endothelial glycocalyx and leukocyte adhesion molecules after depleting pericytes postnatally in mice. Moreover, we investigated hypoxia and gliosis as consequences of capillary stalling. Although there were no differences in the capillary structure and RBC flow, longitudinal optical coherence tomography angiography showed an increased number of stalled segments in capillaries after pericyte loss. Furthermore, the extent of the cerebral endothelial glycocalyx was decreased with increased expression of leukocyte adhesion molecules, suggesting enhanced interaction between leukocytes and endothelial cells. Finally, pericyte loss induced cerebral hypoxia and gliosis. Cumulatively, the results suggest that pericyte loss induces capillary stalling through increased interaction between leukocytes and endothelial cells in the brain.
Research on the Advance Role of Institutional Quality on Achieving Environmental Efficiency in Sub Sahara Africa

The study investigates the impact of institutional quality on environmental efficiency in the presence of the Environmental Kuznets Curve (EKC) using data on desirable and undesirable outputs as well as institutional quality dimensions from the World Governance Indicators (WGI) for 19 Sub-Sahara African (SSA) countries over an annual period from 2005 to 2014. Environmental efficiency was low in eight SSA countries and excellent in eleven others, according to the efficiency results. Two countries had the highest average environmental efficiency over the first period, while one had the lowest. In 2013, the majority of SSA countries had high efficiency indexes, with one country having an index of 2.098 and four countries having efficiency rates of one. After controlling for industrialization, energy consumption, and population variables, the results show that corruption control and regulatory quality lower environmental efficiency while government effectiveness increases. The DH causality test revealed that environmental efficiency, control of corruption, regulatory quality, energy consumption, and population had no causal relationship. There are also one-way causal linkages between environmental efficiency and government effectiveness and industrialization.