Miracle-dz/UniFAR-FTUs huggingface dataset:
Path Learning in Individuals With Down Syndrome: The Floor Matrix Task and the Role of Individual Visuo-Spatial Measures

Environment learning is essential in everyday life. In individuals with Down syndrome (DS), this skill has begun to be examined using virtual exploration. Previous studies showed that individuals with DS can learn and remember paths in terms of sequences of turns and straight stretches, albeit with some difficulty, and this learning is supported by their cognitive abilities. This study further investigates environment learning in the DS population, newly examining their ability to learn a path from actual movements, and to learn increasingly long paths, and how their performance relates to their visuo-spatial abilities and everyday spatial activities. A group of 30 individuals with DS and 30 typically-developing (TD) children matched for receptive vocabulary performed a 4 × 4 Floor Matrix task in a grid comprising 16 squares (total area 2.3 × 2.3 meters). The task involved repeating increasingly long sequences of steps by actually moving in the grid. The sequences were presented in two learning conditions, called Observation (when participants watched the experimenter’s moves), or Map (when they were shown a map reproducing the path). Several visuo-spatial measures were also administered. The results showed a clear difference between the two groups’ performance in the individual visuo-spatial measures. In the Floor Matrix task, after controlling for visuo-spatial reasoning ability, both groups benefited to the same degree from the Observation condition vis-à-vis the Map condition, and no group differences emerged. In the group with DS, visuo-spatial abilities were more predictive of performance in the Floor Matrix task in the Observation condition than in the Map condition. The same was true of the TD group, but this difference was much less clear-cut. The visuo-spatial working memory and visualization tasks were the strongest predictors of Floor Matrix task performance. Finally, the group with DS showed a significant relation between Floor Matrix task performance in the Observation condition and everyday spatial activity. These results enlarge on what we know about path learning in individuals with DS and its relation to their visuo-spatial abilities. These findings are discussed within the frame of spatial cognition and the atypical development domain.
Which Method is Superior in the Diagnosis of Nonalcoholic Fatty Liver and Steatohepatatis in Children

Context: Nonalcoholic fatty liver disease (NAFLD) is increasing with the increased rate of obesity and reduced physical activity in children worldwide. Despite high prevalence of the disease, a standard and acceptable diagnostic method is not available. The current study aimed at collecting all related articles and evaluating the challenges. Methods: The current study searched Scopus, Web of Science, and PubMed. Articles and guidelines in English in the ﬁeld of inva-siveandnoninvasivediagnosticmethodsforNAFLDandnonalcoholicsteatohepatitis(NASH)inchildrenandadolescentsuptoOct 2016 were used. It was tried to evaluate all laboratory and radiologic methods, biomarkers, and scores in addition to mention the challenges. Results: Ultrasonographyandlaboratoryevaluation,whichwereroutinemethodsinearlydiagnosis,didnothaveenoughaccuracy in this ﬁeld. Diagnosis of steatosis and ﬁbrosis and determining the severity of disease were achieved by ﬁbro scan and controlled attenuation parameter (CAP) without the challenges of computed tomography (CT) scan and magnetic resonance imaging (MRI). Fatty liver can be predicted with high accuracy by body analyzer, anthropometric, and DEXA methods. Conclusions: Diagnosisandpredictionof fattylivershouldbedoneinallchildrenwithobesityaged> 3years,andphysicianshould seek the genetic and metabolic causes in children aged < 3 years and/or without overweight.
fMRI-Targeted High-Angular Resolution Diffusion MR Tractography to Identify Functional Language Tracts in Healthy Controls and Glioma Patients

Background MR Tractography enables non-invasive preoperative depiction of language subcortical tracts, which is crucial for the presurgical work-up of brain tumors; however, it cannot evaluate the exact function of the fibers. Purpose A systematic pipeline was developed to combine tractography reconstruction of language fiber bundles, based on anatomical landmarks (Anatomical-T), with language fMRI cortical activations. A fMRI-targeted Tractography (fMRI-T) was thus obtained, depicting the subsets of the anatomical tracts whose endpoints are located inside a fMRI activation. We hypothesized that fMRI-T could provide additional functional information regarding the subcortical structures, better reflecting the eloquent white matter structures identified intraoperatively. Methods Both Anatomical-T and fMRI-T of language fiber tracts were performed on 16 controls and preoperatively on 16 patients with left-hemisphere brain tumors, using a q-ball residual bootstrap algorithm based on High Angular Resolution Diffusion Imaging (HARDI) datasets (b = 3000 s/mm2; 60 directions); fMRI ROIs were obtained using picture naming, verbal fluency, and auditory verb generation tasks. In healthy controls, normalized MNI atlases of fMRI-T and Anatomical-T were obtained. In patients, the surgical resection of the tumor was pursued by identifying eloquent structures with intraoperative direct electrical stimulation mapping and extending surgery to the functional boundaries. Post-surgical MRI allowed to identify Anatomical-T and fMRI-T non-eloquent portions removed during the procedure. Results MNI Atlases showed that fMRI-T is a subset of Anatomical-T, and that different task-specific fMRI-T involve both shared subsets and task-specific subsets – e.g., verbal fluency fMRI-T strongly involves dorsal frontal tracts, consistently with the phonogical-articulatory features of this task. A quantitative analysis in patients revealed that Anatomical-T removed portions of AF-SLF and IFOF were significantly greater than verbal fluency fMRI-T ones, suggesting that fMRI-T is a more specific approach. In addition, qualitative analyses showed that fMRI-T AF-SLF and IFOF predict the exact functional limits of resection with increased specificity when compared to Anatomical-T counterparts, especially the superior frontal portion of IFOF, in a subcohort of patients. Conclusion These results suggest that performing fMRI-T in addition to the ‘classic’ Anatomical-T may be useful in a preoperative setting to identify the ‘high-risk subsets’ that should be spared during the surgical procedure.
Vertically Transferred Immunity in Neonates: Mothers, Mechanisms and Mediators

Over the last years, an increasing number of outbreaks of vaccine-preventable infectious diseases has been reported. Besides elderly and immunocompromised individuals, newborns and small infants are most susceptible to infections, as their immune system is still immature. This vulnerability during infancy can be mitigated by the transplacental transfer of pathogen-specific antibodies and other mediators of immunity from mother to the fetus during pregnancy, followed postnatally by breast milk-derived immunity. Since this largely antibody-mediated passive immunity can prevent the newborn from infections, neonatal immunity depends strongly on the maternal concentration of respective specific antibodies during pregnancy. If titers are low or wane rapidly after birth, the protection transferred to the child may not be sufficient to prevent disease. Moreover, emerging concepts propose that mothers may transfer active immunity to the newborns via vertical transfer of pathogen-specific T cells. Overall, a promising strategy to augment and prolong neonatal immunity is to vaccinate the mother before or during pregnancy in order to boost maternal antibody concentrations or availability of specific T cells. Hence, a large number of pre-and postconceptional vaccine trials have been carried out to test and confirm this concept. We here highlight novel insights arising from recent research endeavors on the influence of prenatal maternal vaccination against pathogens that can pose a threat for newborns, such as measles, pertussis, rubella and influenza A. We delineate pathways involved in the transfer of specific maternal antibodies. We also discuss the consequences for children’s health and long-term immunity resulting from an adjustment of prenatal vaccination regimes.
Characterization of Dysregulated lncRNA-Associated ceRNA Network Reveals Novel lncRNAs With ceRNA Activity as Epigenetic Diagnostic Biomarkers for Osteoporosis Risk

The altered expression of long non-coding RNAs (lncRNAs) has been implicated in the development and human diseases. However, functional roles and regulatory mechanisms of lncRNA as competing endogenous RNAs (ceRNAs) in osteoporosis and their potential clinical implication for osteoporosis risk are largely unexplored. In this study, we performed integrated analysis for paired expression profiles and regulatory relationships of dysregulated lncRNAs, mRNAs, and miRNAs based on “ceRNA hypothesis,” and constructed an osteoporosis-related dysregulated miRNA-mediated lncRNA–mRNA ceRNA network (DysCeNet) composed of 105 nodes (including eight miRNAs, 24 mRNAs, and 73 lncRNAs) and 515 edges. Functional analysis suggested that the DysCeNet was involved in known osteoporosis or bone metabolism-related biological processes and pathways. Then, we performed random forest-based feature selection for 73 lncRNAs with ceRNA activity and identified 25 of 73 lncRNAs as potential diagnostic biomarkers. A random forest-based classifier composed of 25 lncRNA biomarkers (RF-25lncRNA) was developed for predicting osteoporosis risk. Performance evaluation with the leave-one-out cross-validation (LOOCV) procedure showed that the RF-25lncRNA achieved a good performance in distinguishing high- and low-bone mineral density (BMD) subjects in different osteoporosis datasets. Our study for the first time revealed a global view of lncRNA-associated ceRNA regulation in osteoporosis and provided novel lncRNAs with ceRNA activity as candidate epigenetic diagnostic biomarkers for early detection of osteoporosis risk.
Template-Free Synthesis of N-Doped Porous Carbon Materials From Furfuryl Amine-Based Protic Salts

Nitrogen-doped porous carbon materials (NPCMs) are usually obtained by carbonization of complicated nitrogen-containing polymers in the presence of template or physical/chemical activation of the as-synthesized carbon materials. Herein we reported the facile synthesis of NPCMs by direct carbonization of a series of furfuryl amine (FA)-based protic salts ([FA][X], X = NTf2, HSO4, H2PO4, CF3SO3, BF4, NO3, Cl) without any templates, tedious synthetic steps and other advanced techniques. The thermal decomposition of precursors and structure, elemental composition, surface atomic configuration, and porosity of carbons have been carefully investigated by thermogravimetric analysis (TGA), X-ray diffraction (XRD), Raman spectra, X-ray photoelectron spectroscopy (XPS), combustion elemental analysis, energy-dispersive spectrometry, and nitrogen isotherm adsorption. Different from the parent amine FA that was evaporated below 130°C and no carbon was finally obtained, it was found that all the prepared protic precursors yield NPCMs. These carbon materials were found to exhibit anion structure- dependent carbon yield, chemical composition, and porous structure. The obtained NPCMs can be further exploited as adsorbents for dye removal and decoloration. Among all NPCMs, [FA][H2PO4]-derived carbon owing to its high surface area and special pore structure exhibits the highest adsorption capacities toward both Methylene blue and Rhodamine B.
Studies on Haloperidol and Adjunctive α-Mangostin or Raw Garcinia mangostana Linn Pericarp on Bio-Behavioral Markers in an Immune-Inflammatory Model of Schizophrenia in Male Rats

Schizophrenia is a severe brain disorder that is associated with neurodevelopmental insults, such as prenatal inflammation, that introduce redox-immune-inflammatory alterations and risk for psychotic symptoms later in life. Nutraceuticals may offer useful adjunctive benefits. The aim of this study was to examine the therapeutic effects of Garcinia mangostana Linn (GML) and one of its active constituents, α-mangostin (AM), alone and as adjunctive treatment with haloperidol (HAL) on schizophrenia related bio-behavioral alterations in a maternal immune-activation (MIA) model. Sprague–Dawley dams were exposed to lipopolysaccharide (LPS) (n = 18) or vehicle (n = 3) on gestational days 15 and 16. Male offspring (n = 72) were treated from PND 52–66 with either vehicle, HAL (2 mg/kg), GML (50 mg/kg), HAL + GML, AM (20 mg/kg), or HAL + AM. Control dams and control offspring were treated with vehicle. In order to cover the mood–psychosis continuum, prepulse inhibition (PPI) of startle, open field test (locomotor activity), and the forced swim test (depressive-like behavior) were assessed on PND's 64–65, followed by assay of frontal–cortical lipid peroxidation and plasma pro-inflammatory cytokines, viz. interleukin-1 (IL-1) and tumor necrosis factor-α (TNF-α). MIA-induced deficits in sensorimotor gating were reversed by HAL and HAL + GML, but not GML and AM alone. MIA-induced depressive-like behavior was reversed by AM and GML alone and both in combination with HAL, with the combinations more effective than HAL. MIA-induced cortical lipid peroxidation was reversed by HAL and AM, with elevated IL-6 levels restored by GML, AM, HAL, and HAL + GML. Elevated TNF-α was only reversed by GML and HAL + GML. Concluding, prenatal LPS-induced psychotic- and depressive-like bio-behavioral alterations in offspring are variably responsive to HAL, GML, and AM, with depressive (but not psychosis-like) manifestations responding to GML, AM, and combinations with HAL. AM may be a more effective antioxidant than GML in vivo, although this does not imply an improved therapeutic response, for which trials are required.
pheSAG Based Rapid and Efficient Markerless Mutagenesis in Methylotuvimicrobium

Due to their fast growth rate and robustness, some haloalkalitolerant methanotrophs from the genus Methylotuvimicrobium have recently become not only promising biocatalysts for methane conversion but also favorable materials for obtaining fundamental knowledge on methanotrophs. Here, to realize unmarked genome modification in Methylotuvimicrobium bacteria, a counterselectable marker (CSM) was developed based on pheS, which encodes the α-subunit of phenylalanyl-tRNA synthetase. Two-point mutations (T252A and A306G) were introduced into PheS in Methylotuvimicrobium buryatense 5GB1C, generating PheSAG, which can recognize p-chloro-phenylalanine (p-Cl-Phe) as a substrate. Theoretically, the expression of PheSAG in a cell will result in the incorporation of p-Cl-Phe into proteins, leading to cell death. The Ptac promoter and the ribosome-binding site region of mmoX were employed to control pheSAG, producing the pheSAG-3 CSM. M. buryatense 5GB1C harboring pheSAG-3 was extremely sensitive to 0.5 mM p-Cl-Phe. Then, a positive and counterselection cassette, PZ (only 1.5 kb in length), was constructed by combining pheSAG-3 and the zeocin resistance gene. A PZ- and PCR-based strategy was used to create the unmarked deletion of glgA1 or the whole smmo operon in M. buryatense 5GB1C and Methylotuvimicrobium alcaliphilum 20Z. The positive rates were over 92%, and the process could be accomplished in as few as eight days.
Identification of NUDT5 Inhibitors From Approved Drugs

Recent studies have revealed the important role of NUDT5 in estrogen signaling and breast cancer, but research on the corresponding targeted therapy has just started. Drug repositioning strategy can effectively reduce the time and economic resources spent on drug discovery. To find novel inhibitors of NUDT5, we investigated the previously identified connectivity map-based drug association models and found eighteen FDA approved drugs as candidates. The molecular docking and molecular dynamic simulation were performed and revealed that fourteen organic drugs have the potential to bind the NUDT5 target. Eight representative drugs were selected to perform the cell line viability inhibition analysis, and the results showed that seven of them were able to suppress MCF7 breast cancer cells. Two drugs, nomifensine and isoconazole, showed lower IC50 than the known antiestrogens raloxifene and tamoxifen, and they deserve further pharmacodynamic investigations to test their feasibility for use as NUDT5 inhibitors.
Verotoxin Receptor-Based Pathology and Therapies

Verotoxin, VT (aka Shiga toxin,Stx) is produced by enterohemorrhagic E. coli (EHEC) and is the key pathogenic factor in EHEC-induced hemolytic uremic syndrome (eHUS-hemolytic anemia/thrombocytopenia/glomerular infarct) which can follow gastrointestinal EHEC infection, particularly in children. This AB5 subunit toxin family bind target cell globotriaosyl ceramide (Gb3), a glycosphingolipid (GSL) (aka CD77, pk blood group antigen) of the globoseries of neutral GSLs, initiating lipid raft-dependent plasma membrane Gb3 clustering, membrane curvature, invagination, scission, endosomal trafficking, and retrograde traffic via the TGN to the Golgi, and ER. In the ER, A/B subunits separate and the A subunit hijacks the ER reverse translocon (dislocon-used to eliminate misfolded proteins-ER associated degradation-ERAD) for cytosolic access. This property has been used to devise toxoid-based therapy to temporarily block ERAD and rescue the mutant phenotype of several genetic protein misfolding diseases. The A subunit avoids cytosolic proteosomal degradation, to block protein synthesis via its RNA glycanase activity. In humans, Gb3 is primarily expressed in the kidney, particularly in the glomerular endothelial cells. Here, Gb3 is in lipid rafts (more ordered membrane domains which accumulate GSLs/cholesterol) whereas renal tubular Gb3 is in the non-raft membrane fraction, explaining the basic pathology of eHUS (glomerular endothelial infarct). Females are more susceptible and this correlates with higher renal Gb3 expression. HUS can be associated with encephalopathy, more commonly following verotoxin 2 exposure. Gb3 is expressed in the microvasculature of the brain. All members of the VT family bind Gb3, but with varying affinity. VT2e (pig edema toxin) binds Gb4 preferentially. Verotoxin-specific therapeutics based on chemical analogs of Gb3, though effective in vitro, have failed in vivo. While some analogs are effective in animal models, there are no good rodent models of eHUS since Gb3 is not expressed in rodent glomeruli. However, the mouse mimics the neurological symptoms more closely and provides an excellent tool to assess therapeutics. In addition to direct cytotoxicity, other factors including VT–induced cytokine release and aberrant complement cascade, are now appreciated as important in eHUS. Based on atypical HUS therapy, treatment of eHUS patients with anticomplement antibodies has proven effective in some cases. A recent switch using stem cells to try to reverse, rather than prevent VT induced pathology may prove a more effective methodology.
Timing Is Everything—The High Sensitivity of Avian Satellite Cells to Thermal Conditions During Embryonic and Posthatch Periods

Myofiber formation is essentially complete at hatch, but myofiber hypertrophy increases posthatch through the assimilation of satellite cell nuclei into myofibers. Satellite cell proliferation and differentiation occur during the early growth phase, which in meat-type poultry terminates at around 8 days posthatch. Thus, any factor that affects the accumulation of satellite cells during late-term embryogenesis or early posthatch will dictate long-term muscle growth. This review will focus on the intimate relationship between thermal conditions during chick embryogenesis and the early posthatch period, and satellite cell myogenesis and pectoralis growth and development. Satellite cells are highly sensitive to temperature changes, particularly when those changes occur during crucial periods of their myogenic activity. Therefore, timing, temperature, and duration of thermal treatments have a great impact on satellite cell activity and fate, affecting muscle development and growth in the long run. Short and mild thermal manipulations during embryogenesis or thermal conditioning in the early posthatch period promote myogenic cell proliferation and differentiation, and have long-term promotive effects on muscle growth. However, chronic heat stress during the first 2 weeks of life has adverse effects on these parameters and may lead to muscle myopathies.
Chemical Analysis of Pollen by FT-Raman and FTIR Spectroscopies

Pollen studies are important for the assessment of present and past environment, including biodiversity, sexual reproduction of plants and plant-pollinator interactions, monitoring of aeroallergens, and impact of climate and pollution on wild communities and cultivated crops. Although information on chemical composition of pollen is of importance in all of those research areas, pollen chemistry has been rarely measured due to complex and time-consuming analyses. Vibrational spectroscopies, coupled with multivariate data analysis, have shown great potential for rapid chemical characterization, identification and classification of pollen. This study, comprising 219 species from all principal taxa of seed plants, has demonstrated that high-quality Raman spectra of pollen can be obtained by Fourier transform (FT) Raman spectroscopy. In combination with Fourier transform infrared spectroscopy (FTIR), FT-Raman spectroscopy is obtaining comprehensive information on pollen chemistry. Presence of all the main biochemical constituents of pollen, such as proteins, lipids, carbohydrates, carotenoids and sporopollenins, have been identified and detected in the spectra, and the study shows approaches to measure relative and absolute content of these constituents. The results show that FT-Raman spectroscopy has clear advantage over standard dispersive Raman measurements, in particular for measurement of pollen samples with high pigment content. FT-Raman spectra are strongly biased toward chemical composition of pollen wall constituents, namely sporopollenins and pigments. This makes Raman spectra complementary to FTIR spectra, which over-represent chemical constituents of the grain interior, such as lipids and carbohydrates. The results show a large variability in pollen chemistry for families, genera and even congeneric species, revealing wide range of reproductive strategies, from storage of nutrients to variation in carotenoids and phenylpropanoids. The information on pollen’s chemical patterns for major plant taxa should be of outstanding value for various studies in plant biology and ecology, including aerobiology, palaeoecology, forensics, community ecology, plant-pollinator interactions, and climate effects on plants.
PI(3,4)P2 Signaling in Cancer and Metabolism

The phosphatidylinositide 3 kinases (PI3Ks) and their downstream mediators AKT and mammalian target of rapamycin (mTOR) are central regulators of glycolysis, cancer metabolism, and cancer cell proliferation. At the molecular level, PI3K signaling involves the generation of the second messenger lipids phosphatidylinositol 3,4,5-trisphosphate [PI(3,4,5)P3] and phosphatidylinositol 3,4-bisphosphate [PI(3,4)P2]. There is increasing evidence that PI(3,4)P2 is not only the waste product for the removal of PI(3,4,5)P3 but can also act as a signaling molecule. The selective cellular functions for PI(3,4)P2 independent of PI(3,4,5)P3 have been recently described, including clathrin-mediated endocytosis and mTOR regulation. However, the specific spatiotemporal dynamics and signaling role of PI3K minor lipid messenger PI(3,4)P2 are not well-understood. This review aims at highlighting the biological functions of this lipid downstream of phosphoinositide kinases and phosphatases and its implication in cancer metabolism.