Miracle-dz/UniFAR-FTUs huggingface dataset:
Oral and Intra-nasal Administration of Nanoparticles in the Cerebral Ischemia Treatment in Animal Experiments: Considering its Advantages and Disadvantages

Background Over the past few decades, nanotechnology has dramatically advanced; from the precise strategies of synthesizing modern nanostructures to methods of entry into the body. Using nanotechnology in diagnosis, drug delivery, determining signaling pathways, and tissue engineering is great hope for the treatment of stroke. The drug-carrying nanoparticles are a way to increase drug absorption through the mouth or nose in treating the stroke. Objective In this article, in addition to explaining pros and cons of oral and intra-nasal administration of nanoparticles in the brain ischemia treatment of animal models, the researchers introduce some articles in this field and briefly mentioned their work outcomes. Methods A number of relevant published articles 183 were initially collected from three popular databases including PubMed, Google Scholar, and Scopus. The articles not closely related to the main purpose of the present work were removed from the study process. The present data set finally included 125 published articles. Results Direct delivery of the drug to the animal brain through the mouth and nose has more therapeutic effects than systemic delivery of drugs. The strategy of adding drugs to the nanoparticles complex can potentially improve the direct delivery of drugs to the CNS. Conclusion Despite the limitations of oral and intra-nasal routes, the therapeutic potential of oral and intra-nasal administration of nano-medicines is high in cerebral ischemia treatment.
Modelling a crime scene in 3D and adding thermal information

Once a crime has been perpetrated, forensic traces will only be persevered in the crime scene for a limited time frame. It is therefore necessary to record a crime scene meticulously. Usually, photographs and/or videos are taken at the scene to document it, so that later on one will know the exact place of an object. Another possibility is to construct a three dimensional (3D) model of the crime scene. A 3D model has the advantage that you can change the perspective and view the scene from all directions. We use a stereo camera to record the crime scene and use these images to construct a 3D model. A drawback of conventional (color) cameras is that they only capture features that belong to the visible part of electromagnetic spectrum. Interesting traces with strong signatures in other parts of the spectrum could be overlooked. For example; has a lamp or computer screen been turned on previously, is there some fluid on the carpet? Such traces can be observed with an infrared (IR) camera that captures images in the IR part of the spectrum. However, it is not well understood if these traces stay visible for a sufficient amount time. Therefore, a first set of experiments was conducted to gain some insight in the visibility degradation of different IR traces over time. The results are discussed in this paper. Furthermore, it will be shown how adding thermal information to the 3D model can improve crime scene understanding.
Microbial Size Spectra from Diverse Marine Ecosystems.

Abstract : Microbial size spectra serve as synoptic pictures of the organization of the pelagic food web. However, field data sets are limited and the range and variability of size spectra are still relatively unexplored. In this thesis, we examined how the characteristics of microbial size spectra varied with ecosystem productivity, and how size spectra responded to environmental perturbations. Flow cytometry was used to generate size spectra and to study the temporal and spatial dynamics of bacteria and phytoplankton from high nutrient, productive coastal waters in Massachusetts and Cape Cod Bays, and low nutrient, low productivity waters in the oligotrophic Sargasso Sea. Additional data was collected from the equatorial Pacific a high nutrient, low chlorophyll region. In general, a spectrum reflecting the predominance of larger bacteria and phytoplankton cells was observed in winter and early spring, where low temperatures resulted in well- mixed waters and high nutrient concentrations. Seasonal succession was accompanied by a distinct shift in the size spectrum to smaller cells, coinciding with rising temperatures, stratification of the water column and diminishing nutrient concentrations. In stratified waters, larger mean bacteria and phytoplankton sizes were observed in surface and very deep waters, whereas the smallest sizes were typically seen around the chlorophyll maximum.
Effective properties of two‐phase flow in heterogeneous aquifers

The spectral perturbation approach is employed to predict the field‐scale relative permeabilities and the variance of capillary pressure and saturation under steady two‐phase flow conditions. The theoretical analysis treats stationary three‐dimensional variations in pressure and flow produced as a result of spatial variations of permeability and two‐phase flow characteristics. The analysis is developed in a general form that is applied to different commonly used two‐phase flow characterizations, and results are illustrated for two‐phase flow characteristics corresponding to those observed at the Borden site in Canada. For gravity‐driven flow in horizontally layered aquifers, both nonwetting phase flow (dense nonaqueous phase liquid (DNAPL) flow) and wetting phase flow (water, unsaturated flow) show effective vertical relative permeabilities that are substantially decreased in comparison with those corresponding to a homogeneous system. The resulting saturation‐dependent anisotropy of effective permeability is substantially larger for DNAPL flow than for the case of unsaturated flow. The Leverett scaling characterization frequently used in Monte Carlo simulations is shown to underestimate system anisotropy owing to omission of variability of the parameter governing the slope in the capillary pressure–saturation function. Application of the Brooks‐Corey characterization of the relative permeability resulted in significantly greater anisotropy than with the van Genuchten characterization. In contrast to the strong influence of heterogeneity predicted in the case of effective permeabilities, the effective capillary pressure characteristic (mean capillary pressure versus mean saturation curve) is only weakly influenced by heterogeneity.
Genetic colour variation visible for predators and conspecifics is concealed from humans in a polymorphic moth

The definition of colour polymorphism is intuitive: genetic variants express discretely coloured phenotypes. This classification is, however, elusive as humans form subjective categories or ignore differences that cannot be seen by human eyes. We demonstrate an example of a ‘cryptic morph’ in a polymorphic wood tiger moth (Arctia plantaginis), a phenomenon that may be common among well‐studied species. We used pedigree data from nearly 20,000 individuals to infer the inheritance of hindwing colouration. The evidence supports a single Mendelian locus with two alleles in males: WW and Wy produce the white and yy the yellow hindwing colour. The inheritance could not be resolved in females as their hindwing colour varies continuously with no clear link with male genotypes. Next, we investigated if the male genotype can be predicted from their phenotype by machine learning algorithms and by human observers. Linear discriminant analysis grouped male genotypes with 97% accuracy, whereas humans could only group the yy genotype. Using vision modelling, we also tested whether the genotypes have differential discriminability to humans, moth conspecifics and their bird predators. The human perception was poor separating the genotypes, but avian and moth vision models with ultraviolet sensitivity could separate white WW and Wy males. We emphasize the importance of objective methodology when studying colour polymorphism. Our findings indicate that by‐eye categorization methods may be problematic, because humans fail to see differences that can be visible for relevant receivers. Ultimately, receivers equipped with different perception than ours may impose selection to morphs hidden from human sight.
Progesterone attenuates cerebral edema in neonatal rats with hypoxic-ischemic brain damage by inhibiting the expression of matrix metalloproteinase-9 and aquaporin-4

The aim of this study was to investigate the effects of progesterone (PROG) on blood-brain barrier (BBB) permeability, cerebral edema and the expression of matrix metalloproteinase-9 (MMP-9) and aquaporin-4 (AQP-4) in neonatal rats with hypoxic-ischemic brain damage (HIBD) and to explore the mechanism of its neuroprotective effect. Sixty 7-day-old Wistar rats were divided into sham surgery, hypoxic ischemia (HI) and drug prophylaxis (PROG) groups. HIBD animal models were established. All the animals were sacrificed after 24 h. The BBB was assessed using Evans blue. Cerebral moisture capacity was determined using the dry-wet method. MMP-9 was detected in the brain tissues using enzyme-linked immunosorbent assay. The expression of AQP-4 and MMP-9 in the cerebral cortex was observed using immunohistochemistry and real-time polymerase chain reaction. The MMP-9 levels in the cortex, BBB permeability, cerebral moisture capacity and expression of AQP-4 and MMP-9 in the HI group were significantly higher compared with those in the sham surgery group (P<0.01), and they were significantly lower in the drug prophylaxis group compared with those in the HI group (P<0.05). In conclusion, PROG reduces BBB damage and cerebral edema and inhibits MMP-9 generation to protect rat brains against HIBD. The protective effect of PROG may be correlated with downregulated expression of AQP-4 and MMP-9 in the cerebral cortex.
Investigating polymorphisms by bioinformatics is a potential cost-effective method to screen for germline mutations in Chinese familial adenomatous polyposis patients

The aim of this study was to investigate germline mutations of the APC, MUTYH and AXIN2 genes in Chinese patients with familial adenomatous polyposis (FAP), and further assess the value of bioinformatics in screening the pathogenic changes predisposing to FAP. APC genes from 11 unrelated FAP patients in Yunnan province in China were firstly examined by exon-specific DNA sequencing. For samples without already known pathogenic changes predisposing to FAP in the APC gene, whole-gene sequencing of MUTYH and AXIN2 was performed. Mutational analysis of each gene was performed by bioinformatics. Eleven different types of APC polymorphisms were observed in the cohort of families analyzed. Of these polymorphisms, four were missense substitutions (V1822D, V1173G, P1760H and K2057), one was a nonsense substitution (S1196X), and six were silent substitutions (Y486Y, T449T, T1493T, G1678G, S1756S and P1960P). One missense mutation (Q335H) and two intronic substitutions (c.264+11G>A and c.420+35A>G) were detected in the MUTYH gene, and four synonymous mutations (I144I, P455P, P462P and L688L) and three intonic mutations (c.1060–77G>T, c.1060–287A>G and c.1060–282 A>G) of the AXIN2 gene were observed. In addition to the already reported pathogenic mutations, by using function assessment tools and databases, the synonymous substitutions observed in the APC gene of our samples were predicted to affect splicing regulation in the translation of mRNA, while the missense mutations observed in the APC gene and MUTYH gene were predicted to be disease-related polymorphisms; however, no functional effect of the mutations was observed in the AXIN2 gene. Comprehensive screening for germline mutations in APC, MUTYH and AXIN2 genes followed by prediction of pathogenicity using bioinformatic tools contributes to a cost-effective way of screening germline mutations in Chinese familial adenomatous polyposis patients.
Urinary Volatomic Expression Pattern: Paving the Way for Identification of Potential Candidate Biosignatures for Lung Cancer

The urinary volatomic profiling of Indian cohorts composed of 28 lung cancer (LC) patients and 27 healthy subjects (control group, CTRL) was established using headspace solid phase microextraction technique combined with gas chromatography mass spectrometry methodology as a powerful approach to identify urinary volatile organic metabolites (uVOMs) to discriminate among LC patients from CTRL. Overall, 147 VOMs of several chemistries were identified in the intervention groups—including naphthalene derivatives, phenols, and organosulphurs—augmented in the LC group. In contrast, benzene and terpenic derivatives were found to be more prevalent in the CTRL group. The volatomic data obtained were processed using advanced statistical analysis, namely partial least square discriminative analysis (PLS-DA), support vector machine (SVM), random forest (RF), and multilayer perceptron (MLP) methods. This resulted in the identification of nine uVOMs with a higher potential to discriminate LC patients from CTRL subjects. These were furan, o-cymene, furfural, linalool oxide, viridiflorene, 2-bromo-phenol, tricyclazole, 4-methyl-phenol, and 1-(4-hydroxy-3,5-di-tert-butylphenyl)-2-methyl-3-morpholinopropan-1-one. The metabolic pathway analysis of the data obtained identified several altered biochemical pathways in LC mainly affecting glycolysis/gluconeogenesis, pyruvate metabolism, and fatty acid biosynthesis. Moreover, acetate and octanoic, decanoic, and dodecanoic fatty acids were identified as the key metabolites responsible for such deregulation. Furthermore, studies involving larger cohorts of LC patients would allow us to consolidate the data obtained and challenge the potential of the uVOMs as candidate biomarkers for LC.
Formation of Essential Ultrastructural Interface between Cultured Hippocampal Cells and Gold Mushroom-Shaped MEA- Toward “IN-CELL” Recordings from Vertebrate Neurons

Using cultured Aplysia neurons we recently reported on the development of a novel approach in which an extracellular, non-invasive multi-electrode-array system provides multisite, attenuated, intracellular recordings of subthreshold synaptic potentials, and action potentials (APs), the so called “IN-CELL” recording configuration (to differentiate it from intracellular recordings). Because of its non-invasive nature, the configuration can be used for long term semi intracellular electrophysiological monitoring of APs and synaptic potentials. Three principals converge to generate the IN-CELL configuration: (a) engulfment of approximately 1 μm size gold mushroom-shaped microelectrodes (gMμE) by the neurons, (b) formation of high seal resistance between the cell’s plasma membrane and the engulfed gMμE, and (c), autonomous localized increased conductance of the membrane patch facing the gMμE. Using dissociated rat hippocampal cultures we report here that the necessary morphological and ultrastructural relationships to generate the IN-CELL recording configuration are formed between hippocampal cells and the gMμEs. Interestingly, even <1 μm thin branches expand and engulf the gMμE structures. Recordings of spontaneous electrical activity revealed fast ∼2 ms, 0.04–0.75 mV positive monophasic APs (FPMP). We propose that the FPMP are attenuated APs generated by neurons that engulf gMμEs. Computer simulations of analog electrical circuits depicting the cell–gMμE configuration point out the parameters that should be altered to improve the neuron–gMμE electrical coupling.
Seven years of macroinfauna monitoring at Ladeira beach (Corrubedo Bay, NW Spain) after the Prestige oil spill *

Abstract The exposed sandy beach of Ladeira (Corrubedo Bay, NW Spain) was sampled during seven years (2003–2009) after the Prestige oil spill (winter 2002–03), to determine interannual variations in the macroinfaunal community in two ways: (i) through ecological indices (species richness and abundances, Shannon’s diversity and Pielou’s evenness) and (ii) through the density of the most representative species. A clear zonation pattern was found, consisting of two zones: (i) the supralittoral, occupied by talitrid amphipods, isopods and insects, and (ii) the intertidal, where marine crustaceans and polychaetes prevailed. The amphipods Talitrus saltator and Talorchestia deshayesii dominated from the drift line upwards, and isopods ( Eurydice spp.), polychaetes ( Scolelepis spp.) and the amphipod Pontocrates arenarius dominated the intertidal. Univariate indices remained constant throughout the study period in the supralittoral, but they varied widely in the intertidal zone. Multivariate analysis showed that the Prestige oil spill scarcely affected the macroinfaunal community structure during the study period (2003–2009) and its effect was limited just to the first campaign (2003), six months after the Prestige accident.
Molecular Systems Biology Peer Review Process File Metabolic Reconstruction Identifies Strain-specific Regulation of Virulence in Toxoplasma Gondii Transaction Report: the Reviewed Paper Reports the First Large-scale Metabolic Network Reconstruction for Toxoplasma

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Portal to the heritage of astronomy

Abstract Following the Starlight meeting held in La Palma in November 2009, members of the IAU Working Group on Astronomy and World Heritage and the Starlight Initative are working together, with the approval of the UNESCO World Heritage Centre, to produce a new integrated web site for the UNESCO–IAU Astronomy and World Heritage Initiative that will act as a Portal to the Heritage of Astronomy. As such, the portal will be the bridge between the Initiative, the scientific community, National Commissions and experts, and the general public.
Long-Term Exposure to Urban Air Pollution and Mortality in a Cohort of More than a Million Adults in Rome

Background: Few European studies have investigated the effects of long-term exposure to both fine particulate matter (≤ 2.5 µm; PM2.5) and nitrogen dioxide (NO2) on mortality. Objectives: We studied the association of exposure to NO2, PM2.5, and traffic indicators on cause-specific mortality to evaluate the form of the concentration–response relationship. Methods: We analyzed a population-based cohort enrolled at the 2001 Italian census with 9 years of follow-up. We selected all 1,265,058 subjects ≥ 30 years of age who had been living in Rome for at least 5 years at baseline. Residential exposures included annual NO2 (from a land use regression model) and annual PM2.5 (from a Eulerian dispersion model), as well as distance to roads with > 10,000 vehicles/day and traffic intensity. We used Cox regression models to estimate associations with cause-specific mortality adjusted for individual (sex, age, place of birth, residential history, marital status, education, occupation) and area (socioeconomic status, clustering) characteristics. Results: Long-term exposures to both NO2 and PM2.5 were associated with an increase in nonaccidental mortality [hazard ratio (HR) = 1.03 (95% CI: 1.02, 1.03) per 10-µg/m3 NO2; HR = 1.04 (95% CI: 1.03, 1.05) per 10-µg/m3 PM2.5]. The strongest association was found for ischemic heart diseases (IHD) [HR = 1.10 (95% CI: 1.06, 1.13) per 10-µg/m3 PM2.5], followed by cardiovascular diseases and lung cancer. The only association showing some deviation from linearity was that between NO2 and IHD. In a bi-pollutant model, the estimated effect of NO2 on mortality was independent of PM2.5. Conclusions: This large study strongly supports an effect of long-term exposure to NO2 and PM2.5 on mortality, especially from cardiovascular causes. The results are relevant for the next European policy decisions regarding air quality.
To center or not to center? Investigating inertia with a multilevel autoregressive model

Whether level 1 predictors should be centered per cluster has received considerable attention in the multilevel literature. While most agree that there is no one preferred approach, it has also been argued that cluster mean centering is desirable when the within-cluster slope and the between-cluster slope are expected to deviate, and the main interest is in the within-cluster slope. However, we show in a series of simulations that if one has a multilevel autoregressive model in which the level 1 predictor is the lagged outcome variable (i.e., the outcome variable at the previous occasion), cluster mean centering will in general lead to a downward bias in the parameter estimate of the within-cluster slope (i.e., the autoregressive relationship). This is particularly relevant if the main question is whether there is on average an autoregressive effect. Nonetheless, we show that if the main interest is in estimating the effect of a level 2 predictor on the autoregressive parameter (i.e., a cross-level interaction), cluster mean centering should be preferred over other forms of centering. Hence, researchers should be clear on what is considered the main goal of their study, and base their choice of centering method on this when using a multilevel autoregressive model.