Miracle-dz/UniFAR-FTUs huggingface dataset:
Adipokines contribute to central-obesity related reductions in myelin-sensitive MRI indices in the fornix

Midlife obesity is a risk factor of late onset Alzheimer’s disease (LOAD) but why this is the case remains unknown. As systemic inflammation is involved in both conditions, one possibility is that obesity-related neuroinflammation may contribute to the development of LOAD. Neuroinflammation is closely linked to white matter myelin loss, and this can be measured in vivo with quantitative magnetization transfer (qMT) imaging. Here, we investigated whether differences in obesity measures, i.e., in Waist Hip Ratio (WHR), abdominal visceral and subcutaneous fat volume fractions and Body Mass Index (BMI), were associated with reductions in qMT indices of apparent myelin in temporal white matter pathways involved in LOAD (i.e., the fornix, the parahippocampal cingulum and the uncinate fasciculus compared with whole brain and cortico-spinal white matter) in 166 cognitively healthy individuals (38-71 years of age). Obesity-related effects on myelin-sensitive markers were contrasted with differences in apparent axon density from dual-shell diffusion Neurite Orientation Dispersion and Density Imaging (NODDI). Differences in WHR and in visceral fat volume fractions were negatively correlated with differences in qMT estimates of apparent myelin and tissue metabolism in the fornix but not with any other microstructural components. These correlations were not explained by demographic (age, sex, education), health (hypertension, alcohol consumption, sedentary lifestyle) or genetic (APOE genotype, family history of dementia) risk factors of LOAD. Furthermore, differences in the ratio of plasma concentrations of leptin and adiponectin were also positively correlated with differences in C-Reactive Protein concentrations, and contributed significantly to the correlations between central obesity and myelin-sensitive metrics in the fornix. These results are consistent with the view that visceral fat-related chronic inflammation may damage white matter myelin in limbic regions, known to be vulnerable to LOAD pathology.
Phenology of Parasetigena silvestris (Diptera: Tachinidae), gypsy moth (Lymantria dispar) (Lepidoptera: Lymantriidae) larval parasitoid and its efficiency for parasitisation

ABSTRACT Parasetigena silvestris is a univoltine, solitary, larval endoparasitoid which lays its eggs on the surface of gypsy moth larvae. Field collection of the host larvae (2nd through 5th instar) from an artificially established gypsy moth population were made to compare stage specific parasitism between larvae without and with P. silvestris tachinid eggs. The tachinid oviposition rate detected was highest in second instar larvae, and then decreased as larvae developed toward full maturity. The opposite was true for tachinid parasitoid emergence which had no emergence from second through third host instar larvae. Fourth instar gypsy moth larvae, however, experienced significantly higher parasitism by P. silvestris in the larvae with eggs than those without the eggs. The braconid wasp Cotesia melanoscelus caused significantly higher parasitism in early instar larvae with P. silvestris eggs than in those without the eggs. The tachinid prefers to lay more eggs on parasitised larvae by the braconid even though the braconid is a superior competitor to the fly during multiparasitism. Factors influencing parasitism rates by P. silvestris such as host-parasitoid synchronisation and the multiparasitism interaction with C. melanoscelus are discussed.
Text mining and network analysis for discovery of novel genes

Text mining is the process of extracting relevant information from the unstructured data obtained from the published corpora in biomedical literature. A vast amount of literature is available in context of biofilms in PubMed database. It is a very daunting task to extract useful information in the form of genes and proteins from text manually; therefore, text mining approaches are used for this purpose. The extracted relevant information can be appropriately visualized using network biology approaches. Therefore, here we present a framework that would help in discovering novel biomarkers (genes) and gene-drug associations, involved in Staphylococcus biofilm using the available published corpora. We initially utilized COREMINE tool to select biological processes (i
Statistical Analysis of MicroRNA as Markers for Screening of Colon Cancer

Diagnostic screening can potentially reduce mortality from Colon Cancer (CC) detection because it enhances premalignant detection. The commonly used immunological Fecal Occult Blood Test (FOBTi) screening lacks sensitivity and imposes dietary restriction, resulting in decreased compliance. The Gold Standard for ColoRectal Cancer (CRC) screening “Colonoscopy” --not requiring dietary restriction-is invasive, often accompanied by abdominal pain, has potential for complications, is not economical, and could also lead to mortality. Therefore, a noninvasive sensitive screen would be a more convenient test.
World’s fastest brain-computer interface: Combining EEG2Code with deep learning

In this paper, we present a Brain-Computer Interface (BCI) that is able to reach an information transfer rate (ITR) of more than 1200 bit/min using non-invasively recorded EEG signals. By combining the EEG2Code method with deep learning, we present an extremely powerful approach for decoding visual information from EEG. This approach can either be used in a passive BCI setting to predict properties of a visual stimulus the person is viewing, or it can be used to actively control a BCI spelling application. The presented approach was tested in both scenarios and achieved an average ITR of 701 bit/min in the passive BCI approach with the best subject achieving an online ITR of 1237 bit/min. The presented BCI is more than three times faster than the previously fastest BCI and allows to discriminate 500,000 different visual stimuli based on 2 seconds of EEG data with an accuracy of up to 100 %. When using the approach in an asynchronous BCI for spelling, we achieved an average utility rate of 175 bit/min, which corresponds to an average of 35 error-free letters per minute. As we observe a ceiling effect where more powerful approaches for brain signal decoding do not translate into better BCI control anymore, we discuss if BCI research has reached a point where the performance of non-invasive BCI control cannot be substantially improved anymore.
Effect of lighting spectrum and naphthaleneacetic acid (NAA) on in vitro development of cactus pear [Opuntia ficus-indica (L.) Mill]

Modification of in vitro culture environment can improve the development of plants, obtaining higher morphological and physiological quality. The objective of this work was to analyze the influence of different luminous spectrums as well as different doses of auxin NAA on in vitro development of cactus pear (Opuntia ficus-indica (L.) Mill). The experiment was conducted in a completely randomized design in factorial scheme 4 x 3 (Luminous spectrums x NAA doses), corresponding to four luminous spectrums: red, green, blue and white, and three doses of NAA 1, 2 and 3 mg. L -1 . A total of 12 treatments with 6 replications were applied including 1 plant per repetition. Cactus pear plants were introduced on MS culture medium solidified with 7% agar, and pH adjusted to 5.8. We observed higher development of plants (growth and rooting) under luminous spectrums, 30 and 60 days after plant establishment (red and green). At concentrations of 1 and 2 mg L -1 of NAA we observed better height of the plants, 30 and 60 days after establishment. The luminous spectrums red and green influenced the in vitro development of cactus pear plants. The best doses to promote better plant growth are 1 and 2 mg. L -1 of NAA.
Extraction of Microbial and Host DNA, RNA, and Proteins from Oak Bark Tissue

The application of high-throughput nucleic acid and protein sequencing technologies is transforming our understanding of plant microbiomes and their interactions with their hosts in health and disease. However, progress in studying host-microbiome interactions in above-ground compartments of the tree (the phyllosphere) has been hampered due to high concentrations of phenolic compounds, lignin, and other compounds in tree bark that severely limit the success of DNA, RNA, and protein extraction. Here we present modified sample-preparation and kit-based protocols for the extraction of host and microbiome DNA and RNA from oak (Quercus robus and Quercus petraea) bark tissue for subsequent high-throughput sequencing. In addition, reducing the quantity of bark tissue used for an established protein extraction protocol yielded high quality protein for parallel analysis of the oak-microbiota metaproteome. These procedures demonstrate the successful extraction of nucleic acids and proteins from oak tissue using as little as 50 mg of sample input, producing sufficient quantities for nucleic acid sequencing and protein mass spectrometry of tree stem tissues and their associated microbiota.
Relationship between mathematical confidence and academic performance, among undergraduate biology students

Background The interconnectivity between the nature and origins of mathematics and science cannot be overstated. However, studies over the past decade have shown that approx. 50% of life science students lack confidence in their mathematical abilities, and as a result, often adopt a rigid attitude to learning mathematics. This is particularly problematic in undergraduate life sciences, when the focus shifts to data handling and calculations. It was hypothesised that this ‘rigidity’ would relate to lower academic performance in biology and mathematics. Aims This study was framed using Bandura (1977) self-efficacy theory and aimed to determine whether low mathematical confidence amongst undergraduate biology students would relate to low academic performance in biology mathematics. Design and methods Students enrolled in an introductory biology course (n=254) at a major research focused university were surveyed as to their attitudes to mathematics, using a modified version of the Fennema-Sherman Attitude Scale (5-point Likert items). Based on their responses to the confidence sub-scale, students were categorised as either possessing ‘low’ (mean Likert score 3.5) confidence, they were then matched to their mean final grades in mathematics and biology, and compared using a student’s independent samples t-test. Results No differences were found between students who possessed ‘low’ or ‘high’ mathematical confidence, in terms of mean final grades in biology. Interestingly, for mathematics, students who were categorised a possessing ‘high’ mathematical confidence, achieved significantly lower grades compared to those students who possessed ‘low’ mathematical confidence. In other words students who were less mathematically confident, achieved significantly higher grades relative to their more mathematically confident peers. Conclusions The recognition that students possess a high degree of additional complexity, with regards to the learning of mathematics and biology, is beneficial to educators. Such that more effective learning and teaching interventions may be developed, to encourage students to develop attitudes to learning that relate to improved educational outcomes.
Characterisation of anergic B cells in a new mouse model with altered B cell receptor signalling

While the B cell antigen receptor (BCR) membrane IgM (mIgM) transmits signals via Igα/β, the cytoplasmic tail of mIgG is able to transmit signals directly. We have generated mice where the IgG1 cytoplasmic signalling tail was added to the C-terminus of IgM (IgMg1 mouse). During B cell development, IgMg1 B cells experience stronger negative selection resulting in tonic BCR signal transduction being repressed and reduced mIgM expression. BCR stimulation of immature and mature IgMg1 B cells results in reduced signalling. This shows that IgMg1 B cells leave the bone marrow as anergic cells. IgMg1 B cells respond less efficiently to thymus-independent antigens. They do, however, respond well to the thymus-dependent antigen. The anergic pattern of IgMg1 B cells is maintained throughout the GC response and even after they become IgG switched memory B cells (MBCs). These effects may contribute to a delay in the shift of antigen-specificity of GC B cells. These results are in line with recent studies showing that anergic B cells are licensed to participate in Germinal Centre (GC) reactions, where they can undergo clonal redemption. We conclude that IgMg1 mice are a new model to study anergy in B cells with a complete repertoire of BCR-specificities.
Genome-wide Prediction of Potential Polycomb Response Elements and their Functions

The Polycomb-group proteins (PcG) and Trithorax-group proteins (TrxG) are two major epigenetic regulators important for proper differentiation during development (1, 2). In Drosophila melanogaster (D. melanogaster), Polycomb response elements (PREs) are short segments of DNA with a high density of binding sites for transcription factors (TFs) that recruit PcG and TrxG proteins to chromatin. Each PRE has a different number of binding sites for PcG and TrxG, and these binding sites have different topological organizations. It is thus difficult to find general rules to discover the locations of PREs over the entire genome. We have developed a framework to predict the locations and roles of potential PRE regions over the entire D. melanogaster genome using machine learning algorithms. Using a combination of motif-based and simple sequence-based features, we were able to train a random forest (RF) model with very high performance in predicting active PRE regions. This model could distinguish potential PRE regions from non-PRE regions (precision and recall ~0.92 upon cross-validation). In the process, the model suggests that previously unrecognized TFs might contribute to PcG/TrxG recruitment at the PRE locations, as the presence of binding sites for those factors is strongly informative of active PREs. A secondary regression model provides information on features that further differentiate PREs into functional subclasses. Our findings provide both new predictions of 7887 potential PREs in the D. melanogaster genome, and new mechanistic insight into the set of DNA-associated proteins that may contribute to PcG recruitment and/or activity.
The recent past and promising future for data integration methods to estimate species’ distributions

With the advance of methods for estimating species distribution models has come an interest in how to best combine datasets to improve estimates of species distributions. This has spurred the development of data integration methods that simultaneously harness information from multiple datasets while dealing with the specific strengths and weaknesses of each dataset. We outline the general principles that have guided data integration methods and review recent developments in the field. We then outline key areas that allow for a more general framework for integrating data and provide suggestions for improving sampling design and validation for integrated models. Key to recent advances has been using point‐process thinking to combine estimators developed for different data types. Extending this framework to new data types will further improve our inferences, as well as relaxing assumptions about how parameters are jointly estimated. These along with the better use of information regarding sampling effort and spatial autocorrelation will further improve our inferences. Recent developments form a strong foundation for implementation of data integration models. Wider adoption can improve our inferences about species distributions and the dynamic processes that lead to distributional shifts.
Usage of Kombucha ‘Tea Fungus’ for Enhancement of Functional Properties of Herbal Beverages

The following herbal teas were fermented with the Kombucha “tea fungus” for 7 days: Acacia arabica, Aegle marmelos root bark, Aerva lanata, Asteracantha longifolia, Cassia auriculata, Hemidesmus indicus, Hordeum vulgare, Phyllanthus emblica, Tinospora cordifolia. Microbial enumerations of the bacteria and fungi present in the broth and the tea fungal mats were carried out. At the end of the period of fermentation, the pH values ranged from 4.0 to 6.0, while the titratable acidity (TA) ranging from 2.5 to 5.0 g/mL. The TA was within the acceptable limits of consumption for all beverages. The Oxygen radical absorbance capacity (ORAC) assay indicated 5 of the fermented beverages to have statistically significant increases (P < 0.05) by the end of the period of fermentation. By day 7, the IC50 values of the α-amylase inhibitory activities ranged from 52.5 to 67.2 μg/mL, while the α-glucosidase inhibitory activity values ranged from 95.2 to 196.1 μg/mL by this time point. Overall, an enhancement of the antioxidant and starch hydrolase inhibitory potential of the seven herbal teas was observed as a result of the fermentation by addition of the tea fungus. Thus, this fermentation process could be highlighted as a novel and versatile methodology to obtain functional beverages.
Copper and the Skin

Copper and Copper Alloys. Corrosion Chemistry of Copper. Basics of Metal Skin Penetration: Scope and Limitations. Percutaneous Absorption of Copper. Diffusion of Copper Through Human Skin In Vivo. Irritation Potential of Copper Compounds. Copper Hypersensitivity. Copper in Medicine and Personal Care: A Historical Overview. The Role of Copper in Onset, Development, and Control of Acute and Chronic Inflammation. Copper Jewelry and Arthritis. The Role of Copper in Anti-Inflammatory Therapy and the Potential for Its Transdermal Application.
Is the use of supermarket trolleys microbiologically safe? Study of microbiological contamination

ABSTRACT Microbial contamination in shopping trolleys (eighty five) by considering different supermarkets (seven) from three major food companies in Las Palmas de Gran Canaria (Spain) was determined. The two sampled areas were trolley handles and food trolley baskets-child seats. Samples were analyzed by selective and differential microbiological culture media. E. coli four (2.4%) indicative of faecal contamination, Klebsiella pneumoniae twelve (6.5%) and Citrobacter freundii, six (5.1%), which have been isolated from human faecal samples, were isolated from trolleys; Pseudomonas rhodesiae, five (4.25%), and Pseudomonas fluorescens, three (2.55%), which both evidenced environmental contamination. Significant differences among the companies were found for the Enterobacteriaceae and coliforms. Regarding location, these differences (p < 0.003) were observed only for the coliform rates, which were higher in trolleys located outside. The results of this study suggest the implementation of cleaning and disinfection programmes to improve trolley sanitation, and to reduce exposure to both potential pathogenic and transmitting bacterial infections.
Cell size heterogeneity early in development is required for collective cell migration during gastrulation in zebrafish

Metazoan embryos begin life as a single large cell, which divides to generate an entire multicellular organism. This natural progression is characterized by an early, visually striking phenomenon of progressive reduction in cell size, since early cell divisions occur in the absence of cell growth. It is intuitive that early embryogenesis, wherein the phenomenon of growing numbers of progressively smaller cells dominate, cell size may be an important factor for normal development. However, in the absence of experimental efforts directed at altering cell sizes in early embryos, the importance of optimal cell sizes early in development for normal embryogenesis remains an intuitive conjecture at best. We used haploid and tetraploid zebrafish as tools to obtain embryos with smaller or larger than the normal diploid size cells, respectively. Analysis of early development in haploids and tetraploids revealed that when reductive early cell divisions generate a pool of smaller or larger cells in comparison to diploid embryos, embryonic patterning is perturbed due to defective collective migration of cells during gastrulation. During this early phase, the transcriptome of haploid and tetraploid embryos remained largely unperturbed, suggesting that the developmental defects cannot be explained by potential transcriptional changes in response to deviation from a diploid state of the genome. We additionally show that a short exposure to a combination of Aphidicolin and Hydroxyurea during blastoderm stages increases cell sizes in diploid embryos. Such embryos displayed morphological abnormalities that resembled haploid and tetraploid embryos at the end of gastrulation. Conversely, a similar short exposure to a combination of Aphidicolin and Hydroxyurea increased cell sizes in haploid embryos, partially restoring normal patterning. We posit that early reductive divisions set up an optimum range and proportions of cell sizes in early embryos onto which molecular controls are overlaid to execute collective cell migration during gastrulation. Perturbation of the normal cell size landscape triggers aberrant cell migration and gastrulation defects despite normal expression of conserved genes, revealing the importance of optimal cell sizes per se in normal embryonic patterning.
Comparing conceptual frameworks for a fish community MSY (FCMSY) using management strategy evaluation—an example from the North Sea

Maximum sustainable yield (MSY) is a well-established concept that is mandated by legislation, and has a clear theoretical meaning in terms of a single stock. However, its definition is problematic in a multispecies setting, which makes it more difficult to apply the MSY principle. In this study of the North Sea fish community, we consider several possible MSY candidates, and evaluate them in terms of their ability to produce optimum long-term yield whilst avoiding unacceptable risk of stock impairment. We perform this evaluation with an ensemble of size-structured models using a management strategy evaluation approach, in which harvest control rules (HCRs) are used to determine levels of fishing as a function of the proposed MSY target and stock status, taking account of recruitment and model parameter uncertainties. We find that HCRs of the type considered here are always useful in the scenarios we tested, as they reduce overfishing risk much more than average long-term yield. This is independent of the precise form of the HCR, so it is more important to implement one rigorously than obsess over the rule details. For a lax definition of overfishing, which accepts relatively severe stock depletion (B < 10% B0), and using HCRs, risks are “low” across all strategies, and the Nash equilibrium is the best performing MSY approach considered here. For more stringent definitions of “at risk” (e.g. likelihood of B < 20% of B0), the application of HCRs can allow a range of alternative formulations of MSY. Thus, the definition of MSY may be sensitive to judgements about acceptable levels of risk, and consistent application of a sensible management framework may be more important than developing the best possible theoretical definition of MSY.
The Problem of Commercial Application of Perovskite Solar Cells

Despite the power conversion efficiency (PCE) in organometal halide perovskite solar cells (PCSs) has achieved 23.7%, the prospect commercial application is not optimistic. The stability and repeatability of conversion efficiency from small-area devices to large-area devices are the main reasons for preventing commercialization. Here, we will discuss these two aspects in detail.