Miracle-dz/UniFAR-FTUs huggingface dataset:
Loneliness during the Covid-19 pandemic in Germany: Impact of social factors and polygenic risk scores on interpersonal differences in loneliness and mental health

Abstract Objectives The outbreak of Covid-19 negatively affected mental health and increased loneliness. The subjective feeling of loneliness is influenced by genetic and social factors and has a negative impact on mental health. Methods From March 2020 to June 2021 loneliness was investigated in N = 517 individuals using monthly acquired questionnaire data and Latent Growth Curve Analysis. Associations of social factors and polygenic risk scores (PRSs, n = 361) with class membership were investigated. Results Three classes (“average”, 40%; “not lonely”, 38%; “elevated loneliness”, 22%) were identified, that differ significantly regarding loneliness, mental dysfunction, and response to the lockdown phases. Individuals with a high PRS for neuroticism are more likely to belong to the “elevated loneliness” class, living with another person is a protective factor. Conclusion As the “elevated loneliness” class was at the highest risk of mental dysfunction, our findings underscore the importance of identifying those individuals to implement counteractive measures.
Secondary hypertension as a cause of treatment resistance

Abstract In secondary hypertension, elevated blood pressure is caused by a known and/or potentially treatable underlying disease. Although the prevalence of secondary hypertension depends on the patient population and the thoroughness of applied diagnostic approaches, arterial hypertension is classified in 90 to 95% as primary in nature. In young patients, individuals without a family history of hypertension, late onset of hypertension or worsening of a previous well-controlled hypertension as well as in patients who have a difficult to treat hypertension, the prevalence of secondary hypertension is significantly higher. Because the identification and the specific therapy of secondary hypertension may result in normalisation or improvement of elevated blood pressure in many cases, a targeted diagnostics is of great importance. Key messages The prevalence of secondary hypertension is 5-10% of hypertensive patients (lower in the whole population, higher in patients with therapy-resistant hypertension). Patient history, physical examination, and laboratory results are very important to patients with suspected secondary hypertension to identify. After a preliminary screening, the assignment is made recommended for specialist medical clarification. Think about secondary hypertension In young patients, individuals without a family history of hypertension, late onset of hypertension or worsening of a previous well-controlled hypertension as well as in patients who have a difficult to treat hypertension.
Prevalence and Characterization of Legionella pneumophila and Related Species from Water-Based Recreational Sites

Abstract Background and Objectives Legionella is a genus of gram-negative bacteria common in soil and aquatic systems and is associated with protists. They have emerged as a pathogenic group due to the increased use and poor maintenance of artificial water environments. This study aims at phenotypic and molecular identification of Legionella in water and swab samples collected from water-based recreational sites. The biofilm-forming ability of Legionella on exposure to various temperatures and iron concentrations was also studied. Methods A total of 60 samples including 30 swab samples and 30 water samples (decorative fountain ponds, swimming pools, garden sprinklers, drip irrigation system) were collected from in and around Mangalore, Karnataka, India. From each source, swab and water samples were collected as per the Indian standard IS: 1622. The collected samples were processed within 4 hours of collection. The samples were subjected to microbiological and chemical estimation followed by filtration through a 0.2 µm membrane filter. Isolation of Legionella from collected samples was performed as per US Centers for Disease Control and Prevention guidelines 2005. The positive isolates were then checked for biofilm-forming ability at various temperatures (25°C, 35°C, and 45°C) and iron concentration (3 mg/L, 30 mg/L, and 300 mg/L) using crystal violet assay. Results Out of 30, water and swab samples tested, one water sample from a garden sprinkler, swimming pool, and one from both water and swab samples from a decorative fountain showed the presence of Legionella . A biofilm study of Legionella at various temperatures and iron concentrations categorized the bacteria as a moderate biofilm former. Conclusion This study revealed that most of the water and swab samples were found to be negative for Legionella that is quite encouraging and the contamination of water systems in recreational facilities can be reduced by decontamination techniques and proper hygienic practices.
Semi-automatic assessment of lack of control code documentation in automated production systems

Abstract This paper first examines the current state of industrial practice of documentation in automated production systems based on a large-scale survey in machine and plant manufacturing proving that companies still face major challenges in documentation. However, insufficient documentation creates friction since it may increase the risk of malfunction and high costs, and impede system development due to lack of traceability, especially for control software being one of the main functionality carriers. Therefore, secondly, a risk priority indicator RPI4DD is proposed to systematically capture the lack of control code documentation to avoid undesired costs due to inadequate documentation.
Nonlocal Diffusion in Porous Media: A Spatial Fractional Approach

AbstractOne-dimensional diffusion problems in bounded porous media characterized by the presence of nonlocal interactions are investigated by assuming a Darcy’s constitutive equation of convolution integral type. A power law attenuation function is implemented: Analogies and differences of the flow-rate-pressure law with respect to other nonlocal and fractal models are outlined. By means of the continuity relationship, the fractional diffusion equation is then derived. It involves spatial Riemann-Liouville derivatives with a noninteger order consisting of between 1 and 2. The solution is obtained numerically using fractional finite differences, and results are presented in both the transient and the steady-state regimes. Eventually, the physical meaning of fractional operators is discussed and potential applications of the analysis are suggested.
A unified solution for vibration analysis of moderately thick, functionally graded rectangular plates with general boundary restraints and internal line supports

ABSTRACT The objective of this article is to present a Fourier-Ritz method-based solution approach for the free vibration analysis of moderately thick, functionally graded (FG) rectangular plates with general boundary restraints and internal line supports. Under the current framework, regardless of boundary conditions, each of the displacements and rotations of the FG plates is invariantly expressed as a modified Fourier series in both directions. Then, the accurate solutions are obtained using the Ritz procedure based on the energy function of the plates. The convergence and accuracy of the present method are verified by a considerable number of convergence tests and comparisons.
CO2 and CH4 fluxes from forest soil in the northern Da Xing’anling Mountains in Northeast China during the freezing and thawing periods of near-surface soil in 2018–2019

ABSTRACT Under a warming climate, the studies on effects of seasonal freeze–thaw cycles on soil respiration are key to understanding the soil carbon cycles and ecosystem responses and resilience at mid- and high latitudes. In this study, the effluxes of soil surface CO2 and absorption rates of CH4 were measured in the Xing'an larch (Larix gmelinii) forest in the northern Da Xing’anling Mountains, Northeast China using an automatic multichannel soil greenhouse gas measurement system (dynamic gas chamber method) during the periods of October–November 2018 and April–May 2019. The results showed that during the freezing period of near-surface soil, CO2 and CH4 fluxes significantly declined, approaching zero, at the end of November. During the thawing period of near-surface soil, CO2 and CH4 fluxes from surface soil fluctuated markedly at first and then rose rapidly. The respective Q10 values of 3.86 and 4.89 during the freezing and thawing periods of near-surface soil, respectively, indicate the important role of ground freeze–thaw cycles in the modifications of CO2 and CH4 fluxes. The results of this study could help assess the stability of the soil carbon pool and carbon flux strength in taiga-forested permafrost regions in the northern Da Xing’anling Mountains, Northeast China.
Using the stress–vulnerability model to better understand suicide in prison populations

Suicide is the culmination of the interaction of a number of factors with the critical component being distress. The contribution of mental illness as a vulnerability factor in an individual case of suicide by a prisoner may be significant, marginal or non-existent. Because of the high prevalence in prison populations of all risk factors for suicide, relying solely on those factors is of little use in elaborating the risk of suicide for a given prisoner. Whilst a current mental illness or past history of a suicide attempt are two factors that appear to be strongly associated with completed suicide, no screening or risk assessment tool has any proven efficacy in predicting suicide in prison populations. The stress–vulnerability model offers a more sophisticated and comprehensive assessment and also informs a more individualised needs-based management of the risk of suicide with an emphasis on detecting and responding to a prisoner’s distress.
JMnorm: a novel joint multi-feature normalization method for integrative and comparative epigenomics

Combinatorial patterns of epigenetic features reflect transcriptional states and functions of genomic regions. While many epigenetic features have correlated relationships, most existing data normalization approaches analyze each feature independently. Such strategies may distort relationships between functionally correlated epigenetic features and hinder biological interpretation. We present a novel approach named JMnorm that simultaneously normalizes multiple epigenetic features across cell types, species, and experimental conditions by leveraging information from partially correlated epigenetic features. We demonstrate that JMnorm-normalized data can better preserve cross-epigenetic-feature correlations across different cell types and enhance consistency between biological replicates than data normalized by other methods. Additionally, we show that JMnorm-normalized data can consistently improve the performance of various downstream analyses, which include candidate cis-regulatory element clustering, cross-cell-type gene expression prediction, detection of transcription factor binding and changes upon perturbations. These findings suggest that JMnorm effectively minimizes technical noise while preserving true biologically significant relationships between epigenetic datasets. We anticipate that JMnorm will enhance integrative and comparative epigenomics. GRAPHICAL ABSTRACT JMnorm can jointly normalize multiple epigenetic features between the target sample and the reference.
Did Moldehawera flowers evolve through mimicry with oil-producing Malpighiaceae?

Floral mimicry is a captivating phenomenon wherein flowers imitate traits of other species to attract specific pollinators. The Caesalpinioideae legumes in general have relatively unspecialized flowers, which has allowed the development of disparate morphologies associated with adaptation to different types of pollinators. This study describes the pollination of Moldenhawera nutans and explores its potential floral mimicry towards Malpighiaceae flowers. Our investigation revealed that M. nutans is pollinated by species of Centris Fabricius, 1804 and Xylocopa Latreille, 1802. It also presents compelling evidence supporting the hypothesis of floral mimicry, including striking similarities in floral display, shared oil-collecting pollinators, oil collection behavior in M. nutans despite the absence of oil production, and the reliance on exogenous pollen for reproduction. These findings suggest that species of Centris bees visit M. nutans flowers under the mistaken impression of oil availability, subsequently transitioning to pollen collection. We explored other potential cases of floral mimicry with Malpighiaceae in the Caesalpinioideae legumes by optimizing the Malpighiaceae-like floral display on a dated phylogeny of this subfamily. However, current information does not allow us to determine whether the similarities in floral morphology represent cases of floral mimicry, phylogenetic inertia, or simple convergence. Several hypothesis tests are suggested that can guide the study of these fascinating evolutionary processes in the group.
CRISPR/Cas9-Mediated Generation of COL7A1-Deficient Keratinocyte Model of Recessive Dystrophic Epidermolysis Bullosa

Objective Recessive dystrophic epidermolysis bullosa (RDEB) is a genetic skin fragility and ultimately lethal blistering disease caused by mutations in the COL7A1 gene which is responsible for coding type VII collagen. Investigating the pathological mechanisms and novel candidate therapies for RDEB could be fostered by new cellular models. Here, we developed multiple immortalized COL7A1-deficient keratinocyte cell lines using CRISPR/Cas9 technology as RDEB cellular model. Materials and Methods In this experimental study, we used transient transfection to express COL7A1-targeting gRNA and Cas9 in HEK001 immortalized keratinocyte cell line followed by enrichment with fluorescent-activated cell sorting (FACS) via GFP expressing cells (GFP+ HEK001). Homogenous single-cell clones were then isolated, genotyped, and evaluated for type VII collagen expression. We performed a scratch assay to confirm the functional effect of COL7A1 knockout. Results We achieved 46.1% (p < 0.001) efficiency of indel induction in the enriched transfected cell population. Except for 4% of single nucleotide insertions, the remaining indels were deletions of different sizes. Out of nine single clones expanded, two homozygous and two heterozygous COL7A1-deficient cell lines were obtained with defined mutation sequences. No off-target effect was detected in the knockout cell lines. Immunostaining and western blot analysis showed the lack of type VII collagen (COL7A1) protein expression in these cell lines. We also showed that COL7A1-deficient cells had higher motility compared with their wild-type counterparts. Conclusion We reported the first isogenic immortalized COL7A1-deficient keratinocyte lines that provide a useful cell culture model to investigate aspects of RDEB biology and potential therapeutic options.
ADAM11 a novel regulator of Wnt and BMP4 signaling in neural crest and cancer

Introduction: Cranial neural crest (CNC) cells are induced at the border of the neural plate by a combination of FGF, Wnt, and BMP4 signaling. CNC then migrate ventrally and invade ventral structures where they contribute to craniofacial development. Methods: We used loss and gain of function experiments to determine phenotypes associated with the perturbation of Adam11 expression in Xenopus Laevis. Mass spectrometry to identify partners of Adam11 and changes in protein expression in CNC lacking Adam11. We used mouse B16 melanoma to test the function of Adam11 in cancer cells, and published database analysis to study the expression of ADAM11 in human tumors. Results: Here we show that a non-proteolytic ADAM, Adam11, originally identified as a putative tumor suppressor binds to proteins of the Wnt and BMP4 signaling pathway. Mechanistic studies concerning these non-proteolytic ADAM lack almost entirely. We show that Adam11 positively regulates BMP4 signaling while negatively regulating β-catenin activity. In vivo, we show that Adam11 influences the timing of neural tube closure and the proliferation and migration of CNC. Using both human tumor data and mouse B16 melanoma cells, we further show that ADAM11 levels similarly correlate with Wnt or BMP4 activation levels. Discussion: We propose that ADAM11 preserves naïve cells by maintaining low Sox3 and Snail/Slug levels through stimulation of BMP4 and repression of Wnt signaling, while loss of ADAM11 results in increased Wnt signaling, increased proliferation and early epithelium to mesenchyme transition.
Evaluating power to detect recurrent selective sweeps under increasingly realistic evolutionary null models

The detection of selective sweeps from population genomic data often relies on the premise that the beneficial mutations in question have fixed very near the sampling time. As it has been previously shown that the power to detect a selective sweep is strongly dependent on the time since fixation as well as the strength of selection, it is naturally the case that strong, recent sweeps leave the strongest signatures. However, the biological reality is that beneficial mutations enter populations at a rate, one that partially determines the mean wait time between sweep events and hence their age distribution. An important question thus remains about the power to detect recurrent selective sweeps when they are modelled by a realistic mutation rate and as part of a realistic distribution of fitness effects (DFE), as opposed to a single, recent, isolated event on a purely neutral background as is more commonly modelled. Here we use forward-in-time simulations to study the performance of commonly used sweep statistics, within the context of more realistic evolutionary baseline models incorporating purifying and background selection, population size change, and mutation and recombination rate heterogeneity. Results demonstrate the important interplay of these processes, necessitating caution when interpreting selection scans; specifically, false positive rates are in excess of true positive across much of the evaluated parameter space, and selective sweeps are often undetectable unless the strength of selection is exceptionally strong. Teaser Text Outlier-based genomic scans have proven a popular approach for identifying loci that have potentially experienced recent positive selection. However, it has previously been shown that an evolutionarily appropriate baseline model that incorporates non-equilibrium population histories, purifying and background selection, and variation in mutation and recombination rates is necessary to reduce often extreme false positive rates when performing genomic scans. Here we evaluate the power to detect recurrent selective sweeps using common SFS-based and haplotype-based methods under these increasingly realistic models. We find that while these appropriate evolutionary baselines are essential to reduce false positive rates, the power to accurately detect recurrent selective sweeps is generally low across much of the biologically relevant parameter space.
A novel 4D fMRI clustering technique to examine event-related spatiotemporal dynamics of face processing in naturalistic stimuli

Cortical function is complex, nuanced, and involves information processing in a multimodal and dynamic world. However, previous functional magnetic resonance imaging (fMRI) research has generally characterized static activation differences between strictly controlled proxies of real-world stimuli that do not encapsulate the complexity of everyday multimodal experiences. Of primary importance to the field of neuroimaging is the development of techniques that distill complex spatiotemporal information into simple, behaviorally relevant representations of neural activation. Herein, we present a novel 4D spatiotemporal clustering method to examine dynamic neural activity associated with events (specifically the onset of human faces in audiovisual movies). Results from this study showed that 4D spatiotemporal clustering can extract clusters of fMRI activation over time that closely resemble the known spatiotemporal pattern of human face processing without the need to model a hemodynamic response function. Overall, this technique provides a new and exciting window into dynamic functional processing across both space and time using fMRI that has wide applications across the field of neuroscience.
Practical challenges of urban regeneration in China

COPYRIGHT © 2023 Cheshmehzangi, Chen, Mangi and Heath. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Practical challenges of urban regeneration in China
Multisite transformation in Neisseria gonorrhoeae: insights on transformations mechanisms and new genetic modification protocols

Natural transformation, or the uptake of naked DNA from the external milieu by bacteria, holds a unique place in the history of biology. This is both the beginning of the realization of the correct chemical nature of genes and the first technical step to the molecular biology revolution that sees us today able to modify genomes almost at will. Yet the mechanistic understanding of bacterial transformation still presents many blind spots and many bacterial systems lag behind power horse model systems like Escherichia coli in terms of ease of genetic modification. Using Neisseria gonorrhoeae as a model system and using transformation with multiple DNA molecules, we tackle in this paper both some aspects of the mechanistic nature of bacterial transformation and the presentation of new molecular biology techniques for this organism. We show that similarly to what has been demonstrated in other naturally competent bacteria, Neisseria gonorrhoeae can incorporate, at the same time, different DNA molecules modifying DNA at different loci within its genome. In particular, co-transformation of a DNA molecule bearing an antibiotic selection cassette and another non-selected DNA piece can lead to the integration of both molecules in the genome while selecting only through the selective cassette at percentages above 70%. We also show that successive selections with two selection markers at the same genetic locus can drastically reduce the number of genetic markers needed to do multisite genetic modifications in Neisseria gonorrhoeae. Despite public health interest heightened with the recent rise in antibiotic resistance, the causative agent of gonorrhea still does not possess a plethora of molecular techniques. This paper will extend the techniques available to the Neisseria community while providing some insights into the mechanisms behind bacterial transformation in Neisseria gonorrhoeae. We are providing a suite of new techniques to quickly obtain modifications of genes and genomes in the Neisserial naturally competent bacteria.