Miracle-dz/UniFAR-FTUs huggingface dataset:
T cell receptor sequencing specifies psoriasis as a systemic and atopic dermatitis as a skin- 1 focused, disease 2

Background: Atopic dermatitis (AD) and psoriasis represent two of the most common 33 inflammatory skin diseases in developed countries. A hallmark of both diseases is T cell infiltration into the skin. However, it is still not clarified to what extent these infiltrating T cells 35 are antigen-specific skin-homing T cells or unspecific heterogeneous bystander cells. 36 Methods: To elucidate this, T cells from lesional skin and from blood of 9 AD and 10 psoriasis 37 patients were compared by receptor (TCR) sequencing. Therefore, peripheral blood mononuclear 38 cells (PBMC) were cell-sorted according to expression of the cutaneous leukocyte antigen (CLA) 39 into skin-homing (CLA + ) and non-skin-homing (CLA - ) subfractions. Aeroallergen-specific T cell 40 lines were grown from AD patients´ PBMC in parallel. 41 Results: Intra-individual comparison of TCRB CDR3 regions revealed that clonally expanded T 42 cells in skin lesions of both AD and psoriasis patients corresponded to skin-homing circulating T 43 cells. However, in psoriasis patients, these T cell clones were also detectable to a larger extent among CLA - circulating T cells. Up to 28% of infiltrating cells in AD skin were identified as 45 allergen-specific by overlapping TCR sequences. 46 Conclusions: Our data shows that in line with the systemic nature of psoriasis, T cell clones that 47 infiltrate psoriatic skin lesions do not exclusively possess skin-homing ability and are therefore 48 most probably specific to antigens that are not exclusively expressed or located in the skin. T 49 cells driving AD skin inflammation appear to home nearly exclusively to the skin and are, to a 50 certain extent, specific to aeroallergens. 51
A high-gain inkjet-printed UWB LPDA antenna on paper substrate

An ultra-wideband (UWB) log-periodic dipole array (LPDA) antenna inkjet-printed on a 0.5 mm thick photo paper substrate is presented. The overall size of the LPDA antenna is 130 × 60 mm2. The LPDA antenna exhibits stable input-impedance characteristics and a consistent end-fire radiation pattern over the whole operating band of 2.2–11 GHz. Fulfilling the need of high-gain flexible antennas for UWB, a highly directive measured gain of 9.5 dBi on a paper substrate makes it an excellent candidate for flexible wireless devices.
Pharmacological inhibition of the NLRP3 inflammasome reduces Pharmacological inhibition of the NLRP3 inflammasome reduces blood pressure, renal damage, and dysfunction in salt-sensitive blood pressure, renal damage, and dysfunction in salt-sensitive hypertension hypertension

Aims Renal inﬂammation, leading to ﬁbrosis and impaired function is a major contributor to the development of hypertension. The NLRP3 inﬂammasome mediates inﬂammation in several chronic diseases by processing the cytokines pro-interleukin (IL)-1 b and pro-IL-18. In this study, we investigated whether MCC950, a recently-identiﬁed inhibitor of NLRP3 activity, reduces .
Creating Artificial Intelligence Agents for Spelunky using an Artificial Neural Network and a Genetic Algorithm

The research in this paper will focus on the use of artificial neural networks and genetic algorithms in creating an artificial intelligence (AI) agent that is able to successfully handle the various problem domains that exist within an electronic game known as Spelunky. A problem domain being the specific area of challenge within Spelunky such as the domain of terrain navigation, the domain of combat, the domain of planning and others (Scales and Thompson, 2014). This paper begins by giving an introduction which consists of the hypothesis of the paper as well as why this hypothesis is possible and worth researching. The introduction then lays out the aim and objectives of this paper that need to be met so a valid assessment of the accuracy of the hypothesis can be made. A literature review is then conducted which details the concepts of artificial neural networks as well as genetic algorithms. It will also cover their implementation and an example of work they have been used in. Using games as a test bed for AI research will also be reviewed as well why Spelunky should specifically be used. A methodology follows the literature review detailing how an artificial neural network will be implemented into Spelunky as well as what experimentations will be ran and what data will be looked for in the experiments as well as how data is to be retrieved from the experiments. The results of testing are then displayed and an analysis of the results is conducted. A discussion is then conducted which details some of the issues that have been experienced in the research and what the testing data is telling us about the system that has been implemented. Conclusions are then made from all the gathered information about the performance of the AI agents created to tackle Spelunky, what limitations they have, how well met the aim and objectives were and finally the accuracy of the hypothesis of this research will be assessed.
Changes in Lysophospholipid Components in Ulcerative Colitis and Colitis-associated Cancer

Background: In recent years, it has become clear that, in addition to normal cytokines, phospholipid mediators play an important role in the development, growth, infiltration, and metastasis of cancer and in the cancer microenvironment. A phospholipid analysis method using tandem mass spectrometry (LC-MS/MS) with high detection sensitivity has enabled quantification of phospholipids, even when using a very small sample. To date, we had applied this MS technology to colorectal cancer tissue. Therefore, in this study, this mass spectrometry technique was applied to ulcerative colitis (UC) and UC-related colorectal cancer, and an analysis was conducted with the aim of clarifying which lysophospholipids specifically change in each type of tissue. Materials and Methods: UC-associated colorectal cancer tissue and UC mucosa were collected from surgical specimens of colitic cancer (n=3). Cancerous and non-cancerous tissues were collected from surgical specimens from patients with sporadic colorectal cancer (n=11). After extraction from these tissues, the amounts of lysophospholipids were quantified by LC-MS/MS. In addition, lysophosphatidylserine (LPS) and lysophosphatidylinositol (LPI) were quantified for each molecular species of fatty acids. Results: Compared to normal mucosa, LPI was increased 3.8-fold (p<0.001) and LPS 3.5-fold (p<0.001) in UC-related colorectal cancer. Molecular species of LPI which were increased in UC-related colorectal cancer were 18:0 (p=0.001), 16:0 (p=0.03) and 20:4 (p=0.004), and of LPS were 18:0 (p<0.001) and 22:6 (p=0.014). Conclusion: Lysophospholipids increased in colorectal cancer and in UC-associated colorectal cancer. In particular, LPI may have contributed significantly to colitis-associated carcinogenesis.
A review on sensory perception for dexterous robotic manipulation

Sensory perception for dexterous robotic hands is an active research area and recent progress in robotics. Effective dexterous manipulation requires robotic hands to accurately feedback their state or perceive the surrounding environment. This article reviews the state-of-the-art of sensory perception for dexterous robotic manipulation. Two types of sensors, such as intrinsic and extrinsic sensors, are introduced according to their function and layout in robotic hands. These sensors provide rich information to a robotic hand, which contains the posture, the contact information of objects, and the physical information of the environment. Then, a comprehensive analysis of perception methods including planning-level, control-level, and learning-level perceptions is presented. The information obtained from sensory perception can help robotic hands to make decisions effectively. Previously issued reviews mainly focus on the design of tactile senor, while we analyze and discuss the relationship among sensing, perception, and dexterous manipulation. Some potential research topics on sensory perception are also summarized and discussed.
An Umbrella Review of Systematic Reviews With or Without Meta-Analysis Assessing Treatment Outcomes and Efficiency of Self-Ligating Brackets

Introduction Self-ligating bracket systems are popular and seem to demonstrate lesser friction, allowing tooth movement without exerting unwanted forces on surrounding structures. This umbrella review aimed to compare self-ligating and conventional bracket systems for treatment efficiency. Methods An electronic search in 8 databases was performed for literature published between January 1, 1990, and October 1, 2021, with manual hand-searching of references of retrieved articles. Quality assessment was performed using the risk of bias in a systematic tool by 2 independent reviewers. Data were extracted using a prepiloted form (Joanna Briggs Institute) for evidence synthesis. Corrected covered area was calculated to quantify study overlaps across systematic reviews with or without meta-analysis. Results 605 articles were retrieved, of which 16 were selected. Most included studies had a low risk of bias, except for 6 that showed an unclear risk of bias. Data analysis revealed a reduction in lower incisor proclination, bacterial accumulation, and oral malodor using self-ligating appliances. Conclusions Self-ligating systems reduce mandibular incisor proclination, bacterial accumulation, external apical root resorption, chairside time, and oral malodor. No other differences could be demonstrated in comparison with conventional appliance systems.
From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools

In metagenomic analyses of microbiomes, one of the first steps is usually the taxonomic classification of reads by comparison to a database of previously taxonomically classified genomes. While different studies comparing metagenomic taxonomic classification methods have determined that different tools are “best”, there are two tools that have been used the most to-date: Kraken (k-mer based classification against a user-constructed database) and MetaPhlAn (classification by alignment to clade-specific marker genes), the latest versions of which are Kraken2 and MetaPhlAn 3, respectively. We found large discrepancies in both the proportion of reads that were classified as well as the number of species that were identified when we used both Kraken2 and MetaPhlAn 3 to classify reads within metagenomes from human-associated or environmental datasets. We then investigated which of these tools would give classifications closest to the real composition of metagenomic samples using a range of simulated and mock samples and examined the combined impact of tool-parameter-database choice on the taxonomic classifications given. This revealed that there may not be a one-size-fits-all “best” choice. While Kraken2 can achieve better overall performance, with higher precision, recall and F1 scores, as well as alpha- and beta-diversity measures closer to the known composition than MetaPhlAn 3, the computational resources required for this may be prohibitive for many researchers, and the default database and parameters should not be used. We therefore conclude that the best tool-parameter-database choice for a particular application depends on the scientific question of interest, which performance metric is most important for this question and the limit of available computational resources.
Lola-I is a developmentally regulated promoter pioneer factor

While enhancers are often regulated at the level of accessibility by pioneer factors, promoters tend to be constitutively accessible and poised for activation by paused Pol II — thus are often not considered as sites of developmental regulation. Here we show that the accessibility of promoters and the acquisition of paused Pol II can be subject to developmental regulation by pioneer factors. We show that Lola-I, a Drosophila zinc finger transcription factor, is ubiquitously expressed at the end of embryogenesis and causes its target promoters to become accessible and acquire paused Pol II throughout the embryo. This promoter transition is required but not sufficient for tissue-specific target gene expression. Lola-I mediates this function by binding to the edges of the promoter nucleosomes, which leads to their depletion, similar to the action of pioneer factors at enhancers. These results uncover a level of regulation for promoters that is normally found at enhancers, providing further evidence that promoters and enhancers display unexpectedly similar characteristics.
Museomic approaches to genotype historic Cinchona barks

Over the last few centuries, millions of plant specimens have been collected and stored within herbaria and biocultural collections. They therefore represent a considerable resource for a broad range of scientific uses. However, collections degrade over time, and it is therefore increasingly difficult to characterise their genetic signatures. Here, we genotyped highly degraded Cinchona barks and leaves from herbaria using two separate high-throughput sequencing methods (HtS) and compared their performance. We subsequently genotyped specimens using genome skimming, the most commonly performed high-throughput sequencing (HtS) technique. We additionally used a recently developed capture bait set (Angiosperm353) for a target enrichment approach. Specifically, phylogenomic analyses of modern leaf and historical barks of Cinchona were performed, including 23 historical barks and six fresh leaf specimens. We found that samples degraded over time, which directly reduced the quantity and quality of the data produced by both methodologies (in terms of reads mapped to the references). However, we found that both approaches generated enough data to infer phylogenetic relationships, even between highly degraded specimens that are over 230 years old. However, the target capture kit produced data for target nuclear loci and also chloroplast data, which allowed for phylogenies to be inferred from both genomes, whereas it was only possible to use chloroplast data using genome skimming. We therefore find the Angiosperms353 target capture kit a powerful alternative to genome skimming, which can be used to obtain more information from herbarium specimens, and ultimately additional cultural benefits.
Predicting individual skill learning, a cautionary tale

People show vast variability in skill learning. What determines a person’s individual learning ability? In this study we explored the possibility to predict participants’ future learning, based on their behavior during initial skill acquisition. We recruited a large online multi-session sample of participants performing a sequential tapping skill learning task. We trained machine learning models to predict future skill learning from raw data acquired during initial skill acquisition, and from engineered features calculated from the raw data. While the models did not explain learning, strong correlations were observed between initial and final performance. In addition, the results suggest that in correspondence with other empirical fields testing human behavior, canonical experimental tasks developed and selected to detect average effects may constrain insights regarding individual variability, relevant for real-life scenarios. Overall, implementing machine learning tools on large-scale data sets may provide a powerful approach towards revealing what differentiates between high and low innate learning abilities, paving the way for learning optimization techniques which may generalize beyond motor skill learning to broad learning abilities.
Log-order improved in trans hammerhead ribozyme turnover rates: reevaluating therapeutic space for small catalytic RNAs

We discovered an enhanced functionality hammerhead ribozyme (EhhRz), designed to act in trans against human rod opsin (RHO) mRNA, with turnover activity >300 nM min−1 under substrate-excess conditions and physiological Mg2+ levels (1 mM). We developed a real-time moderate-throughput fluorescence quantitative hhRz kinetic assay, which is linear with substrate and product moles and supported by gel-based measures. The EhhRz targets a CUC↓ cleavage site in a substrate with no predicted secondary/tertiary structure and demonstrates classic Michaelis-Menten turnover behavior when the substrate is in 10-fold excess (Vmax/Km up to 1.60 × 108 min−1 M−1), which is comparable to RNase A. EhhRzs show cooperative titration with a Kd of 0.73 ± 0.02 mM at cellular Mg2+ concentrations and a Hill coefficient of 1.73 ± 0.07. The upstream EhhRz antisense flank (bound to a downstream substrate flank) interacts with stem-loop II, and examinations of different variants revealed that a U7 residue in the downstream flank of the substrate is not essential for enhanced activity. Under single-turnover conditions with substrate pre-annealed to enzyme, reaction rates exceeded 1,000 min−1. These findings show that RNA catalysis approaches the efficiency of the ribosome and suggests EhhRz in trans is a druggable nucleic acid therapeutic.
Calcium Determines Lactiplantibacillus plantarum Intraspecies Competitive Fitness

Ecological theory states that the struggle for existence is stronger between closely related species. Contrary to this assertion, fermented foods frequently sustain conspecific individuals, in spite of their high levels of phylogenetic relatedness. ABSTRACT The importance of individual nutrients for microbial strain robustness and coexistence in habitats containing different members of the same species is not well understood. To address this for Lactiplantibacillus plantarum in food fermentations, we performed comparative genomics and examined the nutritive requirements and competitive fitness for L. plantarum strains B1.1 and B1.3 isolated from a single sample of teff injera fermentation batter. Compared to B1.1 and other L. plantarum strains, B1.3 has a smaller genome, limited biosynthetic capacities, and large mobilome. Despite these differences, B1.3 was equally competitive with B1.1 in a suspension of teff flour. In commercially sourced, nutrient-replete MRS (cMRS) medium, strain B1.3 reached 3-fold-higher numbers than B1.1 within 2 days of passage. Because B1.3 growth and competitive fitness were poor in mMRS medium (here called mMRS), a modified MRS medium lacking beef extract, we used mMRS to identify nutrients needed for robust B1.3 growth. No improvement was observed when mMRS was supplemented with nucleotides, amino acids, vitamins, or monovalent metals. Remarkably, the addition of divalent metal salts increased the growth rate and cell yields of B1.3 in mMRS. Metal requirements were confirmed by inductively coupled plasma mass spectrometry, showing that total B1.3 intracellular metal concentrations were significantly (up to 2.7-fold) reduced compared to B1.1. Supplemental CaCl2 conferred the greatest effect, resulting in equal growth between B1.1 and B1.3 over five successive passages in mMRS. Moreover, calcium supplementation reversed a B1.3 strain-specific, stationary-phase, flocculation phenotype. These findings show how L. plantarum calcium requirements affect competitive fitness at the strain level. IMPORTANCE Ecological theory states that the struggle for existence is stronger between closely related species. Contrary to this assertion, fermented foods frequently sustain conspecific individuals, in spite of their high levels of phylogenetic relatedness. Therefore, we investigated two isolates of Lactiplantibacillus plantarum, B1.1 and B1.3, randomly selected from a single batch of teff injera batter. These strains spanned the known genomic and phenotypic range of the L. plantarum species, and in laboratory culture medium used for strain screening, B1.3 exhibited poor growth and was outcompeted by the more robust strain B1.1. Nonetheless, B1.1 and B1.3 were equally competitive in teff flour. This result shows how L. plantarum has adapted for coexistence in that environment. The capacity for the single macronutrient calcium to restore B1.3 competitive fitness in laboratory culture medium suggests that L. plantarum intraspecies diversity found in food systems is fine-tuned to nutrient requirements at the strain level.
The Drosophila Fab-7 boundary element modulates Abd-B gene activity in the genital disc by guiding an inversion of collinear chromatin organization and alternative promoter use

Hox genes encode transcription factors that specify segmental identities along the Antero-Posterior body axis. These genes are organized in clusters, where their order corresponds to their activity along the body axis, an evolutionary conserved feature known as collinearity. In Drosophila, the BX-C cluster contains the three most posterior Hox genes, where their collinear activation incorporates progressive replacement of histone modifications, reorganization of 3D chromatin architecture and sequential activation of boundary elements and cis-regulatory regions. To dissect functional hierarchies, we compared chromatin organization in larvae and in cell lines, with a focus on the Abd-B gene. Our work establishes the importance of the Fab-7 boundary element for insulation between 3D domains marked by different histone modifications. Interestingly, we detected a non-canonical inversion of collinear chromatin dynamics at the Abd-B gene, with the active histone domain decreasing in size. This chromatin organization differentially instructed alternative Abd-B promoter use, thereby expanding the possibilities to regulate transcriptional output.
Quantitative analysis of surface wave patterns of Min proteins

The Min protein system is arguably the best-studied model systems for biological pattern formation. It exhibits pole-to-pole oscillations in E. coli bacteria as well as a variety of surface wave patterns in in vitro reconstitutions. Such Min surface wave patterns pose particular challenges to quantification as they are typically only semi-periodic and non-stationary. Here, we present a methodology for quantitatively analyzing such Min patterns, aiming for reproducibility, user-independence, and easy usage. After introducing pattern-feature definitions and image-processing concepts, we present an analysis pipeline where we use autocorrelation analysis to extract global parameters such as the average spatial wavelength and oscillation period. Subsequently, we describe a method that uses flow-field analysis to extract local properties such as the wave propagation velocity. We provide descriptions on how to practically implement these quantification tools and provide Python code that can directly be used to perform analysis of Min patterns.