Miracle-dz/UniFAR-FTUs huggingface dataset:
c‐di‐GMP regulates activity of the PlzA RNA chaperone from the Lyme disease spirochete

PlzA is a c‐di‐GMP‐binding protein crucial for adaptation of the Lyme disease spirochete Borrelia (Borreliella) burgdorferi during its enzootic life cycle. Unliganded apo‐PlzA is important for vertebrate infection, while liganded holo‐PlzA is important for survival in the tick; however, the biological function of PlzA has remained enigmatic. Here, we report that PlzA has RNA chaperone activity that is inhibited by c‐di‐GMP binding. Holo‐ and apo‐PlzA bind RNA and accelerate RNA annealing, while only apo‐PlzA can strand displace and unwind double‐stranded RNA. Guided by the crystal structure of PlzA, we identified several key aromatic amino acids protruding from the N‐ and C‐terminal domains that are required for RNA‐binding and unwinding activity. Our findings illuminate c‐di‐GMP as a switch controlling the RNA chaperone activity of PlzA, and we propose that complex RNA‐mediated modulatory mechanisms allow PlzA to regulate gene expression during both the vector and host phases of the B. burgdorferi life cycle.
Cross‐cultural adaptation, translation, and validation of the Arabic version of the short form of Neurogenic Bladder Symptoms Score

The Neurogenic Bladder Symptom Score—Short Form (NBSS‐SF) evaluates the impact of disease‐specific symptoms on the quality of life (QoL) in individuals with neurogenic bladder (NB). There is no data on the validity and reliability of the NBSS‐SF questionnaire in the Arabic language, so this study aimed at providing the translation, cultural adaptation, and validation of the Arabic NBSS‐SF in patients with multiple sclerosis (MS) and spinal cord injury (SCI).
Conversion of monoclonal IgG to dimeric and secretory IgA restores neutralizing ability and prevents infection of Omicron lineages

Significance Considering the high risk of breakthrough infections in individuals with an insufficient mucosal immunoglobulin A (IgA) response, we have engineered various forms of monoclonal IgA antibodies for direct administration to the mucosal surface. The dimerization of IgA, potentially through increased avidity, significantly enhances the potency of broadly neutralizing antibodies tested. Importantly, converting IgG to dimeric and secretory forms of IgA restores neutralizing ability against Omicron variants. When administered intranasally, the dimeric IgA antibody DXP-604 provided both prophylactic and therapeutic protection against Omicron BA.5 in transgenic mice expressing human ACE2. Thus, the nasal spray delivery of dimeric or secretory IgA antibodies holds the potential to effectively block viral infection and enhance mucosal immunity against severe acute respiratory syndrome coronavirus 2.
Impaired AMPK activity contributes to the inflammatory phenotype and the reduced phagocytosis capacity of VASP-deficient macrophages

Macrophage polarization plays an important role in tissue regeneration. Numerous factors and signaling molecules affect polarization processes. Here we investigated the consequences of the genetic deletion of vasodilator-stimulated phosphoprotein (VASP), which increases macrophage M1 polarization through augmented signal transducer and activator of transcription 1 (STAT1) signaling, and AMP-activated protein kinase (AMPK), which attenuates inflammation by inhibiting STAT1 expression and signaling. While a basal activity of AMPK (phosphorylation on Thr172) was detected in macrophages from wild-type mice, AMPK phosphorylation was significantly reduced in VASP-deficient M1 macrophages in vitro and the expression of the pro-inflammatory cytokines TNFα and IL-1β was increased in these cells. Consistent with the role of AMPK in macrophage phagocytosis, VASP-/- macrophage phagocytosis was also significantly impaired. Interestingly, impaired phagocytosis could be rescued by exogenous activation of AMPK. Mechanistically, we found that VASP binds directly to protein phosphatase 1 regulatory subunit 6 (PP1-R6) and we hypothesize that VASP-binding to PP1- R6/PP1 limits the PP1-dependent de-phosphorylation of AMPK in wild-type cells. Conversely, AMPK dephosphorylation by the PP1-R6/PP1 complex is enhanced in the absence of VASP. In summary, we have identified a link between VASP and AMP-activated protein kinase (AMPK) activity, which may contribute to the pro-inflammatory phenotype of VASP-deficient macrophages.
Alternative mRNA Splicing Controls the Functions of the Histone H3K27 Demethylase UTX/KDM6A

Background The UTX/KDM6A histone H3K27 demethylase plays an important role in development and is frequently mutated in cancers such as urothelial cancer. Despite many studies on UTX proteins, variations in mRNA splicing have been overlooked. Methods Using Nanopore sequencing, we present a comprehensive analysis of UTX/KDM6A splicing events in human cell lines and in tissue samples from bladder cancer and normal epithelium. Results The central region of UTX mRNAs encoded by exons 12 to 17 undergoes extensive alternative splicing. Up to half of all stable mRNAs (8-48% in bladder tissues and 18-58% in cell lines) are represented by the UTX canonical isoform lacking exon 14 encoding a nuclear localization sequence, hence localize to the nucleus, unlike cytonuclear localization of the canonical isoform. Chromatin association was also higher for exon 14-containing isoform compared to the canonical UTX. Using quantitative mass spectrometry, we found that all UTX isoforms integrated into the MLL3 and MLL4, PR-DUB and MiDAC complexes. Interestingly, one of the novel UTX isoforms, which lacks exons 14 and 16, fails to interact with PR-DUB and MiDAC complex members. Conclusion UTX mRNAs undergo extensive alternative splicing that controls the subcellular localization of UTX and its interactions with other chromatin regulatory complexes. Simple Summary UTX/KDM6A is a histone H3K27 demethylase and plays an important role in mammalian development and human diseases such as urothelial cancer. We identified a region encompassing exons 12-17 of UTX that undergoes extensive splicing events. As a result, a nuclear localization sequence located in exon14 is missing in a considerable part of UTX transcripts in different cell lines and tissues from normal bladder epithelium and bladder cancer. Mass spectrometry analysis showed a role for this region in binding to the epigenetic PR-DUB and MiDAC complexes. UTX was also more extensively bound to chromatin when the alternative splicing region presented. Our study showed that alternative splicing of UTX transcripts plays an important role in its functions.
RBPCA MaxLike : A Novel Statistic Classifier for Face Recognition based on Block-Based PCA and Covariance Matrix Regularization

This paper presents a novel statistical approach for face recognition, called RBPCA MaxLike , by combining covariance matrix regularization, block- based PCA (BPCA) for dimensionality reduction and maximum likelihood for classification. Typically, face recognition is an extremely ill-posed problem, since the data dimensionality is huge in comparison to the number of available samples (small sample size problem). The proposed method performs robust covariance matrices estimation by adopting the Mixed- LOOC2 regularization technique, allowing a more accurate statistical modeling for parametric classification (Maximum Likelihood and Bayesian classifiers), since it avoids the presence of singular matrices. Experiments with two well known face databases (ORL and AR) show good results.
Bivariate Agreement Coefficients for Reliability of Data

The quality of data in content analysis, in surveys with openended questions, in the observation of unstructured social events, and so on, critically depends on the reliability with which primary observations are assigned to categories, scaled, or measured. To help assure valid interpretations, agreement between two independent observers is measured. When agreement is due merely to chance, data may have little to do with the phenomena studied. In order for such data to be empirically meaningful, a high degree of inter-observer agreement must be demonstrated. This paper suggests that several heretofore unrelated bivariate agreement coefficients may in fact be regarded as belonging to one family. It presents a paradigm through which their formal resemblances become transparent and it proposes efficient formulas for their computation.
Probiotics for Neurodegenerative Diseases: A Systemic Review

Neurodegenerative disorders (ND) are a group of conditions that affect the neurons in the brain and spinal cord, leading to their degeneration and eventually causing the loss of function in the affected areas. These disorders can be caused by a range of factors, including genetics, environmental factors, and lifestyle choices. Major pathological signs of these diseases are protein misfolding, proteosomal dysfunction, aggregation, inadequate degradation, oxidative stress, free radical formation, mitochondrial dysfunctions, impaired bioenergetics, DNA damage, fragmentation of Golgi apparatus neurons, disruption of axonal transport, dysfunction of neurotrophins (NTFs), neuroinflammatory or neuroimmune processes, and neurohumoral symptoms. According to recent studies, defects or imbalances in gut microbiota can directly lead to neurological disorders through the gut-brain axis. Probiotics in ND are recommended to prevent cognitive dysfunction, which is a major symptom of these diseases. Many in vivo and clinical trials have revealed that probiotics (Lactobacillus acidophilus, Bifidobacterium bifidum, and Lactobacillus casei, etc.) are effective candidates against the progression of ND. It has been proven that the inflammatory process and oxidative stress can be modulated by modifying the gut microbiota with the help of probiotics. As a result, this study provides an overview of the available data, bacterial variety, gut-brain axis defects, and probiotics’ mode of action in averting ND. A literature search on particular sites, including PubMed, Nature, and Springer Link, has identified articles that might be pertinent to this subject. The search contains the following few groups of terms: (1) Neurodegenerative disorders and Probiotics OR (2) Probiotics and Neurodegenerative disorders. The outcomes of this study aid in elucidating the relationship between the effects of probiotics on different neurodegenerative disorders. This systematic review will assist in discovering new treatments in the future, as probiotics are generally safe and cause mild side effects in some cases in the human body.
Roma, Gypsies, and Travellers As a Community of Difference: Challenging Inclusivity As an Anti-racist Approach

In order to consider how white privilege functions in late modernity, this article engages with issues of identity and political economy to theorise the impact of racist discourse on Roma, Gypsies, and Travellers in the United Kingdmom (UK). The article specifically problematizes the increasing aggregation of Roma, Gypsies, and Travellers as one community of difference in the UK. The article expresses the author’s concern that contemporary discourse and associated policy developments have racialized communities, and in doing so negated them through a failure to acknowledge the breadth of experience of Roma, Gypsies, and Travellers. The article makes a theoretical argument, evidenced by a comprehensive review of literature in the social sciences and key policy documents in the UK. It also incorporates an analysis of reports produced by UKgovernment and civil society organisations over the past 15-year period. The article argues that the categorisation of Roma, Gypsies, and Travellers as one community of difference has occurred due tothe embedded racism within contemporary European society that functions through and is augmented by neoliberal capitalist norms. In conclusion the paper argues that the norms of neoliberal capitalism, that are typified by individualism, competition, and the primacy of capital over human experience, allow the perpetuation of this racist discourse that is not challenged by narratives of inclusion but rather is augmented by them.
Improving Load Forecasting Performance via Sample Reweighting

Load forecasting techniques have been well developed and almost all typical models are trying to minimize the error over all equally weighted data samples. However, treating all data equally in the training process is unreasonable and even harmful to model generalization. This letter investigates the issue of data inequality which is crucial but is overlooked in the field of load forecasting. To this end, we propose a novel load forecasting method via sample reweighting to tackle the data inequality issue. The proposed method determines the weights of samples using their gradients and influence functions in the process of training. Case studies on a real-world load dataset using linear models, artificial neural networks, and long short term memory in both deterministic and probabilistic situations all reveal that assigning different weights to various samples can improve forecasting accuracy.
Values across adolescence: a four-year longitudinal study. The predictive role of community violence and parental acceptance-rejection

Adolescence is critical for values development since transitions in several domains occur during this period. Building upon Schwartz’s circumplex model, this study investigated stability and change of values during adolescence and their environmental precursors (i.e., parental rejection and community violence exposure). A sample of 773 Italian high school students (342 males; M age [Time 1] = 14.19, SD = 0.56) was assessed using self-report questionnaires across four waves. Rank-order stability coefficients were moderate for all values. Latent growth curve analyses revealed a significant linear increase in self-enhancement; all the other values displayed a quadratic shape in change over time, with a decline in the first part of the curve and a subsequent increase across time points. Overall, significant associations were found between environmental factors and the baseline levels of values. Value change over time was not significantly predicted by environmental factors except for openness to change, which was associated with paternal rejection. Specifically, high paternal rejection was linked with a faster decrease and a slower increase of openness to change over time. These findings highlight the importance of longitudinal studies when examining value change over time. Also, they suggest that environmental factors may play a significant role in shaping adolescent values.
Influence of streamwise and spanwise wall magnet arrays on near-wall MHD turbulence

ABSTRACT The effect of a permanent, localised and non-uniform magnetic field on the near-wall turbulence in a fully developed channel flow is analysed through direct numerical simulations. The magnetic field distribution is obtained by an arrangement of magnets placed on the upper and lower channel walls, producing preferentially either a streamwise (i.e. in the main flow direction) or a spanwise magnetic field component. The wall shear stress is drastically reduced under the effect of the streamwise arrangement of the wall magnets wherein both streamwise and wall-normal magnetic fields are involved. The magnetic braking effect leads to an important increase of the body force. Paradoxically enough, the small-scale turbulent activity is significantly increased above the low buffer layer in this case. On the opposite, imposing a magnetic field with a predominant spanwise component reduces tremendously the population of the turbulent shear stress producing eddies by directly affecting the regeneration of the buffer layer quasi-streamwise vortices. The flow is quasi-relaminarised between the magnets in the low-buffer and viscous sublayers. The wall shear increases in a predictable and deterministic way over the magnets, wherein the wall normal magnetic field component induces electric current loops.
Trichoderma asperellum Extract Isolated from Brazil Nuts (Bertholletia excelsa BONPL): In Vivo and In Silico Studies on Melanogenesis in Zebrafish

Endophytic fungi are those that present part of their life cycle in healthy tissues of different plant hosts in symbiosis without causing harm. At the same time, fungus-plant symbiosis makes it possible for microorganisms to synthesize their own bioactive secondary metabolites while in the stationary stage. To accomplish this, the endophytic fungus Trichoderma asperellum was isolated from Bertholletia excelsa (Brazil nut) almonds. The fungus was cultivated and extracted with ethyl acetate, obtaining AM07Ac. Then, using HPTLC (High-performance thin-layer chromatography) and nuclear magnetic resonance (1H NMR), β-amyrin, kaempferol, and brucine were identified as major compounds. Further in vivo assays in zebrafish demonstrated the activity of AM07Ac on melanogenesis by producing a concentration–response inhibitory effect, which, through an in silico study, proved to be related to the noted major compounds known to inhibit tyrosinase activity. The inhibition of tyrosinase prevents melanin accumulation in skin. Therefore, these results imply the importance of investigating microorganisms and their pharmacological activities, in particular the endophytic fungus Trichoderma asperellum as a generator of active metabolites for melanogenesis modulation.
Two-Dimensional Films Based on Graphene/Li4Ti5O12 and Carbon Nanotube/Li4Ti5O12 Nanocomposites as a Prospective Material for Lithium-Ion Batteries: Insight from Ab Initio Modeling

The combination of spinel Li4Ti5O12 (LTO) with carbon nanostructures, such as graphene (G) and carbon nanotubes (CNTs), provides all of the required properties for modern chemical power sources such as Li-ion batteries (LIBs) and supercapacitors (SCs). G/LTO and CNT/LTO composites demonstrate a superior reversible capacity, cycling stability, and good rate performances. In this paper, an ab initio attempt to estimate the electronic and capacitive properties of such composites was made for the first time. It was found that the interaction between LTO particles and CNTs was higher than that with graphene due to the larger amount of transfer charge. Increasing the graphene concentration raised the Fermi level and enhanced the conductive properties of G/LTO composites. For CNT/LTO samples, the radius of CNT did not affect the Fermi level. For both G/LTO and CNT/LTO composites, an increase in the carbon ratio resulted in a similar reduction in quantum capacitance (QC). It was observed that during the charge cycle in the real experiment, the non-Faradaic process prevailed during the charge cycle, while the Faradaic process prevailed during the discharge cycle. The obtained results confirm and explain the experimental data and improve the understanding of the processes occurring in G/LTO and CNT/LTO composites for their usages in LIBs and SCs.
On ill-conditioning in 3D similarity transformation

3D similarity transformations are often used for datum transformation in Geomatic Engineering. The transformations are routinely performed between the point coordinates evaluated from GNSS (Global Navigation Satellite Systems) observations and the point coordinates given in national datum. A mathematical model established among two different 3D coordinate systems contains tree type datum parameters which are translations, rotations and a scale. Coefficients of the parameters reflect large variations from each other’s. So, the unknown coefficient matrix in normal equations is to be ill-conditioned. In this study, it is indicated how the ill-condition structure is reduced to acceptable level by means of choosing at different unit of unknown parameters. Finally, the transformation from Kocaeli Metropolitan Municipality GNSS network coordinates to Turkish Geodetic Datum is used as a numerical example.
Toward understanding the effects of socially aware robot behavior

A key factor for the acceptance of robots as regular partners in human-centered environments is the appropriateness and predictability of their behaviors, which depend partially on the robot behavior’s conformity to social norms. Previous experimental studies have shown that robots that follow social norms and the corresponding interactions are perceived more positively by humans than robots or interactions that do not adhere to social norms. However, the conducted studies only focused on the effects of social norm compliance in specific scenarios. Therefore, this paper aims to guide further research studies by compiling how researchers in relevant research fields think the perception of robots and the corresponding interactions are influenced independently of a specific scenario if a robot’s behavior conforms to social norms. Additionally, this study investigates what characteristics and metrics constitute a good general benchmark to objectively evaluate the behavior of social robots regarding its conformity to social norms according to researchers in relevant research communities. Finally, the paper summarizes how the obtained results can guide future research toward socially aware robot behavior.
Molecular characterisation of three Ixodes (Pholeoixodes) species (Ixodida, Ixodidae) and the first record of Ixodes (Pholeoixodes) kaiseri from Slovakia

﻿Abstract A study of ticks on wildlife was carried out in the area of Levice, Bratislava, Stupava, and Vrbovce (south-western Slovakia) during 2021 and 2022. Overall, 512 ticks were collected from 51 individuals of six wild mammalian species. Eight tick species were identified, namely Dermacentorreticulatus, D.marginatus, Haemaphysalisinermis, H.concinna, Ixodesricinus, I.hexagonus, and two Ixodes spp. Ixodeshexagonus were collected from northern white-breasted hedgehogs (Erinaceusroumanicus), females belonging to Ixodes spp. were collected from red fox (Vulpesvulpes) and nymphs from European badger (Melesmeles). Ixodeshexagonus and the Ixodes spp. were identified morphologically and molecularly based on sequences of fragments of two mitochondrial genes, COI and 16S rRNA. Molecular analysis of Ixodes spp. confirmed the identity of Ixodeskaiseri Arthur, 1957 and I.canisuga (Johnston, 1849). Sequence analyses show that the I.kaiseri isolate from Slovakia is identical to I.kaiseri isolates from Romania, Poland, Germany, Turkey, and Croatia. We demonstrate for the first time the presence of I.kaiseri in Slovakia using both morphological and molecular methods.
Small Molecules Targeting Kidney ClC-K Chloride Channels: Applications in Rare Tubulopathies and Common Cardiovascular Diseases

Given the key role played by ClC-K chloride channels in kidney and inner ear physiology and pathology, they can be considered important targets for drug discovery. Indeed, ClC-Ka and ClC-Kb inhibition would interfere with the urine countercurrent concentration mechanism in Henle’s loop, which is responsible for the reabsorption of water and electrolytes from the collecting duct, producing a diuretic and antihypertensive effect. On the other hand, ClC-K/barttin channel dysfunctions in Bartter Syndrome with or without deafness will require the pharmacological recovery of channel expression and/or activity. In these cases, a channel activator or chaperone would be appealing. Starting from a brief description of the physio-pathological role of ClC-K channels in renal function, this review aims to provide an overview of the recent progress in the discovery of ClC-K channel modulators.