Miracle-dz/UniFAR-FTUs huggingface dataset:
The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation

Significance Modulation of primary root growth is a foraging strategy adapting to NO3− fluctuation in soil. However, how that comes about remains unclear. Here, we identify a unique mechanism involving the interaction of two transporters specific to different substrates (NO3− or auxin). Our study demonstrates that the high-affinity NO3− transporter NRT2.1 directly associates with the auxin transporter PIN7, and antagonizes its activity depending on NO3− levels, thus regulating primary root elongation. Collectively, this work provides insight into the mechanisms regulating root growth adaptation in response to NO3− availability.
Sexual Orientation and Gender Identity/Expression in Adolescent Research: Two Decades in Review

ABSTRACT There is a long history of research among adolescents who are minoritized and marginalized for their sexual orientation and gender identity/expression (SOGIE). However, it remains unclear how we can best conceptualize and assess SOGIE in adolescence, resulting in different subpopulations and findings across studies. Addressing this issue, we present a narrative literature review of the conceptualization and assessment of SOGIE, and provide recommendations for conceptualizing and operationalizing these concepts. Our review indicated that most research with adolescent populations still almost exclusively assesses isolated dimensions of sexuality and gender (e.g., attraction but not identity). We argue that to make research inclusive and equitable, scholars are required to make clear substantiated decisions and be transparent about the SOGIE dimensions and, thus, subpopulations they represent.
MicroRNA-211 Regulates Proliferation, Expansion, and Immune Inhibitory Function of Myeloid-Derived Suppressor Cells via Mediation of CHOP Expression

ABSTRACT Background Myeloid-derived suppressor cells (MDSCs) are capable of effectively repressing immune responses against tumors and orchestrating the tumor microenvironment, which can promote tumor angiogenesis and metastasis. The pathway networks used to modulate tumor-expanded MDSC accumulation and function remain unclear. This study identified microRNA-211 (miR-211), whose expression was significantly decreased by factors derived from tumors. Methods miR-211 was assumed to be critical in modulating the accumulation and activity of MDSCs isolated from ovarian cancer (OC)-bearing mice by targeting C/EBP homologous protein (CHOP). Results The upregulation of miR-211 repressed MDSC proliferation, inhibited MDSC immunosuppressive functions, and increased the number of co-incubated CD4+ and CD8+ cells. Furthermore, overexpression of miR-211 led to decreased activities of the NF-κB, PI3K/Akt, and STAT3 pathways and the subsequent downregulation of matrix metalloproteinases to promote tumor cell invasion and metastasis. CHOP overexpression counteracted the effects of miR-211 elevation on these phenotypic changes. Upregulation of miR-211 also dramatically impaired the activity of MDSCs and suppressed OC tumor growth in vivo. Conclusion These results indicated that the miR-211-CHOP axis in MDSCs plays an essential role in the metastasis and proliferation of tumor-expanded MDSCs and might represent a promising cancer treatment target.
Cross sectional study of vitamin B12 supplementation in Slovak and Czech vegans.

Background The number of vegans in the world is growing and in Slovakia and the Czech Republic they make up 1% of the population. Vegan diet excludes all foods of animal origin and vegans who do not use vitamin B12 supplements are at risk of the vitamin B12 deficiency. Objective The aim of this study was to determine what proportion of Czech and Slovak vegans use vitamin B12 supplements regularly, irregularly or not at all and what is their supplemental cobalamin intake. Materials and methods The research involved 1337 self-identified vegans from Slovakia and the Czech Republic who were interviewed using the CAWI (Computer-Assisted Web Interview) method. Participants were recruited by posts in veganism-themed social media groups. Results Out of 1337 vegans 55.5% supplemented cobalamin regularly, 32.54% irregularly and 11.97% were not supplementing. Rate of not supplementing individuals was 5.04% higher in Slovaks than in Czechs. Short-term vegans had a significantly higher rate of not supplementing individuals (17.99%) compared to medium-term (8.37%) and long-term vegans (7.50%). Mean weekly cobalamin intake from supplements was 2938.34±2566.60 μg in regularly supplementing vegans compared to 1630.31±1949.27 μg in irregularly supplementing vegans, particularly due to the lower weekly supplementation frequency among irregularly (2.93) compared to regularly supplementing vegans (5.27). Conclusions The rate of supplementation in Slovak and particularly Czech vegans was higher than in other countries. The number of not supplementing individuals was significantly higher among short-term vegans, indicating that there is still a need for education on the importance of adequate and regular cobalamin supplementation, especially in new vegans. Our results support the hypothesis that the reason for higher rate of cobalamin deficiency in irregularly compared to regularly supplementing vegans is the lower cobalamin intake caused by lower supplementation frequency.
A stability criterion for power system with time-varying delay based on convex combination

In the wide-area environment, the time-delay of control signal generated in the process of transmission and treatment will produce a negative effects that can not be neglected for the stable operation of power system. A stability criterion for power system with time-varying delay based on the method of convex combination is presented. Firstly, through constructing a new type of Lyapunov-Krasovskii functional and proving its positive definiteness, the parameter constraint is relaxed. Secondly, using slack matrices and a convex combination method, the time-varying delay stability criterion, which is less conservative, is derived in terms of linear matrix inequalities. Finally, simulation results indicate that the presented method reduces the conservatism of some existing results.
Estimation Error Consisting of Motor Imagery and Motor Execution in Patients with Stroke

Abstract Previous studies demonstrate that the difference between motor imagery and actual tasks (estimation error) is related to cognitive and physical functions and that a large estimation error (LE) is related to motor imagery ability, including cognitive and physical functions in healthy subjects. The purpose of this study investigated whether estimation error is related to physical and cognitive function in patients with stroke. The study included 60 patients with stroke. The Timed Up and Go Test (TUGT) was employed to assess estimation error. First, the imagined TUGT (iTUGT) was performed; thereafter, the actual TUGT was performed. The estimation error was calculated by subtracting TUGT from iTUGT, with conversion to the absolute value. The patients were classified into the small estimation error (SE) and LE groups, with comparisons of various clinical scores (Mini-Mental State Examination, Berg Balance Scale, 10-m walking speed, Brunnstrom Recovery Stage, and Functional Independence Measure). As a result, the estimation error was significantly larger in the LE group than in the SE group. Cognitive function and balance ability were significantly lower in the LE group than in the SE group. In conclusion, the estimation error was related to physical and cognitive functions in patients with stroke.
Medial prefrontal cortical PPM1F alters depression‐related behaviors by modifying p300 activity via the AMPK signaling pathway

Protein phosphatase Mg2+/Mn2+‐dependent 1F (PPM1F) is a serine/threonine phosphatase, and its dysfunction in depression in the hippocampal dentate gyrus has been previously identified. Nevertheless, its role in depression of another critical emotion‐controlling brain region, the medial prefrontal cortex (mPFC), remains unclear. We explored the functional relevance of PPM1F in the pathogenesis of depression.
Beta-delayed fission probabilities of transfermium nuclei, involved in the r-process

For the nucleosynthesis of heavy and superheavy nuclei fission becomes very important when the r-process runs in a very high neutron density environment. In part, fission is responsible for the formation of heavy nuclei due to the inclusion of fission products as new seed nuclei (fission cycling). More than that, beta-delayed fission, along with spontaneous fission, is responsible in the late stages of the r-process for the suppression of superheavy element yields. For beta-delayed fission probability calculations a model description of the beta-strength- functions is required. Extended theoretical predictions for astro-physical applications were provided long ago, and new predictions also for superheavy nuclei with uptodate nuclear input are needed. For the further extension of data to heavier transactinides the models of strength- functions should be modified, taking into account more complicated level schemes. In our present calculations the strength-function model is based on the quasi-particle approximation of Finite Fermi Systems Theory. The probabilities of beta-delayed fission and beta-delayed neutron emission are calculated for some transfermium neutron-rich nuclei, and the influence of beta-delayed fission upon superheavy element formation is discussed.
Association between misoprostol and nonsteroidal anti‐inflammatory drug‐induced kidney injury: A systematic review and meta‐analysis

Misoprostol is a prostaglandin E1 analogue that is used to prevent nonsteroidal anti‐inflammatory drug (NSAID)‐induced gastrointestinal disorders. The aim of this systematic review and meta‐analysis was to evaluate whether use of misoprostol also decreases the risk of NSAID‐induced kidney injury.
Global Differences in the Management of Staphylococcus aureus Bacteremia: No International Standard of Care

Abstract Background Despite being the leading cause of mortality from bloodstream infections worldwide, little is known about regional variation in treatment practices for Staphylococcus aureus bacteremia (SAB). The aim of this study was to identify global variation in management, diagnostics, and definitions of SAB. Methods During a 20-day period in 2022, physicians throughout the world were surveyed on SAB treatment practices. The survey was distributed through listservs, e-mails, and social media. Results In total, 2031 physicians from 71 different countries on 6 continents (North America [701, 35%], Europe [573, 28%], Asia [409, 20%], Oceania [182, 9%], South America [124, 6%], and Africa [42, 2%]) completed the survey. Management-based responses differed significantly by continent for preferred treatment of methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA) bacteremia, use of adjunctive rifampin for prosthetic material infection, and use of oral antibiotics (P < .01 for all comparisons). The 18F-FDG PET/CT scans were most commonly used in Europe (94%) and least frequently used in Africa (13%) and North America (51%; P < .01). Although most respondents defined persistent SAB as 3–4 days of positive blood cultures, responses ranged from 2 days in 31% of European respondents to 7 days in 38% of Asian respondents (P < .01). Conclusions Large practice variations for SAB exist throughout the world, reflecting the paucity of high-quality data and the absence of an international standard of care for the management of SAB.
Overview Update: Computational Prediction of Intrinsic Disorder in Proteins

There are over 100 computational predictors of intrinsic disorder. These methods predict amino acid‐level propensities for disorder directly from protein sequences. The propensities can be used to annotate putative disordered residues and regions. This unit provides a practical and holistic introduction to the sequence‐based intrinsic disorder prediction. We define intrinsic disorder, explain the format of computational prediction of disorder, and identify and describe several accurate predictors. We also introduce recently released databases of intrinsic disorder predictions and use an illustrative example to provide insights into how predictions should be interpreted and combined. Lastly, we summarize key experimental methods that can be used to validate computational predictions. © 2023 Wiley Periodicals LLC.
Phosphorylation of DNA-PKcs at the S2056 cluster ensures efficient and productive lymphocyte development in XLF-deficient mice

Significance The S2056 (PQR) cluster is one of the two autophosphorylation clusters on DNA-PKcs. Despite extensive structural and biochemical characterization, the physiological significance of S2056 cluster phosphorylation on chromosomal nonhomologous end-joining (NHEJ) remains elusive in part due to the lack of measurable phenotype in the alanine substitution mouse models. Using the Xlf-deficient background, our study documents a physiological role for the PQR cluster phosphorylation in the end-ligation step of chromosomal NHEJ and suggests an overlapping role between PQR site autophosphorylation and Xlf-mediated end-ligation.
Sex differences in emotion recognition: investigating the moderating effects of stimulus features

ABSTRACT Emotion recognition – a prerequisite for social interactions – varies among individuals. Sex differences have been proposed as a central source of individual differences, although the existing evidence is rather heterogeneous. In the current study (N = 426), we investigated the potential moderating effects of stimulus features, including modality, emotion specificity, and the sex of the encoder (referring to the sex of the actor) on the magnitude of sex differences in emotion recognition. Our findings replicated women’s overall better emotion recognition, particularly evident for negative expressions (fear and anger) compared to men. This outperformance was observed across all modalities, with the largest differences for audiovisually expressed emotions, while the sex of the encoder had no impact. Given our findings, future studies should consider these and other potential moderator variables to better estimate sex differences.
Management and Outcome of Intracranial Dural Arteriovenous Fistulas That Have Caused a Hemorrhage in the Posterior Fossa : A Clinical Study

Objective We evaluated the diagnosis, treatment, and long-term results of patients with dural arteriovenous fistula (dAVF), which is a very rare cause of posterior fossa hemorrhage. Methods This study included 15 patients who underwent endovascular, surgical, combined, or Gamma Knife treatments between 2012 and 2020. Demographics and clinical features, angiographic features, treatment modalities, and outcomes were analyzed. Results The mean age of the patients was 40±17 years (range, 17–68), and 68% were men (11/15). Seven of the patients (46.6%) were in the age group of 50 years and older. While the mean Glasgow coma scale was 11.5±3.9 (range, 4–15), 46.3% presented with headache and 53.7% had stupor/coma. Four patients (26.6%) had only cerebellar hematoma and headache. All dAVFs had cortical venous drainage. In 11 patients (73.3%), the fistula was located in the tentorium and was the most common localization. Three patients (20%) had transverse and sigmoid sinus localizations, while one patient (6.7%) had dAVF located in the foramen magnum. Eighteen sessions were performed on the patients during endovascular treatment. Sixteen sessions (88.8%) were performed with the transarterial (TA) route, one session (5.5%) with the transvenous (TV) route, and one session (5.5%) with the TA+TV route. Surgery was performed in two patients (14.2%). One patient (7.1%) passed away. While there were nine patients (64.2%) with a Rankin score between 0 and 2, the total closure rate was 69.2% in the first year of control angiograms. Conclusion In the differential diagnosis of posterior fossa hemorrhages, the differential diagnosis of dAVFs, which is a very rare entity, should be considered, even in the middle and elderly age groups, in patients presenting with good clinical status and pure hematoma. The treatment of such patients can be done safely and effectively in a multidisciplinary manner with a good understanding of pathological vascular anatomy and appropriate endovascular treatment approaches.
Predicting implicit attitudes with natural language data

Significance For decades, psychologists have studied attitudes with the goal of developing better techniques for measuring and predicting them. Here, we examine how large natural language datasets can be used to predict people’s implicit attitudes, that is, automatic associations between a concept and an evaluation. We apply computational models that use the strength of association of words in language to proxy the associations in people’s minds. We show that these models predict biases in implicit attitudes that cannot be explained using participant self-reports. We also develop a computational method that combines linguistic associations with existing psychological data, and show that it generates especially good predictions, thereby facilitating several practical applications.
A temperature-dependent virus-binding assay reveals the presence of neutralizing antibodies in human cytomegalovirus gB vaccine recipients’ sera

Human cytomegalovirus (HCMV) remains an important cause of mortality in immune-compromised transplant patients and following congenital infection. Such is the burden, an effective vaccine strategy is considered to be of the highest priority. The most successful vaccines to date have focused on generating immune responses against glycoprotein B (gB) – a protein essential for HCMV fusion and entry. We have previously reported that an important component of the humoral immune response elicited by gB/MF59 vaccination of patients awaiting transplant is the induction of non-neutralizing antibodies that target cell-associated virus with little evidence of concomitant classical neutralizing antibodies. Here we report that a modified neutralization assay that promotes prolonged binding of HCMV to the cell surface reveals the presence of neutralizing antibodies in sera taken from gB-vaccinated patients that cannot be detected using standard assays. We go on to show that this is not a general feature of gB-neutralizing antibodies, suggesting that specific antibody responses induced by vaccination could be important. Although we can find no evidence that these neutralizing antibody responses are a correlate of protection in vivo in transplant recipients their identification demonstrates the utility of the approach in identifying these responses. We hypothesize that further characterization has the potential to aid the identification of functions within gB that are important during the entry process and could potentially improve future vaccine strategies directed against gB if they prove to be effective against HCMV at higher concentrations.
Mean-field-like approximations for stochastic processes on weighted and dynamic networks

The explicit use of networks in modelling stochastic processes such as epidemic dynamics has revolutionised research into understanding the impact of contact pattern properties, such as degree heterogeneity, preferential mixing, clustering, weighted and dynamic linkages, on how epidemics invade, spread and how to best control them. In this thesis, I worked on mean-field approximations of stochastic processes on networks with particular focus on weighted and dynamic networks. I mostly used low dimensional ordinary differential equation (ODE) models and explicit network-based stochastic simulations to model and analyse how epidemics become established and spread in weighted and dynamic networks. I begin with a paper presenting the susceptible-infected-susceptible/recovered (SIS, SIR) epidemic models on static weighted networks with different link weight distributions. This work extends the pairwise model paradigm to weighted networks and gives excellent agreement with simulations. The basic reproductive ratio, R0, is formulated for SIR dynamics. The effects of link weight distribution on R0 and on the spread of the disease are investigated in detail. This work is followed by a second paper, which considers weighted networks in which the nodal degree and weights are not independent. Moreover, two approximate models are explored: (i) the pairwise model and (ii) the edge-based compartmental model. These are used to derive important epidemic descriptors, including early growth rate, final epidemic size, basic reproductive ratio and epidemic dynamics. Whilst the first two papers concentrate on static networks, the third paper focuses on dynamic networks, where links can be activated and/or deleted and this process can evolve together with the epidemic dynamics. We consider an adaptive network with a link rewiring process constrained by spatial proximity. This model couples SIS dynamics with that of the network and it investigates the impact of rewiring on the network structure and disease die-out induced by the rewiring process. The fourth paper shows that the generalised master equations approach works well for networks with low degree heterogeneity but it fails to capture networks with modest or high degree heterogeneity. In particular, we show that a recently proposed generalisation performs poorly, except for networks with low heterogeneity and high average degree.
Whole‐genome methylation analysis of aging human tissues identifies age‐related changes in developmental and neurological pathways

Age‐associated changes in the DNA methylation state can be used to assess the pace of aging. However, it is not understood what mechanisms drive these changes and whether these changes affect the development of aging phenotypes and the aging process in general. This study was aimed at gaining a more comprehensive understanding of aging‐related methylation changes across the whole genome, and relating these changes to biological functions. It has been shown that skeletal muscle and blood monocytes undergo typical changes with aging. Using whole‐genome bisulfite sequencing, we sought to characterize the genome‐wide changes in methylation of DNA derived from both skeletal muscle and blood monocytes, and link these changes to specific genes and pathways through enrichment analysis. We found that methylation changes occur with aging at the locations enriched for developmental and neuronal pathways regulated in these two peripheral tissues. These results contribute to our understanding of changes in epigenome in human aging.