Miracle-dz/UniFAR-FTUs huggingface dataset:
A novel geometry‐based analysis of hippocampal morphometry in mesial temporal lobe epilepsy

Hippocampal volumetry is an essential tool in researching and diagnosing mesial temporal lobe epilepsy (mTLE). However, it has a limited ability to detect subtle alterations in hippocampal morphometry. Here, we establish and apply a novel geometry‐based tool that enables point‐wise morphometric analysis based on an intrinsic coordinate system of the hippocampus. We hypothesized that this point‐wise analysis uncovers structural alterations not measurable by volumetry, but associated with histological underpinnings and the neuropsychological profile of mTLE. We conducted a retrospective study in 204 individuals with mTLE and 57 age‐ and gender‐matched healthy subjects. FreeSurfer‐based segmentations of hippocampal subfields in 3T‐MRI were subjected to a geometry‐based analysis that resulted in a coordinate system of the hippocampal mid‐surface and allowed for point‐wise measurements of hippocampal thickness and other features. Using point‐wise analysis, we found significantly lower thickness and higher FLAIR signal intensity in the entire affected hippocampus of individuals with hippocampal sclerosis (HS‐mTLE). In the contralateral hippocampus of HS‐mTLE and the affected hippocampus of MRI‐negative mTLE, we observed significantly lower thickness in the presubiculum. Impaired verbal memory was associated with lower thickness in the left presubiculum. In HS‐mTLE histological subtype 3, we observed higher curvature than in subtypes 1 and 2 (all p < .05). These findings could not be observed using conventional volumetry (Bonferroni‐corrected p < .05). We show that point‐wise measures of hippocampal morphometry can uncover structural alterations not measurable by volumetry while also reflecting histological underpinnings and verbal memory. This substantiates the prospect of their clinical application.
Coupling of Alfven-like Modes and large 2/1 Tearing Modes at TEXTOR

A new class of MHD modes has been observed at TEXTOR(R = 1.75 m, a = 0.46 m). The excitation of intensive 2/1 tearing modes is accompanied with the excitation of high frequency modes. These modes are found for different plasma conditions and appear only in pairs, with
Rewilding of laboratory mice enhances granulopoiesis and immunity through intestinal fungal colonization

The paucity of blood granulocyte populations such as neutrophils in laboratory mice is a notable difference between this model organism and humans, but the cause of this species-specific difference is unclear. We previously demonstrated that laboratory mice released into a seminatural environment, referred to as rewilding, display an increase in blood granulocytes that is associated with expansion of fungi in the gut microbiota. Here, we find that tonic signals from fungal colonization induce sustained granulopoiesis through a mechanism distinct from emergency granulopoiesis, leading to a prolonged expansion of circulating neutrophils that promotes immunity. Fungal colonization after either rewilding or oral inoculation of laboratory mice with Candida albicans induced persistent expansion of myeloid progenitors in the bone marrow. This increase in granulopoiesis conferred greater long-term protection from bloodstream infection by gram-positive bacteria than by the trained immune response evoked by transient exposure to the fungal cell wall component β-glucan. Consequently, introducing fungi into laboratory mice may restore aspects of leukocyte development and provide a better model for humans and free-living mammals that are constantly exposed to environmental fungi. Description Fungal colonization of lab mice, through release into the wild or inoculation with Candida albicans, enhances granulopoiesis. Editor’s summary Although mice represent a valuable model organism for dissecting the immune system, laboratory mice kept in specific pathogen–free facilities lack the complex microbial exposure of humans. Using “rewilded” laboratory mice exposed to a seminatural outdoor environment, Chen et al. found that fungal colonization induces a distinct program of granulopoiesis that could also be elicited by Candida albicans intestinal colonization. C. albicans–induced granulopoiesis was dependent on IL-6 receptor signaling and the hypha-associated factor candidalysin. Fungal colonization led to sustained neutrophil expansion and protected against bloodborne bacterial infection with Staphylococcus aureus, highlighting the impact of environmental fungi on myeloid cell differentiation and innate immunity. —Claire Olingy
Simultaneous tests and confidence bands for Stata estimation commands

Stata estimation commands that implement frequentist methods produce an output table that contains multiple tests and multiple confidence intervals. Presumably, the multiple tests and multiple confidence are designed to help determine which parameters are responsible for a possible rejection of the overall null hypothesis of no effect. When taken by itself, each test and each confidence interval provides valid inference about the null hypothesis of no effect for each parameter at the specified error rate. However, simultaneously using two or more of these tests or confidence intervals provides inference at an error rate that exceeds the one specified. In this article, I discuss the sotable command, which provides p-values that are adjusted for the multiple tests and a confidence band that can be used to simultaneously test multiple parameters for no effect after almost all frequentist estimation commands. I also provide an introduction to the literature on simultaneous inference.
xtnumfac: A battery of estimators for the number of common factors in time series and panel-data models

In this article, we introduce a new community-contributed command, xtnumfac, for estimating the number of common factors in time-series and panel datasets using the methods of Bai and Ng (2002, Econometrica 70: 191–221), Ahn and Horenstein (2013, Econometrica 81: 1203–1227), Onatski (2010, Review of Economics and Statistics 92: 1004–1016), and Gagliardini, Ossola, and Scaillet (2019, Journal of Econometrics 212: 503–521). Common factors are usually unobserved or unobservable. In time series, they influence all predictors, while in paneldata models, they influence all cross-sectional units at different degrees. Examples are shocks from oil prices, inflation, or demand or supply shocks. Knowledge about the number of factors is key for multiple econometric estimation methods, such as Pesaran (2006, Econometrica 74: 967–1012), Bai (2009, Econometrica 77: 1229–1279), Norkute et al. (2021, Journal of Econometrics 220: 416–446), and Kripfganz and Sarafidis (2021, Stata Journal 21: 659–686). This article discusses a total of 10 methods to estimate the number of common factors. Examples based on Kapetanios, Pesaran, and Reese (2021, Journal of Econometrics 221: 510–541) show that U.S. house prices are exposed to up to 10 common factors. Therefore, when one fits models with house prices as a dependent variable, the number of factors must be considered.
Crowd social pressure in the Brazilian soccer league: testing home advantage and referees’ bias during the COVID-19 pandemic

ABSTRACT Although the home advantage is a well-documented phenomenon in soccer, the effect of the home crowd social pressure on teams and referees’ performance remains unclear. The COVID-19 pandemic brought a unique opportunity to test the real effect of the crowd. The aim of the present study was to analyse the home advantage and referee bias in the Brazilian soccer league, comparing whole seasons played with and without spectators. Match data from 2003 to 2020 were compared. The points earned, victories, and goals scored were used to analyse teams’ performance. Referee bias was investigated by the extra time, yellow and red cards awarded. Difference of points and victories, between home and away teams, during the 2020 season was similar to most of the previous seasons and showed a decreasing tendency throughout the seasons. When comparing the 2019 and 2020 seasons, the home advantage, measured by the relative number of points won at home, was present in games played with (60.9 ± 7.7%) and without (60.4 ± 6.3%) spectators. Home teams showed higher number of victories, total points, and goals scored (p < 0.001 each). Away teams were awarded with a higher number of yellow cards (p = 0.008), but this number was smaller during the pandemic (p = 0.049). Games played with spectators received less minutes of extra time in the second half when away teams were losing by a difference of one goal (p = 0.012). In conclusion, the absence of spectators in the Brazilian soccer league during the COVID-19 pandemic did not reduce the home advantage but affected the referee bias.
Civil society’s impact on quality of life

ABSTRACT The purpose of the article is to analyze the impact of three forms of involvement in organized civil society – as ‘participant’, as ‘member’ and as ‘volunteer’ – on self-assessed quality of life when checking for coherence between the three forms of participation. The article is inspired by both Lim and Putnam’s claim that close social networks around meaningful and identity-bearing activities increase self-assessed quality of life and Stebbins’ claim that life satisfaction is an essential by-product of ‘serious leisure’. This article utilizes data from a digital survey study conducted among adult citizens in Denmark, which 2514 citizens answered. The questionnaire contained a broad range of questions regarding participation in leisure activities, membership in associations, engagement in voluntary work, subjective life-satisfaction, self-assessed health and social background of the respondents. The statistical regression analysis shows a correlation between volunteering in general and self-assessed quality of life, but the correlation is relatively weak. However, the analysis does not show a significant correlation between the quality of life and membership in an association and participation in ‘serious leisure’. Of the other variables included, self-assessed health, in particular, contributes to explaining the variation in self-assessed quality of life.
Microhabitat use by Mediterranean ribbed newts: newts in highly fluctuating conditions?

ABSTRACT Ribbed newts (genus Pleurodeles) are among the few species of amphibians present in open, dry and warm southern Mediterranean habitats. However, the factors that determine the presence of these species in such xeric environments remain poorly understood. We characterised the microhabitat niches of the three species of the genus (P. nebulosus, P. poireti and P. waltl). We used temperature–humidity probes and described the variation in the vegetative composition of their habitats. We found that the three species of this genus use sparsely vegetated habitats, exposed to high seasonal temperatures (above 35°C) and to broad intra-annual fluctuations in air temperature and humidity. The capacity of the three species to occupy microclimatically fluctuating environments explains why these urodeles are broadly distributed in disturbed landscapes in southern Mediterranean regions, where no other species of urodeles occur. Ribbed newts are highly adaptable to changing environments, which is advantageous under highly unstable Mediterranean hydrological regimes.
Internet as an ideology: nationalistic discourses, and multiple subject positions of Chinese internet workers

ABSTRACT Ideology works. This article examines how the Internet as a capital actor has become a nationalist ideology in China. Disclosing how nationalism serves to facilitate the expansion of China-based Internet platforms in the age of informational capitalism, we directly confront the Chinese Internet as an ideology apparatus that works to fulfill a dual logic of capital and territorial power. This article contributes to the study of three types of Chinese Internet workers: programmers, white-collar employees (excluding programmers), and assembly-line workers, and focuses on how nationalist discourses are created, which enthrall but at the same time are questioned by different workers who help fabricate nationalism as well as challenge it. We conceptualize topos of threat and referential strategy of collectivization as cultural and media tactics, driven by the nationalistic sentiments that form part of the “common sense” of Chinese users. We further analyze the multiple subject positions of Chinese Internet workers into hegemonic position, negotiated position, and oppositional position to discover the complexity of labor subjectivity which may create discrepancy or sometimes even challenge the Chinese Internet as an ideology. This study sheds light on how subject positions could disrupt a homogenous process of merging nationalism with populist sentiments, a conservative ideology that is prevalent in today’s China.
What Drives Business Cycles in Egypt? An Analysis of Coincident and Leading Indicators

Abstract The paper proposes a chronology for the Egyptian economy by detecting phases of expansions and recessions during the period (2002–2019). It examines the cyclical behavior of variables that are considered potentially useful in measuring or predicting aggregate economic activity. To do so, we combine the National Bureau of Economic Research (NBER) approach together with time series analysis techniques to select the variables best suitable to play the role of coincident and leading indicators. This methodology is found to be the most appropriate when there is no well-established reference chronology as a benchmark for the cyclical analysis, which is the case of Egypt. As a result, two composite indexes are constructed: 1) the composite index of coincident economic indicators (CEI), which can be considered an adequate measure for the Egyptian business cycle; 2) the composite index of leading economic indicators (LEI) that shows good performance in anticipating aggregate economic activity in Egypt. Moreover, the empirical results indicate that total employment, consumption, and investment move coincidently with the reference cycle, while exchange rate and interest rate variables lead the reference cycle and have strong predictive power for economic activity in Egypt.
Analyzing polysemiosis: language, gesture, and depiction in two cultural practices with sand drawing

Abstract Human communication is by default polysemiotic: it involves the spontaneous combination of two or more semiotic systems, the most important ones being language, gesture, and depiction. We formulate an original cognitive-semiotic framework for the analysis of polysemiosis, contrasting this with more familiar systems based on the ambiguous term “multimodality. ” To be fully explicit, we developed a coding system for the analysis of polysemiotic utterances containing speech, gesture, and drawing, and implemented this in the ELAN video annotation software. We used this to analyze 23 video-recordings of sand drawing performances on Paama, Vanuatu and 20 sand stories of the Pitjantjatjara culture in Central Australia. Methodologically we used the conceptual-empirical loop of cognitive semiotics: our theoretical framework guided general considerations, such as distinguishing between the “tiers” of gesture and depiction, and the three kinds of semiotic grounds (iconic, indexical, symbolic), but the precise decisions on how to operationalize these were made only after extensive work with the material. We describe the coding system in detail and provide illustrative examples from the Paamese and Pitjantjatjara data, remarking on both similarities and differences in the polysemiosis of the two cultural practices. We conclude by summarizing the contributions of the study and point to some directions for future research.
Kir2.1 modulation in macrophages sensitises dorsal root ganglion neurons through TNF secretion after nerve injury

Macrophages and satellite glial cells are found between injured and uninjured neurons in the lumbar dorsal root ganglia (DRG). We explored the mechanism of neuro-immune and neuron–glia crosstalk leading to hyperexcitability of DRG neurons. After spared nerve injury (SNI), CX3CR1+ resident macrophages became activated, proliferated and increased inward-rectifying potassium channel Kir2.1 currents. Conditioned medium (CM) by macrophages, obtained from DRG of SNI mice, sensitised small DRG neurons from naïve mice. However, treatment with CM from GFAP+ glial cells did not affect neuronal excitability. When subjected to this macrophage-derived CM, DRG neurons had increased spontaneous activity, current-evoked responses and voltage-gated NaV1.7 and NaV1.8 currents. Silencing Kir2.1 in macrophages after SNI prevented the induction of neuronal hyperexcitability from their CM. Blocking vesicular exocytosis or soluble tumour necrosis factor (TNF) in CM or interfering with the downstream intracellular p38 pathway in neurons, also prevented neuronal hyperexcitability. Blocking protein trafficking in neurons reduced the effect of CM, suggesting that the hyperexcitable state resulted from changes in NaV channel trafficking. These results suggest that DRG macrophages, primed by peripheral nerve injury, contribute to neuron–glia crosstalk, NaV channel dysregulation and neuronal hyperexcitability implicated in the development of neuropathic pain. Graphical abstract
Sexual dimorphism in the social behaviour of Cntnap2-null mice correlates with disrupted synaptic connectivity and increased microglial activity in the anterior cingulate cortex

A biological understanding of the apparent sex bias in autism is lacking. Here we have identified Cntnap2 KO mice as a model system to help better understand this dimorphism. Using this model, we observed social deficits in juvenile male KO mice only. These male-specific social deficits correlated with reduced spine densities of Layer 2/3 and Layer 5 pyramidal neurons in the Anterior Cingulate Cortex, a forebrain region prominently associated with the control of social behaviour. Furthermore, in male KO mice, microglia showed an increased activated morphology and phagocytosis of synaptic structures compared to WT mice, whereas no differences were seen in female KO and WT mice. Our data suggest that sexually dimorphic microglial activity may be involved in the aetiology of ASD, disrupting the development of neural circuits that control social behaviour by overpruning synapses at a developmentally critical period. Sexual dimorphism in the social behaviour of Cntnap2 -null mice correlates with disrupted synaptic connectivity and increased microglial activity in the anterior cingulate cortex of males.
Optimisation of a DNA extraction protocol for improving the bacterial and fungal classification based on Nanopore sequencing

Ribosomal RNA gene amplicon sequencing is commonly used to evaluate microbiome profiles in health and disease and document the impact of interventional treatments. Long-read nanopore sequencing is attractive since it can provide greater classification at the species level. However, optimised protocols to target marker genes for bacterial and fungal profiling are needed. To achieve an increased taxonomic resolution, we developed extraction and long-amplicon PCR-based approaches using Nanopore sequencing. Three sample lysis conditions were applied to a mock microbial community, including known bacterial and fungal species; the 96 MagBead DNA lysis buffer (ML) alone, incorporating bead-beating (MLB) or bead-beating plus MetaPolyzyme enzymatic treatment (MLBE). Profiling of bacterial comparison, MLB had more statistically different bacterial phyla and genera than the others. For fungal profiling, MLB had a significant increase of Ascomycota and a decline of Basidiomycota, subsequently failing to detect Malassezia and Cryptococcus. Also, the principal coordinates analysis (PCoA) plot by the Bray-Curtis index showed a significant difference among groups for bacterial (p = 0.033) and fungal (p = 0.012) profiles. Overall, the microbial profiling and diversity analysis revealed that ML and MLBE have more similarity than MLB for both bacteria and fungi, therefore, bead-beating is not recommended for long-read amplicon sequencing. However, ML alone was suggested as an optimal approach considering DNA yield, classification, reagent cost and hands-on time. This could be an initial proof-of-concept study for simultaneous human microbiome and mycobiome studies.
Drug Resistance without a cost? Common and uncommon routes to fosfomycin resistance in Uropathogenic Escherichia coli

Fosfomycin kills bacteria by blocking the binding of phosphoenolpyruvate (PEP) to the bacterial enzyme MurA and halting peptidoglycan synthesis. While its use has increased with the emergence of antibiotic resistance, the mechanisms leading to fosfomycin resistance remain relatively unexplored. In uropathogenic Escherichia coli (UPEC) that accounts for >75% of urinary tract infections (UTIs), fosfomycin enters the cell primarily through UhpT, which transports glucose-6-phosphate (G6P) glycolysis intermediate into the cell. Mutations in uhpT lead to fosfomycin resistance and have been identified during antimicrobial susceptibility testing (AST) in non-susceptible inner colonies that form within the zone of inhibition. However, EUCAST and CLSI guidelines differ in how to read fosfomycin AST when such resistant colonies arise. Work from our lab and others demonstrated that glycolysis is dispensable during acute UTI. Moreover, G6P is scarce in urine, prompting us to test the hypothesis that uhp mutations may not impart a fitness cost to the pathogen. We report that loss of uhp indeed does not impair UPEC pathogenesis and that clinical isolates exist that lack the uhp locus altogether. Analysis of non-susceptible inner colonies revealed a suite of novel genes involved in fosfomycin resistance. One of them is PykF that converts PEP to pyruvate during glycolysis. Single deletions of pykF or its anaerobic homolog pykA do not attenuate UPEC. Based on our data, we raise the alarm that multiple routes lead to fosfomycin resistance and do not affect pathogenesis and propose that the current EUCAST and CLSI guidelines unify into how they evaluate fosfomycin AST. IMPORTANCE While fosfomycin resistance is rare, the observation of non-susceptible subpopulations among clinical Escherichia coli isolates is a common phenomenon during antimicrobial susceptibility testing (AST) in American and European clinical labs. Previous evidence suggests that mutations eliciting this phenotype are of high biological cost to the pathogen during infection, leading to current recommendations of neglecting non-susceptible colonies during AST. Here we report that the most common route to fosfomycin resistance, as well as novel routes described in this work do not impair virulence in uropathogenic E. coli, the major cause of urinary tract infections, suggesting a re-evaluation of current susceptibility guidelines is warranted.
Advanced methodology for bacterial colonization of 3D organotypic epidermal models: a gateway to long-term host-microbe interaction and intervention studies

Background Following descriptive studies on skin microbiota in health and disease, mechanistic studies on the interplay between skin and microbes are on the rise, for which experimental models are in great demand. Here, we present a novel methodology for microbial colonization of organotypic skin and analysis thereof. Results An inoculation device ensured a standardized application area on the stratum corneum and a homogenous distribution of bacteria, while preventing infection of the basolateral culture medium even during prolonged co-culture periods for up to two weeks at a specific culture temperature and humidity. Hereby, host-microbe interactions and antibiotic interventions could be studied, revealing diverse host responses to various skin-related bacteria and pathogens. Conclusions Our methodology is easily transferable to a wide variety of organotypic skin or mucosal models and different microbes at every cell culture facility at low costs. We envision that this study will kick-start skin microbiome studies using human organotypic skin cultures, providing a powerful alternative to experimental animal models in pre-clinical research.