Miracle-dz/UniFAR-FTUs huggingface dataset:
Incidence and factors for pseudoaccommodation after monofocal lens implantation: the Monofocal Extended Range of Vision study

A combination of low myopic spherical equivalent, lower spherical aberration, shorter axial length, and smaller pupil size increases the chances of pseudoaccommodation. Purpose: To screen patients with a monofocal intraocular lens (IOL) for incidence of unaided 20/40 and 0.3 LogMAR for distance and near (pseudoaccommodation) and to find factors for pseudoaccommodation. Settings: University Hospitals Sussex NHS Foundation Trust, Brighton, United Kingdom. Design: Prospective study. Methods: This was a single-eye study (ClinicalTrials.gov: NCT04011696). At 3 to 9 months, refraction, uncorrected and corrected distance and uncorrected near visual acuity (logMAR), spherical equivalent (SEQ), mesopic pupil size (PS), total eye spherical (Z40), vertical coma (Z3−1) aberrations, reading speed and smallest print size were assessed. Refractive astigmatism (RA) was classified as against-the-rule, with-the-rule, oblique and no astigmatism. Data on preoperative axial length (AL) and anterior chamber depth (ACD) were collected. Results: 29 patients (9.6%, 95% CI, 6.5-13.5) had pseudoaccommodation. In cases vs controls, median SEQ, PS, total Z40, Z3−1, reading speed, smallest print size, preoperative ACD, preoperative AL were: −0.39 vs 0.0 diopters; 3.62 vs 4.10 mm; 0.01 vs 0.02 μm; 0.018 vs 0.022 μm; 106 vs 133 words per minute; 0.30 vs 0.50 logMAR; 2.94 vs 3.13 mm, 23.4 vs 23.7 mm, respectively. RA was not different between the groups. Univariate analysis revealed preoperative ACD (odds ratio [OR], 0.38, 95% CI, 0.16-0.94, P = .04), SEQ (OR, 0.61, 95% CI, 0.42-0.88, P = .01), total Z40 (OR, 0.0003, 95% CI, 0.00-0.39, P = .03) and PS (OR, 0.39, 95% CI, 0.22-0.69, P < .041) to be significant. Whereas multivariable logistic regression identified: preoperative AL (OR, 0.62, 95% CI, 0.42-0.91, P = .02), SEQ (OR, 0.49, 95% CI, 0.31-0.78, P = .01), Z40 (OR, 0.00, 95% CI, 0.0-0.01, P = .01) and PS (OR, 0.41, 95% CI, 0.23-0.75, P = .01) to be significant. Conclusions: A combination of low myopic SEQ, lower Z40, shorter preoperative AL, and smaller PS increases the chances of pseudoaccommodation.
Global ocean thermohaline conveyor at present and in the Late Quaternary

Operation modes of the global ocean thermohaline conveyor at present, at the last glacial maximum, and at a subsequent meltwater event (MWE) are revisited using a combination of a global ocean circulation model and a semi‐Lagrangian trajectory tracing model. The trajectory tracing model helps to visualize the true three‐dimensional water transport that is not accessible within traditional ocean circulation modeling. Our simulations confirm that the glacial mode of the conveyor was substantially weaker as compared to the present day mode. However, the simulations indicate that major changes of the deep global ocean conveyor occurred only at the MWE. These changes led to reversal of the Indian‐Atlantic branch of the deep conveyor due to complete cessation of North Atlantic Deep Water production caused by a very localized meltwater impact.
Morphological alterations of the neuronal Golgi apparatus upon seizures

Epilepsy is one of the most common chronic neurological disorders, affecting around 50 million people worldwide, but its underlying cellular and molecular events are not fully understood. The Golgi is a highly dynamic cellular organelle and can be fragmented into ministacks under both physiological and pathological conditions. This phenomenon has also been observed in several neurodegenerative disorders; however, the structure of the Golgi apparatus (GA) in human patients suffering from epilepsy has not been described so far. The aim of this study was to assess the changes in GA architecture in epilepsy.
Rare-earth elements and yttrium distributions in mangrove coastal water systems: The western Gulf of Thailand

The concentration of rare-earth elements and yttrium (REY) was investigated in dissolved phase, suspended particulate matter, and seafloor sediments of the western coastal area of the Gulf of Thailand. The samples show Eu and Gd positive anomalies in the shale-normalized REY patterns, especially in the suspended particulate matter. On the other hand, a very high REE content was detected in the coastal waters, probably due to the weathering produced by the Mae Klong river waters on rare-earth element (REE)-rich accessory minerals coming from terrains and mineral deposits cropping out in the studied area. The shale-normalized patterns of yttrium and REE estimated for the dissolved phase show an enrichment of medium rare-earth elements (MREE), characteristic of extensive water–rock interactions and weathering occurring in the continental environment. The REE concentrations of suspended particulate, normalized to the REE concentrations in each sediment sampled from the tidal flat, show the same behaviour of the experimentally determined apparent REE bulk distribution coefficients 1 for pH values ranging from about 5.5 to 6.2. Since the REY concentration of the water masses is controlled by the oceanographic features of the studied area, riverine inputs, and ionic straight, we suppose that the dissolved phase represents a mix of truly dissolved and colloidal pool (<0.2 μm) in which REY were enriched during the rock–water interactions of continental environment. In the estuarine system, the salt-induced coagulation of colloidal pool takes place and an authigenic fraction of suspended matter is formed, assuming the typical REE behaviour due to rock–water interactions.
Rooted Divergence-Preserving Branching Bisimilarity is a Congruence for Guarded CCS

Branching bisimilarity is a well-known equivalence relation for labelled transition systems. Based on this equivalence relation, with an additional simple rootedness condition, a congruence relation for calculus of communication system (CCS) processes can be obtained. However, neither branching bisimilarity nor the corresponding congruence relation preserves divergence, and it is still a question whether, based on a divergence-preserving variant of branching bisimilarity, a divergence-preserving congruence relation for CCS processes can be obtained by introducing the same simple rootedness condition. In this article, we present a partial solution by showing that rooted divergence-preserving branching bisimilarity is preserved under the usual CCS operators, including prefixing, summation, parallel composition, relabelling, restriction, and (weakly) guarded recursion.
A method for trend-based change analysis in Arctic tundra using the 25-year Landsat archive

ABSTRACT Remote sensing has provided evidence of vegetation changes in Arctic tundra that may be attributable to recent climate warming. These changes are evident from local scales as expanding shrub cover observed in aerial photos, to continental scales as greening trends based on satellite vegetation indices. One challenge in applying conventional two date, satellite change detection in tundra environments is the short growing season observation window, combined with high inter-annual variability in vegetation conditions. We present an alternative approach for investigating tundra vegetation and surface cover changes based on trend analysis of long-term (1985-present) Landsat TM/ETM+ image stacks. The Tasseled Cap brightness, greenness, and wetness indices, representing linear transformations of the optical channels, are analysed for per-pixel trends using robust linear regression. The index trends are then related to changes in fractional shrub and other vegetation covers using a regression tree classifier trained with high resolution land cover. Fractional trends can be summarised by vegetation or ecosystem type to reveal any consistent patterns. Example results are shown for a 3 000 km2 study area in northern Yukon, Canada where index and fractional changes are related to growth of vascular plants and coastal erosion.
Neuroanatomical, electrophysiological, and morphological characterization of melanin-concentrating hormone cells coexpressing cocaine- and amphetamine-regulated transcript

Melanin-concentrating hormone (MCH) cells in the hypothalamus regulate fundamental physiological functions like energy balance, sleep, and reproduction. This diversity may be ascribed to the neurochemical heterogeneity among MCH cells. One prominent subpopulation of MCH cells coexpresses cocaine- and amphetamine-regulated transcript (CART), and as MCH and CART can have opposing actions, MCH/CART+ and MCH/CART− cells may differentially modulate behavioural outcomes. However, it is not known if there are differences in cellular properties underlying their functional differences, thus we compared the neuroanatomical, electrophysiological, and morphological properties of MCH cells in male and female Mch-cre;L10-Egfp reporter mice. Half of MCH cells expressed CART and were most prominent in the medial hypothalamus. Whole-cell patch-clamp recordings revealed differences in their passive and active membrane properties in a sex-dependent manner. Female MCH/CART+ cells had lower input resistances, but male cells largely differed in their firing properties. All MCH cells increased firing when stimulated, but their firing frequency decreases with sustained stimulation. MCH/CART+ cells showed stronger spike rate adaptation than MCH/CART− cells. The kinetics of excitatory events at MCH cells also differed by cell type, as the rising rate of excitatory events was slower at MCH/CART+ cells. By reconstructing the dendritic arborization of our recorded cells, we found no sex differences, but male MCH/CART+ cells had less dendritic length and fewer branch points. Overall, distinctions in topographical division and cellular properties between MCH cells add to their heterogeneity and help elucidate their response to stimuli or effect on modulating their respective neural networks.
Predicting Beef Tenderness with Computer Vision

A computer vision system was developed to predict cooked-beef tenderness. Our objective was to predict Warner-Bratzler shear force on 14-day aged beef using textural features extracted from 110 fresh beef color images. After ribeye segmentation, images were converted from RGB to CIELAB color space. Gray-level difference histograms were constructed from each L*, a*, and b* color bands and textural features were extracted. The system predicted shear force with an R 2 value of 0.50 and correctly classified 79% of samples into two tenderness categories. Detailed close-up images were also acquired from the final 48 samples. Textural features extracted from these close-up images captured more textural information and predicted shear force with a higher R 2 value of 0.72. Correct classification rate was 92%. Computer vision shows promise for on-line prediction of cooked-beef tenderness.
Pleistocene evolution of the Danube in the Carpathian Basin

The present-day drainage system of the Carpathian Basin originates from the gradual regression of the last marine transgression (brackish Pannonian Sea). The flow directions of the rivers including the Danube, are determined by the varying rates and locations of subsidence within the region. The Danube, which forms the main axis of the drainage network, first filled the depression of the Little Plain Lake and then, further southward, the Slavonian Lake. From the end of the Pliocene, the crustal movements which caused the uplift of the Transdanubian Mountains, forced the Danube to flow in an easterly direction, towards the antecedent Visegrid Gorge, and into the subsiding basins of the Great Plain. Climatic changes during the Pleistocene had the effect of forming up to seven fluvial terraces. The uplift of the mountains is demonstrated by the deformation of the terraces, while the subsidence of the Plains is proven by an accumulation of several hundred metres of sediment. The river only occupied its present position south of Budapest in the latest Pleistocene.
Laboratory mice with a wild microbiota generate strong allergic immune responses

Allergic disorders are caused by a combination of hereditary and environmental factors. The hygiene hypothesis postulates that early-life microbial exposures impede the development of subsequent allergic disease. Recently developed “wildling” mice are genetically identical to standard laboratory specific pathogen–free (SPF) mice but are housed under seminatural conditions and have rich microbial exposures from birth. Thus, by comparing conventional SPF mice with wildlings, we can uncouple the impact of lifelong microbial exposures from genetic factors on the allergic immune response. We found that wildlings developed larger populations of antigen-experienced T cells than conventional SPF mice, which included interleukin-10–producing CD4 T cells specific for commensal Lactobacilli strains and allergy-promoting T helper 2 (TH2) cells. In models of airway exposure to house dust mite (HDM), recombinant interleukin-33, or Alternaria alternata, wildlings developed strong allergic inflammation, characterized by eosinophil recruitment, goblet cell metaplasia, and antigen-specific immunoglobulin G1 (IgG1) and IgE responses. Wildlings developed robust de novo TH2 cell responses to incoming allergens, whereas preexisting TH2 cells could also be recruited into the allergic immune response in a cytokine-driven and TCR-independent fashion. Thus, wildling mice, which experience diverse and lifelong microbial exposures, were not protected from developing pathological allergic immune responses. Instead, wildlings mounted robust allergic responses to incoming allergens, shedding new light on the hygiene hypothesis. Description Allergen exposure in wildling mice induces robust de novo responses and activates an endogenous memory TH2 cell pool. Editor’s summary The hygiene hypothesis proposes that early-life exposure to microbes protects against the development of allergies, a possible explanation for the alarming rise in allergic disorders in developed countries. However, a causal link between early-life infections and allergies is lacking. To uncover the impact of lifelong microbial exposure on the development of allergic inflammation, Ma and Urgard et al. compared experimental wildling mice, which have a representative breadth of naturally occurring pathogens, to specific pathogen–free mice. Surprisingly, when challenged with allergens, wildlings developed robust signs of pathological inflammation and allergic responses, with rapid expansion of TH2 cells in the lungs. The study identifies that increased microbial biodiversity in wildlings did not protect against allergic inflammation, in contrast to what would be predicted by the hygiene hypothesis. —Hannah Isles
Population stratification correction using Bayesian shrinkage priors for genetic association studies

Population stratification (PS) is a major source of confounding in population‐based genetic association studies of quantitative traits. Principal component regression (PCR) and linear mixed model (LMM) are two commonly used approaches to account for PS in association studies. Previous studies have shown that LMM can be interpreted as including all principal components (PCs) as random‐effect covariates. However, including all PCs in LMM may dilute the influence of relevant PCs in some scenarios, while including only a few preselected PCs in PCR may fail to fully capture the genetic diversity.
Mitochondrial Dysfunction and Neuronal Anomalies in POLG Mutant Midbrain Organoids

Human pluripotent stem cell-derived midbrain organoids offer transformative potential for elucidating brain development, disease representation, and therapeutic innovations. We introduce a novel methodology to generate midbrain-specific organoids from both embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). By employing tailored differentiation cues, notably dual-SMAD inhibition combined with FGF-8b and Sonic hedgehog agonist purmorphamine, we direct pluripotent stem cells towards a midbrain lineage. These organoids, growing beyond 2mm in diameter, house diverse neuroepithelial cell populations. Their midbrain character is affirmed by the pronounced expression of midbrain-specific markers and the absence of forebrain and hindbrain indicators. Critically, these organoids differentiate into dopaminergic neurons characteristic of the midbrain, displaying both morphological sophistication and electrophysiological vigor. Additionally, our experiments with POLG iPSC-derived midbrain organoids revealed a marked loss of dopaminergic neurons and diminished expression of genes governing mitochondrial pathways. This evidence underscores the model’s potential in simulating mitochondrial diseases and neurodegenerative conditions, notably Parkinson’s disease. Our protocol thus emerges as a pivotal instrument for crafting functionally adept, midbrain-centric organoids, paving avenues for advanced studies in midbrain evolution, disorders like Parkinson’s disease, and their interplay with mitochondrial dysfunction.
Modified solar flux index for upper atmospheric applications

[1] The F10.7 solar flux index was modified in order to better describe short-term variations in solar extreme ultraviolet (EUV) irradiance for application in ionosphere and thermosphere studies. Several parameters were computed from the F10.7 time series with the assistance of an artificial neural network (ANN) technique, and the daily F10.7 index value was converted to a new solar flux index, MEI10.7. The ANN consists of an input layer that includes an experimental solar input and the day of the year to take seasonal factors into account, one hidden layer, and a target layer of ionospheric total electron content (TEC). The ANN training and validation data set covered one solar cycle from 1997 to 2008. The parameter set that yielded the smallest root-mean-square errors (RMSEs) between the observed and ANN-predicted TECs was adopted for modifying the solar flux index. The MEI10.7 index was evaluated via the same ANN technique. MEI10.7 yielded a smaller RMSE than the magnesium index (Mg II core-to-wing ratio) and a similar RMSE to the EUV index based on the integrated 26–34 nm emission measured by the Solar and Heliospheric Observatory. An advantage of MEI10.7 is long-term availability since the 1940s, unlike satellite measurements. A long-term trend analysis of the ionospheric critical frequency (foF2) at Kokubunji, Japan, conducted for the period from 1957 to 2010 examined the difference between the ANN-modeled and measured foF2 values. The linear regression error when foF2 was modeled by MEI10.7 was appreciably smaller than when it was modeled by F10.7.
Africans’ experiences of international PhDs: making sense of a spectrum of career mobility trajectories

ABSTRACT Globally, countries often view PhD training as building research capacity and may encourage international mobility of potential PhDs as they expect them to return home – not considering individuals as agents negotiating their own intentions. We examined the interaction between such structural factors and 36 PhD graduates’ efforts (from 13 African countries) to negotiate their intentions, particularly around international mobility as they navigated international, national, organisational and day-to-day factors in three periods. Shifts in focus occurred: a) Pre-PhD: international factors around finding a place; b) PhD: host country (national through day-to-day) factors in negotiating a time-limited experience; c) Post-PhD: focus on longer-term, with difference between those returning home and those away (elsewhere in Africa or beyond). Nine trajectories emerged, highlighting the variation in how individuals negotiated asymmetrically within distinct structural factors to advance their careers. Implications for future research as well as policy and practice are explored.
Racial Inequities in Drug Tests Ordered by Clinicians for Pregnant People Who Disclose Prenatal Substance Use

Current practice patterns and protocols such as urine drug testing in pregnancy care deserve review to identify and mitigate areas of racial bias and racism. OBJECTIVE: To measure racial inequities in drug testing among pregnant people during the first prenatal visit based on their drug use disclosure pattern. METHODS: We used data from a cohort study of patient–clinician communication patterns regarding substance use in first prenatal visits from February 2011 to August 2014. We assessed racial differences (Black–White) in the receipt of urine toxicology testing, stratifying on patients' drug use disclosure to the clinician. RESULTS: Among 341 study participants (205 Black [60.1%] and 136 White [39.9%] participants), 70 participants (33 Black [47.1%] and 37 White [52.9%] participants) disclosed drug use, and 271 participants (172 Black [63.5%] and 99 White [36.5%] participants) did not disclose drug use during their first obstetric visit. Of 70 participants who disclosed drug use, 50 (28 Black [56.0%] and 22 White [44.0%] White) had urine drug testing conducted. Black pregnant patients who disclosed drug use were more likely to be tested for drugs than their White counterparts in the adjusted regression analysis (adjusted odds ratio [aOR] 8.9, 95% CI 1.3–58.6). Among the 271 participants who did not disclose drug use, 38 (18 Black [47.4%] and 20 White [52.6%] participants) had urine drug testing conducted. For those who did not disclose drug use, the adjusted model showed no statistically significant differences in urine drug testing by patients’ race (aOR 0.7, 95% CI 0.3–1.6). CONCLUSION: When pregnant people disclosed drug use, clinicians were more likely to order urine drug testing for Black pregnant people compared with their White counterparts, suggesting clinician racial bias. Current practice patterns and protocols such as urine drug testing in pregnancy care deserve review to identify and mitigate areas of potential clinician discrimination.
Matrix Selection for the Visualization of Small Molecules and Lipids in Brain Tumors Using Untargeted MALDI-TOF Mass Spectrometry Imaging

Matrix-assisted laser desorption/ionization mass spectrometry imaging allows the study of metabolic activity in the tumor microenvironment of brain cancers. The detectable metabolites within these tumors are contingent upon the choice of matrix, deposition technique, and polarity setting. In this study, we compared the performance of three different matrices, two deposition techniques, and use of positive and negative polarity in two different brain cancer types and across two species. Optimal combinations were confirmed by comparative analysis of lipid and small molecule abundance using liquid chromatography–mass spectrometry and RNA-sequencing assessing differential metabolites between normal and tumor regions. Our findings indicate that the recrystallized α cyano-4-hydroxycinnamic acid matrix in positive polarity offered superior performance for both detected metabolites and consistency with other techniques. Beyond these implications for brain cancer, our work establishes a workflow to identify optimal matrices for spatial metabolomics studies.