julilili42/papers huggingface dataset:
Multifaceted confidence in exploratory choice
2025-01-09

Our choices are typically accompanied by a feeling of confidence—an internal estimate that they are correct. Correctness, however, depends on our goals. For example, exploration-exploitation problems entail a tension between short- and long-term goals: finding out about the value of one option could mean foregoing another option that is apparently more rewarding. Here, we hypothesised that after making an exploratory choice that involves sacrificing an immediate gain, subjects will be confident that they chose a better option for long-term rewards, but not confident that it was a better option for immediate reward. We asked 250 subjects across 2 experiments to perform a varying-horizon two-arm bandits task, in which we asked them to rate their confidence that their choice would lead to more immediate, or more total reward. Confirming previous studies, we found a significant increase in exploration with increasing trial horizon, but, contrary to our predictions, we found no difference between confidence in immediate or total reward. This dissociation is further evidence for a separation in the mechanisms involved in choices and confidence judgements.
StretchView – A Multi‐Axial Cell‐Stretching Device for Long‐Term Automated Videomicroscopy of Living Cells
2025-01-10

Abstract Incorporating mechanical stretching of cells in tissue culture is crucial for mimicking (patho)‐physiological conditions and understanding the mechanobiological responses of cells, which can have significant implications in areas like tissue engineering and regenerative medicine. Despite the growing interest, most available cell‐stretching devices are not compatible with automated live‐cell imaging, indispensable for characterizing alterations in the dynamics of various important cellular processes. In this work, StretchView is presented, a multi‐axial cell‐stretching platform compatible with automated, time‐resolved live‐cell imaging. Using StretchView, long‐term image acquisition of cells in the relaxed and stretched states is shown for the first time (experimental time of 12 h) without the need for human intervention. Homogeneous and stable strain fields are demonstrated for 18 h of cyclic stretching, highlighting the platform's versatility and robustness. As proof‐of‐principle, the effect of stretching on cell kinematics and spatiotemporal localization of the cell‐cell adhesion protein E‐cadherin is examined for MDCK cells in monolayer. First evidence of a monotonic increase in junctional E‐cadherin localization upon exposure to stretch is presented using live‐cell imaging data acquired during cyclic stretching, suggestive of an increase in barrier integrity of the monolayer. These findings highlight the potential of StretchView in providing insights into cell mechanobiology and beyond.
Comparison of GFR estimation in patients with diabetes mellitus using the EKFC and CKD-EPI equations
2025-01-10

Abstract Background The estimation of glomerular filtration rate (eGFR) is essential in the early detection of diabetic nephropathy. We herein compare the performance of common eGFR formulas against a gold standard measurement of GFR in patients with diabetes mellitus. Methods GFR was measured in 93 patients with diabetes mellitus using iohexol clearance as the reference standard. The performance of the creatinine- and cystatin C-based EKFC formulas (2021, 2023) and the CKD-EPI formulas (2009, 2012) was compared against measured GFR. Results Sixty patients with type 2 diabetes mellitus and 33 patients with type 1 diabetes mellitus were included. The creatinine-based EKFC formula showed lower bias and higher accuracy than the CKD-EPI formula. No significant difference was observed between the cystatin C-based formulas. The combined creatinine- and cystatin C-based formulas had the highest accuracy and lowest bias. Body fat or diabetes type did not significantly influence the accuracy of the cystatin C-based formulas. Conclusions Our study demonstrated a slight advantage of the creatinine-based EKFC formula over the CKD-EPI formula in patients with diabetes. However, both for the CKD-EPI and the EKFC formula, the best performance was achieved by the combined creatinine- and cystatin C-based formulas. Graphical abstract
The evolutionary history of the field vole species complex revealed by modern and ancient genomes
2025-01-10

<title>Abstract</title> Background The field vole, an abundant and widespread microtine rodent, is a complex comprising three cryptic species. The short-tailed field vole (<italic>Microtus agrestis</italic>) is present over much of Eurasia, the Mediterranean field vole (<italic>Microtus lavernedii</italic>) in southern Europe, and the Portuguese field vole (<italic>Microtus rozianus</italic>) is limited to western Spain and Portugal. Previous research has shown high genomic differentiation of these three lineages; however, the details of the process underlying their divergence remain unknown. Results We analysed 46 mitogenomes and 16 nuclear genomes of modern specimens, and 75 mitogenomes and 12 nuclear genomes of ancient specimens spanning the last 75 thousand years, to investigate the evolutionary history of this species complex. We estimated the divergence of Portuguese from short-tailed and Mediterranean field voles to be ca. 220 ka ago and of the latter to be ca. 110 ka ago, earlier than previous estimates involving only modern sequences. The divergence times we obtained match those between major mitochondrial lineages of cold-adapted and steppe rodents in Europe. We found signatures of gene flow within and between field vole lineages, with some analyses suggesting a hybrid origin of the Mediterranean lineage. Ancient specimens from the Italian Peninsula revealed a previously unrecognised lineage that showed evidence of genetic exchange with other populations. Conclusions The pattern of genetic variation in the field vole species complex demonstrates unequivocally the impact of stadial-interstadial cycles in generating recurrent episodes of allopatry and connectivity of populations, a situation which could only be revealed by our dense genomic sampling over time.
Prospective Multicenter Evaluation of the MDS “Suggestive of PSP” Diagnostic Criteria
2025-01-10

Abstract Background The recent Movement Disorders Society (MDS)‐progressive supranuclear palsy (PSP) diagnostic criteria conceptualized three clinical diagnostic certainty levels: “suggestive of PSP” for sensitive early diagnosis based on subtle clinical signs, “possible PSP” balancing sensitivity and specificity, and “probable PSP” highly specific for PSP pathology. Objective The aim of this study was to prospectively validate the criteria against long‐term clinical follow‐up and characterize the diagnostic certainty increase over time. Methods Patients with “possible PSP” or “suggestive of PSP” diagnosis and clinical follow‐up were recruited in two German multicenter longitudinal observational studies (ProPSP and DescribePSP). The cumulative percentage of patients longitudinally increasing diagnostic certainty was assessed over up to 2.5 years of follow‐up. The sample size per arm required to detect 30% attenuated rate in diagnostic certainty increase in trials was estimated over multiple time intervals. Results Of 254 patients with available longitudinal data, 61 patients had low diagnostic certainty at baseline (48 suggestive of PSP, 13 possible PSP) and multiple clinical visits (median: 3, range: 2–4). The cumulative percentage of patients increasing diagnostic certainty progressed with follow‐up duration (30.4% at 6 months, 51.7% at 1 year, 80.4% at 2.5 years). The sample size required to detect 30% reduction in diagnostic certainty increase rate within 1 year was 163, slightly smaller than that required using the PSP rating scale. Conclusions Most “suggestive of PSP” patients increased diagnostic certainty upon longitudinal follow‐up, providing the first prospective multicenter validation of MDS‐PSP diagnostic criteria. Our data support the design of trials tailored for these early‐stage patients, suggesting the PSP rating scale and the diagnostic certainty increase rate as potential endpoint measures. © 2025 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
Long-term stable laser injection locking for quasi-CW applications
2025-01-10

Abstract Generating high output powers while achieving narrow line single mode lasing are often mutual exclusive properties of commercial laser diodes. For this reason, efficient and scalable amplification of narrow line laser light is still a major driving point in modern laser system designs. Commonly, injection locking of high-power semiconductor laser diodes are used for this purpose. However, for many laser diodes it is very challenging to achieve stable operation of the injection locked state due to a complex interplay of non-linearities and thermal effects. Different approaches of active or passive stabilization usually require a large overhead of optical and electrical equipment and are not generally applicable. In our work we present an active, periodically applied stabilization scheme which is generally applicable, technically easy to implement and extremely cost-effective. It is based on the externally synchronized automatic acquisition of the optimal injection state. Central to our simple but powerful scheme is the management of thermalization effects during lock acquisition. By periodical relocking, spectrally pure amplified light is maintained in a quasi-CW manner over long timescales. We characterize the performance of our method for laser diodes amplifying 671 nm light and demonstrate the general applicability by confirming the method to work also for laser diodes at 401 nm, 461 nm and 689 nm. Our scheme enables the scaled operation of injection locks, even in cascaded setups, for the distributed amplification of single frequency laser light.
Exploring the utility of unretouched lithic flakes as markers of cultural change
2025-01-10

Abstract Lithic artefacts provide the principal means to study cultural change in the deep human past. Tools and cores have been the focus of much prior research based on their perceived information content and cultural relevance. Unretouched flakes rarely attract comparable attention in archaeological studies, despite being the most abundant assemblage elements and featuring prominently in ethnographic and experimental work. Here, we examine the potential of flake morphology for tracing cultural change utilising 4,512 flakes, each characterised by 16 standard mixed-scale attributes, from a well-documented cultural sequence at the Middle Stone Age site of Sibhudu, South Africa. We quantified multivariate similarities among flakes using FLEXDIST, a highly versatile method capable of handling mixed, correlated, incomplete, and high-dimensional data. Our findings reveal a significant gradual change in flake morphology that aligns with the documented cultural succession at Sibhudu. Furthermore, our analysis provides new insights into the patterning of variability throughout the studied sequence. The demonstrated potential of flakes to track cultural change opens up additional avenues for comparative research due to their ubiquity, the availability of commonly recorded attributes, and especially in the absence of cores or tools. FLEXDIST, with its versatile applicability to complex lithic datasets, holds particular promise in this regard.
Multiparametric functional MRI of the kidneys – evaluation of test-retest repeatability and effects of different manual and automatic image analysis strategies
2025-01-10

Abstract Multiparametric MRI is a promising technique for noninvasive structural and functional imaging of the kidneys that is gaining increasing importance in clinical research. Still, there are no standardized recommendations for analyzing the acquired images and there is a need to further evaluate the accuracy and repeatability of currently recommended MRI parameters. The aim of the study was to evaluate the test-retest repeatability of functional renal MRI parameters using different image analysis strategies. Ten healthy volunteers were examined twice with a multiparametric renal MRI protocol including arterial spin labeling (ASL), diffusion-weighted imaging (DWI) with intravoxel incoherent motion (IVIM), blood-oxygen-dependent (BOLD) imaging, T1 and T2 mapping, and volumetry with an interval of one week. The quantitative results of both kidneys were determined by manual organ segmentation, ROI analysis, and automatic segmentation based on the nnUNet framework. Test-retest repeatability of each parameter was computed using the within-subject coefficient of variance (wCV) and the intraclass coefficient (ICC). Segmentation accuracy and inter-reader agreement were evaluated using the dice score. Structural tissue parameters (T1, T2) showed wCV (%) between 4 and 11 and an ICC between 0.2 and 0.8. Functional parameters (ASL, BOLD and DWI) showed wCV (%) between 3 and 38 and an ICC between 0.0 and 0.7. The highest variances between test-retest scans were observed in perfusion measurements with ASL and IVIM (wCV: 17–37%). Quantitative analysis of the cortex and medulla showed a better repeatability when acquired using manual segmentation compared to ROI-based image analysis. Comparable repeatability was achieved with manual and automatic segmentation of the total kidney. Reasonable repeatability was achieved for all MR parameters. Structural MR parameters showed better repeatability compared to functional parameters. ROI-based image analysis showed overall lower repeatability compared to manual segmentation. Comparable repeatability to manual segmentation as well as acceptable segmentation accuracy could be achieved with automatic segmentation.
Parental and adolescents’ perspectives on environmental predictors of active commuting to school – findings from the ARRIVE mixed-methods study
2025-01-10

Background Active commuting to school (e.g., walking or cycling) can contribute to an increase in daily physical activity time of adolescents which is associated with positive health effects. However, it is known that the perceived barriers related to the physical and social environment hinder adolescents in participating in active commuting. To obtain more information about these barriers, and therefore be able to address them in the future, the present study aims to investigate how parents’ and adolescents’ perception of the physical and social environment is associated with (active) commuting to school. Methods The ARRIVE study consists of a quantitative online survey with parent-adolescent dyads ( N = 517) followed by qualitative interviews with adolescents and parents ( N = 32). The quantitative part examined adolescents’ travel behaviour to and from school and its predictors. The qualitative part sought to explore the decision-making process in families regarding transport mode choice. To evaluate predictors of active commuting to and from school binary logistic regression analysis and qualitative content analysis were performed. Results In the quantitative part, we found that adolescents and parents perceive especially having much luggage to carry as crucial for adolescents’ active travel. Besides this barrier on active commuting to and from school found in the questionnaires, parents and adolescents reported lack of social support, weather, convenience, lack of traffic safety and getting a lift as barriers in the interviews. Conclusion We found differences and similarities in the perceived barriers of active commuting regarding the physical and social environment between adolescents and parents. To encourage adolescents to actively commute to school, the perception of the physical and social environment, especially from parents, be taken into account.
How Crystallization Additives Govern Perovskite Grain Growth.
2025-01-10

<title>Abstract</title> The preparation of perovskite solar cells from the liquid phase is a cornerstone of their immense potential. However, a clear relationship between the precursor ink and the resulting perovskite is missing. Established theories, such as heterogeneous nucleation and lead complex colloid formation often prove unreliable, which has led to an overreliance on heuristics. Most high-performing perovskites use additives to control crystallization; their role during crystallization is, however, elusive. Here, we provide strong evidence that typical crystallization additives do not predominantly impact the nucleation phase, but rather facilitate coarsening grain growth by increasing ion-mobility across grain boundaries. Drawing from the insights of our unprecedentedly broad study, that combines e and in situ characterization methods, devices and simulations, we propose a concept that proves valid for various additives and perovskite formulations. Moreover, we establish a direct link between additive engineering and perovskite post-processing, offering a unified framework for advancing material design and process engineering.
A Heterozygous 9q34 deletion encompassing SPTAN1 as a cause of distal myopathy
2025-01-10

Abstract We report a family affected with childhood onset distal muscle weakness with a heterozygous chromosome 9q34 deletion encompassing the SPTAN1 gene. The deletion was detected through exome-sequencing based copy number variant detection, segregates in four patients and is non-penetrant in two other relatives. Electromyography, muscle MRI and muscle biopsy revealed a myopathic disease phenotype. Cellular consequences of the deletion were investigated using qPCR and western blotting on patient-derived fibroblasts, which revealed a reduction of RNA but not protein levels. Immunocytochemistry was performed on muscle tissue which did not reveal reduction of α-II-spectrin. SPTAN1 loss-of-function variants have previously been reported to cause distal hereditary motor neuropathy and recently distal myopathy. Here, we confirm the role of SPTAN1 haploinsufficiency as a cause of distal myopathy. We propose an age-dependent lack of α-II-spectrin and suggest CNV detection in repurposed exome sequencing as an important diagnostic tool.
Intestinal interstitial fluid isolation provides novel insight into the human host-microbiome interface
2025-01-10

Abstract Aims The gastrointestinal (GI) tract is composed of distinct sub-regions, which exhibit segment-specific differences in microbial colonization and (patho)physiological characteristics. Gut microbes can be collectively considered as an active endocrine organ. Microbes produce metabolites, which can be taken up by the host and can actively communicate with the immune cells in the gut lamina propria with consequences for cardiovascular health. Variation in bacterial load and composition along the GI tract may influence the mucosal microenvironment and thus be reflected its interstitial fluid (IF). Characterization of the segment-specific microenvironment is challenging and largely unexplored because of lack of available tools. Methods and results Here, we developed methods, namely tissue centrifugation and elution, to collect IF from the mucosa of different intestinal segments. These methods were first validated in rats and mice, and the tissue elution method was subsequently translated for use in humans. These new methods allowed us to quantify microbiota-derived metabolites, mucosa-derived cytokines, and proteins at their site-of-action. Quantification of short-chain fatty acids showed enrichment in the colonic IF. Metabolite and cytokine analyses revealed differential abundances within segments, often significantly increased compared to plasma, and proteomics revealed that proteins annotated to the extracellular phase were site-specifically identifiable in IF. Lipopolysaccharide injections in rats showed significantly higher ileal IL-1β levels in IF compared to the systemic circulation, suggesting the potential of local as well as systemic effect. Conclusion Collection of IF from defined segments and the direct measurement of mediators at the site-of-action in rodents and humans bypasses the limitations of indirect analysis of faecal samples or serum, providing direct insight into this understudied compartment.
Benchmarking R&D success rates of leading pharmaceutical companies: an empirical analysis of FDA approvals (2006–2022)
2025-01-11

Previous analyses provide an industry benchmark of ∼10% for the success rate in clinical development. However, prior analyses were limited by a narrow timeframe, a diverse research focus, biases in phase-to-phase transition methodology or a focus on specific use cases. We calculated unbiased input:output ratios (Phase I to FDA new drug approval) to analyze the likelihood of first approval using data from clinicaltrials.gov, encompassing a total of 2092 active ingredients, 19 927 clinical trials conducted by 18 leading pharmaceutical companies (2006-2022) and 274 new drug approvals. Our study reveals an average likelihood of first approval rate of 14.3% across leading research-based pharmaceutical companies, broadly ranging from 8% to 23%.
Quantifying Differences in Neural Population Activity With Shape Metrics
2025-01-11

Abstract Quantifying differences across species and individuals is fundamental to many fields of biology. However, it remains challenging to draw detailed functional comparisons between large populations of interacting neurons. Here, we introduce a general framework for comparing neural population activity in terms of shape distances . This approach defines similarity in terms of explicit geometric transformations, which can be flexibly specified to obtain different measures of population-level neural similarity. Moreover, differences between systems are defined by a distance that is symmetric and satisfies the triangle inequality, enabling downstream analyses such as clustering and nearest-neighbor regression. We demonstrate this approach on datasets spanning multiple behavioral tasks (navigation, passive viewing of images, and decision making) and species (mice and non-human primates), highlighting its potential to measure functional variability across subjects and brain regions, as well as its ability to relate neural geometry to animal behavior.
Challenging energy transition and green jobs: climate policy obstruction across borders
2025-01-11

Critical policy mobility literature still does not usually account for transnational opposition dedicated to push back against policy transfer. To address this gap, we examine the case of policy instruments and discourses in support of energy transition and green jobs. In the 2000s, countries such as Spain, Germany, and Denmark adopted policies to fund renewable energy expansion. The success of feed-in-tariff and other policies served as an example for the promotion of public renewable energy investment in the US. Yet by the early 2010s, Spain and Germany discarded feed-in tariffs and erected regulatory barriers against renewables. An opposing discourse coalition amplified policy controversies in North America and Europe. The Institute of Energy Research (IER) orchestrated such efforts in opposition to president Obama’s renewable energy program. An IER-led campaign focused on the denial of job market claims related to renewable energy (‘green jobs’). Pursuing a multi-site case study of opposition strategy mobility, we examine the organizational and discursive building blocks of this campaign. The campaign against renewable policy and green jobs undermined popular renewable energy transition arguments in times of financial crisis in the United States, and was also mobilized against renewable programs in Canada and Europe.