julilili42/papers huggingface dataset:
A primer on the use of computational modelling to investigate affective states, affective disorders and animal welfare in non-human animals
2023-11-30

Abstract Objective measures of animal emotion-like and mood-like states are essential for preclinical studies of affective disorders and for assessing the welfare of laboratory and other animals. However, the development and validation of measures of these affective states poses a challenge partly because the relationships between affect and its behavioural, physiological and cognitive signatures are complex. Here, we suggest that the crisp characterisations offered by computational modelling of the underlying, but unobservable, processes that mediate these signatures should provide better insights. Although this computational psychiatry approach has been widely used in human research in both health and disease, translational computational psychiatry studies remain few and far between. We explain how building computational models with data from animal studies could play a pivotal role in furthering our understanding of the aetiology of affective disorders, associated affective states and the likely underlying cognitive processes involved. We end by outlining the basic steps involved in a simple computational analysis.
An Evaluation of the Performance of Stopping Rules in AI-aided Screening for Psychological Meta-Analytical Research
2023-11-30

Several AI-aided screening tools have emerged to tackle the ever-expanding body of literature. These tools employ active learning, where algorithms sort abstracts based on human feedback. However, researchers using these tools face a crucial dilemma: When should they stop screening without knowing the proportion of relevant studies? Although numerous stopping rules have been proposed to guide users in this decision, they have yet to undergo comprehensive evaluation. In this study, we evaluated the performance of three stopping rules: the knee method, a data-driven heuristic, and a prevalence estimation technique. We measured performance via sensitivity, specificity, and screening cost and explored the influence of the prevalence of relevant studies and the choice of the learning algorithm. We curated a dataset of abstract collections from meta-analyses across five psychological research domains. Our findings revealed performance differences between stopping rules regarding all performance measures and variations in the performance of stopping rules across different prevalence ratios. Moreover, despite the relatively minor impact of the learning algorithm, we found that specific combinations of stopping rules and learning algorithms were most effective for certain prevalence ratios of relevant abstracts. Based on these results, we derived practical recommendations for users of AI-aided screening tools. Furthermore, we discuss possible implications and offer suggestions for future research.
Multiple Gestation as a Risk Factor for SARS-CoV-2-Associated Adverse Maternal Outcome: Data From the COVID-19 Related Obstetric and Neonatal Outcome Study (CRONOS)
2023-11-30

Abstract Studies have shown that pregnant women with COVID-19 have a higher risk of intensive care unit admission and invasive mechanical ventilation support than non-pregnant women. Pregnancy-associated physiological changes in respiratory function may contribute to the elevated risk. Alteration in lung volumes and capacities are attributed to the mechanical impediment caused by the growing fetus. Multiple pregnancies may therefore compromise functional lung capacity earlier than singleton pregnancies and contribute to severe respiratory symptoms of COVID-19. A total of 5514 women with a symptomatic SARS-CoV-2 infection during pregnancy registered in the COVID-19 Related Obstetric and Neonatal Outcome Study were included. The COVID-19-related adverse maternal outcomes were compared in 165 multiple versus 5349 singleton pregnancies. Combined adverse maternal outcome was defined as presence of COVID-19-related hospitalization and/or pneumonia and/or oxygen administration and/or transfer to ICU and/or death. Multivariate logistic regression was used to estimate the odds ratios and 95% confidence intervals were calculated. The frequency of dyspnea, likelihood of developing dyspnea in a defined pregnancy week and duration of the symptomatic phase of the COVID-19 infection did not differ between the two groups. On average, COVID-19-related combined adverse outcome occurred earlier during pregnancy in women expecting more than one child than in singleton pregnancies. The overall incidence of singular and combined COVID-19-associated adverse maternal outcomes was not significantly different between groups. However, regression analysis revealed that multiple gestation, preconceptional BMI &gt; 30 kg/m2 and gestational age correlated significantly with an increased risk of combined adverse maternal outcome. Conversely, maternal age and medically assisted reproduction were not significant risk factors for combined adverse maternal outcome. Our data show that multiple gestation alone is a risk factor for COVID-19-associated combined adverse maternal outcome. Moreover, severe courses of COVID-19 in women expecting more than one child are observed earlier in pregnancy than in singleton pregnancies.
The Psychological, Social and Behavioral Impact of Intravitreal Anti-VEGF Therapy: An Analysis from the ALBATROS Data
2023-11-30

Background: Retinal diseases such as neovascular age-related macular degeneration (nAMD), diabetic macular edema (DME), or branch/central retinal vein occlusion (B/CRVO) have significant implications for patients’ social and psychological well-being. The ALBATROS study aimed to assess the care situation of patients who received anti-VEGF (vascular endothelial growth factor) treatment. To gain a comprehensive understanding of patients’ backgrounds and attitudes, we developed an exploratory, structured questionnaire, the Basic Care and Patient Satisfaction Questionnaire (BPZ-9). Methods: The data collection took place at the beginning and after twelve months of anti-VEGF therapy. The BPZ-9 questionnaire comprises nine questions to evaluate patients’ psychological and social situation and satisfaction with treatment. Results: Data were collected from 1478 nAMD (mean 78 years), 445 DME (67 years), 233 BRVO (70 years), and 144 CRVO (71 years) patients at 102 study centers throughout Germany. One in four patients had difficulties walking, and one in five needed an accompanying person for treatment. Anxiety about losing vision was present in three out of four patients at the beginning, and it slightly decreased to two out of three patients over the 12-month treatment period. The distress of having a retinal disease was generally higher than the distress related to the treatment. Most patients reported high treatment satisfaction (73%) and felt well-informed (81%). Conclusions: There is a relevant social and psychological impact related to anti-VEGF treatment. The patients’ perception, attitudes, and commitment need further investigation.
Metabolic Modeling Elucidates Phenformin and Atpenin A5 as Broad-Spectrum Antiviral Drugs
2023-11-30

Abstract:The SARS-CoV-2 pandemic has reemphasized the urgent need for broad-spectrum antiviral therapies. We developed a computational pipeline using scRNA-Seq data to assess cellular metabolism during viral infection. With this pipeline we predicted the capacity of cells to sustain SARS-CoV-2 virion production in patients and found a tissue-wide induction of metabolic pathways that support viral replication. Expanding our analysis to influenza A and dengue viruses, we identified metabolic targets and inhibitors for potential broad-spectrum antiviral treatment. These targets were highly enriched for known interaction partners of all analyzed viruses. Indeed, phenformin, an NADH:ubiquinone oxidoreductase inhibitor, suppressed SARS-CoV-2 and dengue virus replication. Atpenin A5, blocking succinate dehydrogenase, inhibited SARS-CoV-2, dengue virus, respiratory syncytial virus, and influenza A with high selectivity indices. In vivo, phenformin showed antiviral activity against SARS-CoV-2 in a Syrian hamster model. Our work establishes host metabolism as druggable for broad-spectrum antiviral strategies, providing invaluable tools for pandemic preparedness.
Water’s path from moss to soil Vol. 2: How soil-moss combinations affect the soil water balance and soil erosion
2023-11-30

<title>Abstract</title> Mosses are key components of many ecosystems and particularly related to the soil water balance. In principle, the importance of mosses for water-related processes is known; however, their influence is rarely quantified in scientific studies. To fill this research gap, this study concentrates on the influence of mosses of different species on surface runoff, the amount of percolated water, soil erosion, and the temporal dynamics of soil water content. For this purpose, an experimental approach consisting of an ex situ rainfall simulation with infiltration boxes equipped with biocrust wetness probes was applied. On average, mosses significantly reduced surface runoff by 91% and soil erosion by almost 100%, while the amount of percolated water was increased by 85% compared with bare soils. Similarly, the moss treatments tended to have lower water contents in 3 cm soil depth during 30 minutes of rainfall simulations compared to the bare treatments. However, specific effects of moss treatments were superimposed by desiccation cracks as well as soil hydrophobicity, two major factors that clearly override individual species effects. Therefore, it is imperative that further experiments will be conducted to elucidate the apparently underestimated effects of mosses and their specific traits on the soil water balance and sediment transport.
Spontaneous muscle activity classification with delay-based reservoir computing
2023-11-30

Neuromuscular disorders (NMDs) affect various parts of a motor unit, such as the motor neuron, neuromuscular junction, and muscle fibers. Abnormal spontaneous activity (SA) is detected with electromyography (EMG) as an essential hallmark in diagnosing NMD, which causes fatigue, pain, and muscle weakness. Monitoring the effects of NMD calls for new smart devices to collect and classify EMG. Delay-based Reservoir Computing (DRC) is a neuromorphic algorithm with high efficiency in classifying sequential data. This work proposes a new DRC-based algorithm that provides a reference for medical education and training and a second opinion to clinicians to verify NMD diagnoses by detecting SA in muscles. With a sampling frequency of Fs = 64 kHz, we have classified SA with EMG signals of 1 s of muscle recordings. Furthermore, the DRC model of size N = 600 nodes has successfully detected SA signals against normal muscle activity with an accuracy of up to 90.7%. The potential of using neuromorphic processing approaches in point-of-care diagnostics, alongside the supervision of a clinician, provides a more comprehensive and reliable clinical profile. Our developed model benefits from the potential to be implemented in physical hardware to provide near-sensor edge computing.
Forward programming of hiPSCs towards beta-like cells using Ngn3, Pdx1, and MafA
2023-11-30

<title>Abstract</title> Transplantation of stem cell-derived β-cells is a promising therapeutic advancement in the treatment of type 1 diabetes mellitus. A current limitation of this approach is the long differentiation timeline of up to two months that generates a heterogeneous population of pancreatic endocrine cells. To address this limitation, an inducible lentiviral overexpression system of mature β-cell markers was introduced into human induced-pluripotent stem cells (hiPSCs). Following selection of the successfully transduced hiPSCs, the cells were treated with doxycycline in pancreatic progenitor induction medium to support their transition towards the pancreatic lineage. Cells cultured with doxycycline presented the markers of interest, NGN3, PDX1, and MAFA, after five days of culture, and glucose-stimulated insulin secretion assays demonstrated that the cells were glucose-responsive in a monolayer culture. When cultured as a spheroid, the markers of interest and insulin secretion in a parallel glucose-stimulated insulin secretion assay were maintained; however, insulin secretion upon consecutive glucose challenges was limited. Comparison to human fetal and adult donor tissues identified that although the hiPSC-derived spheroids present similar markers to adult insulin-producing cells, they are functionally representative of fetal development. Together, these results suggest that with optimization of the temporal expression of these markers, forward programming of hiPSCs towards insulin-producing cells could be a possible alternative for islet transplantation.
Roadmap for focused ion beam technologies
2023-12-01

The focused ion beam (FIB) is a powerful tool for fabrication, modification, and characterization of materials down to the nanoscale. Starting with the gallium FIB, which was originally intended for photomask repair in the semiconductor industry, there are now many different types of FIB that are commercially available. These instruments use a range of ion species and are applied broadly in materials science, physics, chemistry, biology, medicine, and even archaeology. The goal of this roadmap is to provide an overview of FIB instrumentation, theory, techniques, and applications. By viewing FIB developments through the lens of various research communities, we aim to identify future pathways for ion source and instrumentation development, as well as emerging applications and opportunities for improved understanding of the complex interplay of ion–solid interactions. We intend to provide a guide for all scientists in the field that identifies common research interest and will support future fruitful interactions connecting tool development, experiment, and theory. While a comprehensive overview of the field is sought, it is not possible to cover all research related to FIB technologies in detail. We give examples of specific projects within the broader context, referencing original works and previous review articles throughout.
Microbial phosphorus recycling in soil by intra- and extracellular mechanisms
2023-12-01

Abstract Rising global stoichiometric imbalance between increasing nitrogen (N) availability and depleting phosphorus (P) resources increases the importance of soil microbial P recycling. The contribution of extra- versus intracellular P (re-)cycling depending on ecosystem nutrient status is vastly unclear, making soil microorganisms a blind spot in our understanding of ecosystem responses to increasing P deficiency. We quantified P incorporation into microbial DNA and phospholipids by 33P labeling under contrasting conditions: low/high P soil × low/high carbon (C)NP application. By combining 33P and 14C labeling with tracing of microbial community biomarkers and functional genes, we disengaged the role of DNA and phospholipids in soil P cycling. Microorganisms in low P soil preferentially allocated P to phospholipids with an acceleration of phospholipids metabolism driven by C addition, which was strongly related to high abundances of microbial community members (e.g. some G-) with a fast phospholipids turnover. In high P soil, however, more P was allocated to DNA with a microbial functional shift towards DNA synthesis to support a replicative growth when sufficient C was supplied, which was coupled with a strong enrichment of fungal copiotrophs and microbial genes coding DNA primase. Consequently, adaptation to low P availability accelerated microbial intracellular P recycling through reutilization of the P stored in phospholipids. However, microorganisms under high P availability commonly adopted extracellular P recycling with release and reuse of DNA P by microbial death-growth dynamics. These results advance our understanding on microbial adaptation to P deficiency in soil by regulating component-specific P pathways and reflect the specific functions of phospholipids and DNA for P recycling.
X-Ray Polarization of the BL Lacertae Type Blazar 1ES 0229+200
2023-12-01

Abstract We present polarization measurements in the 2–8 keV band from blazar 1ES 0229+200, the first extreme high synchrotron peaked source to be observed by the Imaging X-ray Polarimetry Explorer (IXPE). Combining two exposures separated by about two weeks, we find the degree of polarization to be Π X = 17.9% ± 2.8% at an electric-vector position angle ψ X = 25.°0 ± 4.°6 using a spectro-polarimetric fit from joint IXPE and XMM-Newton observations. There is no evidence for the polarization degree or angle varying significantly with energy or time on both short timescales (hours) or longer timescales (days). The contemporaneous polarization degree at optical wavelengths was &gt;7× lower, making 1ES 0229+200 the most strongly chromatic blazar yet observed. This high X-ray polarization compared to the optical provides further support that X-ray emission in high-peaked blazars originates in shock-accelerated, energy-stratified electron populations, but is in tension with many recent modeling efforts attempting to reproduce the spectral energy distribution of 1ES 0229+200, which attribute the extremely high energy synchrotron and Compton peaks to Fermi acceleration in the vicinity of strongly turbulent magnetic fields.
The detection of polarized X-ray emission from the magnetar 1E 2259+586
2023-12-01

ABSTRACT We report on IXPE, NICER, and XMM–Newton observations of the magnetar 1E 2259+586. We find that the source is significantly polarized at about or above 20 per cent for all phases except for the secondary peak where it is more weakly polarized. The polarization degree is strongest during the primary minimum which is also the phase where an absorption feature has been identified previously. The polarization angle of the photons are consistent with a rotating vector model with a mode switch between the primary minimum and the rest of the rotation of the neutron star. We propose a scenario in which the emission at the source is weakly polarized (as in a condensed surface) and, as the radiation passes through a plasma arch, resonant cyclotron scattering off of protons produces the observed polarized radiation. This confirms the magnetar nature of the source with a surface field greater than about 1015 G.
Full‐Field Numerical Simulation of Halite Dynamic Recrystallization From Subgrain Rotation to Grain Boundary Migration
2023-12-01

Abstract Full‐field numerical modeling is a useful method to gain understanding of rock salt deformation at multiple scales, but it is quite challenging due to the anisotropic and complex plastic behavior of halite, together with dynamic recrystallization processes. This contribution presents novel results of full‐field numerical simulations of coupled dislocation glide and dynamic recrystallization of halite polycrystalline aggregates during simple shear deformation, including both subgrain rotation and grain boundary migration (GBM) recrystallization. The results demonstrate that the numerical approach successfully replicates the evolution of pure halite microstructures from laboratory torsion deformation experiments at 100–300°C. Temperature determines the competition between (a) grain size reduction controlled by dislocation glide and subgrain rotation recrystallization (at low temperature) and (b) grain growth associated with GBM (at higher temperature), while the resulting crystallographic preferred orientations are similar for all cases. The relationship between subgrain misorientation and strain follows a power law relationship with a universal exponent of 2/3 at low strain. However, dynamic recrystallization causes a progressive deviation from this relationship when strain increases, as revealed by the skewness of the subgrain misorientation distribution. A systematic investigation of the subgrain misorientation evolution shows that strain or temperature prediction from microstructures requires careful calibration.
Organic Matter Matters—The Imaginary Conductivity of Sediments Rich in Solid Organic Carbon
2023-12-01

Abstract Solid organic matter (OM) is a biogeochemically relevant constituent of soils and sediments. It also affects sediments' geophysical properties, but is often overlooked in hydro‐ and biogeophysical approaches for the characterization of the shallow subsurface. Here, we explore the potential of spectral induced polarization (SIP) to delineate OM‐rich zones in the subsurface and provide insights into the mechanisms that drive OM‐polarization using measurements on both field cores and artificial OM‐sand mixtures. Both, field samples and artificial mixtures showed a linear relationship between the total organic carbon (TOC) content and charge storage (imaginary conductivity). The high cation exchange capacity of OM drives the increase in polarization and can help in delineating potentially microbially active OM‐rich zones in cores or field surveys. To avoid misinterpretation of SIP data in unconsolidated media, we strongly suggest quantifying TOC content in sediment samples to accompany the interpretation of field surveys.
Diversity of MIS 3 Levallois technology from Motravulapadu, Andhra Pradesh, India‐implications of MIS 3 cultural diversity in South Asia
2023-12-01

The chronology and hominin association of the South Asian Middle Palaeolithic have attracted much attention in the last few decades. The emergence of Middle Palaeolithic culture in the region has been debated between the local origins (behavioural change) model based on an early date around 380 ka and the diffusion (biological change) model based on Homo sapiens dispersals from Africa around 120–80 ka. The latter has more consensus, whereas the former requires a more robust chronological framework to attribute the emergence of the Middle Palaeolithic to behavioural changes. In the absence of hominin remains, the presence of Middle Palaeolithic technological trajectories are frequently used as behavioural markers of Homo sapiens . Homo sapiens fossil remains from the regions between Africa and South Asia dated to ∼ 200 ka presents more convincing support for the latter model. Here we present contextual, chronological and technological analysis of Middle Palaeolithic assemblages dated to 52 ka from Motravulapadu, Andhra Pradesh, India. Morphometrical analysis of the lithic assemblage indicates diverse Levallois core reductions were practised at the site at the onset of MIS 3. Further this evidence highlights the significance of MIS 3 cultural diversity in South Asia, likely related to changing population dynamics, cultural drift, and the highly variable climatic context of MIS 3.