julilili42/papers huggingface dataset:
banū isrāʾīl, ahl al-kitāb, al-yahūd wa-l-naṣārā: The Qur’anic Community’s Encounters with Jews and Christians
2023-07-20

This paper argues for a new understanding of the Qur’an’s view of Jews and Christians based, firstly, on their developing role in Qur’anic discourse, and, secondly, on the Qur’an’s continuous understanding of the three designations for Jews and Christians: banū isrāʾīl, “the children of Israel,” ahl al-kitāb, “the Scripture People,” and al-yahūd wa-l-naṣārā, “the Jews and the Christians.” Whereas there is a scholarly consensus that the term ahl al-kitāb designates both Jews and Christians, I offer two correctives: first, the term banū isrāʾīl equally designates the Qur’an’s Jewish and Christian contemporaries (or, more often, their common ancestors), and, second, the predominantly collective usage of al-yahūd wa-l-naṣārā shows that the three designations for Jews and Christians most be understood both in their continuity and in the increasing internal differentiation of Jews and Christians from each other.
Influence of [18F]FDG-PET/CT on Clinical Management Decisions in Breast Cancer Patients—A PET/CT Registry Study
2023-07-20

There is a lack of evidence regarding the clinical impact of [18F]fluorodeoxyglucose positron emission tomography/computed tomography ([18F]FDG-PET/CT, hereinafter referred to as PET/CT), especially regarding management changes and their link to overall survival. We analyzed 52 PET/CTs in 47 stage I-IV breast cancer patients, selected from a prospective oncological PET/CT registry. Indications for PET/CT were primary staging (n = 15), restaging (n = 17), and suspected recurrence (n = 20). PET/CT-induced management changes were categorized as major or minor. PET/CT-induced management changes in 41 of 52 scans (78.8%; 38 of 47 patients (80.9%)), of which major changes were suggested in 18 of 52 scans (34.6%, 17 of 47 patients, 36.2%). PET/CT downstaged 6 of 15 primary staging patients, excluding distant metastases. Major management changes were documented in 3 of 17 restaging exams. PET/CT ruled out clinically suspected recurrence in 6 of 20 cases and confirmed it in 11 of 20. In three cases, locoregional recurrence had already been diagnosed via biopsy. In 30 of 52 exams, additional diagnostic tests were avoided, of which 13 were invasive. PET/CT-based management changes resulted in a 5-year survival rate of 72.3% for the whole study group, 93.3% for the staging group, 53.8% for the restaging group, and 68.4% for the recurrence group. This study shows that PET/CT significantly impacts clinical management decisions in breast cancer patients in different clinical scenarios, potentially determining the patient’s tumor stage as the basis for further therapy more reliably and by avoiding unnecessary diagnostic tests.
On estimating the frequency of a target behavior from time-constrained yes/no survey questions: A parametric approach based on the Poisson process.
2023-07-20

We propose a novel method to analyze time-constrained yes/no questions about a target behavior (e.g., "Did you take sleeping pills during the last 12 months?"). A drawback of these questions is that the relative frequency of answering these questions with "yes" does not allow one to draw definite conclusions about the frequency of the target behavior (i.e., how often sleeping pills were taken) nor about the prevalence of trait carriers (i.e., percentage of people that take sleeping pills). Here we show how this information can be extracted from the results of such questions employing a prevalence curve and a Poisson model. The applicability of the method was evaluated with a survey on everyday behavior, which revealed plausible results and reasonable model fit. (PsycInfo Database Record (c) 2023 APA, all rights reserved).
Immunoprecipitation methods impact the peptide repertoire in immunopeptidomics
2023-07-21

Introduction Mass spectrometry-based immunopeptidomics is the only unbiased method to identify naturally presented HLA ligands, which is an indispensable prerequisite for characterizing novel tumor antigens for immunotherapeutic approaches. In recent years, improvements based on devices and methodology have been made to optimize sensitivity and throughput in immunopeptidomics. However, developments in ligand isolation, mass spectrometric analysis, and subsequent data processing can have a marked impact on the quality and quantity of immunopeptidomics data. Methods In this work, we compared the immunopeptidome composition in terms of peptide yields, spectra quality, hydrophobicity, retention time, and immunogenicity of two established immunoprecipitation methods (column-based and 96-well-based) using cell lines as well as primary solid and hematological tumor samples. Results Although, we identified comparable overall peptide yields, large proportions of method-exclusive peptides were detected with significantly higher hydrophobicity for the column-based method with potential implications for the identification of immunogenic tumor antigens. We showed that column preparation does not lose hydrophilic peptides in the hydrophilic washing step. In contrast, an additional 50% acetonitrile elution could partially regain lost hydrophobic peptides during 96-well preparation, suggesting a reduction of the bias towards the column-based method but not completely equalizing it. Discussion Together, this work showed how different immunoprecipitation methods and their adaptions can impact the peptide repertoire of immunopeptidomic analysis and therefore the identification of potential tumor-associated antigens.
Tailoring the Morphology of Monodisperse Mesoporous Silica Particles Using Different Alkoxysilanes as Silica Precursors
2023-07-21

The hard template method for the preparation of monodisperse mesoporous silica microspheres (MPSMs) has been established in recent years. In this process, in situ-generated silica nanoparticles (SNPs) enter the porous organic template and control the size and pore parameters of the final MPSMs. Here, the sizes of the deposited SNPs are determined by the hydrolysis and condensation rates of different alkoxysilanes in a base catalyzed sol–gel process. Thus, tetramethyl orthosilicate (TMOS), tetraethyl orthosilicate (TEOS), tetrapropyl orthosilicate (TPOS) and tetrabutyl orthosilicate (TBOS) were sol–gel processed in the presence of amino-functionalized poly (glycidyl methacrylate-co-ethylene glycol dimethacrylate) (p(GMA-co-EDMA)) templates. The size of the final MPSMs covers a broad range of 0.5–7.3 μm and a median pore size distribution from 4.0 to 24.9 nm. Moreover, the specific surface area can be adjusted between 271 and 637 m2 g−1. Also, the properties and morphology of the MPSMs differ according to the SNPs. Furthermore, the combination of different alkoxysilanes allows the individual design of the morphology and pore parameters of the silica particles. Selected MPSMs were packed into columns and successfully applied as stationary phases in high-performance liquid chromatography (HPLC) in the separation of various water-soluble vitamins.
Accurate Standard Errors in Multilevel Modeling with Heteroscedasticity: A Computationally More Efficient Jackknife Technique
2023-07-21

In random-effects models, hierarchical linear models, or multilevel models, it is typically assumed that the variances within higher-level units are homoscedastic, meaning that they are equal across these units. However, this assumption is often violated in research. Depending on the degree of violation, this can lead to biased standard errors of higher-level parameters and thus to incorrect inferences. In this article, we describe a resampling technique for obtaining standard errors—Zitzmann’s jackknife. We conducted a Monte Carlo simulation study to compare the technique with the commonly used delete-1 jackknife, the robust standard error in Mplus, and a modified version of the commonly used delete-1 jackknife. Findings revealed that the resampling techniques clearly outperformed the robust standard error in rather small samples with high levels of heteroscedasticity. Moreover, Zitzmann’s jackknife tended to perform somewhat better than the two versions of the delete-1 jackknife and was much faster.
Observation of a low energy nuclear recoil peak in the neutron calibration data of the CRESST-III experiment
2023-07-21

New-generation direct searches for low mass dark matter feature detection thresholds at energies well below 100 eV, much lower than the energies of commonly used x-ray calibration sources. This requires new calibration sources with sub-keV energies. When searching for nuclear recoil signals, the calibration source should ideally cause monoenergetic nuclear recoils in the relevant energy range. Recently, a new calibration method based on the radiative neutron capture on W182 with subsequent deexcitation via single γ-emission leading to a nuclear recoil peak at 112 eV was proposed. The CRESST-III dark matter search operated several CaWO4-based detector modules with detection thresholds below 100 eV in the past years. We report the observation of a peak around the expected energy of 112 eV in the data of three different detector modules recorded while irradiated with neutrons from different AmBe calibration sources. We compare the properties of the observed peaks with geant-4 simulations and assess the prospects of using this for the energy calibration of CRESST-III detectors.
AuReTim: an inexpensive and extensible open-source auditory psychomotor vigilance test
2023-07-21

Within a large joint research project aiming for characterizing the nonvisual effects of light (NiviL), AuReTim, a low-cost and extensible open-source portable psychomotor vigilance test using auditory stimuli was developed, tailored for field testing. Currently, an unprepared simple reaction time and a go/no-go paradigm using acoustic stimuli are implemented. AuReTim is based on inexpensive hardware, e.g., its core is a Raspberry Pi leveraging a touch screen as input. Its software is developed in JavaTM using open-source libraries, therefore providing connectivity with other research setups, e.g., EEG, and easy extensibility with other stimulus paradigms. A simulation study proved the precise timing of AuReTim with limits of agreement between −1.86 and 1.67 ms. AuReTim combines the mobility of tablet-based psychomotor vigilance tests with the usability of conventional computer-based tests, which is especially helpful in field studies. AuReTim was successfully applied to study the effects of different lighting on alertness and proved to be a valuable tool for studies using the central nervous activation level as an outcome measure.
Scuba diving after a heart transplant: excessive daring or calculable risk?
2023-07-21

Example for shared decision-making process for tricky questions: First scientific publication about heart transplantation (HTX)-recipient restarting scuba diving. As exercise physiology after HTX combined with specific diving medicine aspects is challenging, we formed a multidisciplinary team to identify, evaluate, and mitigate the risks involved. The results show that today, with the appropriate physical condition and compliance with safety measures, a wide range of activities are possible again after HTX.
Oral fructose intake does not improve exercise, visual, or cognitive performance during acute normobaric hypoxia in healthy humans
2023-07-21

Introduction The ability to metabolize fructose to bypass the glucose pathway in near-anaerobic conditions appears to contribute to the extreme hypoxia tolerance of the naked-mole rats. Therefore, we hypothesized that exogenous fructose could improve endurance capacity and cognitive performance in humans exposed to hypoxia. Methods In a randomized, double-blind, crossover study, 26 healthy adults (9 women, 17 men; 28.8 ± 8.1 (SD) years) ingested 75 g fructose, 82.5 g glucose, or placebo during acute hypoxia exposure (13% oxygen in a normobaric hypoxia chamber, corresponding to oxygen partial pressure at altitude of ~3,800 m) on separate days. We measured exercise duration, heart rate, SpO 2 , blood gasses, and perceived exertion during a 30-min incremental load test followed by Farnsworth-Munsell 100 Hue (FM-100) color vision testing and the unstable tracking task (UTT) to probe eye-hand coordination performance. Results Exercise duration in hypoxia was 21.13 ± 0.29 (SEM) min on fructose, 21.35 ± 0.29 min on glucose, and 21.35 ± 0.29 min on placebo ( p = 0.86). Heart rate responses and perceived exertion did not differ between treatments. Total error score (TES) during the FM-100 was 47.1 ± 8.0 on fructose, 45.6 ± 7.6 on glucose and 53.3 ± 9.6 on placebo ( p = 0.35) and root mean square error (RMSE) during the UTT was 15.1 ± 1.0, 15.1 ± 1.0 and 15.3 ± 0.9 ( p = 0.87). Discussion We conclude that oral fructose intake in non-acclimatized healthy humans does not acutely improve exercise performance and cognitive performance during moderate hypoxia. Thus, hypoxia tolerance in naked mole-rats resulting from oxygen-conserving fructose utilization, cannot be easily reproduced in humans.
Impact of Constructive Narratives About Climate Change on Learned Helplessness and Motivation to Engage in Climate Action
2023-07-21

Climate change is currently one of the most pressing challenges for humanity. This makes the developmentof effective strategies to mitigate climate change of utmost importance. One such strategy is to improve climate change communication especially with respect to increase the public's motivation to engage in climate action. While there has been increased reporting on climate change in recent years, news are dominated by the negative impacts of climate change rather than by solutions. Based on previous research, we assume that the standard way of reporting (problem instead of solution-focused) makes people feel more helpless about climate change and decreases motivation to engage in climate action. On the other hand, using constructive narratives (solution-focused) should decrease helplessness and increase motivation to engage inclimate action. To investigate our hypothesis, we conducted an experiment with N = 1359 participants (quota-based sample of the German population; age and gender). For our intervention, standard and constructive narratives were developed for two crucial climate change topics: energy transition and city development. Results showed that reading constructive narratives significantly decreased participants' helplessness ratings. Furthermore, a decrease in helplessness led to a higher motivation to act. Additionally, the impact of passive risk taking-tendencies on helplessness as well as motivation to act is discussed. Asconstructive narratives effectively reduced helplessness and increased motivation to act, they could supportclimate change mitigation by increasing climate action and thereby become a powerful tool within climate change communication.
Chapter 10. Connectionist Neuroarchitectures in Cognition and Consciousness Theory Based on Integrative (Synchronization) Mechanisms
2023-07-21

The topic of this chapter are cognitive neuroarchitectures, which have been developed since the mid-eighties in connectionism as theoretical models to explain, based on empirical-experimental data, as neurophysiologically plausible as possible perceptual and linguistic performances of self-organizing neuronal networks in the human brain that are related to the binding problem. Thus, neurocognition can be viewed as organized by integrative (phase) synchronization mechanisms that orchestrate the flow of neurocognitive information in self-organizing networks with positive and/or negative feedback loops in subcortical and cortical areas of the brain. This dynamic perspective on cognition contributes significantly to bridging the gap between the discrete, abstract symbolic description of propositions in the mind and their continuous, numerical, and dynamic modeling in terms of cognitive neuroarchitectures in connectionism. This dynamic binding mechanism in connectionist cognitive neuroarchitectures thus has the advantage of enabling more accurate modeling of cognitive processes by conceptualizing these neuroarchitectures as nonlinear dynamical systems. This means that neurocognition is modeled using a neurodynamics in abstract n-dimensional phase spaces in the form of nonlinear vector fields or vector flows.
Reads-per-UMI tables across single-cell RNA sequencing protocols
2023-07-21

&lt;p&gt;Data analyzed in &lt;a href="https://www.biorxiv.org/content/10.1101/2023.08.02.551637v1"&gt;Lause, Ziegenhain et al. (2023)&lt;/a&gt;.&lt;/p&gt; &lt;p&gt;Code to obtain these tables from public data sources is available on &lt;a href="https://github.com/berenslab/read-normalization"&gt;github&lt;/a&gt;.&lt;/p&gt; &lt;p&gt;&nbsp;&lt;/p&gt; &lt;p&gt;Each row in the table is a UMI-tag detected in a certain cell (column RG) attached to a molecule from a specific gene (column GE) with a certain barcode (column UB). Column N gives the number of times the UMI was detected for that gene and cell.&lt;/p&gt; &lt;p&gt;Data sources and protocols are given with the respective file names below.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Johnsson2022_Smartseq3_PE.hd1.txt.gz&lt;/strong&gt;: Mouse fibroblasts profiled with &lt;strong&gt;Smart-seq3&lt;/strong&gt; paired-end; accession E-MTAB-10148, sample plate2,&lt;br&gt; &lt;a href="https://doi.org/10.1038/s41588-022-01014-1"&gt;Paper&lt;/a&gt;&lt;br&gt; &lt;br&gt; &lt;strong&gt;Hagemann-Jensen2020_Smartseq3_SE.hd1.txt.gz: &lt;/strong&gt;Mouse fibroblasts profiled with &lt;strong&gt;Smart-seq3&lt;/strong&gt; single-end; accession E-MTAB-8735, sample Smartseq3.Fibroblasts.smFISH&lt;br&gt; &lt;a href="https://doi.org/10.1038/s41587-020-0497-0"&gt;Paper&lt;/a&gt;&lt;br&gt; &lt;br&gt; &lt;strong&gt;Hagemann-Jensen2022_Smartseq3xpress.hd1.txt.gz: &lt;/strong&gt;HEK293 cells profiled with &lt;strong&gt;Smart-seq3Xpress&lt;/strong&gt;; accession E-MTAB-11467.&lt;br&gt; &lt;a href="https://www.biorxiv.org/content/10.1101/2021.07.10.451889v1"&gt;Paper&lt;/a&gt;&lt;br&gt; &lt;br&gt; &lt;strong&gt;Ziegenhain2017.hd1.txt.gz: &lt;/strong&gt;Mouse embryonic stem cells profiled by &lt;strong&gt;CEL-seq2, Drop-seq, MARS-seq, &lt;/strong&gt;and&lt;strong&gt; SCRB-seq&lt;/strong&gt;; GEO accession GSE75790&lt;br&gt; &lt;a href="https://doi.org/10.1016/j.molcel.2017.01.023"&gt;Paper&lt;/a&gt;&lt;/p&gt;
Low-density lipoprotein receptor-related protein 2 (LRP2) is required for lipid export in the midgut of the migratory locust, Locusta migratoria
2023-07-22

Low-density lipoprotein receptor-related protein 2 (LRP2) is a multifunctional endocytic receptor expressed in epithelial cells. In mammals, it acts as an endocytic receptor that mediates the cellular uptake of cholesterol-containing apolipoproteins to maintain lipid homeostasis. However, little is known about the role of LRP2 in lipid homeostasis in insects. In the present study, we investigated the function of LRP2 in the migratory locust Locusta migratoria (LmLRP2). The mRNA of LmLRP2 is widely distributed in various tissues, including integument, wing pads, foregut, midgut, hindgut, Malpighian tubules and fat body, and the amounts of LmLRP2 transcripts decreased gradually in the early stages and then increased in the late stages before ecdysis during the nymphal developmental stage. Fluorescence immunohistochemistry revealed that the LmLRP2 protein is mainly located in cellular membranes of the midgut and hindgut. Using RNAi to silence LmLRP2 caused molting defects in nymphs (more than 60%), and the neutral lipid was found to accumulate in the midgut and surface of the integument, but not in the fat body, of dsLmLRP2-treated nymphs. The results of a lipidomics analysis showed that the main components of lipids (diglyceride and triglyceride) were significantly increased in the midgut, but decreased in the fat body and hemolymph. Furthermore, the content of total triglyceride was significantly increased in the midgut, but markedly decreased in the fat body and hemolymph in dsLmLRP2-injected nymphs. Our results indicate that LmLRP2 is located in the cellular membranes of midgut cells, and is required for lipid export from the midgut to the hemolymph and fat body in locusts.
Treatment of adult attention-deficit hyperactivity disorder (ADHD) with transcranial direct current stimulation (tDCS): study protocol for a parallel, randomized, double-blinded, sham-controlled, multicenter trial (Stim-ADHD)
2023-07-22

Abstract Transcranial direct current stimulation (tDCS) is a non-invasive brain stimulation treatment used as an alternative or complementary treatment for various neuropsychiatric disorders, and could be an alternative or add-on therapy to psychostimulants in attention-deficit hyperactivity disorder (ADHD). Previous studies provided some evidence for improvements in cognition and clinical symptoms in pediatric and adult ADHD patients. However, data from multi-center randomized controlled trials (RCTs) for this condition are lacking. Thus, our aim is to evaluate short- and mid-term effects of tDCS in this multi-center, randomized, double blind, and sham-controlled, parallel group clinical trial with a 1:1 randomization ratio. Primary endpoint is the total score of DSM-IV scale of the internationally established Conners’ Adult ADHD Rating Scales (German self-report screening version, CAARS-S-SR), at day 14 post-intervention (p.i.) to detect short-term lasting effects analyzed via analyses of covariance (ANCOVAs). In case of significant between-groups differences at day 14 p.i., hierarchically ordered hypotheses on mid-term lasting effects will be investigated by linear mixed models with visit (5 time points), treatment, treatment by visit interaction, and covariates as fixed categorical effects plus a patient-specific visit random effect, using an unstructured covariance structure to model the residual within-patient errors. Positive results of this clinical trial will expand the treatment options for adult ADHD patients with tDCS and provide an alternative or add-on therapy to psychostimulants with a low risk for side effects. Trial Registration The trial was registered on July 29, 2022 in the German Clinical Trials Register (DRKS00028148).
Hyaenid remains from the Late Miocene of Kutschwan (Shanxi Province, China)
2023-07-22

Abstract The hyaenid family reached its peak of spatial range and taxonomic diversity during the Late Miocene, including a very wide range of different forms that were spanning throughout the Old World. Particularly, the fossil record of the family in the Balkans and China has been extremely variable during that time. The present paper deals with cranial and postcranial hyaenid material from the Late Miocene locality of Kutschwan (Shanxi Province, China). The specimens were identified as Hyaenictitherium wongii , a widespread species with well-known occurrences throughout Eurasia during the Vallesian and the Turolian. The material presents some notable features, such as the enlarged M1, M2 and m2 that point towards a more basal form of the species. However, the statistical analysis of the variability of these characters points towards intraspecific divergence based on selective release, instead of taxonomically significant adaptive traits. The postcranial material conforms very well to the known material of H . wongii from other localities, indicating an agile cursorial hunter. This species is the only carnivoran found in Kutschwan, based on the current data.