julilili42/papers huggingface dataset:
OneFlowTraX: A User-Friendly Software for Super-Resolution Analysis of Single-Molecule Dynamics and Nanoscale Organization
2023-08-11

ABSTRACT Super-resolution microscopy (SRM) approaches revolutionize cell biology by providing insights into the nanoscale organization and dynamics of macromolecular assemblies and single molecules in living cells. A major hurdle limiting SRM democratization is post-acquisition data analysis which is often complex and time-consuming. Here, we present OneFlowTraX, a user-friendly and open-source software dedicated to the analysis of single-molecule localization microscopy (SMLM) approaches such as single-particle tracking photoactivated localization microscopy (sptPALM). Through an intuitive graphical user interface, OneFlowTraX provides an automated all-in-one solution for single-molecule localization, tracking, as well as mobility and clustering analyses. OneFlowTraX allows the extraction of diffusion and clustering parameters of millions of molecules in a few minutes. Finally, OneFlowTraX greatly simplifies data management following the FAIR (Findable, Accessible, Interoperable, Reusable) principles. We provide a detailed step-by-step manual and guidelines to assess the quality of single-molecule analyses. Applying different fluorophores including mEos3.2, PA-GFP, and PATagRFP, we exemplarily used OneFlowTraX to analyze the dynamics of plant plasma membrane-localized proteins including an aquaporin, the brassinosteroid receptor Brassinosteroid Insensitive 1 (BRI1) and the Receptor-Like Protein 44 (RLP44).
Survey and Explorations of the Prehistoric Sites in the Highlands of Southwest Angola
2023-08-11

Abstract The area of the escarpment of Angola between Namib and Huíla Province, about 150 km from the Atlantic coast, yields abundant evidence for human activity throughout the Stone Age. There is a high concentration of open-air sites with stone tools classified as Early (ESA) and Middle Stone Age (MSA) by past explorers. At the top of the plateau, the Chela group rocks and particularly the Leba dolomites yield a series of caves and fissures infilled with deposits ranging from the Early Pleistocene to recent times. Considering, the background information, a new project was developed to establish new proxies, we set out to revise this cultural landscape and set the stage for archaeological testing of Stone Age sites. In 2018–2019, our survey documented 45 sites including caves, rock shelters, and open-air locations with evidence of fossil and cultural deposits, including Middle and Later Stone Age (LSA) stone artifacts, faunal remains, pottery, and human burials. A complete map of distribution of caves and their underground topography is presented. Active and fossil speleothems, important for paleoclimatic reconstructions and absolute dating, were found at the caves of Malola and Tchivinguiro. Fossil occurrences were relocated at Tchíua and Cangalongue. Our study shows there is intense recent activity, historical remains, and the use of at least of three caves as burial sites of past herding populations living at the Humpata plateau. Our field assessment shows there is potential to pursue several lines of evidence to reconstruct past human lifeways and environments in this region.
Receptive field sizes and neuronal encoding bandwidth are constrained by axonal conduction delays
2023-08-11

Studies on population coding implicitly assume that spikes from the presynaptic cells arrive simultaneously at the integrating neuron. In natural neuronal populations, this is usually not the case—neuronal signaling takes time and populations cover a certain space. The spread of spike arrival times depends on population size, cell density and axonal conduction velocity. Here we analyze the consequences of population size and axonal conduction delays on the stimulus encoding performance in the electrosensory system of the electric fish Apteronotus leptorhynchus . We experimentally locate p-type electroreceptor afferents along the rostro-caudal body axis and relate locations to neurophysiological response properties. In an information-theoretical approach we analyze the coding performance in homogeneous and heterogeneous populations. As expected, the amount of information increases with population size and, on average, heterogeneous populations encode better than the average same-size homogeneous population, if conduction delays are compensated for. The spread of neuronal conduction delays within a receptive field strongly degrades encoding of high-frequency stimulus components. Receptive field sizes typically found in the electrosensory lateral line lobe of A. leptorhynchus appear to be a good compromise between the spread of conduction delays and encoding performance. The limitations imposed by finite axonal conduction velocity are relevant for any converging network as is shown by model populations of LIF neurons. The bandwidth of natural stimuli and the maximum meaningful population sizes are constrained by conduction delays and may thus impact the optimal design of nervous systems.
STAR SIGN study: Evaluation of COVID‐19 vaccine efficacy against the SARS‐CoV‐2 variants BQ.1.1 and XBB.1.5 in patients with inflammatory bowel disease
2023-08-12

Summary Background Vaccine‐elicited immune responses are impaired in patients with inflammatory bowel disease (IBD) treated with anti‐TNF biologics. Aims To assess vaccination efficacy against the novel omicron sublineages BQ.1.1 and XBB.1.5 in immunosuppressed patients with IBD. Methods This prospective multicentre case–control study included 98 biologic‐treated patients with IBD and 48 healthy controls. Anti‐spike IgG concentrations and surrogate neutralisation against SARS‐CoV‐2 wild‐type, BA.1, BA.5, BQ.1.1, and XBB.1.5 were measured at two different time points (2–16 weeks and 22–40 weeks) following third dose vaccination. Surrogate neutralisation was based on antibody‐mediated blockage of ACE2‐spike protein–protein interaction. Primary outcome was surrogate neutralisation against tested SARS‐CoV‐2 sublineages. Secondary outcomes were proportions of participants with insufficient surrogate neutralisation, impact of breakthrough infection, and correlation of surrogate neutralisation with anti‐spike IgG concentration. Results Surrogate neutralisation against all tested sublineages was reduced in patients with IBD who were treated with anti‐TNF biologics compared to patients treated with non‐anti‐TNF biologics and healthy controls (each p ≤ 0.001) at visit 1. Anti‐TNF therapy (odds ratio 0.29 [95% CI 0.19–0.46]) and time since vaccination (0.85 [0.72–1.00]) were associated with low, and mRNA‐1273 vaccination (1.86 [1.12–3.08]) with high wild‐type surrogate neutralisation in a β‐regression model. Accordingly, higher proportions of patients treated with anti‐TNF biologics had insufficient surrogate neutralisation against omicron sublineages at visit 1 compared to patients treated with non‐anti‐TNF biologics and healthy controls (each p ≤ 0.015). Surrogate neutralisation against all tested sublineages decreased over time but was increased by breakthrough infection. Anti‐spike IgG concentrations correlated with surrogate neutralisation. Conclusions Patients with IBD who are treated with anti‐TNF biologics show impaired neutralisation against novel omicron sublineages BQ.1.1 and XBB.1.5 and may benefit from prioritisation for future variant‐adapted vaccines.
Advanced biomedical imaging for accurate discrimination and prognostication of mediastinal masses
2023-08-12

Abstract Background To investigate the potential of radiomic features and dual‐source dual‐energy CT (DECT) parameters in differentiating between benign and malignant mediastinal masses and predicting patient outcomes. Methods In this retrospective study, we analysed data from 90 patients (38 females, mean age 51 ± 25 years) with confirmed mediastinal masses who underwent contrast‐enhanced DECT. Attenuation, radiomic features and DECT‐derived imaging parameters were evaluated by two experienced readers. We performed analysis of variance (ANOVA) and Chi‐square statistic tests for data comparison. Receiver operating characteristic curve analysis and Cox regression tests were used to differentiate between mediastinal masses. Results Of the 90 mediastinal masses, 49 (54%) were benign, including cases of thymic hyperplasia/thymic rebound ( n = 10), mediastinitis ( n = 16) and thymoma ( n = 23). The remaining 41 (46%) lesions were classified as malignant, consisting of lymphoma ( n = 28), mediastinal tumour ( n = 4) and thymic carcinoma ( n = 9). Significant differences were observed between benign and malignant mediastinal masses in all DECT‐derived parameters ( p ≤ .001) and 38 radiomic features ( p ≤ .044) obtained from contrast‐enhanced DECT. The combination of these methods achieved an area under the curve of .98 (95% CI, .893–1.000; p &lt; .001) to differentiate between benign and malignant masses, with 100% sensitivity and 91% specificity. Throughout a follow‐up of 1800 days, a multiparametric model incorporating radiomic features, DECT parameters and gender showed promising prognostic power in predicting all‐cause mortality (c‐index = .8 [95% CI, .702–.890], p &lt; .001). Conclusions A multiparametric approach combining radiomic features and DECT‐derived imaging biomarkers allows for accurate and noninvasive differentiation between benign and malignant masses in the anterior mediastinum.
Tropical descendant invariants with line constraints
2023-08-12

Abstract Via correspondence theorems, rational log Gromov–Witten invariants of the plane can be computed in terms of tropical geometry. For many cases, there exists a range of algorithms to compute tropically: for instance, there are (generalised) lattice path counts and floor diagram techniques. So far, the cases for which there exist algorithms do not extend to non‐stationary rational descendant log Gromov–Witten invariants, that is, those where Psi‐conditions do not have to be matched up with the evaluation of a point. The case of rational descendant log Gromov–Witten invariants satisfying point conditions (without Psi‐conditions) and one Psi‐condition of any power combined with a line plays a particularly important role, because it shows up in mirror symmetry as contributions to coefficients of the ‐function. We provide recursive formulas to compute those numbers via tropical methods. Our method is inspired by the tropical proof of the WDVV equations. We also extend our study to counts involving two lines, both paired up with a Psi‐condition, appearing with power 1.
A Digital Game-Based Training Improves Spelling in German Primary School Children - A Randomized Controlled Field Trial
2023-08-13

Despite its potential to support reading and spelling development in children with or without dyslexia, research on the effectiveness of digital trainings carried out at home is scarce. This study investigated the effectiveness of a novel digital game-based spelling training for unassisted use at home (Prosodiya). The pedagogical approach differs from similar approaches as it systematically teaches orthographic knowledge in combination with syllable stress awareness. A sample of 116 German second- to fourth-grade children with mainly poor spelling skills participated in a randomized two-period, wait-list controlled field trial, in which children practiced at home over 9–10 weeks with Prosodiya. Results showed high participant engagement, as indicated by behavioral measures of student responsiveness, and they validate our novel pedagogical approach. Most importantly, results revealed significant training effects on syllable stress awareness and spelling abilities in trained and untrained domains. This training may thus expand the traditional pool of training methods.
Evaluation of Data-Dependent MS/MS Acquisition Parameters for Non-Targeted Metabolomics and Molecular Networking of Environmental Samples: Focus on the Q Exactive Platform
2023-08-14

Non-targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a widely used tool for metabolomics analysis, enabling the detection and annotation of small molecules in complex environmental samples. Data-dependent acquisition (DDA) of product ion spectra is thereby currently one of the most frequently applied data acquisition strategies. The optimization of DDA parameters is central to ensuring high spectral quality, coverage, and number of compound annotations. Here, we evaluated the influence of 10 central DDA settings of the Q Exactive mass spectrometer on natural organic matter samples from ocean, river, and soil environments. After data analysis with classical and feature-based molecular networking using MZmine and GNPS, we compared the total number of network nodes, multivariate clustering, and spectrum quality-related metrics such as annotation and singleton rates, MS/MS placement, and coverage. Our results show that <i>automatic gain control</i>, <i>microscans, mass resolving power</i>, and <i>dynamic exclusion</i> are the most critical parameters, whereas <i>collision energy</i>, <i>TopN</i>, and <i>isolation width</i> had moderate and <i>apex trigger</i>, <i>monoisotopic selection</i>, and <i>isotopic exclusion</i> minor effects. The insights into the data acquisition ergonomics of the Q Exactive platform presented here can guide new users and provide them with initial method parameters, some of which may also be transferable to other sample types and MS platforms.
Hyperspectral imaging as a new diagnostic tool for cervical intraepithelial neoplasia
2023-08-14

Abstract Purpose Cervical cancer screening by visual inspection with acetic acid (VIA) during colposcopy can be challenging and is highly dependent on the clinical experience of the examiner. Health-care systems lack qualified physicians able to perform the examination in both industrialized and low- and middle-income countries. Previous work has shown the general potential of hyperspectral imaging (HSI) to discriminate CIN from normal tissue, but clinical translation has been limited due to the lack of medically approved HSI systems. Methods In this study, we evaluate the feasibility of a commercially available HSI system for CIN detection in a prospective monocentric clinical trial. Results By obtaining spectral fingerprints of 41 patients with CIN 1–3 we show that HSI-based differentiation between CIN and normal tissue is possible with high statistical significance. Major spectral differences were seen in the 555–585 wavelength area. Conclusion HSI advances tissue differentiation by associating each pixel with high-dimensional spectra and thereby obtains morphological and biochemical information of the observed tissue. Currently available and medically approved HSI systems may represent a contact- and marker-free examiner-independent method for the diagnosis of CIN.
Further delineation of the rare GDACCF (global developmental delay, absent or hypoplastic corpus callosum, dysmorphic facies syndrome): genotype and phenotype of 22 patients with ZNF148 mutations
2023-08-14

Background Pathogenic variants in the zinc finger protein coding genes are rare causes of intellectual disability and congenital malformations. Mutations in the ZNF148 gene causing GDACCF syndrome (global developmental delay, absent or hypoplastic corpus callosum, dysmorphic facies; MIM #617260) have been reported in five individuals so far. Methods As a result of an international collaboration using GeneMatcher Phenome Central Repository and personal communications, here we describe the clinical and molecular genetic characteristics of 22 previously unreported individuals. Results The core clinical phenotype is characterised by developmental delay particularly in the domain of speech development, postnatal growth retardation, microcephaly and facial dysmorphism. Corpus callosum abnormalities appear less frequently than suggested by previous observations. The identified mutations concerned nonsense or frameshift variants that were mainly located in the last exon of the ZNF148 gene. Heterozygous deletion including the entire ZNF148 gene was found in only one case. Most mutations occurred de novo, but were inherited from an affected parent in two families. Conclusion The GDACCF syndrome is clinically diverse, and a genotype-first approach, that is, exome sequencing is recommended for establishing a genetic diagnosis rather than a phenotype-first approach. However, the syndrome may be suspected based on some recurrent, recognisable features. Corpus callosum anomalies were not as constant as previously suggested, we therefore recommend to replace the term ‘GDACCF syndrome’ with ‘ ZNF148 -related neurodevelopmental disorder’.
Dissipative quantum many-body dynamics in (1+1)D quantum cellular automata and quantum neural networks
2023-08-14

Abstract Classical artificial neural networks, built from elementary units, possess enormous expressive power. Here we investigate a quantum neural network (QNN) architecture, which follows a similar paradigm. It is structurally equivalent to so-called (1+1)D quantum cellular automata, which are two-dimensional quantum lattice systems on which dynamics takes place in discrete time. Information transfer between consecutive time slices—or adjacent network layers—is governed by local quantum gates, which can be regarded as the quantum counterpart of the classical elementary units. Along the time-direction an effective dissipative evolution emerges on the level of the reduced state, and the nature of this dynamics is dictated by the structure of the elementary gates. We show how to construct the local unitary gates to yield a desired many-body dynamics, which in certain parameter regimes is governed by a Lindblad master equation. We study this for small system sizes through numerical simulations and demonstrate how collective effects within the quantum cellular automaton can be controlled parametrically. Our study constitutes a step towards the utilization of large-scale emergent phenomena in large QNNs for machine learning purposes.
Cultural similarities and specificities of finger counting and montring: Evidence from Amazon Tsimane' people
2023-08-14

Numerical cognition might be embodied, that is, grounded in bodily actions. This claim is supported by the observation that, potentially due to our shared biology, finger counting is prevalent among a variety of cultures. Differences in finger counting are apparent even within Western cultures. Relatively few indigenous cultures have been systematically analyzed in terms of traditional finger counting and montring (i.e., communicating numbers with fingers) routines. Even fewer studies used the same protocols across cultures, allowing for a systematic comparison of indigenous and Western finger counting routines. We analyze the finger counting and montring routines of Tsimane' (N = 121), an indigenous people living in the Bolivian Amazon rainforest, depending on handedness, education level, and exposure to mainstream, industrialized Bolivian culture. Tsimane' routines are compared with those of German and British participants. Tsimane' reveal a greater variation in finger counting and montring routines, which seems to be modified by their education level. We outline a framework on how different factors such as handedness and reading direction might affect cross-cultural and within-cultural variation in finger counting.
The Human Mpox Global Outbreak: Available Control Tools and the Opportunity to Break a Cycle of Neglect in Endemic Countries
2023-08-14

ABSTRACT. The 2022 global outbreak of human Mpox (formerly monkeypox) virus (MPXV) infection outside of the usual endemic zones in Africa challenged our understanding of the virus’s natural history, transmission dynamics, and risk factors. This outbreak has highlighted the need for diagnostics, vaccines, therapeutics, and implementation research, all of which require more substantial investments in equitable collaborative partnerships. Global multidisciplinary networks need to tackle MPXV and other neglected emerging and reemerging zoonotic pathogens to address them locally and prevent or quickly control their worldwide spread. Political endorsement from individual countries and financial commitments to maintain control efforts will be essential for long-term sustainability.
Detecting adaptive changes in gene copy number distribution accompanying the human out-of-Africa expansion
2023-08-14

Abstract Genes with multiple copies are likely to be maintained by stabilizing selection that puts a bound to unlimited expansion of copy number. We designed a model where copy number variation is generated by unequal recombination, which fits well to a number of genes, surveyed in three human populations. Based on this theoretical model and on computer simulations, we were interested in answering the question whether gene copy number distribution in the derived European and Asian populations can be explained by a purely demographic scenario or whether shifts in the distribution are signatures of adaptation. Although copy number distribution in most of the analyzed gene clusters can be explained by a bottleneck as in the out of Africa expansion of homo sapiens 60-10kyrs ago, we identified several candidate genes, for instance AMY1A and PGA3 , whose copy numbers are likely to be selected differently among African, Asian and European populations.
Highly Transparent, Yet Photoluminescent: 2D CdSe/CdS Nanoplatelet-Zeolitic Imidazolate Framework Composites Sensitive to Gas Adsorption
2023-08-14

In this work, thin composite films of zeolitic imidazolate frameworks (ZIFs) and colloidal two-dimensional (2D) CdSe/CdS nanoplatelet emitters with minimal scattering are formed by cycled growth and yield highly transparent coatings while retaining the strong and narrow photoluminescence of the nanoplatelets at 546 nm (FWHM: 25 nm) in a solid-state composite structure. The porous ZIF matrix acts as functional encapsulation for the nanoplatelet emitters which is shown by the adsorption of the guest molecules water and ethanol by the ZIF and sensed by a reversable change in the photoluminescence of the embedded nanoplatelets. Additionally, the transmittance of the composite films surpasses the values of uncoated glass substrates at UV-Vis wavelengths where the nanoplatelets show no absorption, rendering it a photoluminescent antireflective coating. The fast formation of smooth films without pre-polymerizing the colloidal nanoplatelet emitters provides a powerful tool for application-oriented photoluminescence-based gas sensing in the composites.
Testing the discrepancy between physical and virtual linear measurements
2023-08-14

Virtual calculations of bone morphology are increasingly becoming the golden standard in anthropological sciences, gradually replacing the performance of direct physical measurements. Nevertheless, the potential discrepancy between the two approaches is rarely addressed. Here, we address this question focusing on the second thoracic vertebrae of 24 well-preserved individuals from the skeletal collection of the Forensic Anthropology Unit of Medical School at the National and Kapodistrian University of Athens, Greece. Following traditional osteometric methods, a series of measurements were taken on the vertebral body, both directly (using a digital caliper) as well as on high-resolution 3D surface models. The arithmetic results of the two measuring techniques were then compared through a number of statistical analyses evaluating inter-method precision (Bland-Altman plots, TEM, %TEM and Wilcoxon test). Moreover, the values obtained from each approach were used to develop discriminant function equations for sex determination to evaluate if both approaches provide the same assessment. Both intraobserver and interobserver tests were performed. Although most statistical analyses showed a significant difference between the two measuring techniques, the discriminant function equations for sex determination provided the same assessment. Overall, the results of this experiment support the use of virtual linear measurements, also suggesting that a refinement of digital measuring protocols could improve their level of agreement with traditional direct osteometry.