julilili42/papers huggingface dataset:
Screening Smarter, Not Harder: A Comparative Analysis of Machine Learning Screening Algorithms and Heuristic Stopping Criteria for Systematic Reviews in Educational Research
2024-02-08

Abstract Systematic reviews and meta-analyses are crucial for advancing research, yet they are time-consuming and resource-demanding. Although machine learning and natural language processing algorithms may reduce this time and these resources, their performance has not been tested in education and educational psychology, and there is a lack of clear information on when researchers should stop the reviewing process. In this study, we conducted a retrospective screening simulation using 27 systematic reviews in education and educational psychology. We evaluated the sensitivity, specificity, and estimated time savings of several learning algorithms and heuristic stopping criteria. The results showed, on average, a 58% ( SD = 19%) reduction in the screening workload of irrelevant records when using learning algorithms for abstract screening and an estimated time savings of 1.66 days ( SD = 1.80). The learning algorithm random forests with sentence bidirectional encoder representations from transformers outperformed other algorithms. This finding emphasizes the importance of incorporating semantic and contextual information during feature extraction and modeling in the screening process. Furthermore, we found that 95% of all relevant abstracts within a given dataset can be retrieved using heuristic stopping rules. Specifically, an approach that stops the screening process after classifying 20% of records and consecutively classifying 5% of irrelevant papers yielded the most significant gains in terms of specificity ( M = 42%, SD = 28%). However, the performance of the heuristic stopping criteria depended on the learning algorithm used and the length and proportion of relevant papers in an abstract collection. Our study provides empirical evidence on the performance of machine learning screening algorithms for abstract screening in systematic reviews in education and educational psychology.
Shear margins in upper half of Northeast Greenland Ice Stream were established two millennia ago
2024-02-08

Abstract Only a few localised ice streams drain most of the ice from the Greenland Ice Sheet. Thus, understanding ice stream behaviour and its temporal variability is crucially important to predict future sea-level change. The interior trunk of the 700 km-long North-East Greenland Ice Stream (NEGIS) is remarkable due to the lack of any clear bedrock channel to explain its presence. Here, we present a 3-dimensional analysis of the folding and advection of its stratigraphic horizons, which shows that the localised flow and shear margins in the upper NEGIS were fully developed only ca 2000 years ago. Our results contradict the assumption that the ice stream has been stable throughout the Holocene in its current form and show that upper NEGIS-type development of ice streaming, with distinct shear margins and no bed topography relationship, can be established on time scales of hundreds of years, which is a major challenge for realistic mass-balance and sea-level rise projections.
Antimicrobial and anti-biofilm activity of a thiazolidinone derivative against Staphylococcus aureus in vitro and in vivo
2024-02-08

ABSTRACT Staphylococcus aureus ( S. aureus ) causes many infections with significant morbidity and mortality. S. aureus can form biofilms, which can cause biofilm-associated diseases and increase resistance to many conventional antibiotics, resulting in chronic infection. It is critical to develop novel antibiotics against staphylococcal infections, particularly those that can kill cells embedded in biofilms. This study aimed to investigate the bacteriocidal and anti-biofilm activities of thiazolidinone derivative (TD-H2-A) against S. aureus . A total of 40 non-duplicate strains were collected, and the minimum inhibitory concentrations (MICs) of TD-H2-A were determined. The effect of TD-H2-A on established S. aureus mature biofilms was examined using a confocal laser scanning microscope (CLSM). The antibacterial effects of the compound on planktonic bacteria and bacteria in mature biofilms were investigated. Other characteristics, such as cytotoxicity and hemolytic activity, were researched. A mouse skin infection model was used, and a routine hematoxylin and eosin (H&amp;E) staining was used for histological examination. The MIC values of TD-H2-A against the different S. aureus strains were 6.3–25.0 μg/mL. The 5 × MIC TD-H2-A killed almost all planktonic S. aureus USA300. The derivative was found to have strong bacteriocidal activity against cells in mature biofilms meanwhile having low cytotoxicity and hemolytic activity against Vero cells and human erythrocytes. TD-H2-A had a good bacteriocidal effect on S. aureus SA113-infected mice. In conclusion, TD-H2-A demonstrated good bacteriocidal and anti-biofilm activities against S. aureus , paving the way for the development of novel agents to combat biofilm infections and multidrug-resistant staphylococcal infections. IMPORTANCE Staphylococcus aureus , a notorious pathogen, can form a stubborn biofilm and develop drug resistance. It is crucial to develop new anti-infective therapies against biofilm-associated infections. The manuscript describes the new antibiotic to effectively combat multidrug-resistant and biofilm-associated diseases.
Allogeneic hematopoietic cell transplantation for adult metachromatic leukodystrophy: a case series
2024-02-08

Abstract Metachromatic leukodystrophy (MLD) is a rare genetic disorder caused by pathogenic variants of the ARSA gene, leading to a deficiency of the arylsulfatase A enzyme (ARSA) and consecutive accumulation of galactosylceramide-3-0-sulfate in the nervous system. The condition leads to severe neurological deficits and subsequently results in profound intellectual and motoric disability. Especially, the adult form of MLD, which occurs in individuals aged &amp;gt;16 years, poses significant challenges for treating physicians because of the rarity of cases, limited therapeutic options, and different allogeneic hematopoietic cell transplantation (allo-HCT) protocols worldwide. Here, we report the results of allo-HCT treatment in 4 patients with a confirmed adult MLD diagnosis. Bone marrow or mobilized peripheral progenitor cells were infused after a reduced intensity conditioning regime consisting of fludarabine and treosulfan. In 3 patients, allo-HCT was followed by an infusion of mesenchymal cells to further consolidate ARSA production. We observed a good tolerability and an increase in ARSA levels up to normal range values in all patients. A full donor chimerism was detected in 3 patients within the first 12 months. In a 1-year follow-up, patients with complete donor chimerism showed a neurological stable condition. Only 1 patient with an increasing autologous chimerism showed neurological deterioration and a decline in ARSA levels in the first year. In summary, allo-HCT offers a therapeutic option for reconstituting ARSA enzyme levels in adult patients with MLD, with tolerable side effects.
Development and validation of a respiratory syncytial virus multiplex immunoassay
2024-02-08

Abstract Purpose Respiratory syncytial virus (RSV) is one of the leading causes of severe respiratory disease in infants and adults. While vaccines and monoclonal therapeutic antibodies either are or will shortly become available, correlates of protection remain unclear. For this purpose, we developed an RSV multiplex immunoassay that analyses antibody titers toward the post-F, Nucleoprotein, and a diverse mix of G proteins. Methods A bead-based multiplex RSV immunoassay was developed, technically validated to standard FDA bioanalytical guidelines, and clinically validated using samples from human challenge studies. RSV antibody titers were then investigated in children aged under 2 and a population-based cohort. Results Technical and clinical validation showed outstanding performance, while methodological developments enabled identification of the subtype of previous infections through use of the diverse G proteins for approximately 50% of samples. As a proof of concept to show the suitability of the assay in serosurveillance studies, we then evaluated titer decay and age-dependent antibody responses within population cohorts. Conclusion Overall, the developed assay shows robust performance, is scalable, provides additional information on infection subtype, and is therefore ideally suited to be used in future population cohort studies.
MP2RAGE vs. MPRAGE surface-based morphometry in focal epilepsy
2024-02-08

In drug-resistant focal epilepsy, detecting epileptogenic lesions using MRI poses a critical diagnostic challenge. Here, we assessed the utility of MP2RAGE–a T1-weighted sequence with self-bias correcting properties commonly utilized in ultra-high field MRI–for the detection of epileptogenic lesions using a surface-based morphometry pipeline based on FreeSurfer, and compared it to the common approach using T1w MPRAGE, both at 3T. We included data from 32 patients with focal epilepsy (5 MRI-positive, 27 MRI-negative with lobar seizure onset hypotheses) and 94 healthy controls from two epilepsy centres. Surface-based morphological measures and intensities were extracted and evaluated in univariate GLM analyses as well as multivariate unsupervised ‘novelty detection’ machine learning procedures. The resulting prediction maps were analyzed over a range of possible thresholds using alternative free-response receiver operating characteristic (AFROC) methodology with respect to the concordance with predefined lesion labels or hypotheses on epileptogenic zone location. We found that MP2RAGE performs at least comparable to MPRAGE and that especially analysis of MP2RAGE image intensities may provide additional diagnostic information. Secondly, we demonstrate that unsupervised novelty-detection machine learning approaches may be useful for the detection of epileptogenic lesions (maximum AFROC AUC 0.58) when there is only a limited lesional training set available. Third, we propose a statistical method of assessing lesion localization performance in MRI-negative patients with lobar hypotheses of the epileptogenic zone based on simulation of a random guessing process as null hypothesis. Based on our findings, it appears worthwhile to study similar surface-based morphometry approaches in ultra-high field MRI (≥ 7 T).
Site-specific sulfations regulate the physicochemical properties of papillomavirus-heparan sulfate interactions for entry
2024-02-08

Abstract Certain human papillomaviruses (HPVs) are etiological agents for several anogenital and oropharyngeal cancers. During initial infection, HPV16, the most prevalent cancer-causing type, specifically interacts with heparan sulfates (HS), not only enabling initial cell attachment but also triggering a crucial conformational change in viral capsids termed structural activation. It is unknown, whether such HS-HPV16 interactions depend on HS sulfation patterns. Thus, we probed potential roles of HS sulfations using cell-based functional and physicochemical assays, including single molecule force spectroscopy. Our results demonstrate that N-sulfation of HS is crucial for virus binding and structural activation by providing high affinity sites, and that additional 6O-sulfation is required to mechanically stabilize the interaction, whereas 2O-sulfation and 3O-sulfation are mostly dispensable. Together, our findings identify the contribution of HS sulfation patterns to HPV16 binding and structural activation and reveal how distinct sulfation groups of HS synergize to facilitate HPV16 entry, which, in turn, likely influences the tropism of HPVs. Teaser Distinct heparan sulfations facilitate HPV16 binding and structural activation through their physico-chemical properties.
Sommerfeld effect for continuum gamma-ray spectra from Dark Matter annihilation
2024-02-08

A bstract We present a calculation of the continuum part of the gamma-ray spectra resulting from Dark Matter annihilation in the framework of the MSSM taking into account Sommerfeld effects. Concentrating on pure wino and pure higgsino scenarios we compare our calculation to existing work and explore the numerical impact of the features not captured by previous approximative descriptions. We find that, in particular for large neutralino masses, when the Sommerfeld enhancement is very large, chargino-antichargino annihilation processes, which have not been considered before, lead to sizable differences with respect to existing calculations. In scenarios with neutralinos in the intermediate-mass range, we find that the role of the charginos is crucial in the endpoint regime. Our calculation provides the currently most accurate prediction for the continuum gamma-ray spectra.
Quality assurance for next-generation sequencing diagnostics of rare neurological diseases in the European Reference Network
2024-02-08

<title>Abstract</title> In the past decade, next-generation sequencing (NGS) has revolutionized genetic diagnostics for rare neurological disorders (RND). However, the lack of standardized technical, interpretative, and reporting standards poses a challenge for ensuring consistent and high-quality diagnostics globally. To address this, the European Reference Network for Rare Neurological Diseases (ERN-RND) collaborated with the European Molecular Genetics Quality Network (EMQN) to establish an external quality assessment scheme for NGS-based diagnostics in RNDs. The scheme, initiated in 2021 with a pilot involving 29 labs and followed by a second round in 2022 with 42 labs, aimed to evaluate the performance of laboratories in genetic testing for RNDs. Each participating lab analysed genetic data from three hypothetical cases, assessing genotyping, interpretation, and clerical accuracy. Despite a majority of labs using exome or genome sequencing, there was considerable variability in gene content, sequencing quality, adherence to standards, and clinical guidance provision. Results showed that while most labs provided correct molecular diagnoses, there was significant variability in reporting technical quality, adherence to interpretation standards, reporting strategies, and clinical commentary. Notably, some labs returned results with the potential for adverse medical outcomes. This underscores the need for further harmonization, guideline development, and external quality assessment in the evolving landscape of genomic diagnostics for RNDs. Overall, the experience with the scheme highlighted the generally good quality of participating labs but emphasized the imperative for ongoing improvement in data analysis, interpretation, and reporting to enhance patient safety.
Peptide-stimulation of autologous T cells reverts immune checkpoint inhibitor resistance of hypermutated colorectal cancer cells
2024-02-08

Abstract Two hypermutated colon cancer cases with patient-derived cell lines, peripheral and tumor-infiltrating T cells available were selected for detailed investigation of immunological response. T cells co-cultured with autologous tumor cells showed only low levels of pro-inflammatory cytokines and failed at tumor recognition. Similarly, treatment of co-cultures with immune checkpoint inhibitors (ICI) did not boost antitumor immune responses. Since proteinase inhibitor 9 (PI-9) was detected in tumor cells, a specific inhibitor (PI-9i) was used in addition to ICI in T cell cytotoxicity testing. However, only pre-stimulation with tumor-specific peptides (cryptic and neoantigenic) significantly increased recognition and elimination of tumor cells by T cells independently of ICI or PI-9i. We showed, that ICI resistant tumor cells can be targeted by tumor-primed T cells and also demonstrated the superiority of tumor-naïve peripheral blood T cells compared to highly exhausted tumor-infiltrating T cells. Future precision immunotherapeutic approaches should include multimodal strategies to successfully induce durable anti-tumor immune responses.
Language Change in Real- and Apparent-Time
2024-02-09

This book makes the case for the value of a combined panel and trend study approach in studying real- and apparent-time language change to reconcile conspicuous disparities between the individual and the community. Through an examination of the Swabian dialect in southwestern Germany in two speech communities over four decades, this volume resolves critical methodological challenges in investigating lifespan and community change. This work affirms the importance of the speech community in shaping change and demonstrating how speakers' notions of local identity and community belonging inform their choice of linguistic variants. Drawing on a comprehensive, integrated methodology, this research brings together diverse approaches for measuring changing social constructs and analyzing linguistic structures using state-of-the-art statistical methods bolstered by participant-observer and ethnographic observations. Beaman explores indexicalities of identity, accommodation, and geographic mobility to investigate how predictable sociolinguistic patterns promote variation and influence language change. Empirically, this volume documents processes of dialect leveling and supraregionalization and the emergence of a "Swabian Renaissance" among younger, well-educated urban speakers who leverage the social indexical status of certain linguistic variables to convey social meanings of local prestige and community belonging. Methodologically, this book offers best practices from a combined panel and trend study, demonstrating the compatibility and complementarity of real- and apparent-time analyses in uncovering the nature, rate, and dispersion of linguistic change. Theoretically, this work links intraspeaker lifespan change and interspeaker community change into a holistic approach, pushing forward our understanding of the role that "orderly heterogeneity" plays in language variation and change. This book will be of interest to students and scholars in sociolinguistics, linguistic anthropology, dialectology, and historical linguistics.
Halide Segregated Crystallization of Mixed-Halide Perovskites Revealed by In Situ GIWAXS
2024-02-09

Mixed-halide perovskites of the composition MAPb(Br<sub><i>x</i></sub>I<sub>1-<i>x</i></sub>)<sub>3</sub>, which seem to exhibit a random and uniform distribution of halide ions in the absence of light, segregate into bromide- and iodide-rich phases under illumination. This phenomenon of halide segregation has been widely investigated in the photovoltaics context since it is detrimental for the material properties and ultimately the device performance of these otherwise very attractive materials. A full understanding of the mechanisms and driving forces has remained elusive. In this work, a study of the crystallization pathways and the mixing behavior during deposition of MAPb(Br<sub><i>x</i></sub>I<sub>1-<i>x</i></sub>)<sub>3</sub> thin films with varying halide ratios is presented. In situ grazing incidence wide-angle scattering (GIWAXS) reveals the distinct crystallization behavior of mixed-halide perovskite compositions during two different fabrication routes: nitrogen gas-quenching and the lead acetate route. The perovskite phase formation of mixed-halide thin films hints toward a segregation tendency since separate crystallization pathways are observed for iodide- and bromide-rich phases within the mixed compositions. Crystallization of the bromide perovskite phase (MAPbBr<sub>3</sub>) is already observed during spin coating, while the iodide-based fraction of the composition forms solvent complexes as an intermediate phase, only converting into the perovskite phase upon thermal annealing. These parallel crystallization pathways result in mixed-halide perovskites forming from initially halide-segregated phases only under the influence of heating.
Nonequilibrium quantum probing through linear response
2024-02-09

The formalism of linear response theory can be extended to encompass physical situations where an open quantum system evolves toward a nonequilibrium steady state. Here, we use the framework put forward by Konopik and Lutz [] to go beyond unitary perturbations of the dynamics. Considering an open system comprised of two coupled quantum harmonic oscillators, we study the system's response to unitary perturbations, affecting the Hamiltonian dynamics, as well as nonunitary perturbations, affecting the properties of the environment, e.g., its temperature and squeezing. We show that linear response, combined with a quantum probing approach, can effectively provide valuable quantitative information about the perturbation and characteristics of the environment, even in cases of nonunitary dynamics. Published by the American Physical Society 2024
PARMESAN: Meteorological Timeseries and TurbulenceAnalysis Backed by Symbolic Mathematics
2024-02-09

PARMESAN (the Python Atmospheric Research Package for MEteorological TimeSeries and Turbulence ANalysis) is a Python package providing common functionality for atmospheric scientists doing time series or turbulence analysis.Several meteorological quantities such as potential temperature, various humidity measures, gas concentrations, wind speed and direction, turbulence and stability parameters can be calculated.Furthermore, signal processing functionality such as properly normed variance spectra for frequency analysis is available.In contrast to existing packages with similar goals, its routines for physical quantities are derived from symbolic mathematical expressions, enabling inspection, automatic rearrangement, reuse and recombination of the underlying equations.Building on this, PARMESAN's functions as well as their comprehensive parameter documentation are mostly auto-generated, minimizing human error and effort.In addition, sensitivity/error propagation analysis is possible as mathematical operations like derivations can be applied to the underlying equations.Physical consistency in terms of units and value domains are transparently ensured for PARMESAN functions.PARMESAN's approach can be reused to simplify implementation of robust routines in other fields of physics.
Brain signal complexity and aperiodicity predict human corticospinal excitability
2024-02-09

Background: Transcranial magnetic stimulation (TMS) holds promise for brain modulation with relevant scientific and therapeutic applications, but it is limited by response variability. Targeting state-dependent EEG features such as phase and power shows potential, but uncertainty remains about the suitable brain states. Objective: This study evaluated broadband EEG measures (BEMs), including the aperiodic exponent (AE) and entropy measures (CTW, LZ), as alternatives to band-limited features, such as power and phase, for predicting corticospinal excitability (CSE). Methods: TMS was delivered with randomly applied single pulses targeting the left primary motor cortex in 34 healthy participants while simultaneously recording EEG and EMG signals. Broadband and band-limited EEG features were evaluated for their ability to predict CSE using motor evoked potentials (MEPs) from the right extensor digitorum communis muscle as the outcome measure. Results: BEMs (AE, CTW) significantly predicted CSE, comparable to beta-band power and phase, the most predictive and spatially specific band-limited markers of motor cortex CSE. Unlike these localized CSE markers at the site of stimulation, BEMs captured more global brain states and greater within-subject variability, indicating sensitivity to dynamic state changes. Notably, CTW was associated with high CSE, while AE was linked to low CSE. Conclusion: This study reveals BEMs as robust predictors of CSE that circumvent challenges of band-limited EEG features, such as narrowband filtering and phase estimation. They may reflect more general markers of brain excitability. With their slower timescale and broader sensitivity, BEMs are promising biomarkers for state-dependent TMS applications, particularly in therapeutic contexts.