julilili42/papers huggingface dataset:
KCl-Mediated Defect Passivation in Vapor-Deposited Perovskites
2025-07-21

Perovskite-based solar cells (PSCs) have reached efficiencies comparable to those of commonly used silicon solar panels. Despite the promise of PSCs, their efficiency and commercial viability are currently restricted by three main factors: nonradiative charge recombinations on defects occurring within the light-absorbing layer and at its boundaries, limited reproducibility, and upscaling due to widely employed wet deposition methods. To address these issues, we investigated the defect passivation strategy by introducing potassium salt (KCl) during perovskite vapor deposition. We observed effective passivation of the defects upon KCl addition, manifested as an immediate and significant enhancement of the real-time photoluminescence (PL) intensity. The efficiency of passivation is related to the ionic nature of the potassium salt and its flux density. On the other hand, the perovskite's crystallographic structure and texture, as observed from the grazing-incidence wide/small-angle X-ray scattering measurements, showed no significant changes due to KCl doping. Our work provides valuable insight into the possible passivation routes for the vapor-deposited perovskite layers, with implications for various chemical compositions or architectures.
The lithic legacy of Loreto: a technological perspective on early hominin toolmaking during the Lower Palaeolithic
2025-07-21

The site of Loreto (Venosa basin, Southern Italy) dates to between MIS 15 and 13, a pivotal phase in the human peopling of Europe. This period marks a moment of change in the Lower Palaeolithic, preceding the glacial break of MIS 12, and the subsequent technological renewal that, from MIS 11 onward, culminated in the transition to the Middle Palaeolithic. Between MIS 15–13, the number of archaeological sites increased, alongside the emergence of bifaces, retouched tools, and more structured land-use strategies. The lithic assemblage from Loreto exemplifies this shift. The technological analysis presented here, focused on layer A, sheds light on hominin behavioural strategies. Core management includes discoid, centripetal, SSDA (Système par surface de débitage alternée), and core-on-flake reduction sequences. Retouched flakes are particularly noteworthy, featuring elaborately worked scrapers and pointed tools with edge rejuvenation, scalariform retouch, and possible soft-hammer use. Beyond its affinities with other coeval sites, the Loreto assemblage may reflect a degree of innovation often linked to biface production, thereby expanding our understanding of Acheulean technical variability. It also contributes to broader discussions on the diversity of lithic strategies adopted by hominins prior to the onset of MIS 11.
Facies and depositional environments of a Holocene floodplain: Implications for modeling biogeochemical reactions in aquifers
2025-07-21

Abstract Aquifer sediments, which are formed under varying depositional conditions, exhibit significant heterogeneity in their sedimentary architecture, causing variability in their hydraulic and biogeochemical properties. The spatial arrangement of these properties controls the net turnover of biogeochemically reactive and environmentally relevant solutes in floodplains. However, the interlinkage between reactive and hydraulic properties is still enigmatic. This study proposes using sedimentary facies analyses to reconstruct the paleoenvironmental conditions that control the abundance and spatial distribution of aquifer materials, their potential as electron donors and their hydraulic conductivity. The approach was applied to a Holocene aquifer in the Ammer floodplain in southwestern Germany, which mainly consists of organic-rich tufa successions with varying total organic carbon (TOC) content, peat lenses, as well as of gravel and clay layers. The spatial extent of sedimentary features and baseline reactive properties (TOC and hydraulic conductivity) was constrained by combining sedimentological observations and bulk geochemical analyses. Unlike most biogeochemical and hydrogeological studies, bioindicators were included to define the paleoenvironmental conditions and related properties of 11 distinct sedimentary facies types. Based on the insights gained from the paleoenvironmental reconstruction, a facies-based virtual aquifer resembling the sedimentological characteristics of the Ammer floodplain was generated and used to perform 3D flow and transport simulations, using groundwater exposure to TOC as a proxy for reactivity. The study demonstrates that the spatial arrangement of facies, along with their combined biogeochemical and hydraulic properties determines which range of nitrate breakthrough times is to be expected, highlighting the importance of sedimentological insights for groundwater quality projections.
MEGaNorm: Normative Modeling of MEG Brain Oscillations Across the Human Lifespan
2025-07-21

<title>Abstract</title> Normative modeling provides a principled framework for quantifying individual deviations from typical brain development and is increasingly used to study heterogeneity in neuropsychiatric conditions. While widely applied to structural phenotypes, functional normative models remain underdeveloped. Here, we introduce MEGaNorm, the first normative modeling framework for charting lifespan trajectories of resting-state magnetoencephalography (MEG) brain oscillations. Using a large, multi-site dataset comprising 1,846 individuals aged 6–88 and spanning three MEG systems, we model relative oscillatory power in canonical frequency bands using hierarchical Bayesian regression, accounting for age, sex, and site effects. To support interpretation at multiple scales, we introduce Neuro-Oscillo Charts, visual tools that summarize normative trajectories at the population level and quantify individual-level deviations, enabling personalized assessment of functional brain dynamics. Applying this framework to a Parkinson’s disease cohort (n = 160), we show that normative deviation scores reveal disease-related abnormalities and uncover a continuum of patients in theta–beta deviation space. This work provides the first lifespan-encompassing normative reference for MEG oscillations, enabling population-level characterization and individualized benchmarking. All models and tools are openly available and designed for federated, continual adaptation as new data become available, offering a scalable resource for precision neuropsychiatry.
Integrated Modeling of Digital‐Motor and Clinician‐Reported Outcomes Using Item Response Theory: Towards Powerful Trials for Rare Neurological Diseases
2025-07-21

ABSTRACT Robust and highly sensitive outcomes are crucial for small trials in rare diseases. Combining different outcome types might improve sensitivity to identify disease severity and progression, yet innovative methodologies are scarce. Here we develop an Item Response Theory framework that allows integrated modeling of both continuous and categorical outcomes (ccIRT). With degenerative ataxias, a group of rare neurological coordination diseases, as a showcase, we developed a ccIRT model integrating two ataxia outcome types: a clinician‐reported outcome (Scale for the Assessment and Rating of Ataxia; SARA; categorical data) and digital‐motor outcomes for gait and limb coordination (continuous data). The ccIRT model leveraged data from 331 assessments from a natural history study for spastic ataxias. The model describes SARA items and digital‐motor outcomes data as functions of a common underlying ataxia severity construct, evaluating 9 gait and 17 limb coordination digital‐motor measures for their ability to add to SARA in estimating individual ataxia severity levels. Based on our proposed workflow for assessing digital‐motor outcomes in ccIRT models, the final model selected three digital gait and three limb coordination measures, reducing average uncertainty in ataxia severity estimates by 49% (10% SD) compared to the SARA‐only IRT model. Trial simulations showed a 49% and 61% reduction in sample sizes needed to detect disease‐modifying effects in two genotypes. Overall, our ccIRT framework for combining multiple outcome domains, even of different variable types, facilitates a more precise estimation of disease severity and a higher power, which is particularly relevant for rare diseases with inherently small and short trials. Trial Registration: ClinicalTrials.gov : NCT04297891
A Complementarity‐Based Approach to De Novo Binder Design
2025-07-21

Abstract De novo design of binders capable of targeting arbitrarily selected epitopes remains a substantial challenge. Here, a generalizable computational strategy is presented to design site‐specific protein binders, obviating steps of extensive empirical optimization or in vitro screening. The dock‐and‐design pipeline retrieves complementary scaffolds from a protein structure database to a given query epitope, where the scaffold is mutated to carve a binding site de novo . The docking step utilizes a novel fingerprint that greatly simplifies and accelerates the surface complementarity evaluation. As proof‐of‐concept, we designed protein binders to target three distinct epitopes on two different oncogenic targets; vascular endothelial growth factor (VEGF) and interleukin‐7 receptor‐α (IL‐7Rα). Experimental characterization of only 24 candidates identified nanomolar binders against each of the target epitopes, where the binders belonged to five different folds. Several designs were active in vitro. Moreover, anti‐VEGF designs showed tumor‐inhibiting activity in vivo, highlighting their therapeutic potential.
Dual-feature selectivity enables bidirectional coding in visual cortical neurons
2025-07-21

Sensory neurons are traditionally viewed as feature detectors that respond with an increase in firing rate to preferred stimuli while remaining unresponsive to others. Here, we identify a dual-feature encoding strategy in macaque visual cortex, wherein many neurons in areas V1 and V4 are selectively tuned to two distinct visual features—one that enhances and one that suppresses activity—around an elevated baseline firing rate. By combining neuronal recordings with functional digital twin models—deep learningbased predictive models of biological neurons—we were able to systematically identify each neuron’s preferred and non-preferred features. These feature pairs served as anchors for a continuous, low-dimensional axis in natural image similarity space, along which neuronal activity varied approximately linearly. Within a single visual area, visual features that strongly or weakly activated individual neurons also had a high probability of modulating the activity of other neurons, suggesting a shared feature selectivity across the population that structures stimulus encoding. We show that this encoding strategy is conserved across species, present in both primary and lateral visual areas of mouse cortex. Dual-feature selectivity is consistent with recent anatomical evidence for feature-specific inhibitory connectivity, suggesting a coding strategy in which selective excitation and inhibition increase the representational capacity of the neuronal population.
The topology of molecular representations and its influence on machine learning performance
2025-07-21

Abstract Advancements in cheminformatics have led to numerous methods for encoding molecules numerically. The choice of molecular representation impacts the accuracy and generalizability of learning algorithms applied to chemical datasets. Designing and selecting the appropriate representation often lacks a systematic approach and follows computationally exhaustive empirical testing. Moreover, research has shown that deep learning models do not substantially outperform traditional approaches across many tasks with no clear explanation for this shortfall. In this work, we present TopoLearn, a model that predicts the effectiveness of representations on datasets based on the topological characteristics of the corresponding feature space. Using interpretability techniques, we find that persistent homology descriptors are linked with the error metrics of trained machine learning models, offering a new method to better understand and select molecular representations. Scientific contribution Our research is the first to establish an empirical connection between the topology of feature spaces and the machine learning performance of molecular representations. In addition, we facilitate future research endeavors by providing open access to our developed model.
Executive Function Deficits in Genetic Frontotemporal Dementia
2025-07-21

Some individuals with <i>C9orf72</i> mutations show difficulties with executive function from very early on in the disease and this continues to deteriorate with disease severity. By contrast, similar difficulties occur only in the later stages of the disease in <i>GRN</i> and <i>MAPT</i> mutation carriers. This differential performance across the genetic groups will be important in neuropsychological task selection in upcoming clinical trials.
No congruency sequence effect across Simon and Eriksen tasks with aligned temporal processing dynamics: Evidence for domain-specific over domain-general cognitive control
2025-07-21

Abstract Previous studies have shown that the congruency sequence effect (CSE) is usually domain-specific, that is, no transfer across different conflict tasks is observed. The goal of the present study was to test whether the lack of a CSE transfer across the Simon and Eriksen flanker tasks can be explained by a confound of conflict type and the temporal dynamics of conflict processing (i.e., the temporal overlap of target and distractor processing). By presenting the target in the Eriksen task before the distractors, we were able to largely align the temporal overlap of distractor-to-target processing (as indexed by delta plots) in the Simon and Eriksen tasks. Nevertheless, across four experiments we found little, if any, evidence for a transfer of the CSE across tasks. Overall, the results demonstrate that cognitive control is highly specific to the type of conflict, even when controlling for the temporal dynamics of conflict processing.
Statistical regularities and the sensory consequences of self-action: A multi-species, multi-modal perspective
2025-07-21

Active sensing is integral for survival in many organisms. While statistical regularities in natural scenes, as well as ecological relevance, are particularly relevant for shaping motor behaviors, significantly less is known about how these factors additionally influence the brain's compensatory mechanisms for the sensory consequences of self-action. Here, using different sensory modalities, species, and timescales, we review recent developments demonstrating that both state estimation and sensory gating, fundamental functions related to sensory processing during movement, are malleable and reflect statistical regularities. Such regularities exist in both the natural environment as well as in the sensory-motor contingencies specific to a given action type. In some species and modalities, the mechanisms for state estimation are well characterized, whereas in others, sensory gating is more developed. We provide a comparative approach that not only identifies common underlying principles, but also highlights upcoming research questions that are relevant for each sensory modality and species.
Studying unconscious processing: Contention and consensus
2025-07-22

Abstract The scope of unconscious processing has long been, and still remains, a hotly debated issue. This is driven in part by the current diversity of methods to manipulate and measure perceptual consciousness. Here, we provide ten recommendations and nine outstanding issues about designing experimental paradigms, analyzing data, and reporting the results of studies on unconscious processing. These were formed through dialogue among a group of researchers representing a range of theoretical backgrounds. We acknowledge that some of these recommendations naturally do not align with some existing approaches and are likely to change following theoretical and methodological development. Nevertheless, we hold that at this stage of the field they are instrumental in evoking a much-needed discussion about the norms of studying unconscious processes and helping researchers make more informed decisions when designing experiments. In the long run, we aim for this paper and future discussions around the outstanding issues to lead to a more convergent corpus of knowledge about the extent – and limits – of unconscious processing.
Confronting recent light compact star observations with color-flavor locked quark matter
2025-07-22

Recent analyses on the properties of the central compact object in the HESS J1731-347 remnant and the PSR J1231-1411 pulsar indicated that these two compact objects are characterized by similar (low) masses and possibly different radii. This paper aims at reconciling the aforementioned measurements by utilizing the widely employed color-flavor locked (CFL) MIT bag model. The main objective is related to the examination of the acceptable values for the color superconducting gap <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="m1"><mml:mrow><mml:mi mathvariant="normal">Δ</mml:mi></mml:mrow></mml:math> and the bag parameter <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="m2"><mml:mrow><mml:mi>B</mml:mi></mml:mrow></mml:math> . Furthermore, our analysis involves two distinct hypotheses for the nature of compact stars. Firstly, we considered the case of absolute stability for strange quark matter and we found that it is possible to explain both measurements, while also respecting the latest astronomical constraints on the masses and radii of compact stars. Secondly, we studied the case of hybrid stellar matter (transition from hadrons to quarks), and concluded that, when early phase transitions are considered, the simultaneous reconciliation of both measurements leads to results that are inconsistent to the existence of massive compact stars. However, we showed that all current constraints may be satisfied under the consideration that the HESS J1731-347 remnant contains a slow stable hybrid star.
TAPAS: Transient Absorption Processing &amp; Analysis Software
2025-07-22

We present TAPAS (Transient Absorption Processing and Analysis Software), an open-source, Python-based graphical platform that covers the entire transient absorption (TA) workflow, from raw data import and preprocessing to visualization, global and target fitting, and statistical evaluation. Users operate TAPAS through an intuitive, seven-tab GUI, yet all underlying modules remain accessible for inspection and extension, merging GUI convenience with script-level flexibility. The fitting engine employs just-in-time compilation via an open-source machine learning compiler ecosystem, delivering 2-20-fold speed gains over established packages. Automatic differentiation and residual-based effective-sample-size calculations yield reliable confidence intervals and correlation matrices, while an integrated sampling routine provides full Bayesian posterior exploration - diagnostics which are rarely available in other TA tools. All raw, processed, and fitted data are written to standardized HDF5 containers and automatically annotated with rich metadata, ensuring complete provenance. An extended case study on Rose Bengal shows how TAPAS first reveals hidden lifetime correlations, then employs broadband global and target analysis to merge TA traces with complementary steady-state and literature data, yielding a single, self-consistent kinetic model. By uniting advanced uncertainty quantification and transparent data management within a user-friendly interface, TAPAS closes the gap between accessibility and rigorous statistical treatment in transient absorption spectroscopy.
Chemical crosslinking extends and complements UV crosslinking in analysis of RNA/DNA nucleic acid–protein interaction sites by mass spectrometry
2025-07-22

Abstract Ultraviolet (UV) crosslinking with mass spectrometry (XL-MS) has been established for identifying RNA- and DNA-binding proteins along with their domains and amino acids involved. Here, we explore chemical XL-MS for RNA–protein, DNA–protein, and nucleotide–protein complexes in vitro and in vivo. We introduce a specialized nucleotide–protein-crosslink search engine, NuXL, for robust and fast identification of such crosslinks at amino acid resolution. Chemical XL-MS complements UV XL-MS by generating different crosslink species, increasing crosslinked protein yields in vivo almost four-fold, and thus it expands the structural information accessible via XL-MS. Our workflow facilitates integrative structural modelling of nucleic acid–protein complexes and adds spatial information to the described RNA-binding properties of enzymes, for which crosslinking sites are often observed close to their cofactor-binding domains. In vivo UV and chemical XL-MS data from E. coli cells analysed by NuXL establish a comprehensive nucleic acid–protein crosslink inventory with crosslink sites at amino acid level for &amp;gt;1500 proteins. Our new workflow combined with the dedicated NuXL search engine identified RNA crosslinks that cover most RNA-binding proteins, with DNA and RNA crosslinks detected in transcriptional repressors and activators.
Case Report: Successful treatment of a novel variant of CARD14-mutated juvenile Pityriasis rubra pilaris with ixekizumab
2025-07-22

Pityriasis rubra pilaris is a rare inflammatory papulosquamous skin disease without any approved treatment options. Variants in the CARD14 (caspase recruitment domain family member 14) gene have been identified to play a role in the pathophysiology of atypical juvenile PRP by activating the IL-23/IL-17A cytokine axis, highlighting this pathway as a potential target of therapy. Here, we present a case of successful treatment with ixekizumab, a humanized monoclonal anti-IL-17A antibody, in an atypical juvenile PRP (type V) patient with a novel variant of CARD14 mutation.
Preventive dendritic cell vaccination induced TGF-βRII frameshift neoantigen-specific T-cells are linked to long-term disease-free survival in Lynch Syndrome patients
2025-07-22

<title>Abstract</title> Despite compliance to surveillance colonoscopies, patients with Lynch Syndrome (LS) remain at a substantial lifetime risk of developing colorectal cancer, with rates as high as 30–52%. This highlights the need for better cancer prevention strategies. To assess the safety, feasibility, and immunogenicity of a preventive (neo)antigen-based dendritic cell (DC) vaccine, a phase I/II clinical trial was conducted involving 3 LS patients with a recent history of colorectal cancer (CRC) and 20 cancer free LS patients. All participants were HLA-A2<sup>+</sup> and received autologous mature DC pulsed with HLA-A2-binding short peptide derived from carcinoembryonic antigen (CEA) and frameshift-derived neoantigens from caspase-5 and TGF-βRII. No grade 4 adverse events occurred in 22/23 patients and (neo)antigen-specific CD8 T cells were detected in nearly all patients. Post-vaccination, patients who developed T cells specific for the TGF-βRII neoantigen (39%) did not develop any LS-associated neoplasia with <italic>TGFBR2</italic> mutation and have remained cancer-free for nearly 10 years. (ClinicalTrials.gov identifier- NCT01885702)