julilili42/papers huggingface dataset:
Individual variation in animal communication: from species averages to unique voices
2025-07-30

ABSTRACT The comparative study of communicative behaviour in non‐human animals, especially primates, has yielded crucial insights into the evolution of human language. This research, mostly focused on the species and population level, has improved our understanding of the various socio‐ecological factors that shape communication systems. However, despite the inherent flexibility of human communication, the impact of individual variation on non‐human communication systems has often been overlooked, along with its potential to shed light on the roots of human language. While the eco‐evolutionary relevance of genetic and phenotypic differences between individuals is well established, animal communication studies have traditionally focused on group averages and treated outliers as noise. In this review, we address this gap by providing a comprehensive overview of the sources of individual variation in animal communicative behaviour (e.g. physiological, sociodemographic, or personality traits), across parameters such as signal forms, repertoires, and usage strategies. In particular, recent evidence from comparative work underscores the potential evolutionary significance of individual plasticity in communicative behaviour. We argue for an explicit focus on within‐individual variation and propose advancing the study of animal communication through multi‐level approaches that integrate intrinsic and environmental factors, as well as between‐ and within‐individual variation. Such approaches not only refine our view of complexity in animal communication systems and their implications for social evolution, but also help trace the evolutionary trajectory of human language through comparative studies.
The “Hottest Ever January” in Germany: Farmers’ Protests and the Discourse on Agriculture and Food Production
2025-07-30

Following the German Federal Government’s announcement of agricultural subsidy cuts in November 2023, farmers mobilized unprecedented protests, creating what their associations celebrated as a “hot January with more protests than the country has ever seen” (“Bauern wollen ‘Kampfansage’ der Ampel annehmen,” 2023). These actions ultimately forced the government to withdraw the proposed policy changes. Our study applies the politicization/depoliticization – policy change model to analyze the theoretical connections between politicization and policy change announcements. Using discourse network analysis, we examine the evolution of politicization/depoliticization dynamics through newspaper articles published between the initial subsidy cut announcement on November 17, 2023, and March 26, 2024. Our findings reveal a dynamic politicization process that farmers strategically amplified through protests to achieve policy reversal. Our research also identifies concerning behavioral patterns of right‐wing actors and ideological infiltration within these protests, opening avenues for further investigation.
Glucagon‐Like Peptide‐1 Receptor Agonists Improve MASH and Liver Fibrosis: A Meta‐Analysis of Randomised Controlled Trials
2025-07-30

ABSTRACT Background/Aims There is uncertainty regarding the hepatic efficacy of glucagon‐like peptide‐1 receptor agonists (GLP‐1RAs) in metabolic dysfunction‐associated steatotic liver disease (MASLD) or steatohepatitis (MASH). We performed a meta‐analysis of randomised controlled trials (RCTs) to examine the efficacy of GLP‐1RAs in treating MASLD or MASH. Methods We systematically searched three electronic databases from inception until April 2025 to identify RCTs examining the efficacy of GLP‐1RAs for the treatment of MASLD or MASH. The outcome measures included MASH resolution without worsening of fibrosis or improvement in at least one stage of fibrosis without worsening of MASH, along with reductions in liver fat content measured using magnetic resonance‐based techniques. Meta‐analysis was conducted using random‐effects models. Results We identified 13 phase 2 or phase 3 RCTs (1811 participants). These trials diagnosed MASLD or MASH through liver biopsy ( n = 4) or magnetic resonance‐based techniques ( n = 9). Regardless of diabetes status, among individuals with MASH and moderate‐to‐advanced fibrosis, GLP‐1RAs (especially semaglutide 2.4 mg/week) for up to 72 weeks were superior to placebo in achieving MASH resolution ( n = 3 RCTs; pooled random‐effects odds ratio 3.48, 95% CI 2.69–4.51; I 2 = 0%), and in improving liver fibrosis (pooled odds ratio 1.79, 95% CI 1.37–2.35; I 2 = 0%). Among individuals with MASH‐related compensated cirrhosis ( n = 1 RCT available only), semaglutide did not lead to MASH resolution or improved fibrosis compared to placebo. Furthermore, GLP‐1RAs reduced magnetic resonance‐measured liver fat content ( n = 9; pooled mean difference: −4.50%, 95% CI −6.60 to −2.40%; I 2 = 95.9%). Conclusions GLP‐1RAs are a promising treatment option for MASLD or MASH. Further research is needed to evaluate the long‐term effects of GLP‐1RAs on liver‐related clinical events.
Protein kinase G inhibition preserves photoreceptor viability and function in a new mouse model for autosomal dominant retinitis pigmentosa
2025-07-30

Abstract Retinitis Pigmentosa (RP) is the most common inherited retinal degeneration, characterized by an initial loss of rod photoreceptor cells. Photoreceptor cell death has been associated with high levels of cyclic guanosine-3′, 5′- monophosphate (cGMP) in animal models of autosomal recessive RP (ARRP) and autosomal dominant RP (ADRP). cGMP analogues inhibiting protein kinase G (PKG) have been found to prevent rod degeneration in ARRP disease models, but their effects on ADRP are unknown. Here, we used the recently generated rhodopsin-mutant Rho I255d/+ ADRP mouse model to study cGMP-signaling and the effects of cGMP analogues targeting PKG. cGMP accumulation was investigated by retinal immunostaining in wild-type (WT), Rho I255d/+ , and Rho I255d/I255d mice. The therapeutic efficacy of the cGMP analogues CN03 and CN238 was evaluated on organotypic retinal explant cultures derived from WT and Rho I255d/+ mice. Readouts included the TUNEL assay and immunostaining for cone arrestin-3. Downstream effectors of cell death were visualized using calpain, poly-ADP-ribose polymerase (PARP), and histone deacetylase (HDAC) in situ assays, as well as caspase-3 immunostaining. Photoreceptor function was assessed using micro-electroretinogram (μERG) recordings. When compared with WT, Rho I255d photoreceptors displayed cGMP accumulation in outer segments. In the Rho I255d/+ ADRP model, CN03 and CN238 significantly reduced the number of dying photoreceptors. However, the relatively small number of photoreceptors exhibiting caspase-3 activity was not changed by the treatment. Remarkably, CN238 effectively provided long-lasting neuroprotection of cone photoreceptors and preserved retinal light responsiveness of Rho I255d/+ retina. Overall, this study suggests caspase-independent but cGMP-dependent cell death as a dominant degenerative mechanism in the Rho I255d/+ ADRP mouse model. PKG inhibition demonstrated robust neuroprotection of both rod and cone photoreceptors, while the marked preservation of retinal function, especially with the compound CN238, highlighted cGMP analogues for the treatment of ADRP.
Perspectives in Computational Mass Spectrometry: Recent Developments and Key Challenges
2025-07-30

Mass spectrometry (MS) is a cornerstone technology in modern molecular biology, powering diverse applications across proteomics, metabolomics, lipidomics, glycomics, and beyond. As the field continues to evolve, rapid advancements in instrumentation, acquisition strategies, machine learning, and scalable computing have reshaped the landscape of computational MS. This perspective reviews recent developments and highlights key challenges, including data harmonization, statistical confidence estimation, repository-scale analysis, multi-omics integration, and privacy in clinical MS. We also discuss the increasing importance of machine learning and the need to build corresponding literacy within the community. Finally, we reflect on the role of the Computational Mass Spectrometry (CompMS) Community of Special Interest of the International Society for Computational Biology in supporting collaboration, innovation, and knowledge exchange. With MS-based technologies now central to both basic and translational research, continued investment in robust and reproducible computational methods will be essential to realize their full potential.
Ordinary muon capture and $$\\gamma $$ competition in76As supporting calculations for $$0\\nu \\beta \\beta $$ decay
2025-07-30

Abstract The compound nucleus model is employed to calculate partial <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mi>γ</mml:mi> </mml:math> -decay width <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub> <mml:mi>Γ</mml:mi> <mml:mi>γ</mml:mi> </mml:msub> </mml:math> of states in 76 As highly excited above the neutron binding energy. The calculations demonstrate the need to observe the <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mi>γ</mml:mi> </mml:math> competition above neutron threshold when extracting the population of low-lying excited states in 76 As after muon capture on 76 Se. Decay and feeding schemata can be modeled to support the extraction of partial muon capture rates. The latter are needed when results of ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:msup> <mml:mi>μ</mml:mi> <mml:mo>-</mml:mo> </mml:msup> <mml:mo>,</mml:mo> <mml:mi>ν</mml:mi> </mml:mrow> </mml:math> ) reactions are used in tests of model calculations for nuclear matrix elements of neutrinoless double beta decay.
Social media feeds as curatorial assemblages: A conceptual framework
2025-07-30

Social media feeds are a central object of analysis and a frequently recurring topic in the study of digital cultures, but their complex and ephemeral nature resists conceptualization. This paper addresses this challenge by approaching feeds as “assemblages.” Using Instagram and TikTok as primary examples, we employ the concept of the “feed-as-assemblage” to understand how a feed’s constitutive elements (e.g., algorithms, data, devices, interfaces, human actors, practices) form relations both at the micro-level of individual feeds and at the macro-level between all the feeds of a given platform. These relations make up intricate sociotechnical ensembles driven by curation, which is to say, the feed-as-assemblage constantly selects specific elements and rearranges their relations in order to generate value. On the basis of this conceptual framework, we focus on three central elements in the feed-as-assemblage – recommender systems, interfaces, and user practices. These elements serve in turn as heuristic access points into the production of (and exchange between) different forms of value. The general aim of this paper is to offer a conceptual approach that brings the strengths of multiple disciplines to bear in analyzing social media feeds.
Proteomic insights into the biology of dopaminergic neurons
2025-07-30

Dopaminergic neurons, primarily located in the substantia nigra, hypothalamus, and ventral tegmental area of the brain, play crucial roles in motor control, reward, motivation, and cognition. Alterations in their function are associated with numerous neurological and psychiatric disorders, such as Parkinson’s disease, but also Schizophrenia, substance use disorders, and bipolar disorder. Recent advances in mass spectrometry-based proteomics have enabled the comprehensive profiling of protein expression, turnover, subcellular localization, and post-translational modifications at an unprecedented depth of analysis. This review summarizes the developments in proteomic approaches taken to study dopaminergic neurons. We cover findings from global and spatial proteomics studies that revealed brain region-specific protein signatures, as well as dynamic turnover of proteins and the importance of mitochondrial and synaptic proteins for the health and vulnerability of dopaminergic neurons. Combined with advanced molecular cell biology tools, such as growth in microfluidic devices, fluorescent-activated synaptosome sorting, and enzymatic proximity labeling, modern proteomics allows for investigation of synaptic and subcellular proteomes. Despite these advancements, the complexity of the human brain and its cell-specific characteristics remain a challenge. The continuing integration of advanced proteomic techniques with other -omics will eventually yield improved and mechanistic understanding of dopaminergic neurons in health and disease.
Declining bird populations are associated with loss of species identification skills in students
2025-07-30

Biodiversity, including bird diversity, is essential for ecosystem stability. However, recent declines in bird populations threaten the balance, additionally reducing opportunities for people to encounter birds in their daily lives and potentially diminishing species identification skills. We here investigate the relationship between bird population trends, and habitats, and students’ bird species identification skills in Baden-Württemberg, Germany, comparing data from 2005 with 2022/2023. Our results suggest that declining populations of bird species are linked to statistically significant reductions in students’ identification skills (Cohen’s d = -0.421, SE = 0.196, p = 0.032). Today, students aged 8 to 21 years are on average 12.2% less familiar with declining bird species than students in 2005. In contrast, stable or increasing bird populations are not related to changes in identification skills. This may be due to reduced direct exposure to nature, a phenomenon known as the extinction of experience. Farmland birds, among the different habitat types, experienced the greatest decline in familiarity (Cohen’s d = -0.254, SE = 0.086, p = 0.003), perhaps mirroring their negative population trends. Our study introduces important ecological factors such as population decline as a previously overlooked but influential driver of species knowledge loss, in contrast to previous research focusing primarily on social variables (education, demography). These results highlight how both population decline, potentially combined with a diminished nature exposure, may contribute to a loss of species identification skills. They underscore the importance of integrating ecological considerations into biodiversity education and conservation efforts.
An explainable artificial intelligence handbook for psychologists: Methods, opportunities, and challenges.
2025-07-31

With more researchers in psychology using machine learning to model large data sets, many are also looking to eXplainable artificial intelligence (XAI) methods to understand how their model works and to gain insights into the most important predictors. However, the methodological approach for establishing predictor importance in a machine learning model is not as straightforward or as well-established as with traditional statistical models. Not only are there a large number of potential XAI methods to choose from, but there are also a number of unresolved challenges when using XAI to understand psychological data. This article aims to provide an introduction to the field of XAI for psychologists. We first introduce explainability from an applied machine learning perspective and contrast it to that in psychology. Then we provide an overview of commonly used XAI approaches, namely permutation importance, impurity-based feature importance, individual conditional expectation graphs, partial dependence plots, accumulated local effect graphs, Local Interpretable Model-agnostic Explanations (LIME), SHapley Additive exPlanations (SHAP), and Deep Learning Important FeaTures (DeepLIFT). Finally, we demonstrate the impact of multicollinearity on different XAI methods using a simulation analysis and discuss the implementation challenges and future directions in psychological research. (PsycInfo Database Record (c) 2025 APA, all rights reserved).
Demographic and Clinical Profiles of Parkinson's Disease in India: Observations from a Nation‐Wide Multicenter Study
2025-07-31

Abstract Background Parkinson's disease (PD) phenotype may vary with genetic, ethno‐geographic, cultural, and environmental factors. Objectives The aim was to develop a clinical database of PD in India and assess the influence of age‐at‐onset (AAO), gender, and motor subtype on the clinical profile of PD. Methods A cross‐sectional study of PD was conducted across 18 Indian hospitals. Standardized assessments were performed by movement disorder specialists. Data were collected using uniform questionnaires during the recruitment visit. A total of 3300 age‐ and gender‐matched case–control pairs were analyzed for environmental exposures, habits, and co‐morbidities. Results We recruited 7918 PD cases with a mean AAO of 54.2 ± 11.8 years and a median disease duration of 5 years (interquartile range: 2–9). Subgroup analyses based on AAO, gender, and motor phenotype revealed significant differences in motor and non‐motor symptoms, exposures, habits, and co‐morbidities. Except coffee consumption, previously known associations were observed for exposure to insecticides/pesticides/fungicides (odds ratio [OR]: 1.67), head injury (OR: 3.11), coffee consumption (OR: 1.73), diabetes (OR: 1.48), hypertension (OR: 1.73), and smoking (OR: 0.74) in the Indian population. Conclusions This large pan‐Indian study highlights the clinical characteristics, environmental exposures, habits, and comorbid diseases associated with PD, which were broadly similar to those observed in European populations. The earlier AAO in Indian PD patients suggests a potentially higher genetic risk, warranting further investigation. A nationwide, community‐based, epidemiological study is needed to achieve a comprehensive understanding of all risk factors for PD in India and to validate the risk factors identified in this hospital‐based study. © 2025 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
Electron acceptors modulate methane oxidation and active methanotrophic communities in anoxic urban wetland sediments
2025-07-31

ABSTRACT Urban wetlands, although often overlooked, are hotspots for CH 4 cycling. However, the understanding of anaerobic CH 4 oxidation and microbial responses to different electron acceptors in urban wetlands remains limited. Here, we employed DNA-stable isotope probing (SIP) and metagenomic techniques to identify the core CH 4 -oxidizing microbial groups in the presence of NO 3 - , SO 4 2- , or ferrihydrite (Fe(III)) in anoxic urban-lake sediments. The addition of NO 3 - to sediment microcosms promoted CH 4 oxidation, whereas SO 4 2- and Fe(III) had minimal or inhibitory effects on CH 4 oxidation rates in anoxic microcosms. The SIP-identified methanotrophs in response to the addition of CH 4 comprised the Marine Benthic Group D (MBG-D), “ Candidatus Methylomirabilis Sh765B-TzT-35 and Z114MB74,” and the putatively aerobic methanotrophs Methylobacter and Methylocystis . The presence of NO 3 - further enriched Methylocaldum , Methylomonas , ‘ Ca . Methylomirabilis Sh765B-TzT-35 and Z114MB74’, Methylococcaceae , and Methylospira . In contrast, SO 4 2- and Fe(III) amendments notably shifted the dominant methanotrophs through the significant labeling of Methylocystis . Furthermore, metagenomic analysis of 13 C-labeled DNA showed enrichment of genes for oxidation of CH 4 and its intermediates, as well as the reduction of NO 3 - , SO 4 2- , Fe(III), and fermentation. These results underscore the activity of NO 3 - -dependent CH 4 -oxidizing microorganisms and highlight their potential metabolic versatility in highly anthropogenically influenced urban wetlands. IMPORTANCE Urban wetlands are critical ecosystems for CH 4 cycling but are increasingly impacted by complex pollutants from urban development, such as nitrates, sulfates, and Fe(III) from industrial runoff, atmospheric deposition, and wastewater discharge. This study reveals how these pollutants act as electron acceptors, modulating microbial metabolic pathways and reshaping methanotrophic communities under anoxic conditions. By uncovering the microbial mechanisms driving CH4 oxidation in urban wetland sediments, our findings provide a deeper understanding of how anthropogenic pollution alters biogeochemical cycles. These insights are crucial for developing targeted strategies to mitigate CH4 emissions and improve greenhouse gas control in rapidly urbanizing regions.
Visual loom caused by self-movement or object-movement elicits distinct responses in mouse superior colliculus
2025-07-31

The meaning of a visual image depends on context-a mouse sees an expanding visual stimulus when approaching a dark refuge or when a cat approaches them, and distinguishing between the two is a matter of life and death. The superior colliculus (SC) is an evolutionarily ancient hub essential for survival behaviors like approach and avoidance of threats.<sup>1</sup><sup>,</sup><sup>2</sup> We therefore combined virtual reality and neural recordings to ask whether matching visual stimuli to self-motion alters behavior and neural activity in SC. We first measured locomotion behavior and neural activity while animals approached an object in virtual reality or while the same object loomed at them. In both contexts, vision dominated activity in the superficial layers of SC (SCs), whereas locomotion had more influence on activity in the intermediate layers (SCim). In addition, animals instinctively slowed their locomotion when nearing the object or when the object neared them. To directly test animals' ability to distinguish self from object motion, we replayed the visual images generated during object approach. Locomotion behavior often changed during replay, showing animals can determine whether visual motion is matched to their self-movement. Further, decoders trained on locomotion behavior or on population activity in SC, particularly in SCim, were able to reliably discriminate self-movement and object movement contexts. We conclude that both mouse behavior and SC activity distinguish the context of visual motion and can thus discriminate motion arising from an animal's own movement and that of an external agent.