bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying benefits of renewable investments for German residential Prosumers in times of volatile energy markets
Authors: van Ouwerkerk Jonas , Celi Cortés Mauricio , Nsir Najet , Gong Jingyu , Figgener Jan , Zurmühlen Sebastian , Bußar Christian , Sauer Dirk Uwe 
Published: September 2024

AbstractThe COVID-19 pandemic and the Russian invasion of Ukraine have led to unseen disruptions in the global energy markets since the end of 2021. Residential renewable investments like photovoltaic systems, battery home storage systems, and heat pumps are therefore gaining traction. However, the benefits of those technologies during the energy crisis and beyond have not been fully quantified yet. Therefore, in this study, we benchmark renewable investments for a broad variety of single-family homes by evaluating potential cost savings and emission reductions. In addition, the study considers the influence of recent political incentives and subsidies. The results show that photovoltaic systems are a no-regret investment decision, both economically and environmentally. At the climax of the energy crisis, a typical German household with a heat pump could save 1850 € and reduce equivalent CO2 emissions by 250 g/kWh annually. Politically introduced price breaks on electricity and natural gas do not reverse this advantage. Furthermore, when owning an electric vehicle renewable investments are often more beneficial.
Dopamine neurons encode trial-by-trial subjective reward value in an auction-like task
Authors: Hill Daniel F. , Hickman Robert W. , Al-Mohammad Alaa , Stasiak Arkadiusz , Schultz Wolfram 
Published: September 2024

AbstractThe dopamine reward prediction error signal is known to be subjective but has so far only been assessed in aggregate choices. However, personal choices fluctuate across trials and thus reflect the instantaneous subjective reward value. In the well-established Becker-DeGroot-Marschak (BDM) auction-like mechanism, participants are encouraged to place bids that accurately reveal their instantaneous subjective reward value; inaccurate bidding results in suboptimal reward (“incentive compatibility”). In our experiment, male rhesus monkeys became experienced over several years to place accurate BDM bids for juice rewards without specific external constraints. Their bids for physically identical rewards varied trial by trial and increased overall for larger rewards. In these highly experienced animals, responses of midbrain dopamine neurons followed the trial-by-trial variations of bids despite constant, explicitly predicted reward amounts. Inversely, dopamine responses were similar with similar bids for different physical reward amounts. Support Vector Regression demonstrated accurate prediction of the animals’ bids by as few as twenty dopamine neurons. Thus, the phasic dopamine reward signal reflects instantaneous subjective reward value.
Distinct mechanisms regulate ventricular and atrial chamber wall formation
Authors: Albu Marga , Affolter Eileen , Gentile Alessandra , Xu Yanli , Kikhi Khrievono , Howard Sarah , Kuenne Carsten , Priya Rashmi , Gunawan Felix , Stainier Didier Y. R. 
Published: September 2024

AbstractTissues undergo distinct morphogenetic processes to achieve similarly shaped structures. In the heart, cardiomyocytes in both the ventricle and atrium build internal structures for efficient contraction. Ventricular wall formation (trabeculation) is initiated by cardiomyocyte delamination. How cardiomyocytes build the atrial wall is poorly understood. Using longitudinal imaging in zebrafish, we found that at least 25% of the atrial cardiomyocytes elongate along the long axis of the heart. These cell shape changes result in cell intercalation and convergent thickening, leading to the formation of the internal muscle network. We tested factors important for ventricular trabeculation including Nrg/ErbB and Notch signaling and found no evidence for their role in atrial muscle network formation. Instead, our data suggest that atrial cardiomyocyte elongation is regulated by Yap, which has not been implicated in trabeculation. Altogether, these data indicate that distinct cellular and molecular mechanisms build the internal muscle structures in the atrium and ventricle.
A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence
Authors: Ivanković Mario , Brand Jeremias N. , Pandolfini Luca , Brown Thomas , Pippel Martin , Rozanski Andrei , Schubert Til , Grohme Markus A. , Winkler Sylke , Robledillo Laura , Zhang Meng , Codino Azzurra , Gustincich Stefano , Vila-Farré Miquel , Zhang Shu , Papantonis Argyris , Marques André , Rink Jochen C. 
Published: September 2024

AbstractThe planarian Schmidtea mediterranea is being studied as a model species for regeneration, but the assembly of planarian genomes remains challenging. Here, we report a high-quality haplotype-phased, chromosome-scale genome assembly of the sexual S2 strain of S. mediterranea and high-quality chromosome-scale assemblies of its three close relatives, S. polychroa, S. nova, and S. lugubris. Using hybrid gene annotations and optimized ATAC-seq and ChIP-seq protocols for regulatory element annotation, we provide valuable genome resources for the planarian research community and a first comparative perspective on planarian genome evolution. Our analyses reveal substantial divergence in protein-coding sequences and regulatory regions but considerable conservation within promoter and enhancer annotations. We also find frequent retrotransposon-associated chromosomal inversions and interchromosomal translocations within the genus Schmidtea and, remarkably, independent and nearly complete losses of ancestral metazoan synteny in Schmidtea and two other flatworm groups. Overall, our results suggest that platyhelminth genomes can evolve without syntenic constraints.
Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements
Authors: Chardon Florence M. , McDiarmid Troy A. , Page Nicholas F. , Daza Riza M. , Martin Beth K. , Domcke Silvia , Regalado Samuel G. , Lalanne Jean-Benoît , Calderon Diego , Li Xiaoyi , Starita Lea M. , Sanders Stephan J. , Ahituv Nadav , Shendure Jay 
Published: September 2024

AbstractCRISPR-based gene activation (CRISPRa) is a strategy for upregulating gene expression by targeting promoters or enhancers in a tissue/cell-type specific manner. Here, we describe an experimental framework that combines highly multiplexed perturbations with single-cell RNA sequencing (sc-RNA-seq) to identify cell-type-specific, CRISPRa-responsive cis-regulatory elements and the gene(s) they regulate. Random combinations of many gRNAs are introduced to each of many cells, which are then profiled and partitioned into test and control groups to test for effect(s) of CRISPRa perturbations of both enhancers and promoters on the expression of neighboring genes. Applying this method to a library of 493 gRNAs targeting candidate cis-regulatory elements in both K562 cells and iPSC-derived excitatory neurons, we identify gRNAs capable of specifically upregulating intended target genes and no other neighboring genes within 1 Mb, including gRNAs yielding upregulation of six autism spectrum disorder (ASD) and neurodevelopmental disorder (NDD) risk genes in neurons. A consistent pattern is that the responsiveness of individual enhancers to CRISPRa is restricted by cell type, implying a dependency on either chromatin landscape and/or additional trans-acting factors for successful gene activation. The approach outlined here may facilitate large-scale screens for gRNAs that activate genes in a cell type-specific manner.
Re-organization of Pacific overturning circulation across the Miocene Climate Optimum
Authors: Holbourn Ann , Kuhnt Wolfgang , Kulhanek Denise K. , Mountain Gregory , Rosenthal Yair , Sagawa Takuya , Lübbers Julia , Andersen Nils 
Published: September 2024

AbstractThe response of the ocean overturning circulation to global warming remains controversial. Here, we integrate a multiproxy record from International Ocean Discovery Program Site U1490 in the western equatorial Pacific with published data from the Pacific, Southern and Indian Oceans to investigate the evolution of deep water circulation during the Miocene Climate Optimum (MCO) and Middle Miocene Climate Transition (MMCT). We find that the northward export of southern-sourced deep waters was closely tied to high-latitude climate and Antarctic ice cover variations. Global warming during the MCO drove a progressive decrease in carbonate ion concentration and density stratification, shifting the overturning from intermediate to deeper waters. In the western equatorial Pacific, carbonate dissolution was compensated by increased pelagic productivity, resulting in overall elevated carbonate accumulation rates after ~16 Ma. Stepwise global cooling and Antarctic glacial expansion during the MMCT promoted a gradual improvement in carbonate preservation and the initiation of a near-modern Pacific overturning circulation. We infer that changes in the latitudinal thermal gradient and in Southern Ocean zonal wind stress and upper ocean stratification drove radically different modes of deep water formation and overturning across the MCO and MMCT.
Examining the photo catalytic potency of annealed and un-annealed ZnO and nickel doped ZnO for degradation of organic pollutants in waste waters
Authors: Gull Fatima , Riaz Rehana , Ansari Komal , Atiq Haleema 
Published: September 2024

AbstractWater scarcity and pollution has increased the need for innovative and effective waste water treatment methods. The presented study aims to tackle this difficulty by synthesizing zinc oxide (ZnO) and nickel (Ni) doped ZnO to improve their photo catalytic capacity. This study examines wastewater treatment and organic pollutant breakdown using nanotechnology. The annealing increases photo catalytic activity by 65%, thereby enhancing efficiency. XRD shows that annealing decreased the average crystal size of pure ZnO and nickel doped ZnO (Ni:ZnO) i.e., for pure ZnO average crystal size is decreased from 23.90 to 20.90 nm and for Ni:ZnO, 34.39–28.65 nm. SEM shows that un annealed samples have agglomerates, while annealed samples are quasi-spherical. Using diffuse reflectance spectroscopy (DRS), the study examines how annealing affects optical band gap. Annealed Ni:ZnO has a band gap of 3.09 eV, which is smaller as compared to un annealed Ni:ZnO (3.18 e V). Similarly, the decline in energy band gap is observed for pure ZnO too. This study highlights the significant capacity of Ni:ZnO, for un annealed and annealed synthesis, to effectively meet the urgent requirements for waste water treatment. The extensive research conducted in this work enhances our comprehension of photo catalytic materials and underscores its potential for practical implementation in addressing waste water-related environmental issues.
Ameliorative effects of silymarin on aflatoxin B1 toxicity in weaned rabbits: impact on growth, blood profile, and oxidative stress
Authors: Imbabi Tharwat A. , El‐Sayed Abdelkarim I. , El-Habbak Mohamed H. , Nasr Mohammed A. , Halawa Eman H. 
Published: September 2024

AbstractNatural plant extracts offer numerous health benefits for rabbits, including improved feed utilization, antimycotic and antiaflatoxigenic effect, antioxidants, immunological modulation, and growth performance. The aim of the current study was to investigate the effects of silymarin on the performance, hemato-biochemical indices, antioxidants, and villus morphology. A total of 45 Moshtohor 4 weeks old weaned male rabbits were randomly allocated into three groups (15 rabbit/each) each group with 5 replicates. The first group served as the control group feed on an infected diet by aflatoxin B1 (AFB1) 0.02 mg/kg BW, while the second and third groups received an infected diet by AFB1 (0.02 mg/kg BW) and was treated with Silymarin 20 mg/kg BW/day or 30 mg/kg BW/day, respectively. Regarding the growth performance, silymarin supplementation significantly improved the final body weight compared with the control group. Physiologically, silymarin induced high level of dose-dependent total red blood cell count, hematocrit, eosinophils, high-density lipoprotein cholesterol, superoxid dismutase, catalase activity, total antioxidant capacityand intestinal villi width and length. Moreover, silymarin significantly restricted oxidative stress indicators, malondialdehyde, Alanine aminotransferase, aspartate aminotransferase, total cholesterol, triglyceridein rabbits treated with (AFB1). In conclusion, silymarin supplementation to AFB1 contaminated rabbit diet may mitigate the negative effect of AFB1 on the rabbit performance and health status and increase growth performance, average daily gain, immunological modulation and antioxidants and provide a theoretical basis for the application of silymarin in livestock production.
Impairment of affective and cognitive empathy in high functioning autism is mediated by alterations in emotional reactivity
Authors: Kimmig Ann-Christin S. , Burger Lina , Schall Marina , Derntl Birgit , Wildgruber Dirk 
Published: September 2024

AbstractEmpathy impairments are considered a key aspect of autism-spectrum disorders (ASD). Previous research consistently shows reduced cognitive empathy, but findings on affective empathy vary, possibly due to experimental design variations (e.g., stimulus modality, social distance) and individual psychological factors (e.g., perceptual abilities, emotional reactivity). This study aims to clarify deficits in affective and cognitive empathy in ASD by addressing these contributing factors. Empathy was examined in 34 autistic individuals and 33 typically developed controls (TDCs) through the Textual Empathy Test (TET). The TET was developed to assess emotional responses when imagining oneself (emotional reactivity) as compared to a target person (friend, stranger) in emotional situations presented via short verbal descriptions. Participants rated emotional states of the target person (cognitive empathy) as well as their own emotional responses when imagining the target person in that situation (affective empathy). Ratings were interpreted relative to normative mean values through standardized regression coefficients. Results showed that high-functioning autism was associated with lower cognitive and affective empathy irrespective of social distance as well as with decreased emotional reactivity compared to controls. Moreover, emotional reactivity mediated the impact of ASD on both empathic components. In summary, altered emotional reactivity may underlie impaired empathy in autistic individuals.
Machine learning based classification of presence utilizing psychophysiological signals in immersive virtual environments
Authors: Saha Shuvodeep , Dobbins Chelsea , Gupta Anubha , Dey Arindam 
Published: September 2024

AbstractIn Virtual Reality (VR), a higher level of presence positively influences the experience and engagement of a user. There are several parameters that are responsible for generating different levels of presence in VR, including but not limited to, graphical fidelity, multi-sensory stimuli, and embodiment. However, standard methods of measuring presence, including self-reported questionnaires, are biased. This research focuses on developing a robust model, via machine learning, to detect different levels of presence in VR using multimodal neurological and physiological signals, including electroencephalography and electrodermal activity. An experiment has been undertaken whereby participants (N = 22) were each exposed to three different levels of presence (high, medium, and low) in a random order in VR. Four parameters within each level, including graphics fidelity, audio cues, latency, and embodiment with haptic feedback, were systematically manipulated to differentiate the levels. A number of multi-class classifiers were evaluated within a three-class classification problem, using a One-vs-Rest approach, including Support Vector Machine, k-Nearest Neighbour, Extra Gradient Boosting, Random Forest, Logistic Regression, and Multiple Layer Perceptron. Results demonstrated that the Multiple Layer Perceptron model obtained the highest macro average accuracy of $$93\pm 0.03\%$$

93
±
0.03
%

. Posthoc analysis revealed that relative band power, which is expressed as the ratio of power in a specific frequency band to the total baseline power, in both the frontal and parietal regions, including beta over theta and alpha ratio, and differential entropy were most significant in detecting different levels of presence.
Reciprocal cognitive and emotional interaction in STEMM university learning and teaching
Authors: Ippolito Kate , Kingsbury Martyn 
Published: September 2024

AbstractUniversity learning and teaching involves contrasting and interacting emotional experiences. Even in disciplines considered as objective as Science and Engineering, emotion plays a significant role in catalysing and sustaining learning. Although emotions are individually felt, they are socially constructed between people. This is especially relevant in group-based learning evident in much contemporary higher education. This paper applies the concept of emotion socialization to illustrate how groups of students and teachers cope and succeed in cognitively and emotionally challenging learning settings. The study is based on qualitative data collected across six STEMM university departments, from 280 students via in-situ questionnaires and from 20 teachers via group and follow-up interviews. Two key findings offer insight into processes of reciprocal influence on cognition and emotion. The first relates to ways in which students’ and teachers’ differing knowledge-related goals and relationships with knowledge influenced cognition and emotion, uncovering previously unacknowledged connections. The second relates to how students’ comparisons of progress towards academic goals with peers contributed considerably to their emotional experiences in cognitively and emotionally helpful and unhelpful ways. Practical implications are presented, including possibilities for capitalising on existing emotion socialization processes and enhancing how they influence cognition and emotional well-being.
Biochemical and crystallographic studies of l,d-transpeptidase 2 from Mycobacterium tuberculosis with its natural monomer substrate
Authors: de Munnik Mariska , Lang Pauline A. , Calvopiña Karina , Rabe Patrick , Brem Jürgen , Schofield Christopher J. 
Published: September 2024

AbstractThe essential l,d-transpeptidase of Mycobacterium tuberculosis (LdtMt2) catalyses the formation of 3$$\to$$
→
3 cross-links in cell wall peptidoglycan and is a target for development of antituberculosis therapeutics. Efforts to inhibit LdtMt2 have been hampered by lack of knowledge of how it binds its substrate. To address this gap, we optimised the isolation of natural disaccharide tetrapeptide monomers from the Corynebacterium jeikeium bacterial cell wall through overproduction of the peptidoglycan sacculus. The tetrapeptides were used in binding / turnover assays and biophysical studies on LdtMt2. We determined a crystal structure of wild-type LdtMt2 reacted with its natural substrate, the tetrapeptide monomer of the peptidoglycan layer. This structure shows formation of a thioester linking the catalytic cysteine and the donor substrate, reflecting an intermediate in the transpeptidase reaction; it informs on the mode of entrance of the donor substrate into the LdtMt2 active site. The results will be useful in design of LdtMt2 inhibitors, including those based on substrate binding interactions, a strategy successfully employed for other nucleophilic cysteine enzymes.
Functional Neuroligin-2-MDGA1 interactions differentially regulate synaptic GABAARs and cytosolic gephyrin aggregation
Authors: Zeppillo Tommaso , Ali Heba , Ravichandran Sowbarnika , Ritter Tamara C. , Wenger Sally , López-Murcia Francisco J. , Gideons Erinn , Signorelli Janetti , Schmeisser Michael J. , Wiltfang Jens , Rhee JeongSeop , Brose Nils , Taschenberger Holger , Krueger-Burg Dilja 
Published: September 2024

AbstractNeuroligin-2 (Nlgn2) is a key synaptic adhesion protein at virtually all GABAergic synapses, which recruits GABAARs by promoting assembly of the postsynaptic gephyrin scaffold. Intriguingly, loss of Nlgn2 differentially affects subsets of GABAergic synapses, indicating that synapse-specific interactors and redundancies define its function, but the nature of these interactions remain poorly understood. Here we investigated how Nlgn2 function in hippocampal area CA1 is modulated by two proposed interaction partners, MDGA1 and MDGA2. We show that loss of MDGA1 expression, but not heterozygous deletion of MDGA2, ameliorates the abnormal cytosolic gephyrin aggregation, the reduction in inhibitory synaptic transmission and the exacerbated anxiety-related behaviour characterizing Nlgn2 knockout (KO) mice. Additionally, combined Nlgn2 and MDGA1 deletion causes an exacerbated layer-specific loss of gephyrin puncta. Given that both Nlgn2 and the MDGA1 have been correlated with many psychiatric disorders, our data support the notion that cytosolic gephyrin aggregation may represent an interesting target for novel therapeutic strategies.
Computational screening of the effects of mutations on protein-protein off-rates and dissociation mechanisms by τRAMD
Authors: D’Arrigo Giulia , Kokh Daria B. , Nunes-Alves Ariane , Wade Rebecca C. 
Published: September 2024

AbstractThe dissociation rate, or its reciprocal, the residence time (τ), is a crucial parameter for understanding the duration and biological impact of biomolecular interactions. Accurate prediction of τ is essential for understanding protein-protein interactions (PPIs) and identifying potential drug targets or modulators for tackling diseases. Conventional molecular dynamics simulation techniques are inherently constrained by their limited timescales, making it challenging to estimate residence times, which typically range from minutes to hours. Building upon its successful application in protein-small molecule systems, τ-Random Acceleration Molecular Dynamics (τRAMD) is here investigated for estimating dissociation rates of protein-protein complexes. τRAMD enables the observation of unbinding events on the nanosecond timescale, facilitating rapid and efficient computation of relative residence times. We tested this methodology for three protein-protein complexes and their extensive mutant datasets, achieving good agreement between computed and experimental data. By combining τRAMD with MD-IFP (Interaction Fingerprint) analysis, dissociation mechanisms were characterized and their sensitivity to mutations investigated, enabling the identification of molecular hotspots for selective modulation of dissociation kinetics. In conclusion, our findings underscore the versatility of τRAMD as a simple and computationally efficient approach for computing relative protein-protein dissociation rates and investigating dissociation mechanisms, thereby aiding the design of PPI modulators.