bluuebunny/crossref_metadata_2025_split huggingface dataset:
A marine cryptochrome with an inverse photo-oligomerization mechanism
Authors: Vu Hong Ha , Behrmann Heide , Hanić Maja , Jeyasankar Gayathri , Krishnan Shruthi , Dannecker Dennis , Hammer Constantin , Gunkel Monika , Solov’yov Ilia A. , Wolf Eva , Behrmann Elmar 
Published: October 2023

AbstractCryptochromes (CRYs) are a structurally conserved but functionally diverse family of proteins that can confer unique sensory properties to organisms. In the marine bristle worm Platynereis dumerilii, its light receptive cryptochrome L-CRY (PdLCry) allows the animal to discriminate between sunlight and moonlight, an important requirement for synchronizing its lunar cycle-dependent mass spawning. Using cryo-electron microscopy, we show that in the dark, PdLCry adopts a dimer arrangement observed neither in plant nor insect CRYs. Intense illumination disassembles the dimer into monomers. Structural and functional data suggest a mechanistic coupling between the light-sensing flavin adenine dinucleotide chromophore, the dimer interface, and the C-terminal tail helix, with a likely involvement of the phosphate binding loop. Taken together, our work establishes PdLCry as a CRY protein with inverse photo-oligomerization with respect to plant CRYs, and provides molecular insights into how this protein might help discriminating the different light intensities associated with sunlight and moonlight.
Localization and interaction of interlayer excitons in MoSe2/WSe2 heterobilayers
Authors: Fang Hanlin , Lin Qiaoling , Zhang Yi , Thompson Joshua , Xiao Sanshui , Sun Zhipei , Malic Ermin , Dash Saroj P. , Wieczorek Witlef 
Published: October 2023

AbstractTransition metal dichalcogenide (TMD) heterobilayers provide a versatile platform to explore unique excitonic physics via the properties of the constituent TMDs and external stimuli. Interlayer excitons (IXs) can form in TMD heterobilayers as delocalized or localized states. However, the localization of IX in different types of potential traps, the emergence of biexcitons in the high-excitation regime, and the impact of potential traps on biexciton formation have remained elusive. In our work, we observe two types of potential traps in a MoSe2/WSe2 heterobilayer, which result in significantly different emission behavior of IXs at different temperatures. We identify the origin of these traps as localized defect states and the moiré potential of the TMD heterobilayer. Furthermore, with strong excitation intensity, a superlinear emission behavior indicates the emergence of interlayer biexcitons, whose formation peaks at a specific temperature. Our work elucidates the different excitation and temperature regimes required for the formation of both localized and delocalized IX and biexcitons and, thus, contributes to a better understanding and application of the rich exciton physics in TMD heterostructures.
Electrochemical carbon–carbon coupling with enhanced activity and racemate stereoselectivity by microenvironment regulation
Authors: Kong Kejian , Li An-Zhen , Wang Ye , Shi Qiujin , Li Jing , Ji Kaiyue , Duan Haohong 
Published: October 2023

AbstractEnzymes are characteristic of catalytic efficiency and specificity by maneuvering multiple components in concert at a confined nanoscale space. However, achieving such a configuration in artificial catalysts remains challenging. Herein, we report a microenvironment regulation strategy by modifying carbon paper with hexadecyltrimethylammonium cations, delivering electrochemical carbon–carbon coupling of benzaldehyde with enhanced activity and racemate stereoselectivity. The modified electrode–electrolyte interface creates an optimal microenvironment for electrocatalysis—it engenders dipolar interaction with the reaction intermediate, giving a 2.2-fold higher reaction rate (from 0.13 to 0.28 mmol h−1 cm−2); Moreover, it repels interfacial water and modulates the conformational specificity of reaction intermediate by facilitating intermolecular hydrogen bonding, affording 2.5-fold higher diastereomeric ratio of racemate to mesomer (from 0.73 to 1.82). We expect that the microenvironment regulation strategy will lead to the advanced design of electrode–electrolyte interface for enhanced activity and (stereo)selectivity that mimics enzymes.
Stress-induced red nucleus attenuation induces anxiety-like behavior and lymph node CCL5 secretion
Authors: Shi Dong-Dong , Zhang Ying-Dan , Zhang Sen , Liao Bing-Bing , Chu Min-Yi , Su Shanshan , Zhuo Kaiming , Hu Hao , Zhang Chen , Wang Zhen 
Published: October 2023

AbstractPrevious studies have speculated that brain activity directly controls immune responses in lymphoid organs. However, the upstream brain regions that control lymphoid organs and how they interface with lymphoid organs to produce stress-induced anxiety-like behavior remain elusive. Using stressed human participants and rat models, we show that CCL5 levels are increased in stressed individuals compared to controls. Stress-inducible CCL5 is mainly produced from cervical lymph nodes (CLN). Retrograde tracing from CLN identifies glutamatergic neurons in the red nucleus (RN), the activities of which are tightly correlated with CCL5 levels and anxiety-like behavior in male rats. Ablation or chemogenetic inhibition of RN glutamatergic neurons increases anxiety levels and CCL5 expression in the serum and CLNs, whereas pharmacogenetic activation of these neurons reduces anxiety levels and CCL5 synthesis after restraint stress exposure. Chemogenetic inhibition of the projection from primary motor cortex to RN elicits anxiety-like behavior and CCL5 synthesis. This brain-lymph node axis provides insights into lymph node tissue as a stress-responsive endocrine organ.
PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks
Authors: Ponce-de-Leon Miguel , Montagud Arnau , Noël Vincent , Meert Annika , Pradas Gerard , Barillot Emmanuel , Calzone Laurence , Valencia Alfonso 
Published: October 2023

AbstractIn systems biology, mathematical models and simulations play a crucial role in understanding complex biological systems. Different modelling frameworks are employed depending on the nature and scales of the system under study. For instance, signalling and regulatory networks can be simulated using Boolean modelling, whereas multicellular systems can be studied using agent-based modelling. Herein, we present PhysiBoSS 2.0, a hybrid agent-based modelling framework that allows simulating signalling and regulatory networks within individual cell agents. PhysiBoSS 2.0 is a redesign and reimplementation of PhysiBoSS 1.0 and was conceived as an add-on that expands the PhysiCell functionalities by enabling the simulation of intracellular cell signalling using MaBoSS while keeping a decoupled, maintainable and model-agnostic design. PhysiBoSS 2.0 also expands the set of functionalities offered to the users, including custom models and cell specifications, mechanistic submodels of substrate internalisation and detailed control over simulation parameters. Together with PhysiBoSS 2.0, we introduce PCTK, a Python package developed for handling and processing simulation outputs, and generating summary plots and 3D renders. PhysiBoSS 2.0 allows studying the interplay between the microenvironment, the signalling pathways that control cellular processes and population dynamics, suitable for modelling cancer. We show different approaches for integrating Boolean networks into multi-scale simulations using strategies to study the drug effects and synergies in models of cancer cell lines and validate them using experimental data. PhysiBoSS 2.0 is open-source and publicly available on GitHub with several repositories of accompanying interoperable tools.
Climate change exacerbates nutrient disparities from seafood
Authors: Cheung William W. L. , Maire Eva , Oyinlola Muhammed A. , Robinson James P. W. , Graham Nicholas A. J. , Lam Vicky W. Y. , MacNeil M. Aaron , Hicks Christina C. 
Published: October 2023

AbstractSeafood is an important source of bioavailable micronutrients supporting human health, yet it is unclear how micronutrient production has changed in the past or how climate change will influence its availability. Here combining reconstructed fisheries databases and predictive models, we assess nutrient availability from fisheries and mariculture in the past and project their futures under climate change. Since the 1990s, availabilities of iron, calcium and omega-3 from seafood for direct human consumption have increased but stagnated for protein. Under climate change, nutrient availability is projected to decrease disproportionately in tropical low-income countries that are already highly dependent on seafood-derived nutrients. At 4 oC of warming, nutrient availability is projected to decline by ~30% by 2100 in low income countries, while at 1.5–2.0 oC warming, decreases are projected to be ~10%. We demonstrate the importance of effective mitigation to support nutritional security of vulnerable nations and global health equity.
The molecular basis of drug selectivity for α5 subunit-containing GABAA receptors
Authors: Kasaragod Vikram Babu , Malinauskas Tomas , Wahid Ayla A. , Lengyel Judith , Knoflach Frederic , Hardwick Steven W. , Jones Charlotte F. , Chen Wan-Na , Lucas Xavier , El Omari Kamel , Chirgadze Dimitri Y. , Aricescu A. Radu , Cecere Giuseppe , Hernandez Maria-Clemencia , Miller Paul S. 
Published: October 2023

Abstractα5 subunit-containing γ-aminobutyric acid type A (GABAA) receptors represent a promising drug target for neurological and neuropsychiatric disorders. Altered expression and function contributes to neurodevelopmental disorders such as Dup15q and Angelman syndromes, developmental epilepsy and autism. Effective drug action without side effects is dependent on both α5-subtype selectivity and the strength of the positive or negative allosteric modulation (PAM or NAM). Here we solve structures of drugs bound to the α5 subunit. These define the molecular basis of binding and α5 selectivity of the β-carboline, methyl 6,7-dimethoxy-4-ethyl-β-carboline-3-carboxylate (DMCM), type II benzodiazepine NAMs, and a series of isoxazole NAMs and PAMs. For the isoxazole series, each molecule appears as an ‘upper’ and ‘lower’ moiety in the pocket. Structural data and radioligand binding data reveal a positional displacement of the upper moiety containing the isoxazole between the NAMs and PAMs. Using a hybrid molecule we directly measure the functional contribution of the upper moiety to NAM versus PAM activity. Overall, these structures provide a framework by which to understand distinct modulator binding modes and their basis of α5-subtype selectivity, appreciate structure–activity relationships, and empower future structure-based drug design campaigns.
A novel approach for predicting upstream regulators (PURE) that affect gene expression
Authors: Nguyen Tuan-Minh , Craig Douglas B. , Tran Duc , Nguyen Tin , Draghici Sorin 
Published: October 2023

AbstractExternal factors such as exposure to a chemical, drug, or toxicant (CDT), or conversely, the lack of certain chemicals can cause many diseases. The ability to identify such causal CDTs based on changes in the gene expression profile is extremely important in many studies. Furthermore, the ability to correctly infer CDTs that can revert the gene expression changes induced by a given disease phenotype is a crucial step in drug repurposing. We present an approach for Predicting Upstream REgulators (PURE) designed to tackle this challenge. PURE can correctly infer a CDT from the measured expression changes in a given phenotype, as well as correctly identify drugs that could revert disease-induced gene expression changes. We compared the proposed approach with four classical approaches as well as with the causal analysis used in Ingenuity Pathway Analysis (IPA) on 16 data sets (1 rat, 5 mouse, and 10 human data sets), involving 8 chemicals or drugs. We assessed the results based on the ability to correctly identify the CDT as indicated by its rank. We also considered the number of false positives, i.e. CDTs other than the correct CDT that were reported to be significant by each method. The proposed approach performed best in 11 out of the 16 experiments, reporting the correct CDT at the very top 7 times. IPA was the second best, reporting the correct CDT at the top 5 times, but was unable to identify the correct CDT at all in 5 out of the 16 experiments. The validation results showed that our approach, PURE, outperformed some of the most popular methods in the field. PURE could effectively infer the true CDTs responsible for the observed gene expression changes and could also be useful in drug repurposing applications.
Identifying target areas for risk-based surveillance and control of transboundary animal diseases: a seasonal analysis of slaughter and live-trade cattle movements in Uganda
Authors: González-Gordon Lina , Porphyre Thibaud , Muwonge Adrian , Nantima Noelina , Ademun Rose , Ochwo Sylvester , Mwiine Norbert Frank , Boden Lisa , Muhanguzi Dennis , Bronsvoort Barend Mark de C. 
Published: October 2023

AbstractAnimal movements are a major driver for the spread of Transboundary Animal Diseases (TADs). These movements link populations that would otherwise be isolated and hence create opportunities for susceptible and infected individuals to meet. We used social network analysis to describe the seasonal network structure of cattle movements in Uganda and unravel critical network features that identify districts or sub-regions for targeted risk-based surveillance and intervention. We constructed weighted, directed networks based on 2019 between-district cattle movements using official livestock mobility data; the purpose of the movement (‘slaughter’ vs. ‘live trade’) was used to subset the network and capture the risks more reliably. Our results show that cattle trade can result in local and long-distance disease spread in Uganda. Seasonal variability appears to impact the structure of the network, with high heterogeneity of node and edge activity identified throughout the seasons. These observations mean that the structure of the live trade network can be exploited to target influential district hubs within the cattle corridor and peripheral areas in the south and west, which would result in rapid network fragmentation, reducing the contact structure-related trade risks. Similar exploitable features were observed for the slaughter network, where cattle traffic serves mainly slaughter hubs close to urban centres along the cattle corridor. Critically, analyses that target the complex livestock supply value chain offer a unique framework for understanding and quantifying risks for TADs such as Foot-and-Mouth disease in a land-locked country like Uganda. These findings can be used to inform the development of risk-based surveillance strategies and decision making on resource allocation. For instance, vaccine deployment, biosecurity enforcement and capacity building for stakeholders at the local community and across animal health services with the potential to limit the socio-economic impact of outbreaks, or indeed reduce their frequency.
Cytotoxicity, mutagenicity and genotoxicity of electronic cigarettes emission aerosols compared to cigarette smoke: the REPLICA project
Authors: Emma Rosalia , Fuochi Virginia , Distefano Alfio , Partsinevelos Konstantinos , Rust Sonja , Zadjali Fahad , Al Tobi Mohammed , Zadjali Razan , Alharthi Zaina , Pulvirenti Roberta , Furneri Pio Maria , Polosa Riccardo , Sun Ang , Caruso Massimo , Li Volti Giovanni ,   the Replica Project Group, Li Volti Giovanni , Caruso Massimo , Emma Rosalia , Giordano Antonio , Sun Ang , Volarevic Vladislav , Lesmana Ronny , Poulas Konstantinos , Distefano Alfio , Partsinevelos Konstantinos , Pulvirenti Roberta , Costa Aurora , Arsenijevic Aleksandar , Barliana Melisa I. , Mesiakaris Konstantinos , Albalushi Najwa , Giardina Chiara , Furnari Salvatore 
Published: October 2023

AbstractConcerns have recently increased that the integrity of some scientific research is questionable due to the inability to reproduce the claimed results of some experiments and thereby confirm that the original researcher's conclusions were justified. This phenomenon has been described as 'reproducibility crisis' and affects various fields from medicine to basic applied sciences. In this context, the REPLICA project aims to replicate previously conducted in vitro studies on the toxicity of cigarette smoke and e-cigarette aerosol, sometimes adding experiments or conditions where necessary, in order to verify the robustness and replicability of the data. In this work the REPLICA Team replicated biological and toxicological assessment published by Rudd and colleagues in 2020. As in the original paper, we performed Neutral Red Uptake (NRU) assay for the evaluation of cytotoxicity, Ames test for the evaluation of mutagenesis and In Vitro Micronuclei (IVMN) assay for the evaluation of genotoxicity on cells treated with cigarette smoke or e-cigarette aerosol. The results showed high cytotoxicity, mutagenicity and genotoxicity induced by cigarette smoke, but slight or no cytotoxic, mutagenic and genotoxic effects induced by the e-cigarette aerosol. Although the two studies presented some methodological differences, the findings supported those previously presented by Rudd and colleagues.
Observation of momentum-dependent charge density wave gap in a layered antiferromagnet $${\textrm{Gd}}{\textrm{Te}}_{3}$$
Authors: Regmi Sabin , Bin Elius Iftakhar , Sakhya Anup Pradhan , Jeff Dylan , Sprague Milo , Mondal Mazharul Islam , Jarrett Damani , Valadez Nathan , Agosto Alexis , Romanova Tetiana , Chu Jiun-Haw , Khondaker Saiful I. , Ptok Andrzej , Kaczorowski Dariusz , Neupane Madhab 
Published: October 2023

AbstractCharge density wave (CDW) ordering has been an important topic of study for a long time owing to its connection with other exotic phases such as superconductivity and magnetism. The $$R{\textrm{Te}}_{3}$$

R

Te
3

(R = rare-earth elements) family of materials provides a fertile ground to study the dynamics of CDW in van der Waals layered materials, and the presence of magnetism in these materials allows to explore the interplay among CDW and long range magnetic ordering. Here, we have carried out a high-resolution angle-resolved photoemission spectroscopy (ARPES) study of a CDW material $${\textrm{Gd}}{\textrm{Te}}_{3}$$

Gd

Te
3

, which is antiferromagnetic below $$\sim \mathrm {12~K}$$

∼

12

K

, along with thermodynamic, electrical transport, magnetic, and Raman measurements. Our ARPES data show a two-fold symmetric Fermi surface with both gapped and ungapped regions indicative of the partial nesting. The gap is momentum dependent, maximum along $${\overline{\Gamma }}-\mathrm{\overline{Z}}$$

Γ
¯

-

Z
¯

and gradually decreases going towards $${\overline{\Gamma }}-\mathrm{\overline{X}}$$

Γ
¯

-

X
¯

. Our study provides a platform to study the dynamics of CDW and its interaction with other physical orders in two- and three-dimensions.
Psychometric investigation of the gamification Hexad user types scale with Brazilian Portuguese adolescents speakers
Authors: Santos Ana Cláudia Guimarães , Muramatsu Pedro Kenzo , Oliveira Wilk , Joaquim Sivaldo , Hamari Juho , Isotani Seiji 
Published: October 2023

AbstractGamification has been applied in different fields over the last years, impacting the development of technologies, services, and products towards a more game-like world. Albeit its success, some results indicated personal differences influencing the success of its application, leading to the creation of user models (e.g., Hexad), a way to represent user profiles in gamified environments. Even though a great effort has been made to create and discuss instruments to represent these user models, many of them lack investigation into their psychometric properties. At the same time, although gamification can be particularly interesting in engaging adolescents, few attempts analyzed instruments considering this population. Addressing this lack, in this study, we evaluated the psychometric properties of the gamification Hexad scale in Brazilian Portuguese considering a sample ($$N = 110$$

N
=
110

) of adolescents aged between 13 and 16 years old. Through a quantitative study (i.e., confirmatory factor analysis and correlation), we analyzed the psychometric properties of the scale and the correlations between user types when using data collected from adolescents. Results demonstrated that the current version of the scale needs improvements to better assess the user types of the Brazilian adolescent population, especially regarding the Disruptor user type. Also, the user types presented fewer correlations when compared with the adult sample. At the same time that the results of this study can be used in the academy and industry as a source of measurement of user types from Brazilian adolescents, it also opens several possibilities for new studies in personalized gamification considering this population.
High-resolution geoelectrical characterization and monitoring of natural fluids emission systems to understand possible gas leakages from geological carbon storage reservoirs
Authors: Salone Rosanna , De Paola Claudio , Carbonari Rolando , Rufino Francesco , Avino Rosario , Caliro Stefano , Cuoco Emilio , Santi Alessandro , Di Maio Rosa 
Published: October 2023

AbstractGas leakage from deep geologic storage formations to the Earth’s surface is one of the main hazards in geological carbon sequestration and storage. Permeable sediment covers together with natural pathways, such as faults and/or fracture systems, are the main factors controlling surface leakages. Therefore, the characterization of natural systems, where large amounts of natural gases are released, can be helpful for understanding the effects of potential gas leaks from carbon dioxide storage systems. In this framework, we propose a combined use of high-resolution geoelectrical investigations (i.e. resistivity tomography and self-potential surveys) for reconstructing shallow buried fracture networks in the caprock and detecting preferential gas migration pathways before it enters the atmosphere. Such methodologies appear to be among the most suitable for the research purposes because of the strong dependence of the electrical properties of water-bearing permeable rock, or unconsolidated materials, on many factors relevant to CO2storage (i.e. porosity, fracturing, water saturation, etc.). The effectiveness of the suggested geoelectrical approach is tested in an area of natural gas degassing (mainly CH4) located in the active fault zone of the Bolle della Malvizza (Southern Apennines,Italy), which could represent a natural analogue of gas storage sites due to the significant thicknesses (hundreds of meters) of impermeable rock (caprock) that is generally required to prevent carbon dioxide stored at depth from rising to the surface. The obtained 3D geophysical model, validated by the good correlation with geochemical data acquired in the study area and the available geological information, provided a structural and physical characterization of the investigated subsurface volume. Moreover, the time variations of the observed geophysical parameters allowed the identification of possible migration pathways of fluids to the surface.