bluuebunny/crossref_metadata_2025_split huggingface dataset:
CryoRhodopsins: a comprehensive characterization of a group of microbial rhodopsins from cold environments
Authors: Lamm G.H.U. , Marin E. , Alekseev A. , Schellbach A.V. , Stetsenko A. , Bourenkov G. , Borshchevskiy V. , Asido M. , Agthe M. , Engilberge S. , Rose S.L. , Caramello N. , Royant A. , Schneider T. R. , Bateman A. , Mager T. , Moser T. , Wachtveitl J. , Guskov A. , Kovalev K. 
Published: January 2024

ABSTRACTMicrobial rhodopsins are omnipresent on Earth, however the vast majority of them remain uncharacterized. Here we describe a new rhodopsin group from cold-adapted organisms and cold environments, such as glaciers, denoted as CryoRhodopsins (CryoRs). Our data suggest that CryoRs have dual functionality switching between inward transmembrane proton translocation and photosensory activity, both of which can be modulated with UV light. CryoR1 exhibits two subpopulations in the ground state, which upon light activation lead to transient photocurrents of opposing polarities. A distinguishing feature of the group is the presence of a buried arginine residue close to the cytoplasmic face of its members. Combining single-particle cryo-electron microscopy and X-ray crystallography with the rhodopsin activation by light, we demonstrate that the arginine stabilizes a UV-absorbing intermediate of an extremely slow CryoRhodopsin photocycle. Together with extensive spectroscopic characterization, our investigations on CryoR1 and CryoR2 proteins reveal mechanisms of photoswitching in the newly identified group and demonstrate principles of the adaptation of these rhodopsins to low temperatures.
Empirical evidence of resource dependent evolution of payoff matrices inSaccharomyces cerevisiaepopulations
Authors: Venkataraman Pavithra , Mahilkar Anjali , Raj Namratha , Saini Supreet 
Published: January 2024

AbstractIn evolutionary game theory, a relative comparison of the cost and benefit associated with obtaining a resource, called payoff, is used as an indicator of fitness of an organism. Such payoff matrices are used to understand complex inter-species and intra-species interactions like cooperation, mutualism, and altruism. In the absence of any empirical data, the evolution of these payoff matrices has been investigated theoretically by tweaking well-established game theory models. In this paper, we present empirical evidence of three types of resource-dependent changes in the payoff matrices of evolvingSaccharomyces cerevisiaepopulations. We show that depending on the carbon source and participating genotypes, the payoff matrix could either (a) evolve quantitatively yet maintain a cheater-cooperator game, (b) change qualitatively such that the cheater-cooperator game collapses, or (c) change qualitatively to result in the birth of a cheater-cooperator game. Our results highlight the need to consider the dynamic nature of payoff matrices while making even short-term predictions about population interactions and dynamics.
Epileptic phenotypes inslc13a5loss-of-function zebrafish are rescued by blocking NMDA receptor signaling
Authors: Dogra Deepika , Phan Van Anh , Gavrilovici Cezar , DiMarzo Nadia , Ibhazehiebo Kingsley , Kurrasch Deborah M. 
Published: January 2024

AbstractSLC13A5encodes a citrate transporter highly expressed in the brain important for regulating intra- and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures, developmental delays, behavioral deficits, poor motor progression, and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here, we used CRISPR/Cas9 to create loss-of-function mutations inslc13a5aandslc13a5b, the zebrafish paralogs to humanSLC13A5.slc13a5mutant larvae showed cognitive dysfunction and sleep disturbances, consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum, a region important for sensory processing.slc13a5mutants displayed hallmark features of epilepsy, including an imbalance in glutamatergic and GABAergic excitatory-inhibitory gene expression, disrupted neurometabolism, and neuronal hyperexcitation as measuredin vivoby extracellular field recordings and live calcium imaging. Mechanistically, we tested the involvement of NMDA signaling inslc13a5mutant epilepsy-like phenotypes. Slc13a5 protein co-localizes with excitatory NMDA receptors in wild-type zebrafish and blocking NMDA receptors inslc13a5mutant larvae rescued bioenergetics, hyperexcitable calcium events, and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over-chelates the ions needed to regulate NMDA receptor function, leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility ofslc13a5mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery.
Informative Presence Bias in Comorbidity Data of Medicare Advantage-Enrolled Beneficiaries
Authors: Schaffer Justin M. , Kluis Austin , Squiers John J. , Banwait Jasjit K. , Gaudino Mario F. L. , Mack Michael J. , DiMaio J. Michael 
Published: January 2024

ABSTRACTBackgroundAnalyses of Medicare administrative claims data are faced with methodological challenges, including accounting for the potential effect of insurance status on documented comorbidities. We present an example of how failing to account for informative presence bias related to beneficiary enrollment status in such analyses may lead to flawed results.MethodsIn this retrospective observational study of Medicare beneficiaries undergoing isolated coronary artery bypass grafting (CABG) from 1999-2019, we compare the distribution of documented comorbidities between beneficiaries with Medicare Advantage (MA) and Traditional Medicare (TM) plans. Long-term survival was then compared in both unweighted and overlap weighted analyses with and without the inclusion of documented comorbidities.ResultsAmong 3,015,066 Medicare beneficiaries undergoing CABG from 1999-2019, 2,345,476 underwent isolated CABG and had suitable data for analysis. The annual proportion of MA-enrolled beneficiaries undergoing CABG remained stable from 1999-2007 (1.1-4.5%) and then progressively increased annually, reaching 38.2% in 2019. The incidences of documented comorbidities were substantially lower among MA-enrolled versus TM-enrolled beneficiaries. Among MA-enrolled and TM-enrolled beneficiaries, respectively, the unweighted median survival difference was only 8 [-12,28] days (10.02 [9.96,10.07] vs 10.00 [9.98,10.01] years); the weighted (adjusted for demographics and procedural characteristics, but not beneficiary comorbidities) median survival difference was also minimal at -2 [-28,24] days (10.00 [9.95,10.06] vs 10.01 [9.98,10.04] years). However, the weighted (with adjustments including beneficiary comorbidities) median survival difference demonstrated a substantial survival disadvantage for MA-enrolled beneficiaries compared to their TM-enrolled counterparts: -604 [-626,-575] days (9.78 [9.73,9.83] vs 11.44 [11.41,11.47] years), respectively.Conclusions and RelevanceComorbidities in MA-enrolled beneficiaries may be severely under-reported in Medicare data. Studies failing to account for this are susceptible to informative presence bias with a significant treatment effect. In the absence of policy changes, increasing enrollment in MA plans will continue to decrease the population of Medicare beneficiaries with suitable data for study in comparative analyses.
Wastelands or Preferred-lands? Indicators for redefining Desert conservation
Authors: Mukherjee Manasi , Banerjee Dhriti , Sharma Indu , Mukerji Mitali 
Published: January 2024

AbstractDesert ecosystems though crucial in shaping global climate, are often perceived to have limited function and are frequently designated as wastelands due to low biotic diversity and abundance. We explore the functional properties of desert through assessment of spatio-temporal variations of avian species richness and insect abundance of the relatively understudied Thar in Rajasthan. The study was conducted across four contrasting ecoregions (Western Thar (WT), Eastern Thar (ET), Transitional Zone (TZ), and Cultivated Zone (CZ) spanning 33 counties of Rajasthan. Monthly avian diversity were obtained from crowdsourced eBird data. Insect diversity and abundance accross the ecoregions were curated from the annual surveys of ZSI, India. The leads were corroborated with five years feeding behaviour observational data recorded from a representative site spanning 852 acres. There was a significant seasonal differences in bird species richness between the ecoregions with the most pronounced variations between summer and winter and CZ exhibiting the highest spatial variability followed by WT. WT also recorded the highest insect diversity and abundance, especially the orders Orthoptera, Hymenoptera, Coleoptera, Lepidotera and Diptera. The correlation matrix between bird and insect abundance and Kernel Density Estimation (KDE) plot indicated the relation between diverse dietary preferences and migratory patterns. These observations challenge the conventional notion that resource-limited environments harbour lesser biodiversity especially in arid environments. The dominance of insectivory among winter migrants aligns with the higher density of resident arthropods and emphasizes the pivotal role of insects as a food source during the migratory period. The adaptability of resident species to varied food sources, particularly arthropods, provides a means to strategically navigate during resource constraints. This study thus provides a unique framework to (a) redefine the functional importance of desert using migratory birds as prominent ecological indicators. (b) include an ecological criteria during policy formulation for biodiversity conservation. It also emphasizes reevaluation of deserts during designation of wastelands especially in the unique WT eco-regions when evolving developmental as well as ecological restoration strategies.
eDITH: an R-package to spatially project eDNA-based biodiversity across river networks with minimal prior information
Authors: Carraro Luca , Altermatt Florian 
Published: January 2024

AbstractEcological and ecosystem monitoring is rapidly shifting towards using environmental DNA (eDNA) data, particularly in aquatic systems. This approach enables a combined coverage of biodiversity across all major organismal groups and the assessment of ecological indices. Yet, most current approaches are not exploiting the full potential of eDNA data, largely interpreting results in a localized perspective. In riverine networks, by explicitly modelling hydrological transport and associated DNA decay, hydrology-based models enable upscaling eDNA-based diversity information, providing spatially integrated inference. To capitalize from these unprecedented biodiversity data and translate into space-filling biodiversity projections, a streamlined implementation is needed.Here, we introduce theeDITHR-package, implementing the eDITH model to project biodiversity across riverine networks with minimal prior information. eDITH couples a species distribution model relating a local taxon’s eDNA shedding rate in streamwater to environmental covariates, a mass balance expressing the eDNA concentration at a river’s cross-section as a weighted sum of upstream contributions, and an observational model accounting for uncertainties in eDNA measurements. By leveraging on spatially replicated eDNA measurements and minimal hydromorphological data, eDITH enables disentangling the various upstream eDNA sources, and produces space-filling maps of a taxon’s spatial distribution at any chosen resolution. eDITH is applicable to both eDNA concentration and metabarcoding data, and to any taxon whose DNA can be retrieved in streamwater.TheeDITHpackage provides user-friendly functions for single-run execution and fitting of eDITH to eDNA data with both Bayesian methods (via theBayesianToolspackage) and non-linear optimization. An interface to theDHARMapackage allows model validation via posterior predictive checks. Necessary preliminary steps such as watershed delineation and hydrological characterization are implemented via therivnetpackage. We illustrateeDITH’s workflow and functionalities with two case studies from published fish eDNA data.TheeDITHpackage provides a user-friendly implementation of eDITH, specifically intended for ecologists and conservation biologists. It can be used without previous modelling knowledge but also allows customization for experienced users. Ultimately, eDITH allows upscaling eDNA biodiversity data for any river globally, transforming how state and change of biodiversity in riverine systems can be tracked at high resolution in a highly versatile manner.
Unveiling common transcriptomic features between melanoma brain metastases and neurodegenerative diseases
Authors: Soler-Sáez Irene , Karz Alcida , Hidalgo Marta R. , Gómez-Cabañes Borja , López-Cerdán Adolfo , Català-Senent José F. , de la Iglesia-Vayá María , Hernando Eva , García-García Francisco 
Published: January 2024

ABSTRACTMelanoma represents a critical clinical challenge due to its high incidence rates and unfavorable clinical outcomes. This type of skin cancer presents unique adaptability to the brain microenvironment, but its underlying molecular mechanisms are poorly understood. To further characterize its tumor neurobiology, we explore the relation between the transcriptional profiles of melanoma brain metastasis (MBM) and the neurodegenerative diseases Alzheimer’s disease, Parkinson’s disease, and multiple sclerosis. Through anin silicoapproach, we unveiled the neurodegenerative signature of MBM when compared to melanoma non-brain metastasis (53 dysregulated genes enriched in 11 functional terms) and to non tumor-bearing brain controls (195 dysregulated genes, mostly involved in development and cell differentiation, chromatin remodeling and nucleosome organization, and translation). Two genes, ITGA10 and DNAJC6, emerged as key potential markers, as they are dysregulated in both scenarios. Lastly, we developed a user-friendly web tool (https://bioinfo.cipf.es/metafun-mbm/) as an open source, so that any user can interactively delve into the results.
Dissecting the molecular puzzle of the editosome core in Arabidopsis organelles
Authors: Baudry Kevin , Monachello Dario , Castandet Benoît , Majeran Wojciech , Lurin Claire 
Published: January 2024

ABSTRACTOver the last decade, the composition of the C-to-U RNA editing complex in embryophyte organelles has turned out to be much more complex than first expected. While PPR proteins were initially thought to act alone, significant evidences have clearly depicted a sophisticated mechanism with numerous protein-protein interaction involving PPR and non-PPR proteins. Moreover, the identification of specific functional partnership between PPRs also suggests that, in addition to the highly specific PPRs directly involved in the RNA target recognition, non-RNA-specific ones are required. Although some of them, such as DYW1 and DYW2, were shown to be the catalytic domains of the editing complex, the molecular function of others, such as NUWA, remains elusive. It was suggested that they might stabilize the complex by acting as a scaffold. We here performed functional complementation of thecrr28-2mutant with truncated CRR28 proteins mimicking PPR without the catalytic domain and show that they exhibit a specific dependency to one of the catalytic proteins DYW1 or DYW2. Moreover, we also characterized the role of the PPR NUWA in the editing reaction and show that it likely acts as a scaffolding factor. NUWA is no longer required for efficient editing of the CLB19 editing sites once this RNA specific PPR is fused to the DYW catalytic domain of its partner DYW2. Altogether, our results strongly support a flexible, evolutive and resilient editing complex in which RNA binding activity, editing activity and stabilization/scaffolding function can be provided by one or more PPRs.
Population-based cancer incidence and mortality rates and ratios among adults with intellectual disabilities in Scotland
Authors: Ward L. A. , Cooper S-A. , Sosenko F. , Morrison D. , Fleming M. , McCowan C. , Robb K. , Hanna C. , Hughes-McCormack L. , Dunn K. , Conway D. , Henderson A. , Smith G. , Truesdale M. , Cairns D. 
Published: January 2024

Structured AbstractObjectiveTo provide contemporary data on cancer mortality rates within the context of incidence in the population with intellectual disabilities.MethodsScotland’s 2011 Census was used to identify adults with intellectual disabilities and controls with records linked to the Scottish Cancer Registry and death certificate data (March 2011-December 2019). The control cohort without intellectual disabilities and/or autism were used for indirect standardisation and calculation of Crude Incident Rates/Crude Mortality Rates (CIR/CMR), and age-sex Standardized Incident Rate Ratios/ Standardized Mortality Ratios (SIR/SMR), with 95% Confidence Intervals (CI).ResultsAdults with intellectual disabilities were most likely diagnosed cancers of digestive, specifically colorectal (14.2%), lung (9.3%), breast (female 22.9%), body of the uterus (female 9.3%) and male genital organs (male 17.6%). Higher incident cancers included metastatic cancer of unknown primary origin (female SIR=1.70, male SIR=2.08), body of uterus (female SIR=1.63), ovarian (female SIR=1.59), kidney (female SIR=1.85), and testicular (male SIR=2.49). SMRs were higher, regardless of a higher, similar, or lower incidence (female SMR=1.34, male SMR=1.07). Excess mortality risk was found for colorectal (male SMR=1.59), kidney (female SMR=2.85u), female genital organs (ovarian SMR=2.86u, body of uterus SMR=2.11), breast (female SMR=1.58), and metastatic cancer of unknown primary origin (female SMR=2.50u, male SMR=2.84).ConclusionsAdults with intellectual disabilities were more likely to die of cancer than the general population. Reasons for this may include later presentation/diagnosis (so poorer outcomes), poorer treatment/compliance, or both. Accessible public health approaches are important for people with intellectual disabilities, and healthcare professionals need to be aware of the different cancer experiences faced by this population.Summary boxStrengths and limitations of this studyOur key strength is the comprehensive coverage of Scotland’s entire adult population with intellectual disabilities, and inclusion of a representative general population comparison group.By using nationwide robust data linkage of high-quality electronic health records, we provide reliable data with minimal bias.Limitations include our inability to account for cancer incidence before the census date. However, prospective collection of data over nearly 9 years provided well-powered person-time for rate calculation, allowing for a meaningful interpretation of mortality rates in the context of incidence.Death certificate data imprecision is considered, but our dual-analysis (main-cause and all-cause analyses), mitigates differences and indeed have similar interpretations.
Strategizing as polarity management: biographical analysis of leadership in the Polish furniture industry (1989–2015)
Authors: Bednarz-Łuczewska Paulina , Łuczewski Michał 
Published: January 2024

PurposeThis article aims to analyze the strategic work of Polish entrepreneurs in the furniture industry following the political changes in 1989. The authors examined how these entrepreneurs transitioned from local craftsmen or importers into leaders of international manufacturing companies and how their strategizing contributed to the unprecedented growth of the Polish furniture sector.Design/methodology/approachThe authors examined extant data, specifically biographical interviews conducted with 11 prominent leaders in the Polish furniture industry (Hryniewicki, 2015, 2018). They analyzed within a theoretical framework that integrates J.C. Spender’s theory of strategic management with Barry Johnson’s concept of polarity management. Polarity is a way of understanding and managing interdependent, opposing pairs of values or perspectives that give rise to conflict.FindingsThe analysis reveals key patterns of strategic challenges at the level of human agency, history and sense-making. The authors identified four key polarities: life and business, knowledge presence and absence, concordance and discordance, and instrumental and non-instrumental sense-making.Originality/valueThe polarity concept illuminates the interplay of agency and determinism in strategic decision-making, offering valuable insights for methodology and a deeper understanding of Poland’s furniture industry.
A hybrid method for forecasting coal price based on ensemble learning and deep learning with data decomposition and data enhancement
Authors: Tang Jing , Guo Yida , Han Yilin 
Published: January 2024

PurposeCoal is a critical global energy source, and fluctuations in its price significantly impact related enterprises' profitability. This study aims to develop a robust model for predicting the coal price index to enhance coal purchase strategies for coal-consuming enterprises and provide crucial information for global carbon emission reduction.Design/methodology/approachThe proposed coal price forecasting system combines data decomposition, semi-supervised feature engineering, ensemble learning and deep learning. It addresses the challenge of merging low-resolution and high-resolution data by adaptively combining both types of data and filling in missing gaps through interpolation for internal missing data and self-supervision for initiate/terminal missing data. The system employs self-supervised learning to complete the filling of complex missing data.FindingsThe ensemble model, which combines long short-term memory, XGBoost and support vector regression, demonstrated the best prediction performance among the tested models. It exhibited superior accuracy and stability across multiple indices in two datasets, namely the Bohai-Rim steam-coal price index and coal daily settlement price.Originality/valueThe proposed coal price forecasting system stands out as it integrates data decomposition, semi-supervised feature engineering, ensemble learning and deep learning. Moreover, the system pioneers the use of self-supervised learning for filling in complex missing data, contributing to its originality and effectiveness.