bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reproductive cycle of the golden carpet shell (Polititapes aureus) in the Ria Formosa lagoon (southern Portugal)
Authors: Moura Paula , Matias Ana Margarete , Vasconcelos Paulo , Roque Cláudia , Joaquim Sandra , Matias Domitília , Gaspar Miguel B. 
Published: June 2022

AbstractThe present study described the gametogenesis and assessed the pattern of energy storage throughout the reproductive cycle of the golden carpet shell (Polititapes aureus) from the Ria Formosa lagoon (southern Portugal). Monthly sampling was performed for two years (March 2016–February 2018) and the study was based on gonad histology, complemented by the estimation of the mean gonadal index, body condition index and biochemical composition. The species’ reproductive cycle presented a seasonal pattern, with a resting period mainly between October and January and gametogenesis beginning around February–March. The spawning season of P. aureus was shorter in 2016 (June–September) than in 2017 (May–October). Furthermore, ripe individuals were very scarce (1.3%) in 2017 compared with the previous year (11.4%). Mean gonadal index (GI) reflected the species’ reproductive cycle and the body condition index (CI) and biochemical composition of the individuals exhibited high variation between years. Regarding the biochemical composition, proteins ranged between 190.6 and 595.2 μg mg−1, glycogen from 5.7 to 102.6 μg mg−1 and total lipids between 31.6 and 80.7 μg mg−1. The reproduction of P. aureus was strongly influenced by fluctuations in both seawater temperature and chlorophyll a, as reflected through the temporal variation in the gonadal cycle, condition index and biochemical composition. Overall, the information gathered in this study is valuable to propose scientifically based harvesting management measures for the long-term sustainable exploitation of this shellfish resource, further reinforcing the importance of implementing adaptive fishery management strategies to cope with global climate change.
Trajectories of depression and generalised anxiety symptoms over the course of cognitive behaviour therapy in primary care: an observational, retrospective cohort
Authors: Bauer-Staeb Clarissa , Griffith Emma , Faraway Julian J. , Button Katherine S. 
Published: June 2022

AbstractBackgroundCognitive-behavioural therapy (CBT) has been shown to be an effective treatment for depression and anxiety. However, most research has focused on the sum scores of symptoms. Relatively little is known about how individual symptoms respond.MethodsLongitudinal models were used to explore how depression and generalised anxiety symptoms behave over the course of CBT in a retrospective, observational cohort of patients from primary care settings (n = 5306). Logistic mixed models were used to examine the probability of being symptom-free across CBT appointments, using the 9-item Patient Health Questionnaire and the 7-item Generalised Anxiety Disorder scale as measures.ResultsAll symptoms improve across CBT treatment. The results suggest that low mood/hopelessness and guilt/worthlessness improved quickest relative to other depressive symptoms, with sleeping problems, appetite changes, and psychomotor retardation/agitation improving relatively slower. Uncontrollable worry and too much worry were the anxiety symptoms that improved fastest; irritability and restlessness improved the slowest.ConclusionsThis research suggests there is a benefit to examining symptoms rather than sum scores alone. Investigations of symptoms provide the potential for precision psychiatry and may explain some of the heterogeneity observed in clinical outcomes when only sum scores are considered.
Automatic golden device selection and measurement smoothing algorithms for microwave transistor small-signal noise modeling
Authors: Salnikov Andrei S. , Dobush Igor M. , Popov Artem A. , Bilevich Dmitry V. , Goryainov Aleksandr E. , Kalentyev Alexey A. , Metel Aleksandr A. 
Published: June 2022

AbstractWe propose the techniques for automatic processing of measurement results in the context of golden (typical) device selection and noise figure measurement. These techniques are for golden (typical) device selection and noise figure measurement processing. Automation of measurement result processing and microwave element modeling speeds up a modeling routine and decreases the risk of possible errors. The techniques are validated through modeling of 0.15 μm GaAs pHEMTs with 4 × 40 μm and 4 × 75 μm total gate widths. Two test amplifiers were designed using the developed models. The amplifier modeling results agree well with measurements which confirms the validity of the proposed techniques. The proposed algorithm is potentially applicable to other circuit types (switches, digital, power amplifiers, mixers, oscillators, etc.) but may require different settings in those cases. However, in the presented work, we validated the algorithm for the linear and low-noise amplifiers only.
Populism and Candidate Support in the US: The Effects of “Thin” and “Host” Ideology
Authors: Castanho Silva Bruno , Neuner Fabian Guy , Wratil Christopher 
Published: June 2022

AbstractMuch of the contemporary literature on populism focuses on its status as a “thin” ideology comprising three key components: people-centrism, anti-elitism, and anti-pluralism. Populist politicians pair this “thin” ideology with extreme positions on policy issues such as immigration or taxation (referred to as “host” or “thick” ideologies). A recent study using German samples leveraged conjoint experiments to disentangle the effects of these appeals on vote choice. The results not only showed that extreme host-ideological positions mattered more than so-called “thin” populist appeals, but also that effects of populist appeals were nearly identical among populist and non-populist voters. Our replication in the US context reaffirms both the importance of host-ideological positions and the lack of heterogeneous effects by voters’ “thin” populist attitudes. Furthermore, by uncovering some divergence from the German case (e.g. anti-elite appeals trumping people-centric appeals), we highlight the need to experimentally examine the effects of populism’s constituent components across contexts.
Impact of Short‐Term Hydrological Components on Landscape Pattern of Waterbird Habitat in Floodplain Wetlands
Authors: Yao Siyang , Chen Cheng , Chen Qiuwen , Cui Zhen , Zhang Jianyun , Zeng Yuhong 
Published: June 2022

AbstractPeriodic flooding in floodplain wetlands dominates the landscape pattern, creating rich and diverse habitats for waterbirds. However, most studies on floodplain wetland landscape are conducted at interannual scale, while few researches investigate the effect of short‐term changes of hydrological components, such as maximum continuous flooding day, average flooding depth, maximum continuous drought day, and distance from water body. This study developed an effective approach by integrating a two‐dimensional hydrodynamic model and a geographic detector model to investigate the single and interactive effects of short‐term hydrological components on the landscape pattern of waterbird habitat in floodplain wetlands. The developed approach was demonstrated in the Poyang Lake in Jiangxi province of China, an important conservation floodplain wetland in the Ramsar Convention. We found the short‐term hydrological components could impose a significant impact on the landscape pattern of waterbird habitat. Particularly, the interactive effects of multiple hydrological components were stronger than that of a single component, showing nonlinear enhancement. The developed approach could provide a viable way to study the ecological impacts of short‐term hydrological components on the landscape pattern of waterbird habitat in floodplain wetlands, thus offer scientific references for waterbird habitat management in floodplain wetlands.
JAK2 gene knockout inhibits corneal allograft rejection in mice by regulating dendritic cell-induced T cell immune tolerance
Authors: Hu Jun , Zhang Wanping , Xu Lingjuan , Hu Lihua 
Published: June 2022

AbstractCorneal allograft rejection can be seen in some patients after corneal transplantation. The present study intends to investigate whether JAK2 gene knockout affects corneal allograft rejection through regulation of dendritic cells (DCs)-induced T cell immune tolerance. In order to identify the target gene related to corneal allograft rejection, high-throughput mRNA sequencing and bioinformatics analysis were performed. JAK2 knockout mice were constructed and subjected to corneal allograft transplantation. The incidence of immune rejection was observed, the percentage of CD4+ T cells was detected, and the expression of Th1 cytokine interferon γ (IFN-γ) was determined. Flow cytometry and ELISA were performed to analyze the effects of JAK2 gene knockout on bone marrow-derived DCs (BMDCs). JAK2 was the target gene related to corneal allograft rejection. JAK2 gene knockout contributed to significantly prolonged survival time of corneal grafts in mice and inhibited corneal allograft rejection. The in vitro cell experiment further confirmed that JAK2 gene knockout contributed to the inactivation of CD4+ T cells and induced IFN-γ expression, accompanied by inhibition of DC immune function, development, maturation, and secretion of inflammatory cytokines. Collectively, JAK2 gene knockout inactivates CD4+ T cells to decrease IFN-γ expression, as well as inhibits DC development, maturation, and secretion of inflammatory cytokines, thereby reducing corneal allograft rejection.
GPI-anchored FGF directs cytoneme-mediated bidirectional contacts to regulate its tissue-specific dispersion
Authors: Du Lijuan , Sohr Alex , Li Yujia , Roy Sougata 
Published: June 2022

AbstractHow signaling proteins generate a multitude of information to organize tissue patterns is critical to understanding morphogenesis. In Drosophila, FGF produced in wing-disc cells regulates the development of the disc-associated air-sac-primordium (ASP). Here, we show that FGF is Glycosylphosphatidylinositol-anchored to the producing cell surface and that this modification both inhibits free FGF secretion and promotes target-specific cytoneme contacts and contact-dependent FGF release. FGF-source and ASP cells extend cytonemes that present FGF and FGFR on their surfaces and reciprocally recognize each other over distance by contacting through cell-adhesion-molecule (CAM)-like FGF-FGFR binding. Contact-mediated FGF-FGFR interactions induce bidirectional responses in ASP and source cells that, in turn, polarize FGF-sending and FGF-receiving cytonemes toward each other to reinforce signaling contacts. Subsequent un-anchoring of FGFR-bound-FGF from the source membrane dissociates cytoneme contacts and delivers FGF target-specifically to ASP cytonemes for paracrine functions. Thus, GPI-anchored FGF organizes both source and recipient cells and self-regulates its cytoneme-mediated tissue-specific dispersion.
Light-sheet photonic force optical coherence elastography for high-throughput quantitative 3D micromechanical imaging
Authors: Lin Yuechuan , Leartprapun Nichaluk , Luo Justin C. , Adie Steven G. 
Published: June 2022

AbstractQuantitative characterisation of micro-scale mechanical properties of the extracellular matrix (ECM) and dynamic cell-ECM interactions can significantly enhance fundamental discoveries and their translational potential in the rapidly growing field of mechanobiology. However, quantitative 3D imaging of ECM mechanics with cellular-scale resolution and dynamic monitoring of cell-mediated changes to pericellular viscoelasticity remain a challenge for existing mechanical characterisation methods. Here, we present light-sheet photonic force optical coherence elastography (LS-pfOCE) to address this need by leveraging a light-sheet for parallelised, non-invasive, and localised mechanical loading. We demonstrate the capabilities of LS-pfOCE by imaging the micromechanical heterogeneity of fibrous collagen matrices and perform live-cell imaging of cell-mediated ECM micromechanical dynamics. By providing access to 4D spatiotemporal variations in the micromechanical properties of 3D biopolymer constructs and engineered cellular systems, LS-pfOCE has the potential to drive new discoveries in mechanobiology and contribute to the development of novel biomechanics-based clinical diagnostics and therapies.
Identifying plant genes shaping microbiota composition in the barley rhizosphere
Authors: Escudero-Martinez Carmen , Coulter Max , Alegria Terrazas Rodrigo , Foito Alexandre , Kapadia Rumana , Pietrangelo Laura , Maver Mauro , Sharma Rajiv , Aprile Alessio , Morris Jenny , Hedley Pete E. , Maurer Andreas , Pillen Klaus , Naclerio Gino , Mimmo Tanja , Barton Geoffrey J. , Waugh Robbie , Abbott James , Bulgarelli Davide 
Published: June 2022

AbstractA prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere, the interface between roots and soil. Here, we use metagenomics information as an external quantitative phenotype to map the host genetic determinants of the rhizosphere microbiota in wild and domesticated genotypes of barley, the fourth most cultivated cereal globally. We identify a small number of loci with a major effect on the composition of rhizosphere communities. One of those, designated the QRMC-3HS, emerges as a major determinant of microbiota composition. We subject soil-grown sibling lines harbouring contrasting alleles at QRMC-3HS and hosting contrasting microbiotas to comparative root RNA-seq profiling. This allows us to identify three primary candidate genes, including a Nucleotide-Binding-Leucine-Rich-Repeat (NLR) gene in a region of structural variation of the barley genome. Our results provide insights into the footprint of crop improvement on the plant’s capacity of shaping rhizosphere microbes.
Ductile deformation during carbonation of serpentinized peridotite
Authors: Menzel Manuel D. , Urai Janos L. , Ukar Estibalitz , Hirth Greg , Schwedt Alexander , Kovács András , Kibkalo Lidia , Kelemen Peter B. 
Published: June 2022

AbstractCarbonated serpentinites (listvenites) in the Samail Ophiolite, Oman, record mineralization of 1–2 Gt of CO2, but the mechanisms providing permeability for continued reactive fluid flow are unclear. Based on samples of the Oman Drilling Project, here we show that listvenites with a penetrative foliation have abundant microstructures indicating that the carbonation reaction occurred during deformation. Folded magnesite veins mark the onset of carbonation, followed by deformation during carbonate growth. Undeformed magnesite and quartz overgrowths indicate that deformation stopped before the reaction was completed. We propose deformation by dilatant granular flow and dissolution-precipitation assisted the reaction, while deformation in turn was localized in the weak reacting mass. Lithostatic pore pressures promoted this process, creating dilatant porosity for CO2transport and solid volume increase. This feedback mechanism may be common in serpentinite-bearing fault zones and the mantle wedge overlying subduction zones, allowing massive carbonation of mantle rocks.
The 3D architecture of the pepper genome and its relationship to function and evolution
Authors: Liao Yi , Wang Juntao , Zhu Zhangsheng , Liu Yuanlong , Chen Jinfeng , Zhou Yongfeng , Liu Feng , Lei Jianjun , Gaut Brandon S. , Cao Bihao , Emerson J. J. , Chen Changming 
Published: June 2022

AbstractThe organization of chromatin into self-interacting domains is universal among eukaryotic genomes, though how and why they form varies considerably. Here we report a chromosome-scale reference genome assembly of pepper (Capsicum annuum) and explore its 3D organization through integrating high-resolution Hi-C maps with epigenomic, transcriptomic, and genetic variation data. Chromatin folding domains in pepper are as prominent as TADs in mammals but exhibit unique characteristics. They tend to coincide with heterochromatic regions enriched with retrotransposons and are frequently embedded in loops, which may correlate with transcription factories. Their boundaries are hotspots for chromosome rearrangements but are otherwise depleted for genetic variation. While chromatin conformation broadly affects transcription variance, it does not predict differential gene expression between tissues. Our results suggest that pepper genome organization is explained by a model of heterochromatin-driven folding promoted by transcription factories and that such spatial architecture is under structural and functional constraints.
Mitigating the detrimental effects of galvanic corrosion by nanoscale composite architecture design
Authors: Renk Oliver , Weißensteiner Irmgard , Cihova Martina , Steyskal Eva-Maria , Sommer Nicole G. , Tkadletz Michael , Pogatscher Stefan , Schmutz Patrik , Eckert Jürgen , Uggowitzer Peter J. , Pippan Reinhard , Weinberg Annelie M. 
Published: June 2022

AbstractWidespread application of magnesium (Mg) has been prevented by its low strength and poor corrosion resistance. Core of this limitation is Mg’s low electrochemical potential and low solubility for most elements, favoring secondary phase precipitation acting as effective micro-galvanic elements. Mg-based metal–metal composites, while benefiting strength, are similarly active galvanic couples. We show that related detrimental corrosion susceptibility is overcome by nanoscale composite architecture design. Nanoscale phase spacings enable high-strength Mg–Fe composites with degradation rates as low as ultra-high purity Mg. Our concept thus fundamentally changes today’s understanding of Mg’s corrosion and significantly widens the property space of Mg-based materials.
Datasets of skills-rating questionnaires for advanced service design through expert knowledge elicitation
Authors: Nguyen Hien Ngoc , Lasa Ganix , Iriarte Ion , Atxa Ariane , Unamuno Gorka , Galfarsoro Gurutz 
Published: June 2022

AbstractThis article presents a dataset of service design skills which service design experts value as important requirements for design team members. Purposive sampling and a chain referral approach were used to recruit appropriate experts to conduct questionnaire-based research. Using the analytical hierarchy process (AHP), pairwise skills-rating questionnaires were designed to elicit the experts’ responses. The resulting dataset was processed using AHP algorithms programmed in R programming language. The transparent data and available codes of the research may be reused by design practitioners and researchers for replication and further analysis. This paper offers a reproduceable research process and associated dataset for conducting multiple-criteria decision analysis with expert purposive sampling.
A dataset of simulated patient-physician medical interviews with a focus on respiratory cases
Authors: Fareez Faiha , Parikh Tishya , Wavell Christopher , Shahab Saba , Chevalier Meghan , Good Scott , De Blasi Isabella , Rhouma Rafik , McMahon Christopher , Lam Jean-Paul , Lo Thomas , Smith Christopher W. 
Published: June 2022

AbstractArtificial Intelligence (AI) is playing a major role in medical education, diagnosis, and outbreak detection through Natural Language Processing (NLP), machine learning models and deep learning tools. However, in order to train AI to facilitate these medical fields, well-documented and accurate medical conversations are needed. The dataset presented covers a series of medical conversations in the format of Objective Structured Clinical Examinations (OSCE), with a focus on respiratory cases in audio format and corresponding text documents. These cases were simulated, recorded, transcribed, and manually corrected with the underlying aim of providing a comprehensive set of medical conversation data to the academic and industry community. Potential applications include speech recognition detection for speech-to-text errors, training NLP models to extract symptoms, detecting diseases, or for educational purposes, including training an avatar to converse with healthcare professional students as a standardized patient during clinical examinations. The application opportunities for the presented dataset are vast, given that this calibre of data is difficult to access and costly to develop.
A database of animal metagenomes
Authors: Hu Ruirui , Yao Rui , Li Lei , Xu Yueren , Lei Bingbing , Tang Guohao , Liang Haowei , Lei Yunjiao , Li Cunyuan , Li Xiaoyue , Liu Kaiping , Wang Limin , Zhang Yunfeng , Wang Yue , Cui Yuying , Dai Jihong , Ni Wei , Zhou Ping , Yu Baohua , Hu Shengwei 
Published: June 2022

AbstractWith the rapid development of high-throughput sequencing technology, the amount of metagenomic data (including both 16S and whole-genome sequencing data) in public repositories is increasing exponentially. However, owing to the large and decentralized nature of the data, it is still difficult for users to mine, compare, and analyze the data. The animal metagenome database (AnimalMetagenome DB) integrates metagenomic sequencing data with host information, making it easier for users to find data of interest. The AnimalMetagenome DB is designed to contain all public metagenomic data from animals, and the data are divided into domestic and wild animal categories. Users can browse, search, and download animal metagenomic data of interest based on different attributes of the metadata such as animal species, sample site, study purpose, and DNA extraction method. The AnimalMetagenome DB version 1.0 includes metadata for 82,097 metagenomes from 4 domestic animals (pigs, bovines, horses, and sheep) and 540 wild animals. These metagenomes cover 15 years of experiments, 73 countries, 1,044 studies, 63,214 amplicon sequencing data, and 10,672 whole genome sequencing data. All data in the database are hosted and available in figshare https://doi.org/10.6084/m9.figshare.19728619.
Simulating epileptic seizures using the bidomain model
Authors: Schreiner Jakob , Mardal Kent-Andre 
Published: June 2022

AbstractEpileptic seizures are due to excessive and synchronous neural activity. Extensive modelling of seizures has been done on the neuronal level, but it remains a challenge to scale these models up to whole brain models. Measurements of the brain’s activity over several spatiotemporal scales follow a power-law distribution in terms of frequency. During normal brain activity, the power-law exponent is often found to be around 2 for frequencies between a few Hz and up to 150 Hz, but is higher during seizures and for higher frequencies. The Bidomain model has been used with success in modelling the electrical activity of the heart, but has been explored far less in the context of the brain. This study extends previous models of epileptic seizures on the neuronal level to the whole brain using the Bidomain model. Our approach is evaluated in terms of power-law distributions. The electric potentials were simulated in 7 idealized two-dimensional models and 3 three-dimensional patient-specific models derived from magnetic resonance images (MRI). Computed electric potentials were found to follow power-law distributions with slopes ranging from 2 to 5 for frequencies greater than 10–30 Hz.