bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variability‐based constraint on ocean primary production models
Authors: Cael B. B. 
Published: June 2021

AbstractPrimary production (PP) is fundamental to ocean biogeochemistry, but challengingly variable. Satellite models are unique tools for investigating PP, but are difficult to compare and validate because of the scale separation between in situ and remote measurements, which also are rarely coincident. Here, I argue that satellite estimates should be log‐skew‐normally distributed, because of this scale separation and because PP measurements are log‐normally distributed. Whether they conform to this distributional shape is therefore a powerful variability‐based constraint on such models. Satellite models that do follow a log‐skew‐normal may then also be concisely characterized by three parameters (log‐mean, log‐standard deviation, and log‐skewness). I show that the output from a recent satellite model (CAFE) over 2019 agrees excellently with the log‐skew‐normal, globally and for most spatiotemporal subsets investigated here. The exception is the Northern Hemisphere winter, which may suggest future model improvements. PP by plankton is essential to ocean ecology and biogeochemistry, so satellite models that estimate PP from remote sensing data are indispensable in numerous scientific applications. However, because the corresponding in situ data are rarely measured when a satellite passes overhead, are measured on a much smaller spatial scale, and are highly variable, it is very difficult to compare different satellite models, evaluate how accurate they are, or to constrain their parameters. Here, a different approach to evaluating, comparing, and constraining these models is described, which accounts for or avoids all of these issues with the standard approach. This approach finds excellent agreement overall with a recent satellite model, while also identifying room for improvement.
The Emerging Role of Phosphodiesterases in Movement Disorders
Authors: Erro Roberto , Mencacci Niccoló E. , Bhatia Kailash P. 
Published: June 2021

ABSTRACTCyclic nucleotide phosphodiesterase (PDE) enzymes catalyze the hydrolysis and inactivation of the cyclic nucleotides cyclic adenosine monophosphate and cyclic guanosine monophosphate, which act as intracellular second messengers for many signal transduction pathways in the central nervous system. Several classes of PDE enzymes with specific tissue distributions and cyclic nucleotide selectivity are highly expressed in brain regions involved in cognitive and motor functions, which are known to be implicated in neurodegenerative diseases, such as Parkinson's disease and Huntington's disease. The indication that PDEs are intimately involved in the pathophysiology of different movement disorders further stems from recent discoveries that mutations in genes encoding different PDEs, including PDE2A, PDE8B, and PDE10A, are responsible for rare forms of monogenic parkinsonism and chorea. We here aim to provide a translational overview of the preclinical and clinical data on PDEs, the role of which is emerging in the field of movement disorders, offering a novel venue for a better understanding of their pathophysiology. Modulating cyclic nucleotide signaling, by either acting on their synthesis or on their degradation, represents a promising area for development of novel therapeutic approaches. The study of PDE mutations linked to monogenic movement disorders offers the opportunity of better understanding the role of PDEs in disease pathogenesis, a necessary step to successfully benefit the treatment of both hyperkinetic and hypokinetic movement disorders. © 2021 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society
Pyruvate dehydrogenase deficiency disease detected by the enzyme activity of peripheral leukocytes
Authors: Ma YanYan , Zhang YaoGang , Zhang Tao , Man Zhu , Su XiaoMing , Hao ShuJing , Wang TianZe 
Published: June 2021

AbstractBackgroundPyruvate dehydrogenase complex (PDHC) deficiency is a common neurodegenerative disease associated with abnormal mitochondrial energy metabolism. The diagnosis of PDHC is difficult because of the lack of a rapid, accurate, and cost‐effective clinical diagnostic method.MethodsA 4‐year‐old boy was preliminarily diagnosed with putative Leigh syndrome based on the clinical presentation. PDHC activity in peripheral blood leukocytes and a corresponding gene analysis were subsequently undertaken. Sodium pyruvate 1‐13C was used for the analysis of PDHC activity in peripheral leukocytes. The genes encoding PDHC were then scanned for mutations.ResultsThe results showed that the corresponding PDHC activity was dramatically decreased to 10.5 nmol/h/mg protein as compared with that of healthy controls (124.6 ± 7.1 nmol/h/mg). The ratio of PDHC to citrate synthase was 2.1% (control: 425.3 ± 27.1). The mutation analysis led to the identification of a missense mutation, NM_000284.4:g214C>T, in exon 3 of PDHC.ConclusionThe peripheral blood leukocyte PDHC activity assay may provide a practical enzymatic diagnostic method for PDHC‐related mitochondrial diseases.
Reliability‐based optimization of a prestressed concrete roof girder using a surrogate model and the double‐loop approach
Authors: Slowik Ondřej , Lehký David , Novák Drahomír 
Published: June 2021

AbstractThe paper describes the reliability‐based optimization of a TT‐shaped precast roof girder produced in Austria. An extensive experimental programme was performed using laboratory specimens to gain information on the mechanical fracture parameters of the utilized concrete. Subsequently, destructive shear tests were performed on scaled‐down and full‐scale girders under laboratory conditions. The experiments helped in the development of an accurate numerical model of the girder. The developed model was consequently used for the advanced stochastic analysis of structural response, followed by reliability‐based optimization, which was used to maximize the shear and bending capacities of the girder and minimize production cost under defined reliability constraints. The enormous computational requirements of the double‐loop optimization approach were significantly reduced by the utilization of an artificial neural network‐based surrogate model instead of the original nonlinear finite element model of the optimized structure.
Pioneer settlement of the cold-water coral Desmophyllum dianthus (Esper, 1794) on plastic
Authors: Bergami Elisa , Caroselli Erik , Vaccari Lisa , Corsi Ilaria , Semenov Alexander , Macali Armando 
Published: June 2021

AbstractLarval settlement is a critical step for sessile benthic species such as corals, whose ability to thrive on diverse natural and anthropogenic substrates may lead to a competitive advantage in the colonization of new environments with respect to a narrow tolerance for a specific kind of substratum. Plastic debris, widespread in marine waters, provides a large, motile, and solid substratum supporting a highly diverse biological community. Here we present the first observation of a floating plastic bottle colonized by the deep-sea coral Desmophyllum dianthus. The density pattern and co-occurring species composition suggest a pioneer behavior of this coral species, whose peculiar morphologic plasticity response when interacting with the plastic substrate (i.e., low density polyethylene) has not been observed before. The tolerance of D. dianthus for such plastic substrate may affect ecological processes in deep water environments, disrupting interspecific substrate competition in the benthic community.
Burden of illness associated with eosinophilic granulomatosis with polyangiitis: a systematic literature review and meta-analysis
Authors: Jakes Rupert W. , Kwon Namhee , Nordstrom Beth , Goulding Rebecca , Fahrbach Kyle , Tarpey Jialu , Van Dyke Melissa K. 
Published: June 2021

Abstract
Eosinophilic granulomatosis with polyangiitis (EGPA) is a rare disease associated with vascular inflammation and multisystem organ damage. The literature reporting EGPA incidence or prevalence is limited. We performed a systematic literature review and meta-analysis to describe the incidence, prevalence, and disease burden associated with EGPA. Real-world, observational, English-language studies in MEDLINE, MEDLINE In-Process, and Embase up to 6 June, 2019, were included. A single investigator screened all identified titles/abstracts and extracted data; an additional, independent investigator repeated the screening and validated the extracted data. A random-effects meta-analysis was conducted to generate pooled estimates for EGPA incidence and prevalence. Data from 100 eligible publications were extracted (32 with incidence/prevalence data, 65 with morbidity/healthcare resource data; 3 with both types of data). Significant evidence of between-study heterogeneity for reported incidence (p = 0.0013–0.0016) and prevalence (p = 0.0001–0.0006) estimates was observed. Global and European pooled estimates (95% confidence interval) of EGPA incidence were 1.22 (0.93, 1.60) and 1.07 (0.94, 1.35) cases per million person-years, respectively; global and European pooled estimates (95% confidence interval) for EGPA prevalence were 15.27 (11.89, 19.61) and 12.13 (6.98, 21.06) cases per million individuals, respectively. The proportions of patients experiencing relapses, or who had nasal polyps or severe asthma, varied considerably across studies. EGPA healthcare resource use was high, with inpatient admissions and emergency department visits reported for 17–42% and 25–42% of patients, respectively. Our results indicate that although global and European EGPA incidence and prevalence is low, the associated disease burden is substantial.

Key points• We performed a systematic literature review and meta-analysis of real-world, observational studies describing the incidence, prevalence, and disease burden associated with eosinophilic granulomatosis with polyangiitis (EGPA).• Based on meta-analysis data from 35 eligible studies reporting incidence and prevalence, the incidence and prevalence of EGPA were low (globally 1.22 cases per million person-years and 15.27 cases per million individuals, respectively).• Among the 49 studies with morbidity and/or healthcare resource data, most reported a large proportion of patients with EGPA relapses and comorbidities of nasal polyps and severe asthma.• Healthcare resource use was also high among patients with EGPA in these studies, with inpatient admissions and emergency department visits reported for 17–42% and 25–42% of patients, respectively. Taken together, these data indicate the substantial disease burden associated with EGPA.
Simultaneous removal of heavy metals from drinking water by banana, orange and potato peel beads: a study of biosorption kinetics
Authors: Nathan Risha Jasmine , Martin Candace E. , Barr Dave , Rosengren Rhonda J. 
Published: June 2021

AbstractBanana, orange and potato peels (BP, OP and PP, respectively) were immobilised to produce biosorbent beads that were employed for the biosorption of heavy metals from a cocktail solution containing As(V), Cd(II), Cr(VI), Cu(II), Hg(II) and Ni(II) ions. Drinking water conditions were maintained with neutral initial pH and low concentration of the ions. Batch experiments were performed for evaluating the effect of pH in the drinking water range (6.5–8.5). Results showed a significant increase in the biosorption capacity of the beads with respective to the uptake of As and Pb, whereas it decreased significantly for Cd, Cu, Hg and Ni ions at basic pH values. Approximate equilibrium biosorption of Cd, Cu, Hg and Ni was 89–92%, 79–87%, 84% and 71–80% by BP, OP and PP beads. The physisorption-based PFO model was the most suitable for the ions with biosorption capacities closer to the experimental values. BP and OP beads had better biosorption efficiencies relative to PP bead due to the higher surface heterogeneity observed by scanning electron microscopy coupled with energy-dispersive spectroscopy. An increase in the biosorbent concentration from one to ten BP beads significantly increased the biosorption percentage of the ions. The biosorption capacities of Cd, Hg and Ni uptake by one BP bead from a 1 mgL−1 cocktail solution were 3.4 ± 0.0, 5.3 ± 0.1 and 3.0 ± 0.0 mgg−1, respectively. Thus, BP beads were the most effective than for the simultaneous removal of heavy metals from drinking water.
Extended Authorization Policy for Graph-Structured Data
Authors: Mohamed Aya , Auer Dagmar , Hofer Daniel , Küng Josef 
Published: June 2021

AbstractThe high increase in the use of graph databases also for business- and privacy-critical applications demands for a sophisticated, flexible, fine-grained authorization and access control (AC) approach. Attribute-based access control (ABAC) supports a fine-grained definition of authorization rules and policies. Attributes can be associated with the subject, the requested resource and action, but also the environment. Thus, this is a promising starting point. However, specific characteristics of graph-structured data, such as attributes on vertices and edges along a path from a given subject to the resource to be accessed, are not yet considered. The well-established eXtensible Access Control Markup Language (XACML), which defines a declarative language for fine-grained, attribute-based authorization policies, is the basis for our proposed approach—XACML for Graph-structured data (XACML4G). The additional path-specific constraints, described in graph patterns, demand for specialized processing of the rules and policies as well as adapted enforcement and decision-making in the access control process. To demonstrate XACML4G and its enforcement process, we present a scenario from the university domain. Due to the project’s environment, the prototype is built with the multi-model database ArangoDB. Finally, compliance of XACML4G with quality standards for access control systems administration and enforcement is assessed. The results are promising and further studies concerning performance and use in practice are planned.
Mecapalapa Tepehua
Authors: Zendejas Esther Herrera 
Published: June 2021

Mecapalapa Tepehua (ISO code: tee) is a language of Mexico that belongs to the Huehuetla branch of the Totonac-Tepehua linguistic family. It is spoken in the town of Mecapalapa, Puebla, Mexico. This linguistic family is composed of the Tepehua and Totonac branches (see MacKay & Trechsel 2014 and references there). The Tepehua branch consists of three main languages and their respective varieties: Pisaflores and Tlachichilco Tepehua are located in Veracruz, and Huehuetla Tepehua is located in Hidalgo and Puebla (see Figure 1). In comparison with Totonac, Tepehua has been poorly studied (see a comprehensive list of references in MacKay & Trechsel 2012). Representative works include Watters (1988), on Tlachichilco morpho-syntax with a brief phonological survey; Gutiérrez, Jiménez & García (2013), on a Tepehua-Spanish vocabulary, which is a vocabulary for the Tepehua variety spoken in Tlachichilco; MacKay & Trechsel (2013, 2018), providing detailed accounts of the phonological structures of Pisaflores and discussion of previous reconstructions of proto-Totonac-Tepehua sounds; and Kryder (1987) and Smythe (2007), offering a detailed description of Huehuetla phonology.
Prolactin receptor regulates the seasonal reproduction of striped hamsters
Authors: Xue Huiliang , Xu Jinhui , Wu Ming , Chen Lei , Xu Laixiang 
Published: June 2021

SummaryIn this study, differential mRNA expression patterns of prolactin receptor (PRLR) in the hypothalamus and gonads, and the correlation with follicle stimulating hormone (FSH) and luteinizing hormone (LH) in striped hamster serum from spring, summer, autumn and winter were analyzed. Mature female and male striped hamsters in oestrus were used. Expression levels of PRLR in the hypothalamus, ovaries and testis from the summer and winter individuals were significantly higher compared with levels from the spring and autumn, whereas FSH and LH serum concentrations from summer and winter individuals were significantly lower compared with that from the spring and autumn. PRLR expression levels in hypothalamus, ovaries and testis were negatively correlated with FSH and LH serum concentrations, illustrating that PRLR might negatively regulate seasonal reproductive activity. PRLR expression levels in ovaries and testes were significantly higher compared with levels in the hypothalamus, suggesting that the regulative effects of PRLR in gonads might be significantly higher compared with that in the hypothalamus. Furthermore, PRLR expression levels from the spring, summer, autumn and winter seasons in the hypothalamus and gonads were significantly higher in females compared with levels in males, indicating that the regulative effect of PRLR might be sex dependent. Taken together, this study helps to understand in depth the seasonal regulative reproduction mechanism of striped hamsters to reasonably control population abundance.
Development of an embryo germination protocol for shy-seeded grape (Vitis vinifera L.)
Authors: Benke Ashwini P. , Krishna Ram , Samarth Roshni R. , Dhumal Shweta S. , Ansari Waquar A. , Shelke Poonam V. , Dukare Somnath S. , Singh Major 
Published: June 2021

AbstractAcquisition and germination of seeds are the most desired targets for the improvement of vegetatively propagated crops. In the present study, we developed a potential embryo germination protocol for the Red Globe grape cultivar having a low seed germination rate. Three grape berries at different developmental stages, viz. 50, 60 and 70 days after flowering (DAF), were selected for in-vitro embryo germination. Three growth media, namely Emershad and Ramming (ER), Nitsch and Nitsch (NN) and Murashige and Skoog (MS), and plant growth regulators (benzyl amino purine (BA), 0.5, 0.7 and 0.9 mg/l; indole butyric acid (IBA), 1.0, 1.5 and 2.0 mg/l; and gibberellic acid (GA), 0.1, 0.3 and 0.9 mg/l) were screened individually in different combinations with three amino acids, namely cysteine, glutamine and proline (2.0 μmol/l each). The maximum embryos germination percentage recorded at 70 DAF was 63.33, 47.78 and 45.56% in ER, NN and MS media, respectively, supplemented with 0.9 mg/l BA, 2.0 mg/l IBA, 0.9 mg/l GA and 2.0 μmol glutamine. Glutamine was found to have the most significant impact, and it improved the rescued embryos germination. The present study provides a potential recipe for a medium that can facilitate efficient germination of grape embryos.
Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment
Authors: Schmid Robin , Petras Daniel , Nothias Louis-Félix , Wang Mingxun , Aron Allegra T. , Jagels Annika , Tsugawa Hiroshi , Rainer Johannes , Garcia-Aloy Mar , Dührkop Kai , Korf Ansgar , Pluskal Tomáš , Kameník Zdeněk , Jarmusch Alan K. , Caraballo-Rodríguez Andrés Mauricio , Weldon Kelly C. , Nothias-Esposito Melissa , Aksenov Alexander A. , Bauermeister Anelize , Albarracin Orio Andrea , Grundmann Carlismari O. , Vargas Fernando , Koester Irina , Gauglitz Julia M. , Gentry Emily C. , Hövelmann Yannick , Kalinina Svetlana A. , Pendergraft Matthew A. , Panitchpakdi Morgan , Tehan Richard , Le Gouellec Audrey , Aleti Gajender , Mannochio Russo Helena , Arndt Birgit , Hübner Florian , Hayen Heiko , Zhi Hui , Raffatellu Manuela , Prather Kimberly A. , Aluwihare Lihini I. , Böcker Sebastian , McPhail Kerry L. , Humpf Hans-Ulrich , Karst Uwe , Dorrestein Pieter C. 
Published: June 2021

AbstractMolecular networking connects mass spectra of molecules based on the similarity of their fragmentation patterns. However, during ionization, molecules commonly form multiple ion species with different fragmentation behavior. As a result, the fragmentation spectra of these ion species often remain unconnected in tandem mass spectrometry-based molecular networks, leading to redundant and disconnected sub-networks of the same compound classes. To overcome this bottleneck, we develop Ion Identity Molecular Networking (IIMN) that integrates chromatographic peak shape correlation analysis into molecular networks to connect and collapse different ion species of the same molecule. The new feature relationships improve network connectivity for structurally related molecules, can be used to reveal unknown ion-ligand complexes, enhance annotation within molecular networks, and facilitate the expansion of spectral reference libraries. IIMN is integrated into various open source feature finding tools and the GNPS environment. Moreover, IIMN-based spectral libraries with a broad coverage of ion species are publicly available.
Comprehensive identification of transposable element insertions using multiple sequencing technologies
Authors: Chu Chong , Borges-Monroy Rebeca , Viswanadham Vinayak V. , Lee Soohyun , Li Heng , Lee Eunjung Alice , Park Peter J. 
Published: June 2021

AbstractTransposable elements (TEs) help shape the structure and function of the human genome. When inserted into some locations, TEs may disrupt gene regulation and cause diseases. Here, we present xTea (x-Transposable element analyzer), a tool for identifying TE insertions in whole-genome sequencing data. Whereas existing methods are mostly designed for short-read data, xTea can be applied to both short-read and long-read data. Our analysis shows that xTea outperforms other short read-based methods for both germline and somatic TE insertion discovery. With long-read data, we created a catalogue of polymorphic insertions with full assembly and annotation of insertional sequences for various types of retroelements, including pseudogenes and endogenous retroviruses. Notably, we find that individual genomes have an average of nine groups of full-length L1s in centromeres, suggesting that centromeres and other highly repetitive regions such as telomeres are a significant yet unexplored source of active L1s. xTea is available at https://github.com/parklab/xTea.
Artificially engineered antiferromagnetic nanoprobes for ultra-sensitive histopathological level magnetic resonance imaging
Authors: Liang Zeyu , Wang Qiyue , Liao Hongwei , Zhao Meng , Lee Jiyoung , Yang Chuang , Li Fangyuan , Ling Daishun 
Published: June 2021

AbstractHistopathological level imaging in a non-invasive manner is important for clinical diagnosis, which has been a tremendous challenge for current imaging modalities. Recent development of ultra-high-field (UHF) magnetic resonance imaging (MRI) represents a large step toward this goal. Nevertheless, there is a lack of proper contrast agents that can provide superior imaging sensitivity at UHF for disease detection, because conventional contrast agents generally induce T2 decaying effects that are too strong and thus limit the imaging performance. Herein, by rationally engineering the size, spin alignment, and magnetic moment of the nanoparticles, we develop an UHF MRI-tailored ultra-sensitive antiferromagnetic nanoparticle probe (AFNP), which possesses exceptionally small magnetisation to minimize T2 decaying effect. Under the applied magnetic field of 9 T with mice dedicated hardware, the nanoprobe exhibits the ultralow r2/r1 value (~1.93), enabling the sensitive detection of microscopic primary tumours (<0.60 mm) and micrometastases (down to 0.20 mm) in mice. The sensitivity and accuracy of AFNP-enhanced UHF MRI are comparable to those of the histopathological examination, enabling the development of non-invasive visualization of previously undetectable biological entities critical to medical diagnosis and therapy.