bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monitoring of spatiotemporal occupancy patterns of fish and amphibian species in a lentic aquatic system using environmental DNA
Authors: Brys Rein , Haegeman Annelies , Halfmaerten David , Neyrinck Sabrina , Staelens Ariane , Auwerx Johan , Ruttink Tom 
Published: November 2020

AbstractTo effectively monitor, manage and protect aquatic species and understand their interactions, knowledge of their spatiotemporal distribution is needed. In this study, we used a fine‐scale spatiotemporal water sampling design, followed by environmental DNA (eDNA) 12S metabarcoding, to investigate occupancy patterns of a natural community of fish and amphibian species in a lentic system. In the same system, we experimentally estimated the spatial and temporal dispersion of eDNA by placing a community of different fish and amphibian species in cages at one side of the pond, creating a controlled point of eDNA emission. Analyses of this cage community revealed a sharp spatial decline in detection rates and relative eDNA quantities at a distance of 5–10 m from the source, depending on the species and its abundance. In addition, none of the caged species could be detected 1 week after removal from the system. This indicates high eDNA decay rates and limited spatial eDNA dispersal, facilitating high local resolution for monitoring spatial occupancy patterns of aquatic species. Remarkably, for seven of the nine cage species, the presence of a single individual could be detected by pooling water of subsamples taken across the whole water body, illustrating the high sensitivity of the eDNA sampling and detection method applied. Finally, our work demonstrated that a fine‐scale sampling design in combination with eDNA metabarcoding can cover total biodiversity very precisely and allows the construction of consistent spatiotemporal patterns of relative abundance and local distribution of free‐living fish and amphibian species in a lentic ecosystem.
The genomic signature of ecological divergence along the benthic‐limnetic axis in allopatric and sympatric threespine stickleback
Authors: Härer Andreas , Bolnick Daniel I. , Rennison Diana J. 
Published: November 2020

AbstractThe repeated occurrence of similar phenotypes in independent lineages (i.e., parallel evolution) in response to similar ecological conditions can provide compelling insights into the process of adaptive evolution. An intriguing question is to what extent repeated phenotypic changes are underlain by repeated changes at the genomic level and whether patterns of genomic divergence differ with the geographic context in which populations evolve. Here, we combined genomic, morphological and ecological data sets to investigate the genomic signatures of divergence across populations of threespine stickleback (Gasterosteus aculeatus) that adapted to contrasting ecological niches (benthic or limnetic) in either sympatry or allopatry. We found that genome‐wide differentiation (FST) was an order of magnitude higher and substantially more repeatable for sympatric benthic and limnetic specialists compared to allopatric populations with similar levels of ecological divergence. We identified genomic regions consistently differentiated between sympatric ecotypes that were also differentiated between or associated with benthic vs. limnetic niche in allopatric populations. These candidate regions were enriched on three chromosomes known to be involved in the benthic‐limnetic divergence of threespine stickleback. Some candidate regions overlapped with QTL for body shape and trophic traits such as gill raker number, traits that strongly differ between benthic and limnetic ecotypes. In summary, our study shows that magnitude and repeatability of genomic signatures of ecological divergence in threespine stickleback highly depend on the geographic context. The identified candidate regions provide starting points to identify functionally important genes for the adaptation to benthic and limnetic niches.
A key cytosolic iron–sulfur cluster synthesis protein localizes to the mitochondrion of Toxoplasma gondii
Authors: Aw Yi Tong Vincent , Seidi Azadeh , Hayward Jenni A. , Lee Jiwon , Makota F. Victor , Rug Melanie , van Dooren Giel G. 
Published: November 2020

AbstractIron–sulfur (Fe‐S) clusters are prosthetic groups on proteins that function in a range of enzymatic and electron transfer reactions. Fe‐S cluster synthesis is essential for the survival of all eukaryotes. Independent Fe‐S cluster biosynthesis pathways occur in the mitochondrion, plastid, and cytosolic compartments of eukaryotic cells. Little is known about the cytosolic Fe‐S cluster biosynthesis in apicomplexan parasites, the causative agents of diseases such as malaria and toxoplasmosis. NBP35 serves as a key scaffold protein on which cytosolic Fe‐S clusters assemble, and has a cytosolic localization in most eukaryotes studied thus far. Unexpectedly, we found that the NBP35 homolog of the apicomplexan Toxoplasma gondii (TgNBP35) localizes to the outer mitochondrial membrane, with mitochondrial targeting mediated by an N‐terminal transmembrane domain. We demonstrate that TgNBP35 is critical for parasite proliferation, but that, despite its mitochondrial localization, it is not required for Fe‐S cluster synthesis in the mitochondrion. Instead, we establish that TgNBP35 is important for the biogenesis of cytosolic Fe‐S proteins. Our data are consistent with TgNBP35 playing a central and specific role in cytosolic Fe‐S cluster biosynthesis, and imply that the assembly of cytosolic Fe‐S clusters occurs on the cytosolic face of the outer mitochondrial membrane in these parasites.
Resistant Starch Production and Glucose Release from Pre‐Prepared Chilled Food: The SPUD Project
Authors: Robertson T. M. , Brown J. E. , Fielding B. A. , Hovorka R. , Robertson M. D. 
Published: November 2020

AbstractWith an increasing prevalence of diabetes worldwide, effective dietary strategies for blood glucose control are crucial. As carbohydrates make up approximately 50% of the diet, it is neither practical nor advisable to avoid them altogether. Most of the carbohydrate in the diet is derived from starch, found in potatoes, pasta, rice and bread. These foods are often processed in some way before consumption, yet little is known about the effects processing, such as chilling and reheating, has on the glycaemic response, particularly when the food is consumed in the context of a mixed meal. This article introduces the SPUD project, a BBSRC DRINC‐funded initiative. Taking the potato as the model carbohydrate, this project will investigate, via in vitro and in vivo studies, the effects of domestic food processing techniques on the glycaemic response. A final study, utilising intrinsically labelled potato and a dual stable isotope methodology, will model glucose flux data to determine the underlying mechanisms of action.
Recommendations by the Asian Pacific society of nephrology (APSN) on the appropriate use of HIF‐PH inhibitors
Authors: Yap Desmond Y. H. , McMahon Lawrence P. , Hao Chuan‐Ming , Hu Nan , Okada Hirokazu , Suzuki Yusuke , Kim Sung Gyun , Lim Soo Kun , Vareesangthip Kriengsak , Hung Chi‐Chih , Nangaku Masaomi ,   for the APSN HIF‐PHI Recommendation Committee
Published: November 2020

AbstractRenal anaemia is a common and important complication in patients with chronic kidney disease (CKD). The current standard‐of‐care treatment for renal anaemia in CKD patients involves ensuring adequate iron stores and administration of erythropoietin stimulating agents (ESA). Hypoxia inducible factor (HIF) is a key transcription factor primarily involved in the cellular regulation and efficiency of oxygen delivery. Manipulation of the HIF pathway by the use of HIF‐prolyl hydroxylase inhibitors (HIF‐PHI) has emerged as a novel approach for renal anaemia management. Despite it being approved for clinical use in various Asia‐Pacific countries, its novelty mandates the need for nephrologists and clinicians generally in the region to well understand potential benefits and harms when prescribing this class of drug. The Asian Pacific society of nephrology HIF‐PHI Recommendation Committee, formed by a panel of 11 nephrologists from the Asia‐Pacific region who have clinical experience or have been investigators in HIF‐PHI studies, reviewed and deliberated on the clinical and preclinical data concerning HIF‐PHI. This recommendation summarizes the consensus views of the committee regarding the use of HIF‐PHI, taking into account both available data and expert opinion in areas where evidence remains scarce.
Oxidized phospholipids affect small intestine neuromuscular transmission and serotonergic pathways in juvenile mice
Authors: Marsilio Ilaria , Caputi Valentina , Latorre Eva , Cerantola Silvia , Paquola Andrea , Alcalde Ana I. , Mesonero José E. , O'Mahony Siobhain M. , Bertazzo Antonella , Giaroni Cristina , Giron Maria Cecilia 
Published: November 2020

AbstractBackgroundOxidized phospholipid derivatives (OxPAPCs) act as bacterial lipopolysaccharide (LPS)–like damage‐associated molecular patterns. OxPAPCs dose‐dependently exert pro‐ or anti‐inflammatory effects by interacting with several cellular receptors, mainly Toll‐like receptors 2 and 4. It is currently unknown whether OxPAPCs may affect enteric nervous system (ENS) functional and structural integrity.MethodsJuvenile (3 weeks old) male C57Bl/6 mice were treated intraperitoneally with OxPAPCs, twice daily for 3 days. Changes in small intestinal contractility were evaluated by isometric neuromuscular responses to receptor and non–receptor‐mediated stimuli. Alterations in ENS integrity and serotonergic pathways were assessed by real‐time PCR and confocal immunofluorescence microscopy in longitudinal muscle‐myenteric plexus whole‐mount preparations (LMMPs). Tissue levels of serotonin (5‐HT), tryptophan, and kynurenine were measured by HPLC coupled to UV/fluorescent detection.Key ResultsOxPAPC treatment induced enteric gliosis, loss of myenteric plexus neurons, and excitatory hypercontractility, and reduced nitrergic neurotransmission with no changes in nNOS+ neurons. Interestingly, these changes were associated with a higher functional response to 5‐HT, altered immunoreactivity of 5‐HT receptors and serotonin transporter (SERT) together with a marked decrease in 5‐HT levels, shifting tryptophan metabolism toward kynurenine production.Conclusions and InferencesOxPAPC treatment disrupted structural and functional integrity of the ENS, affecting serotoninergic tone and 5‐HT tissue levels toward a higher kynurenine content during adolescence, suggesting that changes in intestinal lipid metabolism toward oxidation can affect serotoninergic pathways, potentially increasing the risk of developing functional gastrointestinal disorders during critical stages of development.
Key root traits of Poaceae for adaptation to soil water gradients
Authors: Yamauchi Takaki , Pedersen Ole , Nakazono Mikio , Tsutsumi Nobuhiro 
Published: November 2020

Summary

Drought and flooding are contrasting abiotic stressors for plants. Evidence is accumulating for root anatomical traits being essential for the adaptation to drought or flooding. However, an integrated approach to comprehensively understand root anatomical traits has not yet been established.

Here we analysed the root anatomical traits of 18 wild Poaceae species differing in adaptation to a range of soil water content. Regression model analyses revealed the optimal anatomical traits that were required by the plants to adapt to low or high soil water content.

While the area and number of each root tissue (e.g. stele, cortex, xylem or aerenchyma) were not strongly correlated to the soil water content, the ratio of the root tissue areas (cortex to stele ratio (CSR), xylem to stele ratio (XSR) and aerenchyma to cortex ratio (ACR)) could fully explain the adaptations of the wild Poaceae species to the soil water gradients.

Our results demonstrate that the optimal anatomical traits for the adaptations to soil water content can be determined by three indices (i.e. CSR, XSR and ACR), and thus we propose that these root anatomical indices can be used to improve the tolerance of crops to drought and flooding stresses.
Linking canopy‐scale mesophyll conductance and phloem sugar δ13C using empirical and modelling approaches
Authors: Schiestl‐Aalto Pauliina , Stangl Zsofia R. , Tarvainen Lasse , Wallin Göran , Marshall John , Mäkelä Annikki 
Published: November 2020

Summary

Interpreting phloem carbohydrate or xylem tissue carbon isotopic composition as measures of water‐use efficiency or past tree productivity requires in‐depth knowledge of the factors altering the isotopic composition within the pathway from ambient air to phloem contents and tree ring. One of least understood of these factors is mesophyll conductance (gm).

We formulated a dynamic model describing the leaf photosynthetic pathway including seven alternative gm descriptions and a simple transport of sugars from foliage down the trunk. We parameterised the model for a boreal Scots pine stand and compared simulated gm responses with weather variations. We further compared the simulated δ13C of new photosynthates among the different gm descriptions and against measured phloem sugar δ13C.

Simulated gm estimates of the seven descriptions varied according to weather conditions, resulting in varying estimates of phloem δ13C during cold/moist and warm/dry periods. The model succeeded in predicting a drought response and a postdrought release in phloem sugar δ13C indicating suitability of the model for inverse prediction of leaf processes from phloem isotopic composition.

We suggest short‐interval phloem sampling during and after extreme weather conditions to distinguish between mesophyll conductance drivers for future model development.
Preferential meiotic chromosome pairing among homologous chromosomes with cryptic sequence variation in tetraploid maize
Authors: Braz Guilherme T. , Yu Fan , Zhao Hainan , Deng Zuhu , Birchler James A. , Jiang Jiming 
Published: November 2020

Summary

Meiotic chromosome pairing between homoeologous chromosomes was reported in many nascent allopolyploids. Homoeologous pairing is gradually eliminated and replaced by exclusive homologous pairing in well‐established allopolyploids, an evolutionary process referred to as the diploidization of allopolyploids. A fundamental question of the diploidization of allopolyploids is whether and to what extent the DNA sequence variation among homoeologous chromosomes contribute to the establishment of exclusive homologous chromosome pairing.

We developed aneuploid tetraploid maize lines that contain three copies of chromosome 10 derived from inbred lines B73 and H99. We were able to identify the parental origin of each copy of chromosome 10 in the materials using oligonucleotide‐based haplotype‐specific chromosome painting.

We demonstrate that the two identical copies of chromosome 10 from H99 pair preferentially over chromosome 10 from B73 in different stages of prophase I and metaphase I during meiosis. Thus, homologous chromosome pairing is favored to partners with the most similar DNA sequences and can be discriminated based on cryptic sequence variation.

We propose that innate preference of homologous chromosome pairing exists in nascent allopolyploids and serves as the first layer that would eventually block all homoeologous chromosome pairing in allopolyploids.
Regulatory challenges with biosimilars: an update from 20 countries
Authors: Kang Hye‐Na , Thorpe Robin , Knezevic Ivana , Casas Levano Mary , Chilufya Mumbi Bernice , Chirachanakul Parichard , Chua Hui Ming , Dalili Dina , Foo Freddie , Gao Kai , Habahbeh Suna , Hamel Hugo , Kim Gi Hyun , Perez Rodriguez Violeta , Putri Desi Eka , Rodgers Jacqueline , Savkina Maria , Semeniuk Oleh , Srivastava Shraddha , Tavares Neto João , Wadhwa Meenu , Yamaguchi Teruhide 
Published: November 2020

AbstractThe World Health Organization (WHO) issued guidelines for the regulatory evaluation of biosimilars in 2009 and has provided considerable effort toward helping member states implement the evaluation principles in the guidelines into their regulatory practices. Despite this effort, a recent WHO survey (conducted in 2019–2020) has revealed four main remaining challenges: unavailable/insufficient reference products in the country; lack of resources; problems with the quality of some biosimilars (and even more with noninnovator products); and difficulties with the practice of interchangeability and naming of biosimilars. The following have been identified as opportunities/solutions for regulatory authorities to deal with the existing challenges: (1) exchange of information on products with other regulatory authorities and accepting foreign licensed and sourced reference products, hence avoiding conducting unnecessary (duplicate) bridging studies; (2) use of a “reliance” concept and/or joint review for the assessment and approval of biosimilars; (3) review and reassessment of the products already approved before the establishment of a regulatory framework for biosimilar approval; and (4) setting appropriate regulatory oversight for good pharmacovigilance, which is essential for the identification of problems with products and establishing the safety and efficacy of interchangeability of biosimilars.
Injury prevention among young people in nursing homes: Recommendations following expert consultation forums
Authors: Cartwright Anna , Bugeja Lyndal , Ibrahim Joseph E. 
Published: November 2020

AbstractBackgroundApproximately 6,000 people under the age of 65 years reside in nursing homes each year in Australia. These young people in nursing homes are at risk of premature death and preventable morbidity from injuries. Choking and falls are the leading causes of premature deaths in this cohort with reported rates of 44% and 33%, respectively.ObjectivesTo develop injury prevention recommendations for young people in Australian nursing homes.MethodsThis mixed‐methods study comprised two expert consultation panels and a follow‐up survey. Two expert and stakeholder consultation panels used a modified nominal group technique to formulate recommendations. A short survey was subsequently given to participants to validate responses from the panels and to provide an opportunity to evaluate and rank recommendations.ResultsTen recommendations were formulated for consideration that focused on system‐wide reforms. Four were ranked as most important for implementation: education and training for nursing home staff; implementation of National Disability Insurance Scheme; support for coordinated care; and increasing residential housing stock that is appropriately designed.ConclusionExtensive changes are needed to prevent injury for young people in nursing homes. Implementation should reduce the risk of injury and lead to an improved quality of life for this cohort.Implications for practiceThis study provides an evidence base for aged care practitioners to improve practice within nursing homes to reduce fatal and non‐fatal injuries for young people in nursing homes.
Dry eye symptoms in children: can we reliably measure them?
Authors: Chidi‐Egboka Ngozi Charity , Golebiowski Blanka , Lee Sun‐Young , Vi Mimi , Jalbert Isabelle 
Published: November 2020

AbstractPurposeMany dry eye questionnaires are available, but these may not be suitable for paediatric eye care. The feasibility of use and repeatability of symptom questionnaires administered to children was examined.MethodsParticipants aged 6‐15 years (n = 62; 25M:37F; 40% male) completed six questionnaires twice in random order at a single visit: Symptoms assessment in dry eye (SANDE), ocular surface disease index (OSDI), numerical rating scale (NRS), ocular comfort index (OCI, n = 30), dry eye questionnaire 5 (DEQ‐5) and the instant ocular symptoms survey (IOSS). Completion time and need for assistance were recorded and relationships with age examined (Pearson correlation, independent t‐test). The number of participants requiring assistance and with which items were compared (linear mixed model, pairwise test). Repeatability (coefficient of repeatability (CoR), limit of agreement, bias) and intraclass correlation coefficient (ICC) were examined.ResultsCompletion time was ≤2 min for each individual questionnaire. Younger participants took longer to complete (r = −0.43 to −0.60, p ≤ 0.01), and required more assistance (p ≤ 0.001). Forty‐eight participants required assistance with at least one questionnaire. Older children (13–15 years) only required assistance with OSDI (p ≤ 0.004) and NRS (p ≤ 0.003). Participants required more assistance with SANDE, OSDI and NRS than with DEQ‐5 and IOSS (p ≤ 0.02) and with gritty (OSDI, 77% of participants; OCI, 100%) and foreign body sensation (NRS, 92%) items. CoR was similar for all questionnaires with no evidence of a learning effect (p > 0.05). ICC was moderate to excellent.ConclusionsDry eye questionnaires can be used reliably in paediatric eye care; more time and assistance may be required for younger children. The DEQ‐5 and IOSS are recommended for use in younger age children.
Lung function testing and inflammation markers for wheezing preschool children: A systematic review for the EAACI Clinical Practice Recommendations on Diagnostics of Preschool Wheeze
Authors: Elenius Varpu , Chawes Bo , Malmberg Pekka L. , Adamiec Aleksander , Ruszczyński Marek , Feleszko Wojciech , Jartti Tuomas ,   EAACI Preschool Wheeze Task Force for Diagnostics of Preschool Wheeze
Published: November 2020

AbstractBackgroundPreschool wheeze is highly prevalent; 30%–50% of children have wheezed at least once before age six. Wheezing is not a disorder; it is a symptom of obstruction in the airways, and it is essential to identify the correct diagnosis behind this symptom. An increasing number of studies provide evidence for novel diagnostic tools for monitoring and predicting asthma in the pediatric population. Several techniques are available to measure airway obstruction and airway inflammation, including spirometry, impulse oscillometry, whole‐body plethysmography, bronchial hyperresponsiveness test, multiple breath washout test, measurements of exhaled NO, and analyses of various other biomarkers.MethodsWe systematically reviewed all the existing techniques available for measuring lung function and airway inflammation in preschool children to assess their potential and clinical value in the routine diagnostics and monitoring of airway obstruction.ResultsIf applicable, measuring FEV1 using spirometry is considered useful. For those unable to perform spirometry, whole‐body plethysmography and IOS may be useful. Bronchial reversibility to beta2‐agonist and hyperresponsiveness test with running exercise challenge may improve the sensitivity of these tests.ConclusionsThe difficulty of measuring lung function and the lack of large randomized controlled trials makes it difficult to establish guidelines for monitoring asthma in preschool children.