bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimizing and applying high‐resolution, in‐line laboratory phase‐contrast X‐ray imaging for low‐density material samples
Authors: Zboray Robert 
Published: November 2020

AbstractIn‐line, or propagation‐based phase‐contrast X‐ray imaging (PBI) is an attractive alternative to the attenuation‐based modality for low‐density, soft samples showing low attenuation contrast. With the growing availability of micro‐ and nano‐focus X‐ray tubes, the method is increasingly applied in the laboratory. Here, we discuss the technique and demonstrate its advantages for selected low‐density, low attenuation material samples using a lab‐based micro‐ and nano‐computed tomography systems Easytom XL Ultra, providing micron and sub‐micron range resolution PBI images. We demonstrate a multi‐step optimization of the lab‐based PBI technique on our scanner that includes choosing the optimal detector‐source hardware combination available in the setup, then optimizing the imaging geometry and finally the phase retrieval process through a parametric study. We point out and elaborate on the effect of noise correlation and texturing due to phase retrieval. We demonstrate the overall benefits of using the phase image and the phase retrieval for the selected samples such as improved image quality, increased contrast‐to‐noise ratio while only marginally influencing the spatial resolution. The improvement in image quality also enables further image processing steps for detailed structural analysis of the samples, which would be much more complicated if not impossible based on the transmission image.
Associations of methylenetetrahydrofolate reductase gene (MTHFR) rs1801131 and rs1801133 polymorphisms with susceptibility to vitiligo: A meta‐analysis
Authors: Zhang Hua‐Zhu , Wu Jiang‐Hai , Huang Qian , Yang Qin , Sima Quan , Chen Ke‐Yan , Li Zhi‐Ran , He Gong‐Hao 
Published: November 2020

AbstractBackgroundVitiligo is a common pigmentary skin disorder, and genetic factors were acknowledged to be greatly associated with the pathogenesis of this disease. Recently, increasing studies investigated the associations of methylenetetrahydrofolate reductase (MTHFR) rs1801131 and rs1801133 polymorphisms with risks of vitiligo, but the results still remained controversial.AimThe current meta‐analysis was conducted to further evaluate the association ofMTHFRpolymorphisms with risk of vitiligo.MethodsEligible studies were searched in PubMed, EMBASE, Cochrane library, Chinese National Knowledge Infrastructure (CNKI), Technology of Chongqing (VIP), and Wan Fang Database until October 2020. All analyses were carried out using the Review Manager 5.3 software.ResultsA total of 6 studies that involvedMTHFRrs1801131 and/or rs1801133 polymorphism were finally included, which enrolled 3599 participants. Our results showed that no correlations were found betweenMTHFRrs1801131, rs1801133 polymorphisms and vitiligo risks in overall group. However, subgroup analysis revealed that rs1801131 polymorphism was significantly associated with increased vitiligo risk in the allelic (C vs A: OR = 1.15, 95% CI = 1.02‐1.29,P = .02) and homozygous models (CC vs AA: OR = 1.48, 95% CI = 1.10‐2.01,P = .01) in Asian population and that the rs1801133 polymorphism was significantly associated with decreased vitiligo risk in the allelic model (T vs C: OR = 0.82, 95% CI = 0.74‐0.92,P = .0005) also in Asian population.ConclusionsThis meta‐analysis confirmed the associations ofMTHFRrs1801131 and rs1801133 polymorphisms with vitiligo risks and provided comprehensive insight into the pathogenesis of vitiligo.
Estimated salt intake and risk of atrial fibrillation in a prospective community‐based cohort
Authors: Wuopio J. , Orho‐Melander M. , Ärnlöv J. , Nowak C. 
Published: November 2020

AbstractIntroductionHypertension predisposes to atrial fibrillation (AF) – a major risk factor for ischaemic stroke. Since a high dietary salt consumption is associated with hypertension, we investigated the association between urinary sodium excretion as a marker for dietary sodium intake and risk of new‐onset AF in community‐dwelling adults.MethodThe UK Biobank includes 40‐ to 69‐year‐old British residents recruited 2006–2010. Participants were divided into sex‐specific quintiles according to 24‐hour sodium excretion estimated based on spot samples with the Kawasaki equation. We excluded participants with AF at baseline. Cox regression adjusted for cardiovascular risk factors was used to assess associations with risk of AF, using the third quintile as reference.ResultsA total of 257 545 women and 215 535 men were included. During up to 10 years' follow‐up, 2221 women and 3751 men were diagnosed with AF. There was a tendency for an increased risk of AF in the lowest and highest quintiles of estimated daily salt intake in both women and men. In the fully adjusted model, significant associations were seen amongst men in the lowest and highest quintiles of sodium excretion (hazard ratio, HRQv1, 1.20; 95% CI, 1.08–1.32, P < 0.001, and HRQv5 1.15, 95% CI, 1.03–1.27, P = 0.011).ConclusionWe found evidence for a U‐shaped association between estimated daily salt intake and AF risk amongst men. A suggestive J‐shaped association in women was not statistically confirmed, but analyses were likely underpowered. Our results suggest that above a certain physiological minimum level progressively higher salt intake is associated with increasing risk of AF.
miRNA for the assessment of lymph node metastasis in patients with oral squamous cell carcinoma: Systematic review and metanalysis
Authors: Jadhav Kiran B. , Nagraj Sumanth K. , Arora Shelly 
Published: November 2020

AbstractBackgroundmiRNA is one of the advanced epigenetic molecular markers correlating with lymph node metastasis in patients with Oral squamous cell carcinoma (OSCC). Numerous published papers are showing correlation of miRNA with metastasis. There is a need to analyze and validate such correlation.MethodEnglish language literature in major databases from the last 20 years was searched using controlled vocabulary and keywords. Strict inclusion and exclusion criteria were followed for selection of studies. The quality assessment was done as per the QUADAS tool 2 by three independent reviewers. The metanalysis was performed by using random effect model. Standardized mean difference (SMD) was considered as the effect measure. Statistical software used was STATA version 13.1.ResultsWith all inclusion and exclusion criteria, eight studies could qualify for metanalysis. The pooled estimate is found to be 0.13 (−0.35, 0.62), P = .585, which is statistically not significant. This indicates that there is a no significant difference in the fold change between metastasis and no metastasis groups. P‐value of chi‐square statistic for heterogeneity is <.001 (significant), and I‐squared statistic is 87.2%, which indicates that heterogeneity is present to a considerable extent. Egger's test shows there is no publication bias involved (P = .819).ConclusionThe metanalysis showed no significant difference in the fold change of miRNA expression between metastasis and non‐metastasis OSCC patients. Future studies can be directed to eliminate the heterogeneity among the studies noted in this analysis to confirm the role of miRNA for assessment of regional metastasis with special focus on tongue squamous cell carcinoma.
The potential role of Photodynamic therapy in oral premalignant and malignant lesions: A systematic review
Authors: Romano Antonio , Di Stasio Dario , Gentile Enrica , Petruzzi Massimo , Serpico Rosario , Lucchese Alberta 
Published: November 2020

AbstractBackgroundPhotodynamic therapy (PDT) is considered as a valid treatment option in various branches of dentistry. This systematic review aims to evaluate the usefulness of PDT for treatment of oral premalignant and malignant lesions.MethodsThe MeSH terms “Photodynamic therapy” and “PDT,” in combination with other terms, have been searched by three search engines (PubMed, ISI Web of Science, and the Cochrane Library), and a systematic review has been performed. The Population, Intervention, Comparison, Outcomes, and Study design (PICOS) has been applied as method to outline our study eligibility criteria. Risk of Bias in Non‐randomized Studies of Intervention (ROBINS‐I) has been performed too.ResultsInitial results were 1513. Definitely, 27 studies met our selection criteria.ConclusionsTopical PDT is an easy to perform technique, well‐tolerated treatment and it appears to be an effective method with encouraging achievements in the treatment of premalignant and malignant lesions of the soft tissues of the oral cavity; nevertheless more studies are required to integrate the up‐to‐date experience of this application.
Effect of Inlays, Onlays and Endocrown Cavity Design Preparation on Fracture Resistance and Fracture Mode of Endodontically Treated Teeth: An In Vitro Study
Authors: Kassis Cynthia , Khoury Pierre , Mehanna Carina Z , Baba Nadim Z. , Bou Chebel Fadi , Daou Maha , Hardan Louis 
Published: November 2020

AbstractPurposeTo evaluate the fracture resistance and failure modes of endodontically treated mandibular molars restored with different designs of inlays, onlays and endocrowns.Materials and MethodsExtracted mandibular third molars (n = 180) were used. An access cavity was prepared on the occlusal surface of each tooth and the roots were obturated with gutta percha. All specimens were randomly divided into 6 groups (n = 30/group) according to the cavity design and the restoration material used. C: control group without access cavity preparation. IE: MOD inlay preparation with EverX Posterior (GC Europe) in the pulp chamber. IG: MOD inlay preparation with G‐aenial Universal Flo (GC America) in the pulp chamber. OE: onlay preparation with EverX Posterior (GC Europe) in the pulp chamber. OG: onlay preparation with G‐aenial Universal Flo (GC America) in the pulp chamber. EC: endocrown with an empty pulp chamber. All restorations were fabricated with CAD/CAM system using CERASMART® (GC Dental products Europe, Belgium) CAD/CAM blocks. Specimens were thermal‐cycled and were subjected to a compressive load applied at 30° angle relative to the long axis of the tooth with a universal testing machine. Results were statistically analyzed by ANOVA followed by Tukey post hoc tests. Chi‐square test and Fisher Exact tests were used for the comparisons among groups.ResultsThe mean fracture strength was significantly different between the groups (p < 0.001); it was significantly highest for intact teeth, followed by endocrowns (p = 0.021). The strength was significantly lower for inlays (with G‐aenial Universal Flo and EverX Posterior), intermediate for onlays with EverX Posterior followed by onlays with G‐aenial Universal Flo.ConclusionsEndocrowns exhibited higher fracture resistance than other tested composite resin groups. Endocrowns and onlays showed a more favorable failure mode than inlay restorations.
Using ultraconserved elements to track the influence of sea‐level change on leafy seadragon populations
Authors: Stiller Josefin , da Fonseca Rute R. , Alfaro Michael E. , Faircloth Brant C. , Wilson Nerida G. , Rouse Greg W. 
Published: November 2020

AbstractDuring the Last Glacial Maximum (LGM), global sea levels were 120–130 m lower than today, resulting in the emergence of most continental shelves and extirpation of subtidal organisms from these areas. During the interglacial periods, rapid inundation of shelf regions created a dynamic environment for coastal organisms, such as the charismatic leafy seadragon (Phycodurus eques, Syngnathidae), a brooder with low dispersal ability inhabiting kelp beds in temperate Australia. Reconstructions of the palaeoshoreline revealed that the increase of shallow areas since the LGM was not uniform across the species' range and we investigated the effects of these asymmetries on genetic diversity and structuring. Using targeted capture of 857 variable ultraconserved elements (UCEs, 2,845 single nucleotide polymorphisms) in 68 individuals, we found that the regionally different shelf topographies were paralleled by contrasting population genetic patterns. In the west, populations may not have persisted through sea‐level lows because shallow seabed was very limited. Shallow genetic structure, weak expansion signals and a westward cline in genetic diversity indicate a postglacial recolonization of the western part of the range from a more eastern location following sea‐level rise. In the east, shallow seabed persisted during the LGM and increased considerably after the flooding of large bays, which resulted in strong demographic expansions, deeper genetic structure and higher genetic diversity. This study suggests that postglacial flooding with rising sea levels produced locally variable signatures in colonizing populations.
Activity, delivery, and diversity of Type VI secretion effectors
Authors: Jurėnas Dukas , Journet Laure 
Published: November 2020

AbstractThe bacterial type VI secretion system (T6SS) system is a contractile secretion apparatus that delivers proteins to neighboring bacterial or eukaryotic cells. Antibacterial effectors are mostly toxins that inhibit the growth of other species and help to dominate the niche. A broad variety of these toxins cause cell lysis of the prey cell by disrupting the cell envelope. Other effectors are delivered into the cytoplasm where they affect DNA integrity, cell division or exhaust energy resources. The modular nature of T6SS machinery allows different means of recruitment of toxic effectors to secreted inner tube and spike components that act as carriers. Toxic effectors can be translationally fused to the secreted components or interact with them through specialized structural domains. These interactions can also be assisted by dedicated chaperone proteins. Moreover, conserved sequence motifs in effector‐associated domains are subject to genetic rearrangements and therefore engage in the diversification of the arsenal of toxic effectors. This review discusses the diversity of T6SS secreted toxins and presents current knowledge about their loading on the T6SS machinery.
Selection and validation of reference genes for qPCR in the human dermatophyte Trichophyton rubrum exposed to different carbon sources which promote adhesion‐inducing conditions
Authors: Ciesielska Anita , Stączek Paweł 
Published: November 2020

AbstractObjectiveThe present study aimed to identify reference genes for qPCR analysis of T. rubrum growth in culture media which promote adhesion‐inducing conditions to the host tissue.MethodsWe investigated the suitability of six candidate reference genes: β‐act, β‐tub, ef1‐α, gapdh, sdha and rpl2 in reference strain of Trichophyton rubrum in response to different environmental stimuli. The stability of these genes was determined by NormFinder, geNorm and BestKeeper software.ResultsOur data obtained from the three algorithms revealed that mRNA expression levels of two candidate reference genes, ef1‐α and β‐tub, remained the most stable in response to different carbon sources, while different sample sets had their own most stable reference genes, highlighting the importance of the choice of internal controls in qPCR experiments. We then checked the stability of ef1‐α and β‐tub reference genes expression in different T. rubrum strains, suggesting that these two genes are reliable for normalisation of qPCR. Finally, we validated the suitability of selected reference genes as internal controls for target gene (SUB3) using the 2‐ΔΔCt method. The best result indicating an increase of SUB3 transcript of T. rubrum was found when the two the most stable reference (ef1‐α and β‐tub ) genes were used, as revealed by all three algorithms.ConclusionsWe recommend the use of ef1‐α and β‐tub as reference genes for qPCR analysis of target gene expression in T. rubrum exposed to different carbon sources which promote adhesion‐inducing conditions.
Plant tropisms as a window on plant computational processes
Authors: Meroz Yasmine 
Published: November 2020

SummaryPlants are living information‐processing organisms with highly adaptive behavior, allowing them to prosper in a harsh and fluctuating environment in spite of being sessile. Lacking a central nervous system, plants are distributed systems orchestrating complex computational processes performed at the tissue level. Here I consider plant tropisms as a useful input–output system boasting a robust mathematical description, naturally permitting a dialogue between mathematical modeling and biological observations. I propose tropisms as an ideal framework for the study of plant computational processes, allowing us to infer the relationship between observed tropic responses and known stimuli. I concentrate on macroscopic models, and elucidate this approach by presenting recent examples focusing on computational processes involved at different hierarchical levels of interactions: a plant's interaction with itself and its internal state, with the abiotic environment, and with neighboring plants.
The goo‐d stuff: Plantago as a myxospermous model with modern utility
Authors: Cowley James M. , Burton Rachel A. 
Published: November 2020

SummaryMucilage, a gel‐like layer formed around wetted seeds in a process called myxospermy, has importance as a proxy for studying cell wall polysaccharide biosynthesis and interactions and as a source of valuable health supplements and hydrocolloids. Arabidopsis thaliana has provided unrivalled insight into mucilage/cell wall synthesis, but its lack of commercial utility presents an opportunity to develop an alternative myxospermous model linking genetics, chemistry and functionality. Here, we discuss recent advances in the understanding of mucilage production, composition and properties of Plantago, a promising candidate as an alternative model with economic relevance. We outline how genomic/transcriptomic and chemical analysis advances could be made to strengthen Plantago's use as a model system, through challenging but achievable approaches.
Identification of a tractable model system and oxalic acid‐dependent symptom development of the dollar spot pathogen Clarireedia jacksonii
Authors: Rioux Renée A. , Stephens Cameron M. , Koch Paul L. , Kabbage Mehdi , Kerns James P. 
Published: November 2020

AbstractClarireedia jacksonii causes dollar spot disease of cool‐season turfgrasses in the United States and produces the phytotoxin oxalic acid. The role of oxalic acid in host–pathogen interactions of C. jacksonii is unknown and there are multiple challenges to studying these interactions in natural turfgrass hosts. Consequently, identification of model plants to study C. jacksonii–host interactions and the role of oxalic acid in pathogenesis is necessary. Controlled environment inoculation assays were used to evaluate pathogenesis of C. jacksonii in various model plants and investigate the role of oxalic acid in symptom development. Observations at microscopic and macroscopic levels demonstrated that infection progressed similarly in all monocots tested (creeping bentgrass, wheat, barley, rice, Brachypodium distachyon) but not in the dicot Arabidopsis thaliana. Plant oxalic acid content increased from near zero to around 0.2–0.4 mM following inoculation with C. jacksonii in creeping bentgrass, barley, and wheat. Conversely, oxalic acid content remained near zero in A. thaliana and was not well correlated with inoculation in rice and B. distachyon, both of which had higher endogenous oxalic acid levels than other monocots. Time‐course oxalic acid quantification experiments with creeping bentgrass and B. distachyon further supported a link between symptom development and in planta oxalic acid content and identified 48 hr postinoculation as a critical time‐point for investigating the role of oxalic acid in C. jacksonii pathogenesis. These studies demonstrate that various monocots can serve as tractable model systems for studying C. jacksonii–host interactions and that increases in oxalic acid content are associated with C. jacksonii symptom development.
Susceptibility of native New Zealand Myrtaceae to the South African strain of Austropuccinia psidii: A biosecurity threat
Authors: Soewarto Julia , Somchit Chanatda , du Plessis Esna , Barnes Irene , Granados Ginna M. , Wingfield Michael J. , Shuey Louise , Bartlett Michael , Fraser Stuart , Scott Peter , Miller Elizabeth , Waipara Nick , Sutherland Roanne , Ganley Beccy 
Published: November 2020

AbstractAustropuccinia psidii, cause of myrtle rust, has spread globally where Myrtaceae occur. Multiple strains of A. psidii have been identified, including a unique strain found only in South Africa. The South African strain is a biosecurity concern for species of Myrtaceae worldwide. This is because preliminary testing of South African Myrtaceae suggests it could have a wide host range, and thus has the potential to be invasive. In this study, we assessed the ability of the South African strain to infect other species of Myrtaceae by testing the susceptibility of New Zealand provenance Myrtaceae. Seedlings of four native New Zealand Myrtaceae species (Metrosideros excelsa, Leptospermum scoparium, Kunzea robusta, and Kunzea linearis) were artificially inoculated in South Africa with a single‐uredinium isolate of the South African strain. Fourteen days after inoculation, uredinia, and in many cases telia, had developed on the young leaves and stems of all four host species, which led to shoot tip dieback in the more severe cases. When comparisons were made between the species, K. robusta was the least susceptible to the South African strain of A. psidii, while L. scoparium and M. excelsa were the most susceptible. While only a limited number of seed families were tested, only a small proportion of the seedlings showed resistance to infection by the South African strain. This preliminary testing highlights the potential invasive risk the South African strain poses to global Myrtaceae communities, including New Zealand Myrtaceae.
Supplemental carbon sources applied in biofloc technology aquaculture systems: types, effects and future research
Authors: Abakari Godwin , Luo Guozhi , Kombat Emmanuel O. , Alhassan Elliot H. 
Published: November 2020

AbstractBiofloc technology (BFT) systems have been driven towards increased sustainability in the last decade. BFT depends on maintenance of the optimal carbon‐to‐nitrogen (C/N) ratio through supplementation with organic carbon sources. The types of carbon sources and addition strategies are critical considerations in BFT systems. Thus for the purpose of this review, a thorough search of the literature was conducted to gather relevant information from reliable sources, ranging from reputable journals to books and useful reports in the field of BFT. Keywords used for the literature search include: ‘biofloc technology systems’, ‘carbon sources’, ‘solid carbon sources’, ‘effects of carbons sources’, ‘carbon source addition strategies’, ‘nutritional quality of bioflocs’, ‘carbon sources and water quality’, ‘C/N ratio in BFT’, and ‘carbon sources and bacterial community’. Among the several peer‐reviewed articles, books and technical reports consulted, 147 (dated from 1987 to 2020) were relevant for the preparation of this review. The current review thus examines the subject of supplemental carbon sources in BFT systems and discusses the various effects of their application with respect to the culture organism, microorganisms, water quality and the nutritional quality of flocs. The benefits and challenges associated with the types of carbon sources used in BFTs are also presented. Suggested organic carbon sources and their addition strategies are provided, and further research directions are proposed.