bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanopore sequencing for the detection and identification of Xylella fastidiosa subspecies and sequence types from naturally infected plant material
Authors: Faino Luigi , Scala Valeria , Albanese Alessio , Modesti Vanessa , Grottoli Alessandro , Pucci Nicoletta , Doddi Andrea , L’Aurora Alessia , Tatulli Giuseppe , Reverberi Massimo , Loreti Stefania 
Published: June 2021

AbstractXylella fastidiosa (Xf) is a gram‐negative bacterial plant pathogen that can infect over 500 plant species. While it is endemic in America, X. fastidiosa subsp. pauca was reported for the first time in Europe in 2013 on olive trees in southern Italy. The availability of fast, sensitive, and reliable diagnostic tools is indispensable for managing current and future outbreaks of Xf. In this paper, we use the OXford Nanopore Technologies (ONT) MinION platform for detecting and identifying Xf at species, subspecies, and sequence type (ST) level. Two workflows were developed: the first one provided a “shotgun” strategy, that is, exploring the possibility of detecting Xf within DNA extracted from plant samples. This allowed detection of Xf by direct DNA sequencing and identifying the subspecies only in samples with high bacterial levels. Nanopore amplicon sequencing was pursued as a second workflow. This consists of PCR amplification of a set of seven multilocus sequence typing (MLST) fragments, officially adopted for identifying Xf at type strain level, followed by Nanopore‐sequencing of the amplicons and an ad hoc pipeline to generate MLST consensus calls. This combined approach, which takes only a few hours, allowed the detection and identification of Xf at ST level in plant material with low bacterial infection.
System Analysis of Wildfire‐Water Supply Risk in Colorado, USA with Monte Carlo Wildfire and Rainfall Simulation
Authors: Gannon Benjamin M. , Wei Yu , Thompson Matthew P. , Scott Joe H. , Short Karen C. 
Published: June 2021

AbstractWater supply impairment from increased contaminant mobilization and transport after wildfire is a major concern for communities that rely on surface water from fire‐prone watersheds. In this article we present a Monte Carlo simulation method to quantify the likelihood of wildfire impairing water supplies by combining stochastic representations of annual wildfire and rainfall activity. Water quality impairment was evaluated in terms of turbidity limits for treatment by modeling wildfire burn severity, postfire erosion, sediment transport, and suspended sediment dilution in receiving waterbodies. Water supply disruption was analyzed at the system level based on the impairment status of water supply components and their contributions to system performance. We used this approach to assess wildfire‐water supply impairment and disruption risks for a system of water supply reservoirs and diversions in the Front Range Mountains of Colorado, USA. Our results indicate that wildfire may impair water quality in a concerning 15.7–19.4% of years for diversions from large watersheds. Reservoir impairment should be rare for off‐network reservoirs—ranging from at most 0.01% of years for large reservoirs to nearly 2% of years for small reservoirs. System redundancy meaningfully reduced disruption risk for alternative conveyance routes (4.3–25.0% reduction) and almost eliminated disruption risk for a pair of substitutable terminal sources (99.9% reduction). In contrast, dependency among reservoirs on a conveyance route nearly doubled risk of disruption. Our results highlight the importance of considering water system characteristics when evaluating wildfire‐water supply risks.
Linearization and Variance Estimation of the Bonferroni Inequality Index
Authors: Dong Ziqing , Tillé Yves , Giorgi Giovanni M. , Guandalini Alessio 
Published: June 2021

Abstract
The study of income inequality is important for predicting the wealth of a country. There is an increasing number of publications where the authors call for the use of several indices simultaneously to better account for the wealth distribution. Due to the fact that income data are usually collected through sample surveys, the sampling properties of income inequality measures should not be overlooked. The most widely used inequality measure is the Gini index, and its inferential aspects have been deeply investigated. An alternative inequality index could be the Bonferroni inequality index, although less attention on its inference has been paid in the literature. The aim of this paper is to address the inference of the Bonferroni index in a finite population framework. The Bonferroni index is linearized by differentiation with respect to the sample indicators which allows for conducting a valid inference. Furthermore, the linearized variables are used to evaluate the effects of the different observations on the Bonferroni and Gini indices. The result demonstrates once for all that the former is more sensitive to the lowest incomes in the distribution than the latter.
Inequality Measurement with Grouped Data: Parametric and Non-Parametric Methods
Authors: Jorda Vanesa , Sarabia José María , Jäntti Markus 
Published: June 2021

AbstractGrouped data in the form of income shares have conventionally been used to estimate income inequality due to the lack of individual records. We present a systematic evaluation of the performance of parametric distributions and non-parametric techniques to estimate economic inequality using more than 3300 data sets. We also provide guidance on the choice between these two approaches and their estimation, for which we develop the GB2group R package. Our results indicate that even the simplest parametric models provide reliable estimates of inequality measures. The non-parametric approach, however, fails to represent income distributions accurately.
Hospital‐acquired pressure ulcers prevention: What is needed for patient safety? The perceptions of nurse stakeholders
Authors: Gaspar Susana , Botelho Guedes Fábio , Vitoriano Budri Aglécia Moda , Ferreira Carlos , Gaspar de Matos Margarida 
Published: June 2021

AbstractAimThe aim of this study was to understand the perceptions of 11 Portuguese nurses’ stakeholders regarding pressure ulcers prevention practice and reality in the hospital setting.MethodsConvenience sampling was used to recruit nursing stakeholders for a heterogeneous focus group. A semi‐structured interview was conducted with 11 nursing stakeholders involved in pressure ulcers prevention and/or patient safety. MaxQda 2020 qualitative analysis software was used in the content analysis and data processing. Informed consent was obtained, and anonymity was guaranteed.ResultsFour themes were approached in the interview: (1) Pressure ulcer risk assessment; (2) Nurses and doctors pressure ulcers monitoring; (3) Pressure ulcer risk profiles; and (4) Effective interventions to improve patient safety. The categorisation of the four themes was created aposteriori based on the ‘Awareness/Knowledge/Competence, Opportunity, and Motivation – Behaviour Change Wheel’ (adapted COM‐B system). Interest, responsibility, autonomy, leadership and prioritisation for decision‐making were some categories linked to motivation. Braden scale operationalisation, education given during undergraduate degree continued professional health education, missing care, reliability of the records and patients’ clinical characteristics emerged as categories associated with awareness/knowledge/competence. Understaffing/nursing hours, health policies, electronic health records systems and clinical language used, access to appropriate equipment and resources, teamwork and clinical support specialist on tissue viability/wound care were some categories related to opportunity.ConclusionsPressure ulcer prevention is complex and requires a focussed attitude, robust evidenced‐based knowledge and enhanced skills in risk assessment, communication and team collaboration. The highlighted categories could be further analysed at an organisational level to develop tailored strategies that could contribute to successful evidence‐based practice implementation.Relevance to clinical practiceThe findings provide directions for behavioural change in the hospital context related to pressure ulcers prevention through awareness/knowledge/competence, motivation and opportunity to improve care delivered.
Sand and mud generation from continental flood basalts in contrasting landscapes and climatic conditions (Paraná–Etendeka conjugate igneous provinces, Uruguay and Namibia)
Authors: Garzanti Eduardo , Dinis Pedro , Vezzoli Giovanni , Borromeo Laura 
Published: June 2021

AbstractThis article presents a detailed petrographic, mineralogical and geochemical study of clay, silt, sand and fine gravel generated in the Paraná–Etendeka large igneous province, once united and today exposed in contrasting climatic and orographic conditions on conjugate sides of the Atlantic Ocean. The comparison between low‐relief wetter Uruguay and steeper hyper‐dry Namibia allows to investigate the influence of weathering on basalt‐derived sediments spanning in grain size from <2 μm to >2000 μm. In Namibia, as in Uruguay, X‐ray diffraction analyses of mud samples from streams draining basaltic lavas show only smectitic clay minerals. Macroscopic and microscopic observations indicate that sand is composed in variable proportions of glassy to lathwork volcanic rock fragments, plagioclase and augitic clinopyroxene with minor pigeonite, and gravel dominantly consists of volcanic clasts with chalcedony or quartz geodes occurring locally. Geochemical data highlight the strong grain‐size dependence of weathering intensity. Whereas fine gravel closely reflects source‐rock composition in both Namibia and Uruguay, and mobile elements in sand are moderately depleted, αAlE indices increase notably in silt and reach maximum in clay, with mobility sequence Na >> Ca ≥ Mg > Sr > K. Differences in sand versus mud generation potential in the two regions are prominent. Namibian rivers draining the dry Etendeka Plateau carry purely volcaniclastic sand, whereas streams draining even exclusively the Paraná lava field carry sediments containing invariably significant and even overwhelming amounts of recycled quartz, testifying to the much greater sand‐generation potential of the very‐locally‐exposed underlying, interbedded or overlying quartz‐rich sandstones and loess deposits. Smectite is dominant throughout the Uruguay River catchment, even in the lower course where sand is pure quartzose and pyroxene negligible. A comparison with basaltic provinces worldwide indicates that, especially in low‐relief wet regions where weathering is intense, basalt generates gravel, very minor sand and abundant smectite. Kaolinite forms where chemical leaching is extreme.
Molecular phylogeny and historical biogeography of Apicotermitinae (Blattodea: Termitidae)
Authors: Romero Arias Johanna , Boom Arthur , Wang Menglin , Clitheroe Crystal , Šobotník Jan , Stiblik Petr , Bourguignon Thomas , Roisin Yves 
Published: June 2021

AbstractSoil‐feeding termites are abundant in tropical regions and play an important role in soil bioturbation and in the organic matter cycle. The Apicotermitinae are arguably the most diverse lineage of soil‐feeding termites, but they are also the most understudied, probably because many species are soldierless, which makes identification difficult. Although the backbone of the termite phylogenetic tree is now well‐resolved, the relationships among representatives of Apicotermitinae are still largely unknown. Here, we present phylogenetic trees inferred from 113 mitochondrial genomes of Apicotermitinae representative of the group diversity. Our analyses confirm the monophyly of the Apicotermitinae and the basal position of soldiered taxa, within which two lineages of soldierless species are nested. We describe two new monotypic genera, whose phylogenetic position appeared of special interest:Koutabatermesgen. n., lies on a long branch among soldiered taxa, andApolemotermesgen. n., is sister toAdaiphrotermes. We resolved, with high support, the position of Asian genera as sister group of a clade comprising the monophyletic neotropicalAnoplotermes‐group and the small African clade includingAdaiphrotermesandApolemotermesgen. n.. Our trees cast light on the intergeneric and interspecific relationships within Apicotermitinae and reveal the polyphyly of several genera, includingRuptitermes,AstalotermesandAnoplotermes. Biogeographic reconstructions revealed two dispersal events out of Africa, one to the Oriental realm and one to the Neotropical realm. Overall, the timing of Apicotermitinae diversification and dispersal, following the Eocene–Oligocene boundary, matches that found for other groups of Neoisoptera. Nomenclatural acts are registered in ZooBank:http://zoobank.org/urn:lsid:zoobank.org:pub:CA1A21B6‐573E‐4855‐8C88‐372453C922F7.
Multivariable analysis of the influence of cross‐reactive carbohydrate determinant inhibition and other factors on intradermal and serological allergen test results: a prospective, multicentre study
Authors: Canning Peter , Brame Bailey , Stefanovski Darko , Lee Kenneth W. , Cain Christine L. , Rook Katherine , Morris Daniel O. 
Published: June 2021

BackgroundSerological allergen testing (SAT) is used widely to formulate allergen‐specific immunotherapy for atopic dogs. Serum immunoglobulin (Ig)E specific for cross‐reactive carbohydrate determinants (CCD) can produce false‐positive reactions, creating discrepancy between SAT and intradermal allergen test (IDAT) results.ObjectivesThe primary objective was to determine if inhibition of anti‐CCD IgE in a commercial assay improved correlation with IDAT. The secondary objective was to assess the influence of dog‐ and clinic‐specific factors, environmental factors, putative allergen exposure and prior medications on intradermal and SAT reactivity.AnimalsTwo‐hundred and eleven client‐owned dogs were enrolled from eight North American dermatology specialty practices.Methods and materialsCollection of serum samples and IDAT were performed on the same day. Sera were assayed for detection of IgE specific to 25 allergens, before and after treatment with a proprietary inhibitor of anti‐CCD IgE. Data for each dog were collected via a questionnaire filled out by veterinary personnel.ResultsThe correlation between the testing modalities was fair before (Spearman’s rho, ρ = 0.2092) and after (ρ = 0.3042) inhibition of anti‐CCD IgE. Ciclosporin dose (P = 0.003), independent of duration of use, and duration of lokivetmab use (P = 0.001), independent of dose administered, were associated with statistically significant decreases in IgE concentrations across all allergen types.Conclusions and clinical relevanceContrary to previous reports, this study demonstrated unchanged correlation between SAT and IDAT after inhibition of anti‐CCD IgE. Ciclosporin dose and lokivetmab treatment duration may have unexplored effects on IgE concentration during SAT.
Mathematical Modeling and simulation of MED without TVC Applied to Zuara Desalination Plant
Authors: Muftah Ali , Dhahri Hacen , Ghedira Leila , Abugderah Mabruk 
Published: June 2021

Abstract
Mathematical thermodynamic modeling is used in desalination systems to obtain unknown values and predict various properties such as enthalpy or phase equilibrium. These models are useful to understand system behavior. Zuara desalination plant is a multi-effect evaporation plant without vapor pressure (MED) with three total units of 40,000 m3/day. A mathematical modeling of the desalination plant thermal components was performed to simulate and forecast the temperatures, mass flow rates, and the productivity of each cell of steam. The total productivity of the desalination unit and the performance rate in different operating conditions was also found. A Python program was used to solve the model equations. The obtained results show that the productivity of the system and the gain output ratio are directly proportional to seawater temperature and inversely proportional to plant load.
New field, geochemical, and petrographic evidence from the Bon Accord nickel body: Contamination of a komatiite by deep mantle or meteorite source?
Authors: Huber* Matthew S. , Roelofse Frederick , Koeberl Christian , Tredoux† Marian 
Published: June 2021

ABSTRACT
The Bon Accord nickel body has been known since the 1920s to contain rocks with up to 50 wt% NiO. Numerous nickel-rich minerals have been described from this deposit. However, none of these minerals contains significant Cu or S, making the deposit chemically distinct from all other known Ni deposits. The origin of the Bon Accord nickel body is highly contentious, with previous studies suggesting three major possible origins: (1) a hydrothermal origin; (2) an Fe-Ni meteorite that fell into and was altered by an active ultramafic lava flow; or (3) a deep mantle plume that contained a fragment of nickel-rich material. Here, we present new field, petrographic, and geochemical data in an attempt to constrain the origin of this enigmatic body. Based on our fieldwork, there are at least two distinct Ni-rich bodies. Based on the trace-element chemistry, the protolith of the body was a komatiite, likely belonging to the Weltevreden Formation. Because the Ni end member of olivine (liebenbergite) is present in the form of euhedral crystals, this mineral most likely crystallized from a Ni-rich melt. The redistribution of the nickel appears to be due to hydrothermal activity that occurred during the intrusion of the Stentor pluton. Consistent with previous studies, we find that the komatiitic affinity of the host rocks, the stratigraphic controls on the deposit, and the regional distribution of Ni-rich material are inconsistent with a meteorite origin; instead, a komatiite plume sampling a Ni-rich portion of the mantle is currently the best explanation for the origin of the Ni-rich material.
Effect of breathing on venous return during delayed cord clamping: an observational study
Authors: Brouwer Emma , Knol Ronny , Kroushev Annie , Van Den Akker Thomas , Hooper Stuart B , Roest Arno A , te Pas Arjan B 
Published: June 2021

ObjectiveTo investigate the effect of spontaneous breathing on venous return in term infants during delayed cord clamping at birth.MethodsEchocardiographic ultrasound recordings were obtained directly after birth in healthy term-born infants. A subcostal view was used to obtain an optimal view of the inferior vena cava (IVC) entering the right atrium, including both the ductus venosus (DV) and the hepatic vein (HV). Colour Doppler was used to assess flow direction and flow velocity. Recordings continued until the umbilical cord was clamped and were stored in digital format for offline analyses.ResultsUltrasound recordings were obtained in 15 infants, with a median (IQR) gestational age of 39.6 (39.0–40.9) weeks and a birth weight of 3560 (3195–4205) g. Flow was observed to be antegrade in the DV and HV in 98% and 82% of inspirations, respectively, with flow velocity increasing in 74% of inspirations. Retrograde flow in the DV was observed sporadically and only occurred during expiration. Collapse of the IVC occurred during 58% of inspirations and all occurred caudal to the DV inlet (100%).ConclusionSpontaneous breathing was associated with collapse of the IVC and increased antegrade DV and HV flow velocity during inspiration. Therefore, inspiration appears to preferentially direct blood flow from the DV into the right atrium. This indicates that inspiration could be a factor driving placental transfusion in infants.
Evaluation of dry eye subtypes and characteristics using conventional assessments and dynamic tear interferometry
Authors: Ji Yong Woo , Seong Hyojin , Seo Jeong Gi , Park Si Yoon , Alotaibi Mutlaq , Choi Moonjung , Nam Sangmin , Kim Tae-Im , Lee Hyung Keun , Seo Kyoung Yul 
Published: June 2021

Background/aimsTo evaluate subtypes and characteristics of dry eye (DE) using conventional tests and dynamic tear interferometry, and to investigate determinants of disease severity in each DE subtype.Methods309 patients diagnosed with DE and 69 healthy controls were prospectively enrolled. All eyes were evaluated using Ocular Surface Disease Index (OSDI), Schirmer’s test I (ST1) and Meibomian gland dysfunction (MGD) grade were analysed. The tear interferometric pattern and lipid layer thickness were determined using DR-1α and LipiView II, respectively.ResultsDynamic interferometric analysis revealed 56.6% of patients with DE exhibited Jupiter patterns, indicative of aqueous-deficiency, while 43.4% exhibited crystal patterns, indicative of lipid deficiency. These findings were in accordance with classification based on ST1 scores and MGD grade. Conventional assessment indicated 286 patients exhibited evidence of evaporative DE (EDE) due to MGD, while only 11 exhibited signs of pure aqueous-deficient DE (pure ADDE, only ST1 ≤5 mm). Interestingly, of 286 patients with EDE, 144 were categorised into the mixed-ADDE/EDE group, in which ST1 was identified as a strong negative determinant of OSDI. In contrast, 72.2% of patients with mixed-ADDE/EDE exhibited Jupiter patterns (Jupiter mixed), while 27.8% exhibited crystal patterns (crystal mixed). OSDI values were significantly higher in the crystal-mixed group than in the Jupiter mixed, in which OSDI scores were independently associated with ST1 values only.ConclusionsOur findings indicate that majority of EDE patients also exhibit aqueous deficiency, which can aggravate symptoms even in patients with lipid-deficient mixed-ADDE/EDE. Conventional assessments should be combined with interferometric tear analysis to determine the most appropriate treatment for each DE patient.
Faecal immunochemical tests safely enhance rational use of resources during the assessment of suspected symptomatic colorectal cancer in primary care: systematic review and meta-analysis
Authors: Pin-Vieito Noel , Tejido-Sandoval Coral , de Vicente-Bielza Natalia , Sánchez-Gómez Cristina , Cubiella Joaquín 
Published: June 2021

ObjectiveImplementation of faecal immunochemical tests (FIT) as a triage test in primary healthcare may improve the efficiency of referrals without missing cases of colorectal cancer (CRC). We aim to summarise the performance characteristics of FITs for CRC in symptomatic patients presenting to primary healthcare.DesignWe performed a systematic literature review of Medline and EMBASE databases from May 2018 to November 2020. Previous related systematic searches were also adapted to this aim and completed with reference screening. We identified studies performed on adult patients consulting for abdominal symptoms in primary care which reported data such that the FIT diagnostic performance parameters for CRC could be obtained. Bivariate models were used to synthesise available evidence. Meta-regression analysis was performed to evaluate the causes of heterogeneity.ResultsTwenty-three studies (69 536 participants) were included (CRC prevalence 0.3%–6.2%). Six studies (n=34 691) assessed FIT as rule in test (threshold of ≥150 µg Hb/g faeces) showing a sensitivity of 64.1% (95% CI 57.8% to 69.9%) and a specificity of 95.0% (95% CI 91.2% to 97.2%). A threshold of 10 µg/g (15 studies; n=48 872) resulted in a sensitivity of 87.2% (95% CI 81.0% to 91.6%) and a specificity of 84.4% (95% CI 79.4% to 88.3%) for CRC. At a 20 µg Hb/g faeces threshold (five studies; n=24 187) less than one additional CRC would be missed per 1000 patients investigated compared with 10 µg Hb/g faeces threshold (CRC prevalence 2%).ConclusionFIT is the test of choice to evaluate patients with new-onset lower gastrointestinal symptoms in primary healthcare.