bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing
Authors: Alonge Michael , Lebeigle Ludivine , Kirsche Melanie , Aganezov Sergey , Wang Xingang , Lippman Zachary B. , Schatz Michael C. , Soyk Sebastian 
Published: November 2021

AbstractAdvancing crop genomics requires efficient genetic systems enabled by high-quality personalized genome assemblies. Here, we introduce RagTag, a toolset for automating assembly scaffolding and patching, and we establish chromosome-scale reference genomes for the widely used tomato genotype M82 along with Sweet-100, a rapid-cycling genotype that we developed to accelerate functional genomics and genome editing. This work outlines strategies to rapidly expand genetic systems and genomic resources in other plant species.
Associations and prognostic accuracy of electrolyte imbalances in predicting poor COVID-19 outcome: a systematic review and meta-analysis
Authors: Song Harris Jun Jie Muhammad Danial , Chia Alys Zhi Qin , Tan Benjamin Kye Jyn , Teo Chong Boon , Chua Horng Ruey , Samuel Miny , Kee Adrian 
Published: November 2021

ABSTRACTBackgroundSerum electrolyte imbalances are highly prevalent in COVID-19 patients. However, their associations with COVID-19 outcomes are inconsistent, and of unknown prognostic value.ObjectivesTo systematically clarify the associations and prognostic accuracy of electrolyte imbalances (sodium, calcium, potassium, magnesium, chloride and phosphate) in predicting poor COVID-19 clinical outcome.MethodsPubMed, Embase and Cochrane Library were searched. Odds of poor clinical outcome (a composite of mortality, intensive-care unit (ICU) admission, need for respiratory support and acute respiratory distress syndrome) were pooled using mixed-effects models. The associated prognostic sensitivity, positive and negative likelihood ratios (LR+, LR-) and predictive values (PPV, NPV; assuming 25% pre-test probability), and area under the curve (AUC) were computed.ResultsWe included 28 observational studies from 953 records with low to moderate risk-of-bias. Hyponatremia (OR=2.08, 95%CI=1.48-2.94, I2=93%, N=8), hypernatremia (OR=4.32, 95%CI=3.17-5.88, I2=45%, N=7) and hypocalcemia (OR=3.31, 95%CI=2.24-4.88, I2=25%, N=6) were associated with poor COVID-19 outcome. These associations remained significant on adjustment for covariates such as demographics and comorbidities. Hypernatremia was 97% specific in predicting poor outcome (LR+ 4.0, PPV=55%, AUC=0.80) despite no differences in CRP and IL-6 levels between hypernatremic and normonatremic patients. Hypocalcemia was 76% sensitive in predicting poor outcome (LR- 0.44, NPV=87%, AUC=0.71). Overall quality of evidence ranged from very low to moderate.ConclusionHyponatremia, hypernatremia and hypocalcemia are associated with poor COVID-19 clinical outcome. Hypernatremia is 97% specific for a poor outcome and the association is independent of inflammatory marker levels. Further studies should evaluate if correcting these imbalances help improve clinical outcome.
Wearable technologies in the fashion value ecosystem: a conceptual model
Authors: Serrano Rosiane , Fortunati Larissa , Lacerda Daniel Pacheco 
Published: November 2021

PurposeThe fashion sector is complex. It involves multiple actors with distinct and potentially conflicting interests, forming a value ecosystem. Thus, knowing the interested parties and belonging to the fashion sector may be a means to promote technological innovation, such as products with wearables. The purpose of this paper to identify the participants of the fashion ecosystem from the perspective of wearable technologies and develop a conceptual model.Design/methodology/approachThe present work aims to identify the participants (actors) and develop a conceptual model of the fashion ecosystem from the perspective of wearable technologies. The systematic literature review is the recommended method to qualitatively analyze documents and identify the interested parties (actors) in the fashion sector in order to design the proposed conceptual model.FindingsFrom the studies, the conceptual model of the fashion value ecosystem was designed, and the wearable product was considered its core business. The studies identified addressed ecosystems of fashion value in general but not specific to wearable products and their relations with other complementary industries.Research limitations/implicationsThe model was designed using secondary data only. Its validation is relevant through interviews with experts.Originality/valueIn terms of relevance, when conducting a systematic literature review, there were no studies that included wearable technologies in the fashion ecosystems discussed and their relations with other industries. The topic of wearables is an emerging subject that needs further research aiming to insert this technology in productive sectors.
Genotyping of intraspecies polymorphisms of Sporothrix globosa using partial sequence of mitochondrial DNA
Authors: Mochizuki Hirokazu , Anzawa Kazushi , Mochizuki Takashi 
Published: November 2021

AbstractRestriction fragment length polymorphism (RFLP) of mitochondrial DNA (mtDNA) had been used for molecular identification of Sporothrix spp., which is the causative fungi of sporotrichosis and the most prevalent deep‐seated dermatomycosis. Also, mtDNA‐RFLP had been used to investigate the molecular epidemiology of sporotrichosis. While the current standard for molecular diagnosis is performed by sequence analysis of the calmodulin gene (CAL), correspondence between the results from CAL and mtDNA is of diagnostic and epidemiological interest. Here, we investigated the correspondence between CAL and mtDNA used for molecular identification of Sporothrix globosa and S. schenckii, which are two major species. We also investigated and propose molecular markers suitable to describe the epidemiology of S. globosa, which is considered as a species with few intraspecific polymorphisms. Eighty‐seven strains morphologically identified as S. schenckii sensu lato were investigated. They were identified as group A (17 types, 17 strains) or B (14 types, 70 strains) by mtDNA‐RFLP. Partial sequences of CAL, internal transcribed spacer, and spacer between atp9 and cox2 genes of mtDNA of these strains were determined. All group A strains corresponded to S. schenckii, and group B to S. globosa. The sequences of the amplicons targeted on the spacer region in mtDNA of S. globosa ranged 510–515 bp in length and exhibited 10 molecular variations, whereas CAL indicated seven molecular variations. In conclusion, most of the S. schenckii sensu lato strains isolated from Japanese sporotrichosis patients were confirmed as S. globosa, because group B, which comprised the majority of strains, matched perfectly with S. globosa by the CAL sequencing study. We proposed sequence variations in the spacer between atp9 and cox2 genes of mtDNA as a suitable molecular epidemiological marker for S. globosa.
The hidden legacy of megafaunal extinction: Loss of functional diversity and resilience over the Late Quaternary at Hall’s Cave
Authors: Hedberg Carson P. , Lyons S. Kathleen , Smith Felisa A. 
Published: November 2021

AbstractAimFunctional traits mediate the interactions of species among themselves and with their environment, providing a link between diversity and ecosystem function. Crucially, the loss of biodiversity can jeopardize the functionality of ecosystems. Much focus is on predicting the impacts of current and future species loss; however, modern ecosystems have undergone biodiversity decline throughout the Late Quaternary, starting with the Pleistocene megafaunal extinctions. Thus, the fossil record offers the opportunity to investigate the long‐term legacy of biodiversity erosion and how this is affecting modern ecosystems in a cumulative manner. We aimed to investigate changes in functional diversity and redundancy of a local mammal community at Hall’s Cave, a site with a continuous record from 21,000 years ago to the present. Additionally, we included several common introduced species in the modern community to test whether they restore some lost ecological function.LocationCentral Texas.Time periodLate Pleistocene to Present.Major taxa studiedMammals.MethodsWe used eight functional traits (mass, diet, arboreality, cursoriality, soil disturbance, group size, activity period and migration habit), which, collectively, describe the ecological role of a species and its influence on ecosystem processes, to construct a multidimensional functional space. The functional richness, range and distribution of the Hall’s Cave community and the degree of functional redundancy were characterized statistically over time.ResultsWe found that declines in functional diversity were greater than expected given the decrease in species richness, implying that lost taxa contributed higher than average distinct ecological function. Functional distances between the remaining species increased through time, leading to reduced functional redundancy in younger communities. However, recently introduced taxa increased functional diversity to levels similar to those in the Holocene and partly restored the functional space occupied by Late Pleistocene fauna.Main conclusionsOur local‐scale analysis demonstrates how prolonged biodiversity erosion not only leads to functionally depauperate communities, but, crucially, lowers ecological resilience to future disturbance.
Avoidable healthcare costs of spinning‐induced rhabdomyolysis: a case series
Authors: Saparamadu Amarasinghe Arachchige Don Nalin Samandika , Teo Winnie Z. Y. , Arsad Asrie 
Published: November 2021

AbstractSpinning‐induced rhabdomyolysis (SIR) is a well documented cause of exertional rhabdomyolysis. We aim to raise awareness and to call for preventive action towards avoidable healthcare costs associated with SIR. To this end, we describe three cases of SIR, associated healthcare costs and possible preventive strategies. We propose that community‐based preventive measures should be considered in addressing the economic consequences of SIR.
Atelectasis and lung recruitment in pediatric anesthesia: An educational review
Authors: Bruins Suze , Sommerfield David , Powers Neil , von Ungern‐Sternberg Britta S. 
Published: November 2021

AbstractGeneral anesthesia is associated with development of pulmonary atelectasis. Children are more vulnerable to the development and adverse effects of atelectasis. We review the physiology and risk factors for the development of atelectasis in pediatric patients under general anesthesia. We discuss the clinical significance of atelectasis, the use and value of recruitment maneuvers, and other techniques available to minimize lung collapse. This review demonstrates the value of a recruitment maneuver, maintaining positive end‐expiratory pressure (PEEP) until extubation and lowering FiO2 where possible in the daily practice of the pediatric anesthetist.
Seed coat lignification level is crucial in Capsicum spp seed longevity
Authors: Bissoli Gaetano , Bono Mar , Martínez‐Almonacid Irene , Moreno‐Peris Estela , Renard Joan , Espinosa Ana , Naranjo Miguel Ángel , Yenush Lynne , Fita Ana , Serrano Ramón , Rodríguez‐Burruezo Adrián , Bueso Eduardo 
Published: November 2021

AbstractCapsicum (pepper) is known for its poor seed germination, particularly seed longevity is usually much shorter than other Solanaceae. However, the molecular mechanisms involved are mostly unknown in these species. The present study examines the differences in seed longevity among Capsicum species and varietal types. Feral or less domesticated species, such as Capsicum chinense and particularly Capsicum frutescens, showed higher germination rates than the more domesticated Capsicum annuum after accelerated seed aging treatments. In addition, variability was detected in the expression of genes involved in the response to seed deterioration. The differences observed in ASPG1 expression led us to study the seed protein profile in dry and germinating seeds. Seed storage protein mobilization during germination was faster in seed aging‐resistant genotypes. Similarly, the transcriptional change observed for the orthologous gene of the trans‐species regulator AtHB25 prompted us to study the structure and molecular components of the seed coat in peppers. All the Capsicum pepper accessions analyzed presented very lignified testa and we observed a positive correlation between the amount of lignin and seed viability. Our results provide essential information to explain the poor germination observed in pepper seeds and provide an experimental framework for future improvements in this important character.
Globalisation, economic uncertainty and labour market regulations: Implications for the COVID‐19 crisis
Authors: Fang Jianchun , Gozgor Giray , Nolt James H. 
Published: November 2021

AbstractThis paper empirically analyses the effects of globalisation on labour market regulations. We also interact globalisation measures with economic uncertainty, and they serve as potential determinants of de jure labour market conditions. For this purpose, we consider new innovative globalisation and economic uncertainty indices (the Revisited KOF Globalisation and the World Uncertainty) in a panel dataset of 136 countries from 2000 to 2017. The findings indicate that globalisation promotes labour market flexibility, while economic uncertainty decreases it. We also find that the interaction of globalisation with economic uncertainty positively affects labour market flexibility. The findings are robust to various sensitivity analyses, that is, different estimation procedures and globalisation indicators, including various controls and excluding outliers.
Primary & Secondary Reference Fuel Effects as a Function of Compression Ratio in a CFR Diesel Engine
Authors: Burnett Kevin , Gupta Ashwani , Luning Prak Dianne , Cowart Jim 
Published: November 2021

Abstract
Primary Reference Fuels (PRFs) and Secondary Reference Fuels (SRFs) in the range of cetane from 30 to 60 were operated in a Waukesha Diesel Cooperative Fuels Research (CFR) engine under operating conditions that emulate the cetane rating test. Due to the large number of test points in this study, the exact ASTM cetane rating protocol was not followed precisely, however these results are representative of cetane characterization testing with very similar equivalence ratio and combustion phasing across a broad range of Ignition Delays (IGDs) that varied as a result of Compression Ratio (CR) changes in the eleven to twenty-two range. Intake air temperature was operated both heated, as in the cetane rating test, as well as at ambient laboratory conditions. Additional research instrumentation was added beyond the standard CFR equipment for advanced combustion analysis. Combustion analysis shows that engine torque and efficiency increase significantly with increases in CR. At longer IGDs representative of the cetane rating test (13 deg IGD), the increase in IGD with reduced cetane number is relatively linear. For all of the fuels tested, IGD steadily monotonically decreases with increased CR significantly by more than a factor of two. Shorter IGDs lead to longer burn durations; fuel effect differences become less important at very high CRs. Associated companion analysis shows that at the time of fuel injection (Start Of Injection – SOI), cylinder pressure roughly doubles over the CRs studied, however, cylinder charge temperature only moderately increases. This effect leads to a doubling in cylinder air charge concentration at the highest CRs showing an important effect on the fast kinetics at high CRs. A common IGD correlation was evaluated showing good agreement except for the high CN fuel. New IGD correlations are also presented.
Adapting an Internal Combustion Engine to Oxy-Fuel Combustion With In-Situ Oxygen Production
Authors: Arnau Francisco , Novella Ricardo , García-Cuevas Luis Miguel , Gutiérrez Fabio 
Published: November 2021

Abstract
In transport applications, reciprocating internal combustion engines still have important advantages in terms of endurance and refueling time and available infrastructure when compared against fuel cell or battery-based powertrains. Although conventional internal combustion engine configurations produce important amounts of greenhouse gases and pollutant emissions, oxyfuel combustion can be used to mitigate to a great extent such emissions, mainly producing NOx-free, CO2 and H2O exhaust gases. However, the oxygen needed for the combustion, which is mixed with flue gases before entering the cylinder, has to be stored in an additional tank, which hinders the adoption of this technology. Fortunately, the latest developments in gas separation membranes are starting to produce extremely-high selectivity and high permeability oxygen-separation membranes. Using the waste heat of the exhaust gases to heat up a mixed ionic-electronic conducting membrane, and feeding it with pressurized air, it is possible to produce all the oxygen needed by the combustion process while keeping the whole system compact. This works presents a design of an oxy-fuel combustion engine with in-situ oxygen production. The numerical simulations show also that this concept keeps a competitive brake specific fuel consumption, while the high concentration of CO2 in the exhaust gases facilitates the introduction of carbon sequestration technologies, leading to potentially carbon-neutral internal combustion engines.
Direct Numerical Simulation of Partial Fuel Stratification Assisted Lean Premixed Combustion for Assessment of Hybrid G-Equation/Well-Stirred Reactor Model
Authors: Xu Chao , Ameen Muhsin , Pal Pinaki , Som Sibendu 
Published: November 2021

Abstract
Partial fuel stratification (PFS) is a promising fuel injection strategy to stabilize lean premixed combustion in spark-ignition (SI) engines. PFS creates a locally stratified mixture by injecting a fraction of the fuel, just before spark timing, into the engine cylinder containing homogeneous lean fuel/air mixture. This locally stratified mixture, when ignited, results in complex flame structure and propagation modes similar to partially premixed flames, and allows for faster and more stable flame propagation than a homogeneous lean mixture. This study focuses on understanding the detailed flame structures associated with PFS-assisted lean premixed combustion. First, a two-dimensional direct numerical simulation (DNS) is performed using detailed fuel chemistry, experimental pressure trace, and realistic initial conditions mapped from a prior engine large-eddy simulation (LES), replicating practical lean SI operating conditions. DNS results suggest that conventional triple flame structures are prevalent during the initial stage of flame kernel growth. Both premixed and non-premixed combustion modes are present with the premixed mode contributing dominantly to the total heat release. Detailed analysis reveals the effects of flame stretch and fuel pyrolysis on the flame displacement speed. Based on the DNS findings, the accuracy of a hybrid G-equation/well-stirred reactor (WSR) combustion model is assessed for PFS-assisted lean operation in the LES context. The G-equation model qualitatively captures the premixed branches of the triple flame, while the WSR model predicts the non-premixed branch of the triple flame. Finally, potential needs for improvements to the hybrid G-equation/WSR modeling approach are discussed.
The QUality of Interhospital Transportation in the Euregion Meuse-Rhine (QUIT-EMR) score: a cross-validation study
Authors: Strauch Ulrich , Florack Micheline C D M , Jansen Jochen , van Bussel Bas C T , Beckers Stefan K , Habers Joachim , Winkens Bjorn , van der Horst Iwan C C , van Mook Walther N K A , Bergmans Dennis C J J 
Published: November 2021

ObjectivesInterhospital transports of critically ill patients are high-risk medical interventions. Well-established parameters to quantify the quality of transports are currently lacking. We aimed to develop and cross-validate a score for interhospital transports.SettingAn expert panel developed a score for interhospital transport by a Mobile Intensive Care Unit (MICU), the QUality of Interhospital Transportation in the Euregion Meuse-Rhine (QUIT-EMR) score. The QUIT-EMR score is an overall sum score that includes component scores of monitoring and intervention variables of the neurological (proxy for airway patency), respiratory and circulatory organ systems, ranging from −12 to +12. A score of 0 or higher defines an adequate transport. The QUIT-EMR score was tested to help to quantify the quality of transport.ParticipantsOne hundred adult patients were randomly included and the transport charts were independently reviewed and classified as adequate or inadequate by four transport experts (ie, anaesthetists/intensivists).Outcome measuresSubsequently, the level of agreement between the QUIT-EMR score and expert classification was calculated using Gwet’s AC1.ResultsFrom April 2012 to May 2014, a total of 100 MICU transports were studied. The median (IQR) QUIT-EMR score was 1 (0–2). Experts classified six transports as inadequate. The percentage agreement between the QUIT-EMR score and experts’ classification for adequate/inadequate transport ranged from 84% to 92% (Gwet’s AC10.81–0.91). The interobserver agreement between experts was 87% to 94% (Gwet’s AC10.89–0.98).ConclusionThe QUIT-EMR score is a novel validated tool to score MICU transportation adequacy in future studies contributing to quality control and improvement.Trial registration numberNTR 4937.
Prestroke physical activity and outcomes after intracerebral haemorrhage in comparison to ischaemic stroke: protocol for a matched cohort study (part of PAPSIGOT)
Authors: Viktorisson Adam , Buvarp Dongni , Sunnerhagen Katharina S 
Published: November 2021

IntroductionPiling evidence suggests that a higher level of prestroke physical activity can decrease stroke severity, and reduce the risk of poststroke mortality. However, prior studies have only included ischaemic stroke cases, or a majority of such. We aim to investigate how premorbid physical activity influences admission stroke severity and poststroke mortality in patients with intracerebral haemorrhage, compared with ischaemic stroke. A prespecified analysis plan counteract some inherent biases in observational studies, and promotes transparency.Methods and analysisThis is a statistical analysis protocol for a matched cohort study, including all adult patients with intracerebral haemorrhage, and matched ischaemic stroke controls, treated at Sahlgrenska University Hospital in Sweden between 1 November 2014 and 30 June 2019. All patients have been identified in the Väststroke register, and the data file has been sent for merging with national registries. The follow-up of time for survival will be approximately 2–7 years. The sample size calculation indicates that a minimum of 628 patients with intracerebral haemorrhage is needed for power of 80% at an alpha level of 0.01. Multiple imputation by chained equations will be used to handle missing data. The entire cohort of patients with intracerebral haemorrhage will be matched with consecutive ischaemic stroke controls (1:3 ratio) using nearest neighbour propensity score matching. The association between prestroke physical activity and admission stroke severity will be evaluated using multivariable ordinal regression models, and risk for all-cause mortality will be analysed using multivariable Cox proportional-hazards models. Potential confounders include age, ethnicity, income, educational level, comorbidity, medical treatments, alcohol-related disorders, drug abuse and smoking.EthicsData collection for the Physical Activity Pre-Stroke In GOThenburg project was approved by the Regional Ethical Board on 4 May 2016. An additional application was approved by the National Ethical Review Authority on 7 July 2021.