bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting bycatch of Chinook salmon in the Pacific hake fishery using spatiotemporal models
Authors: Shirk Philip L , Richerson Kate , Banks Michael , Tuttle Vanessa
Published: December 2022

Fisheries bycatch is a global problem, and the ability to avoid incidental catch of non-target species is important to fishermen, managers, and conservationists. In areas with sufficient data, spatiotemporal models have been used to identify times and locations with high bycatch risk, potentially enabling fishing operations to shift their effort in response to the dynamic ocean landscape. Here, we use 18 years of observer data from the Pacific hake (Merluccius productus) fishery, the largest by tonnage on the US West Coast, to evaluate our ability to predict bycatch of the commercially, culturally, and ecologically important Chinook salmon (Oncorhynchus tshawytscha). Using multiple approaches (regression models, tree-based methods, and model averages), we tested our ability to predict bycatch at weekly and yearly timescales and found that spatiotemporal models can have good predictive ability. Gradient boosting trees (GBTs) and model averages typically had higher performance, while generalized linear models and generalized additive models (without interaction terms) did less well. Using a GBT model to remove 1% of hauls with the highest predicted bycatch reduced the bycatch-to-hake ratio by 20%. Our results indicate that spatiotemporal models may be a useful forecasting tool that can help fishing operations avoid bycatch while minimizing losses from target catches.
Bilinear Fourier Multipliers of Bounded Variation
Authors: Baena-Miret Sergi , Carro María J , Luque Teresa , Sánchez-Pascuala Laura
Published: December 2022

In this paper, we obtain weighted estimates for bilinear Fourier multipliers of bounded variation that provide new restricted weak-type bounds. We also study their boundedness on the setting of the weighted Lorentz spaces. The results are obtained using Rubio de Francia extrapolation as the main tool.
Structural equation modelling the impact of antimicrobials on the human microbiome. Colonization resistance versus colonization susceptibility as case studies
Authors: Hurley James C
Published: December 2022

The impact of antimicrobials on the human microbiome and its relationship to human health are of great interest. How antimicrobial exposure might drive change within specific constituents of the microbiome to effect clinically relevant endpoints is difficult to study. Clinical investigation of each step within a network of causation would be challenging if done ‘step-by-step’. An analytic tool of great potential to clinical microbiome research is structural equation modelling (SEM), which has a long history of applications to research questions arising within subject areas as diverse as psychology and econometrics. SEM enables postulated models based on a network of causation to be tested en bloc by confrontation with data derived from the literature. Case studies for the potential application of SEM techniques are colonization resistance (CR) and its counterpart, colonization susceptibility (CS), wherein specific microbes within the microbiome are postulated to either impede (CR) or facilitate (CS) invasive infection with pathogenic bacteria. These postulated networks have three causation steps: exposure to specific antimicrobials are key drivers, clinically relevant infection endpoints are the measurable observables and the activity of key microbiome constituents mediating CR or CS, which may be unobservable, appear as latent variables in the model. SEM methods have potential application towards evaluating the activity of specific antimicrobial agents within postulated networks of causation using clinically derived data.
Combining text mining with clinical decision support in clinical practice: a scoping review
Authors: van de Burgt Britt W M , Wasylewicz Arthur T M , Dullemond Bjorn , Grouls Rene J E , Egberts Toine C G , Bouwman Arthur , Korsten Erik M M
Published: December 2022

Objective

Combining text mining (TM) and clinical decision support (CDS) could improve diagnostic and therapeutic processes in clinical practice. This review summarizes current knowledge of the TM-CDS combination in clinical practice, including their intended purpose, implementation in clinical practice, and barriers to such implementation.

Materials and Methods

A search was conducted in PubMed, EMBASE, and Cochrane Library databases to identify full-text English language studies published before January 2022 with TM-CDS combination in clinical practice.

Results

Of 714 identified and screened unique publications, 39 were included. The majority of the included studies are related to diagnosis (n = 26) or prognosis (n = 11) and used a method that was developed for a specific clinical domain, document type, or application. Most of the studies selected text containing parts of the electronic health record (EHR), such as reports (41%, n = 16) and free-text narratives (36%, n = 14), and 23 studies utilized a tool that had software “developed for the study”. In 15 studies, the software source was openly available. In 79% of studies, the tool was not implemented in clinical practice. Barriers to implement these tools included the complexity of natural language, EHR incompleteness, validation and performance of the tool, lack of input from an expert team, and the adoption rate among professionals.

Discussion/Conclusions

The available evidence indicates that the TM-CDS combination may improve diagnostic and therapeutic processes, contributing to increased patient safety. However, further research is needed to identify barriers to implementation and the impact of such tools in clinical practice.
Influence of a sodium-saccharin sweetener on the rumen content and rumen epithelium microbiota in dairy cattle during heat stress
Authors: Koester Lucas R , Hayman Kris , Anderson Chiron J , Tibbs-Cortes Bienvenido W , Daniels Karrie M , Seggerman Faith M , Gorden Patrick J , Lyte Mark , Schmitz-Esser Stephan
Published: December 2022

The effect of a saccharin-based artificial sweetener was tested on animal performance measures and on the microbial communities associated with the rumen content and with the rumen epithelium during heat stress. Ten cannulated Holstein-Friesian milking dairy cattle were supplemented with 2 g of saccharin-based sweetener per day, top-dressed into individual feeders for a 7-day adaptation period followed by a 14-day heat stress period. A control group of ten additional cows subjected to the same environmental conditions but not supplemented with sweetener were included for comparison. 16S rRNA gene amplicon sequencing was performed on rumen content and rumen epithelium samples from all animals, and comparisons of rumen content microbiota and rumen epithelial microbiota were made between supplemented and control populations. Supplementation of the saccharin-based sweetener did not affect the rumen content microbiota, but differences in the rumen epithelial microbiota beta-diversity (PERMANOVA, P = 0.003, R2 = 0.12) and alpha-diversity (Chao species richness, P = 0.06 and Shannon diversity, P = 0.034) were detected between the supplemented and control experimental groups. Despite the changes detected in the microbial community, animal performance metrics including feed intake, milk yield, and short-chain fatty acid (acetic, propionic, and butyric acid) concentrations were not different between experimental groups. Thus, under the conditions applied, supplementation with a saccharin-based sweetener does not appear to affect animal performance under heat stress. Additionally, we detected differences in the rumen epithelial microbiota due to heat stress when comparing initial, prestressed microbial communities to the communities after heat stress. Importantly, the changes occurring in the rumen epithelial microbiota may have implications on barrier integrity, oxygen scavenging, and urease activity. This research adds insight into the impact of saccharin-based sweeteners on the rumen microbiota and the responsivity of the rumen epithelial microbiota to different stimuli, providing novel hypotheses for future research.
Autologous Skin Cell Suspension in Toxic Epidermal Necrolysis: A Case Series
Authors: Pang Alan , Abla Habib , Felan Sarah , Griswold John
Published: December 2022

Toxic epidermal necrolysis (TEN) is a dermatological process which has lacked both clear pathophysiological definition and efficacious medical treatment. This leads to metabolic dysfunction due to the inability to regulate fluid and electrolytes after the loss of skin. It is a deadly and costly disease which is associated with long lengths of stay and high-mortality rates. The depth of TEN mimics that of a partial-thickness burn. There has been documentation of successful usage of autologous skin cell suspension (ASCS) in TEN. This study expands upon our previous experience using ASCS in TEN to a series of three. Dermatology is consulted for biopsy along with the burn surgery team for wound care, where a Score for TEN is performed for risk stratification. Aggressive operative debridement is performed in the operative suite and a healthy, uninvolved donor site is harvested and processed per standard protocol. Dressings are taken down at postoperative day 4 for evaluation. The average length of stay when compared to historical data in literature is a reduction by 48%. ICU days were reduced by 64%. Cost was reduced by 54%. There was no mortality in our population of three. ASCS is both therapeutically and cost effective at treating TEN. The question of type of dressing and decision to operate is mitigated by this intervention. As an efficacious intervention, it reduces hospital stay, reduces wound cares, speeds healing, and provides a cosmetically acceptable outcome.
A passive planar model with rolling contact and its application for bounding and pronking on a quadruped robot
Authors: Huang Chun-Kai , Hu Chia-Jui , Chang I-Chia , Lin Pei-Chun
Published: December 2022

The development and investigation of a quadruped robot's dynamic bounding and pronking gaits using a sagittal planar model that captures the robot's natural dynamics are presented. The proposed reduced-order model, termed the Two-rolling-leg (TRL) model, is a 3-DOF planar rigid-body model consisting of two half-circular compliant legs with pure rolling contact. Throughout the non-dimensional steps-to-fall and fixed-point analysis, the model with feasible intrinsic parameters can passively perform the periodic dynamic behavior of bounding and pronking, revealing a relationship between the body parameters and the preferred dynamic behaviors. Dynamic bounding and pronking on a quadruped robot were initiated by developing a model-based control strategy based on the searched periodic dynamic behaviors of the TRL model. The experimental results showed that the robot can initiate its dynamic bounding and pronking behaviors at various forward speeds merely by causing the motor to track a preset trajectory derived from the fixed-point motion of the TRL model using position control. The higher success rate of the robot in stable bounding than in pronking is in line with the results from the analysis of the model. This paper confirms that the dynamic multi-gait locomotion of a quadrupedal robot can be initiated by utilizing a reduced-order model for control guidance and that the body configuration plays an important role in determining the characteristics of the dynamic behaviors.
A root functional–structural model allows assessment of the effects of water deficit on water and solute transport parameters
Authors: Bauget Fabrice , Protto Virginia , Pradal Christophe , Boursiac Yann , Maurel Christophe
Published: December 2022

Root water uptake is driven by a combination of hydrostatic and osmotic forces. Water transport was characterized in primary roots of maize seedlings grown hydroponically under standard and water deficit (WD) conditions, as induced by addition of 150 g l–1 polyethylene glycol 8000 (water potential= –0.336 MPa). Flow measurements were performed using the pressure chamber technique in intact roots or on progressively cut root system architectures. To account for the concomitant transport of water and solutes in roots under WD, we developed within realistic root system architectures a hydraulic tree model integrating both solute pumping and leak. This model explains the high spontaneous sap exudation of roots grown in standard conditions, the non-linearity of pressure–flow relationships, and negative fluxes observed under WD conditions at low external hydrostatic pressure. The model also reveals the heterogeneity of driving forces and elementary radial flows throughout the root system architecture, and how this heterogeneity depends on both plant treatment and water transport mode. The full set of flow measurement data obtained from individual roots grown under standard or WD conditions was used in an inverse modeling approach to determine their respective radial and axial hydraulic conductivities. This approach allows resolution of the dramatic effects of WD on these two components.
Mechanisms for high spin in black-hole neutron-star binaries and kilonova emission: inheritance and accretion
Authors: Steinle Nathan , Gompertz Benjamin P , Nicholl Matt
Published: December 2022

A black-hole neutron-star binary merger can lead to an electromagnetic counterpart called a kilonova if the neutron star is disrupted prior to merger. The observability of a kilonova depends on the amount of neutron star ejecta, which is sensitive to the aligned component of the black hole spin. We explore the dependence of the ejected mass on two main mechanisms that provide high black hole spin in isolated stellar binaries. When the black hole inherits a high spin from a Wolf–Rayet star that was born with least $\sim 10{{\ \rm per\ cent}}$ of its breakup spin under weak stellar core-envelope coupling, relevant for all formation pathways, the median of the ejected mass is ≳10−2 M⊙. Though only possible for certain formation pathways, similar ejected mass results when the black hole accretes $\gtrsim 20{{\ \rm per\ cent}}$ of its companion’s envelope to gain a high spin. Together, these signatures suggest that a population analysis of black-hole neutron-star binary mergers with observed kilonovae may help distinguish between mechanisms for spin and possible formation pathways. We show that these kilonovae will be difficult to detect with current capabilities, but that future facilities, such as the Vera Rubin Observatory, can do so even if the aligned dimensionless spin of the black hole is as low as ∼0.2. Our model predicts kilonovae as bright as Mi ∼ −14.5 for an aligned black hole spin of ∼0.9 and mass ratio Q = 3.6.
AGN cool feedback and analogy with X-ray binaries: from radiation pressure to cosmic ray-driven outflows
Authors: Ishibashi W , Fabian A C
Published: December 2022

Cool outflows are now commonly observed in galaxies, but their physical origin and driving mechanism remain unclear. Active galactic nucleus (AGN) feedback can potentially accelerate cool galactic outflows via cosmic rays (CR) and radiation pressure on dust. Here we investigate the relative importance of CR and radiation feedback in AGNs, and we analyse the physical conditions for outflow launching as a function of the black hole accretion flow mode. We assume CRs from AGN jet origin and consider the analogy with Galactic X-ray binaries, whereby the jet is prominent at low accretion rates (hard state) and quenched at high accretion rates (soft state). We show that CR-driven outflows can be powered at low accretion rates and at large radii, whereas radiation pressure-driven outflows dominate at high accretion rates and small radii. Thus the two AGN feedback mechanisms – CRs and radiation pressure on dust – may play complementary roles in driving cool outflows on galactic scales. The transition from radiation pressure-driven outflows at higher accretion rates to CR-driven outflows at lower accretion rates likely corresponds to a transition in the underlying accretion flow modes (from a radiatively efficient accretion disc to a radiatively inefficient jet-dominated flow) over cosmic time.
Targeted bacterial conjugation mediated by synthetic cell-to-cell adhesions
Authors: Robledo Marta , Álvarez Beatriz , Cuevas Ana , González Sheila , Ruano-Gallego David , Fernández Luis Ángel , de la Cruz Fernando
Published: December 2022

Genetic interventions on microbiomes, for clinical or biotechnological purposes, remain challenging. Conjugation-based delivery of genetic cargo is still unspecific and limited by low conjugation rates. Here we report an approach to overcome these problems, based on a synthetic bacterial adhesion system. Mating assemblers consist on a synthetic adhesion formed by the expression on the surface of donor and target cells of specific nanobodies (Nb) and their cognate antigen (Ag). The Nb–Ag bridge increased 1–3 logs transfer of a variety of plasmids, especially in liquid media, confirming that cell-cell docking is a main determinant limiting mating efficiency. Synthetic cell-to-cell adhesion allows efficient conjugation to targeted recipients, enhancing delivery of desired genes to a predefined subset of prey species, or even specific pathogenic strains such as enterohemorrhagic Escherichia coli (EHEC), within a bacterial community. The synthetic conjugation enhancer presented here optimizes plasmid delivery by selecting the target hosts with high selectivity.
Firearms and the State in Sixteenth-Century Italy: Gun Proliferation and Gun Control
Authors: Fletcher Catherine
Published: December 2022

Small firearms proliferated on the Italian peninsula in the context of the Italian Wars of 1494–1559. States were faced with significant challenges in managing this new technology. On the one hand, guns swiftly became important to civic defence. On the other, they raised serious concerns about social order. Archive material from Bologna, Brescia, Florence, Modena and Rome illustrates the routes through which firearms proliferated and sometimes were actively promoted as a means of defence, for example via the development of civic militias and shooting contests. Yet state promotion of shooting skills led to a dangerous expansion of access to weapons, and regimes began to restrict the use of firearms, especially wheel-locks, which could be concealed on the person and thus posed a particular risk to public order. Rank and social status were important in negotiating exemptions to the gun laws, but increasingly those outside the nobility began to assert a need for firearms for self-defence. Guns offer a prism through which it is possible to discern significant tensions in the priorities of early modern regimes and to shed light on the processes through which, in the later years of the sixteenth century, Italy came to suffer high rates of violence.
The Origin of Lattice Rotation during Dendritic Crystallization of Clinopyroxene
Authors: Griffiths Thomas A , Habler Gerlinde , Ageeva Olga , Sutter Christoph , Ferrière Ludovic , Abart Rainer
Published: December 2022

Understanding dendritic crystallization is key to obtaining petrological information about rapid crystallization events. Clinopyroxene dendrites from a basaltic rock fulgurite from Nagpur, India, exhibit curved branches with corresponding lattice rotation that exceeds 180° for some branches. This paper combines crystallographic orientation mapping with microstructural observations and compositional information to determine the dendrites’ 3-D morphology and their bending mechanism. Dendrites exhibit a network of branches in the (010) plane, following either {001}* (normal to {001} planes, strong lattice curvature) or < 10–1 > (weak lattice curvature). Three or more orders of branches are observed in the (010) plane, alternating between {001}* and < 10–1>. Side branches with weak lattice curvature extend sub-perpendicular to the (010) plane, following either {021}* (sprouting from {001}* branches) or < 12–1 > (from <10–1 > branches) and defining curved ‘ribbons’ containing their respective central branch. All branches rotate about [010], with a consistent rotation sense regardless of elongation direction in sample or crystal coordinates. Bending must therefore be caused by local asymmetric thermal and compositional fields in the melt, generated by dendritic growth itself, not by sample-scale compositional, thermal or mechanical gradients. The most likely cause of bending is asymmetric distribution of melt supersaturation around branch tips, related to unequal growth rates perpendicular to different facets. Lattice rotation is inferred to occur via preferential incorporation of high densities of [001] (100) edge dislocations of one sign. High inferred dislocation densities imply that the preservation of bent dendrites requires rapid quenching. Higher inferred degree of undercooling (based on microstructural observations) correlates with greater lattice curvature. Bent dendrites can thus potentially be used to deliver information about spatial variations in degree of undercooling and place limits on the history of a sample after dendritic crystallization. Finally, finding lattice rotation exclusively about [010] is a new criterion to identify cryptic dendritic growth stages in euhedral crystals.
Tomato receptor-like cytoplasmic kinase Fir1 is involved in flagellin signaling and preinvasion immunity
Authors: Sobol Guy , Majhi Bharat Bhusan , Pasmanik-Chor Metsada , Zhang Ning , Roberts Holly M , Martin Gregory B , Sessa Guido
Published: December 2022

Detection of bacterial flagellin by the tomato (Solanum lycopersicum) receptors Flagellin sensing 2 (Fls2) and Fls3 triggers activation of pattern-triggered immunity (PTI). We identified the tomato Fls2/Fls3-interacting receptor-like cytoplasmic kinase 1 (Fir1) protein that is involved in PTI triggered by flagellin perception. Fir1 localized to the plasma membrane and interacted with Fls2 and Fls3 in yeast (Saccharomyces cerevisiae) and in planta. CRISPR/Cas9-generated tomato fir1 mutants were impaired in several immune responses induced by the flagellin-derived peptides flg22 and flgII-28, including resistance to Pseudomonas syringae pv. tomato (Pst) DC3000, production of reactive oxygen species, and enhanced PATHOGENESIS-RELATED 1b (PR1b) gene expression, but not MAP kinase phosphorylation. Remarkably, fir1 mutants developed larger Pst DC3000 populations than wild-type plants, whereas no differences were observed in wild-type and fir1 mutant plants infected with the flagellin deficient Pst DC3000ΔfliC. fir1 mutants failed to close stomata when infected with Pst DC3000 and Pseudomonas fluorescens and were more susceptible to Pst DC3000 than wild-type plants when inoculated by dipping, but not by vacuum-infiltration, indicating involvement of Fir1 in preinvasion immunity. RNA-seq analysis detected fewer differentially expressed genes in fir1 mutants and altered expression of jasmonic acid (JA)-related genes. In support of JA response deregulation in fir1 mutants, these plants were similarly susceptible to Pst DC3000 and to the coronatine-deficient Pst DC3118 strain, and more resistant to the necrotrophic fungus Botrytis cinerea following PTI activation. These results indicate that tomato Fir1 is required for a subset of flagellin-triggered PTI responses and support a model in which Fir1 negatively regulates JA signaling during PTI activation.
The Impact of Risk Cycles on Business Cycles: A Historical View
Authors: Danielsson Jon , Valenzuela Marcela , Zer Ilknur
Published: December 2022

We investigate the effects of financial risk cycles on business cycles, using a panel spanning 73 countries since 1900. Agents use a Bayesian learning model to form their beliefs about risk. We construct a proxy of these beliefs and show that perceived low risk encourages risk-taking, augmenting growth at the cost of accumulating financial vulnerabilities, and, therefore, a reversal in growth follows. The reversal is particularly pronounced when the low-risk environment persists and credit growth is excessive. Global risk cycles have a stronger effect on growth than local risk cycles via their impact on capital flows, investment, and debt-issuer quality.

Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
The promise of artificial intelligence in combating public corruption in the emerging economies: A conceptual framework
Authors: Adobor Henry , Yawson Robert
Published: December 2022

In this conceptual paper, we explore how artificial intelligence (AI) holds promise as an important and additional tool for combating corruption in public procurement in emerging economies. We aim to extend the understanding of how the emergent technology of AI may be another important tool in the fight against corruption in emerging economies. We discuss how AI and related emergent technologies can help build greater accountability and transparency regimes in public procurement, a key source of public corruption. We argue that there are infrastructural, social, ethical, and political challenges to the successful use of emerging technologies of AI in the fight against public corruption. We make inferences from the discussion and provide some tentative guidelines for policymakers. We suggest that using AI as part of a program of institutional reforms in the public sector would increase technology’s role and contributions to the fight against systemic corruption in public procurement in emerging economies.
Mission incomplete: Layered practices of monitoring and evaluation in Swedish transformative innovation policy
Authors: Rohracher Harald , Coenen Lars , Kordas Olga
Published: December 2022

Research and innovation policies (IPs) across Europe, particularly in Sweden, are increasingly framed by an orientation towards societal challenges, missions, and transformative change. Innovation-funding agencies are adapting to these new approaches but struggle with a host of new questions and challenges on how to re-structure public policy interventions and develop new structures for monitoring, learning, and evaluation. In this article, we investigate how this IP paradigm shift is dealt with in the IP discourse and practice in Sweden and how an incomplete shift creates mismatches and tensions with existing structures for programme evaluation and monitoring. Despite the new paradigm, the implementation of evaluation strategies mostly follows a traditional ‘summative’ framing. The ongoing discussions in Swedish IP demonstrate that a paradigm shift towards transformative innovation cannot unfold its potential unless it is also followed by a shift in the practices of programme implementation and evaluation.
Technology entrepreneurship and innovation hubs: Perspectives on the universal regulatory sandbox
Authors: Hemphill Thomas A
Published: December 2022

In the USA, state governments have long focused on how they can provide an attractive operating environment for enterprises to locate and expand business operations within their respective political jurisdiction. In recent years, however, a new focus of state governments is on nurturing technology entrepreneurship creating long-term organizational success that translates into sustainable local- and state-level economic growth. To this end, there has been an expansion of ‘innovation hubs’ across the country. These innovation hubs are considered local and regional ‘laboratories’ for technology-focused, entrepreneurial businesses to gestate their new products and services within state-level political boundaries. A recently emerging phenomenon has been the development of the ‘regulatory sandbox’ concept as a further enhancement of the public policy operating environment for nurturing technology entrepreneurship, with a further conceptual extension—to the ‘universal regulatory sandbox’—now being legislatively enacted and implemented.
Double screening for syphilis and HIV in pregnant women in a priority municipality for the elimination of vertical transmission in Brazil: incidence, risk factors and spatial analysis
Authors: Fava Lidiane Martins Gonçalves , Guedes Ana Lúcia de Lima , Ribeiro Luiz Cláudio , Pinto Carmen Perches Gomide , Souza e Guimarães Ricardo José de Paula , Nogueira Mário Círio , Alves Márcio José Martins , Silva Márcio Roberto
Published: December 2022

Background

The Brazilian Ministry of Health (MoH) recommends double screening (DS) for syphilis and HIV during the first and third trimesters of antenatal care (ANC) to mitigate vertical transmission. We surveyed DS outcomes and their associated factors in a priority Brazilian municipality with >100 000 inhabitants who face challenges for both health problems.

Methods

A total of 399 women were followed up throughout pregnancy using medical records. Spatial and multinomial logistic analyses were performed.

Results

There was an incidence rate of 24.8%, 59.4% and 15.8% for ‘full DS’, ‘partial DS’ and ‘without DS’, respectively. Younger women and those with a history of both prematurity and multiparity were less likely to be in the ‘full DS’ category. There was an overlap of high-density clusters of ‘full DS’ and ‘ANC in better quality basic health units’, adherent to both the Family Health Strategy and the National Program for Access and Quality Improvement in Primary Care.

Conclusions

The poor DS outcomes presented in 75% of the cases were mostly linked to delays in starting ANC appointments or their discontinuity. Thus, the MoH recommendations, accompanied by ongoing training, technical assistance and the periodic evaluation of their implementation, need to effectively reach providers and promote counseling and awareness about the importance of DS for pregnant women.
Gap-Free Nuclear and Mitochondrial Genomes of Ustilaginoidea virens JS60-2, a Fungal Pathogen Causing Rice False Smut
Authors: Wang Yin , Yang Lei , Yang Qun , Dong Jie , Wang Yufu , Duan Yuhang , Yin Weixiao , Zheng Lu , Sun Wenxian , Fan Jing , Luo Chao-Xi , Li Guotian
Published: December 2022

Rice false smut (RFS), caused by Ustilaginoidea virens, has become a major disease in recent years, and mycotoxins produced by U. virens often threaten food safety. To study fungal pathogenesis and identify potential targets for developing new fungicides, gap-free nuclear and complete mitochondrial genomes of U. virens JS60-2 were sequenced and assembled. Using the second and third generation sequencing data, we assembled a 38.02-Mb genome that consists of seven contigs with the contig N50 being 6.32-Mb. In total, 8,486 protein-coding genes were annotated in the genome, including 21 secondary metabolism gene clusters. We also assembled the complete mitochondrial genome, which is 102,498 bp, with 28% GC content. The JS60-2 genomes assembled in this study will facilitate research on U. virens and contribute to RFS control.

[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
A Genome Resource for Ciborinia camelliae, the Causal Agent of Camellia Flower Blight
Authors: Valenti Irene , Saracchi Marco , Degradi Luca , Kunova Andrea , Cortesi Paolo , Pasquali Matias
Published: December 2022

Ciborinia camelliae Kohn is a camellia pathogen belonging to family Sclerotiniaceae, infecting only flowers of camellias. To better understand the virulence mechanism in this species, the draft genome sequence of the Italian strain of C. camelliae was obtained with a hybrid approach, combining Illumina HiSeq paired reads and MinIon Nanopore long-read sequencing. This combination improved significantly the existing National Center for Biotechnology Information reference genome. The assembly contiguity was implemented decreasing the contig number from 2,604 to 49. The N50 contig size increased from 31,803 to 2,726,972 bp and the completeness of assembly increased from 94.5 to 97.3% according to BUSCO analysis. This work is foundational to allow functional analysis of the infection process in this scarcely known floral pathogen.

[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Genome Sequence Resource of Pectobacterium polaris QK413-1 that Causes Blackleg on Potato in Fujian Province, China
Authors: Lin Zhijian , Li Huawei , Luo Wenbin , Xu Yongqing , Xu Guochun , Ji Rongchang , Liu Zhonghua , Zhang Hong , Lin Zhaomiao , Li Guoliang , Qiu Yongxiang , Tang Hao , Qiu Sixin
Published: December 2022

The Pectobacterium pathogens cause soft rot and blackleg diseases on many plants and crops, including potatoes. Here, we first report a high-quality genome assembly and announcement of the P. polaris strain QK413-1, which causes blackleg disease in potatoes in China. The QK413-1 genome was sequenced and assembled using the PacBio Sequel II and Illumina sequencing platform. The assembled genome has a total size of 5,005,507 bp with a GC content of 51.81%, encoding 4,782 open reading frames, including 639 virulence genes, 273 drug resistance genes, and 416 secreted proteins. The QK413-1 genome sequence provides a valuable resource for the control of potato blackleg and research into its mechanism.
A Shift in Pathotype Diversity and Complexity of Phytophthora sojae in Brazil
Authors: Batista Izabel C. A. , Silva Maria P. C. , Silva Junior Amarildo L. , Arrigada Mariela P. G. , de Camargo Meyriele. P. , Figueiredo Adriana , Júnior Braz T. H. , Mizubuti Eduardo S. G.
Published: December 2022

Soybean root and stem rot caused by the oomycete Phytophthora sojae is a destructive disease worldwide that can affect plants at any growth stage. The use of resistant cultivars is the most effective method of controlling the disease. Therefore, monitoring changes in the population of P. sojae regarding the dynamics of avirulence genes capable of overcoming resistance genes (Rps) is important to reduce yield losses and to enhance the effectiveness of the Rps genes. Forty isolates of P. sojae sampled from a region of high incidence of soybean root and stem rot in Brazil were characterized using 14 soybean differentials, and 28 pathotypes were identified. Compared with a study conducted a decade ago, there was a major shift in pathotype diversity and complexity toward both higher numbers of different pathotypes and of avirulence genes in a given individual in the current population of P. sojae. Breeding programs aiming at developing soybean cultivars with resistance to root and stem rot should consider the high variability in the population of P. sojae and seek for strategic deployment of genes and germplasm.
Identification and Characterization ofPythium,Globisporangium, andPhytopythiumSpecies Present in Floricultural Crops from Long Island, New York
Authors: Garrido Patricia A. , Proaño-Cuenca Fernanda , Flor Francisco J. Flores , Benítez Edinson A. Díaz , Torres Ivanna F. Sánchez , Kaiser Alma R. Koch , Sain Linda , Peñaloza Yaneth Amparo Muñoz , Marek Stephen M. , Melouk Hassan , Daughtrey Margery , Garzon Carla D.
Published: December 2022

Several Pythium, Globisporangium, and Phytopythium species cause Pythium diseases in greenhouse floricultural crops, resulting in significant seasonal losses. Four hundred and eighteen Pythium, Globisporangium, and Phytopythium isolates from flowering crops, growing media, or bench and floor debris were collected from Long Island greenhouses or clinic samples between 2002 and 2013. Isolates were identified to species based on morphology and internal transcribed spacer barcoding. Twenty-two species of Pythium, Phytopythium, and Globisporangium were identified, with Globisporangium irregulare sensu lato (s.l.) being the most common. To determine the origin of inoculum during the 2011 cropping season, 11 microsatellite loci were analyzed in 124 G. irregulare s.l. isolates collected in four greenhouses and six previously collected from clinic samples. Cluster analyses grouped G. irregulare s.l. isolates into four groups: G. irregulare sensu stricto, plus three G. cryptoirregulare clusters. The population structure defined by greenhouse and host was found in two clades. Additionally, the population dynamics of G. irregulare s.l. isolates associated with Pelargonium spp. from 2011 to 2013 were examined using 85 isolates and nine informative microsatellite loci to assess inoculum survival over multiple cropping seasons. Although most isolates had unique genotypes, closely related genotypes were found in the same locations over different years. Our results indicate that G. irregulare s.l. inocula have local as well as remote origins. Isolates may be initially brought into ornamental operations from common sources, such as infected plant materials or infested potting mixes. Our results support the hypothesis that established strains can serve as inocula and survive in greenhouse facilities over multiple seasons.
The Golden Goal of Soil Management: Disease-Suppressive Soils
Authors: Sagova-Mareckova Marketa , Omelka Marek , Kopecky Jan
Published: December 2022

Disease-suppressive soils encompass specific plant−pathogen−microbial interactions and represent a rare example of an agroecosystem where soil conditions and microbiome together prevent the pathogen from causing disease. Such soils have the potential to serve as a model for characterizing soil pathogen-related aspects of soil health, but the mechanisms driving the establishment of suppressive soils vary and are often poorly characterized. Yet, they can serve as a resource for identifying markers for beneficial activities of soil microorganisms concerning pathogen prevention. Many recent studies have focused on the nature of disease-suppressive soils, but it has remained difficult to predict where and when they will occur. This review outlines current knowledge on the distribution of these soils, soil manipulations leading to pathogen suppression, and markers including bacterial and fungal diversity, enzymes, and secondary metabolites. The importance to consider soil legacy in research on the principles that define suppressive soils is also highlighted. The goal is to extend the context in which we understand, study, and use disease-suppressive soils by evaluating the relationships in which they occur and function. Finally, we suggest that disease-suppressive soils are critical not only for the development of indicators of soil health, but also for the exploration of general ecological principles about the surrounding landscape, effects of deeper layers of the soil profile, little studied soil organisms, and their interactions for future use in modern agriculture.
Family–Educator Partnership in the Development of Entrustable Professional Activities in Complex Care
Authors: Huth Kathleen , Henry Duncan , Cribb Fabersunne Camila , Coleman Cara L. , Frank Brigit , Schumacher Daniel J. , Shah Neha
Published: December 2022

Problem

Incorporating patient and family voices in the development of entrustable professional activities (EPAs) is not standard practice. Care of children with medical complexity (CMC) is an area of pediatrics that relies on family partnership, and families of CMC are ideal partners in EPA development given their expertise in their child’s care and experience interacting with the health care system. The authors describe their model for partnering with families to develop EPAs and reflect on the unique contributions of family leaders to the process.

Approach

After recruitment of family leaders from a national organization of families and friends of children with special health care needs, the authors used a multistage process for EPA development from June 2019 to February 2021. Family leaders were integrated throughout the process, including creating EPA descriptions, revising content across all EPAs, appraising EPAs through virtual focus groups with other key stakeholders, and finalizing and publishing EPAs. The authors used content analysis to identify recommendations for patient- and family-integrated EPA development.

Outcomes

Family leaders and educators partnered in every phase of developing EPAs for the care of CMC, including as content experts, editors, focus group facilitators, and coauthors. Family leaders recommended substantive changes to all EPAs, including revising language, augmenting content, and modifying scope of practice. In addition, content analysis of family leaders’ revisions yielded 10 recommendations to ensure that written EPA descriptions are patient- and family-centered.

Next Steps

The described process of EPA development for the care of CMC models how families can be integrated into competency framework development and highlights their contributions. Family leader recommendations for embedding patient and family voices in EPA descriptions can serve as a guide for EPA development in other specialties.
Impact of Pediatric Orthopaedic Fellowship Training on Pediatric Supracondylar Humerus Fracture Treatment and Outcomes: A Meta-analysis
Authors: Bram Joshua T. , DeFrancesco Christopher J. , Pascual-Leone Nicolas , Gross Preston W. , Doyle Shevaun M. , Fabricant Peter D.
Published: December 2022

Background:

Supracondylar humerus (SCH) fractures are common pediatric injuries, typically requiring closed reduction and percutaneous pinning or open reduction. These injuries are managed frequently by both pediatric-trained (PTOS) and nonpediatric-trained (NTOS) orthopaedic surgeons. However, some literature suggests that complications for pediatric injuries are lower when managed by PTOS. Therefore, this meta-analysis sought to compile existing literature comparing patients treated by PTOS and NTOS to better understand differences in management and clinical outcomes.

Methods:

Using preferred reporting items for systematic reviews and meta-analyses (PRISMA) methodology, a systematic review was conducted for all articles comparing SCH fractures managed by PTOS and NTOS in 4 online databases (PubMed, Embase, CINAHL, Cochrane). Study quality was assessed through the use of the Newcastle-Ottawa Scale. Meta-analyses were then performed for postoperative outcomes using pooled data from the included studies. Statistics were reported as odds ratios and 95% CI.

Results:

This search strategy yielded 242 unique titles, of which 12 underwent full-text review and 7 met final inclusion. All studies were retrospective and evaluated patients treated in the United States. There were a total of 692 and 769 patients treated by PTOS and NTOS, respectively. PTOS had shorter operative times [mean difference, 13.6 min (CI, −23.9 to −3.4), P=0.01] and less frequently utilized a medial-entry pin [odds ratios, 0.36 (CI, 0.2 to 0.9), P=0.03]. There were no differences in time to treatment, the necessity of open reduction, postoperative Baumann angle, or complications including surgical site infection or iatrogenic nerve injury.

Conclusions:

Despite shorter operative times and lower frequency of cross-pinning when treated by PTOS, pediatric SCH fracture outcomes are similar when treated by PTOS and NTOS. These findings demonstrate that these fractures may possibly be treated safely by both PTOS and experienced fellowship-trained academic NTOS who are comfortable managing these injuries in pediatric patients.

Level of Evidence:

Level III; Meta-analysis.
Outcomes and Safety of Traditional Growing Rod Technique in the Treatment of Early-onset Dystrophic Scoliosis Secondary to Type 1 Neurofibromatosis With Intraspinal Rib Head Dislocation in Children
Authors: Gao Rongxuan , Bai Yunsong , Zhang Xuejun , Cao Jun , Guo Dong , Yao Ziming , Liu Haonan
Published: December 2022

Purpose:

The purpose of this study was to investigate the outcomes and safety of traditional growing rod (TGR) in the treatment of early-onset dystrophic scoliosis secondary to type 1 neurofibromatosis (NF1-EOS) with intraspinal rib head dislocation (IRH) in children.

Methods:

From September 2006 to June 2020, 21 patients with NF1-EOS were treated with TGR. The patients comprised 13 boys and 8 girls with a mean age of 7.1±1.5 years. Two patients had IRH-induced nerve injury [American Spinal Injury Association (ASIA) grade D]. No neurological symptoms were found in the other patients. The intraspinal rib proportion, apical vertebral rotation, apical vertebral translation, coronal main thoracic curve, trunk shift, thoracic kyphosis, lumbar lordosis, sagittal balance, and T1-S1 height were measured before and after TGR implantation and at the last follow-up. Complications were also evaluated.

Results:

The mean follow-up time was 3.4±2.0 years. An average of 3.1 times (range: 1 to 8 times) lengthening procedures were performed in each patient. The intraspinal rib proportion was significantly lower postoperatively than preoperatively (22±11% vs. 33±18%, respectively; P<0.001), and no significant correction loss was found at the last follow-up (24±12%, P=0.364). Compared with the measurements before TGR implantation, the major coronal curve and T1-S1 height after TGR implantation and at the last follow-up were significantly different (P<0.05). Significant correction of apical vertebral translation, thoracic kyphosis, lumbar lordosis, and sagittal balance were noted after TGR implantation, and no significant correction loss was found at the last follow-up (P>0.05). Ten complications occurred in 7 patients. Two patients with nerve injury recovered after the operation. No neurological complications were found during the follow-up.

Conclusions:

TGR is a safe and effective therapy for NF1-EOS with IRH where there was no direct compression of the spinal cord, which was confirmed by preoperative magnetic resonance imaging. Through this procedure, IRH could be partly removed from the spinal canal.

Level of Evidence:

Level III.
Office-based Plastic Surgery—Evidence-based Clinical and Administrative Guidelines
Authors: Zhang Kevin K. , Reddy Nihaal , Janis Jeffrey E.
Published: December 2022

Outpatient procedures are extremely prevalent in plastic surgery, with an estimated 82% of cosmetic plastic surgery occurring in this setting. Given that patient safety is paramount, this practical review summarizes major contemporary, evidence-based recommendations regarding office-based plastic surgery. These recommendations not only outline clinical aspects of patient safety guidelines, but administrative, as well, which in combination will provide the reader/practice with a structure and culture that is conducive to the commitment to patient safety. Proper protocols to address potential issues and emergencies that can arise in office-based surgery, and staff familiarity with thereof, are also necessary to be best prepared for such situations.