bluuebunny/crossref_metadata_2025 huggingface dataset:
A Microbial Signature for Paediatric Perianal Crohn’s Disease
Authors: Breton Jessica , Tanes Ceylan , Tu Vincent , Albenberg Lindsey , Rowley Sarah , Devas Nina , Hwang Rosa , Kachelries Kelly , Wu Gary D , Baldassano Robert N , Bittinger Kyle , Mattei Peter
Published: February 2022

Background and Aims

Perianal fistulising disease can affect up to 25% of patients with Crohn’s disease [CD] and lead to significant morbidity. Although the role of the gut microbiota in inflammatory bowel disease [IBD] has been increasingly recognised, its role in fistula development has scarcely been studied. Here, we aimed to define the microbial signature associated with perianal fistulising CD in children.

Methods

A prospective observational study including children age 6-18 years with a diagnosis of perianal fistulising CD was conducted. Stool samples and rectal and perianal fistula swabs were collected. Stool samples and rectal swabs from children with CD without perianal disease and healthy children were included as comparison. Whole shotgun metagenomic sequencing was performed.

Results

A total of 31 children [mean age 15.5 ± 3.5 years] with perianal CD were prospectively enrolled. The fistula-associated microbiome showed an increase in alpha diversity and alteration in the abundance of several taxa compared with the rectal- and faecal-associated microbiome with key taxa belonging to the Proteobacteria phylum. Genes conferring resistance to the clinically used antibiotic regimen ciprofloxacin and metronidazole were found in the three sample types. In comparison with children without the perianal phenotype [N = 36] and healthy controls [N = 41], the mucosally-associated microbiome of children with perianal CD harboured a reduced butyrogenic potential. Linear discriminant analysis identified key taxa distinguishing the rectal mucosally-associated microbiome of children with perianal CD from children without this phenotype.

Conclusions

The microbial community within CD-related anorectal fistula is compositionally and functionally unique. Taken together, these findings emphasise the need to better understand the ecosystem of the fistula milieu to guide development of novel microbiome-based strategies in this CD phenotype.
New York in Slices: The Victorian Origins of The Bonfire of the Vanities
Authors: Abraham Adam
Published: February 2022

The Bonfire of the Vanities, Tom Wolfe’s first novel, was a bestseller in the 1980s, when it captured its historical moment of yuppie excess, urban corruption, and vanity. Less recognized today are the book’s origins as an experiment in reviving Victorian modes of publication. Taking Dickens and Thackeray, Balzac and Zola as his models, Wolfe planned to write what he conceived of as a new nineteenth-century novel—multiplot and multivalent—an anatomy of New York City. What is more, The Bonfire of the Vanities was first published serially, in Rolling Stone magazine, from 1984 to 1985. This article will explore the Victorian provenance of Wolfe’s novel, in particular by rereading the original serial parts.
Circadian nuclear receptor Rev-erbα is expressed by platelets and potentiates platelet activation and thrombus formation
Authors: Shi Jianfeng , Tong Renyang , Zhou Meng , Gao Yu , Zhao Yichao , Chen Yifan , Liu Wenhua , Li Gaoxiang , Lu Dong , Meng Guofeng , Hu Liuhua , Yuan Ancai , Lu Xiyuan , Pu Jun
Published: February 2022

Aims

Adverse cardiovascular events have day/night patterns with peaks in the morning, potentially related to endogenous circadian clock control of platelet activation. Circadian nuclear receptor Rev-erbα is an essential and negative component of the circadian clock. To date, the expression profile and biological function of Rev-erbα in platelets have never been reported.

Methods and results

Here, we report the presence and functions of circadian nuclear receptor Rev-erbα in human and mouse platelets. Both human and mouse platelet Rev-erbα showed a circadian rhythm that positively correlated with platelet aggregation. Global Rev-erbα knockout and platelet-specific Rev-erbα knockout mice exhibited defective in haemostasis as assessed by prolonged tail-bleeding times. Rev-erbα deletion also reduced ferric chloride-induced carotid arterial occlusive thrombosis, prevented collagen/epinephrine-induced pulmonary thromboembolism, and protected against microvascular microthrombi obstruction and infarct expansion in an acute myocardial infarction model. In vitro thrombus formation assessed by CD41-labelled platelet fluorescence intensity was significantly reduced in Rev-erbα knockout mouse blood. Platelets from Rev-erbα knockout mice exhibited impaired agonist-induced aggregation responses, integrin αIIbβ3 activation, and α-granule release. Consistently, pharmacological inhibition of Rev-erbα by specific antagonists decreased platelet activation markers in both mouse and human platelets. Mechanistically, mass spectrometry and co-immunoprecipitation analyses revealed that Rev-erbα potentiated platelet activation via oligophrenin-1-mediated RhoA/ERM (ezrin/radixin/moesin) pathway.

Conclusion

We provided the first evidence that circadian protein Rev-erbα is functionally expressed in platelets and potentiates platelet activation and thrombus formation. Rev-erbα may serve as a novel therapeutic target for managing thrombosis-based cardiovascular disease.

Key question

Adverse cardiovascular events have day/night patterns with peaks in the morning, potentially related to endogenous circadian clock control of platelet activation. Whether circadian nuclear receptor Rev-erba is present in platelets and regulates platelet function remains unknown.

Key finding

We provide the first evidence that Rev-erba is functionally expressed in platelets and acts as a positive regulator of platelet activation/thrombus formation through the oligophrenin-1-mediated RhoA/ERM signalling pathway.

Take home message

Our observations highlight the importance of circadian clock machinery in platelet physiology and support the notion that Rev-erba may serve as a novel therapeutic target for managing thrombosis-based cardiovascular diseases.
An experimental test of disease resistance function in the skin-associated bacterial communities of three tropical amphibian species
Authors: Hughey Myra C , Rebollar Eria A , Harris Reid N , Ibáñez Roberto , Loftus Stephen C , House Leanna L , Minbiole Kevin P C , Bletz Molly C , Medina Daniel , Shoemaker William R , Swartwout Meredith C , Belden Lisa K
Published: February 2022

Variation in the structure of host-associated microbial communities has been correlated with the occurrence and severity of disease in diverse host taxa, suggesting a key role of the microbiome in pathogen defense. However, whether these correlations are typically a cause or consequence of pathogen exposure remains an open question, and requires experimental approaches to disentangle. In amphibians, infection by the fungal pathogen Batrachochytrium dendrobatidis (Bd) alters the skin microbial community in some host species, whereas in other species, the skin microbial community appears to mediate infection dynamics. In this study, we completed experimental Bd exposures in three species of tropical frogs (Agalychnis callidryas, Dendropsophus ebraccatus,andCraugastor fitzingeri) that were sympatric with Bd at the time of the study. For all three species, we identified key taxa within the skin bacterial communities that were linked to Bd infection dynamics. We also measured higher Bd infection intensities in D. ebraccatus and C. fitzingeri that were associated with higher mortality in C. fitzingeri. Our findings indicate that microbially mediated pathogen resistance is a complex trait that can vary within and across host species, and suggest that symbiont communities that have experienced prior selection for defensive microbes may be less likely to be disturbed by pathogen exposure.
A Structured Approach to Optimizing Animal Model Selection for Human Translation: The Animal Model Quality Assessment
Authors: Storey Joanne , Gobbetti Thomas , Olzinski Alan , Berridge Brian R
Published: February 2022

Animal studies in pharmaceutical drug discovery are common in preclinical research for compound evaluation before progression into human clinical trials. However, high rates of drug development attrition have prompted concerns regarding animal models and their predictive translatability to the clinic. To improve the characterization and evaluation of animal models for their translational relevance, the authors developed a tool to transparently reflect key features of a model that may be considered in both the application of the model but also the likelihood of successful translation of the outcomes to human patients. In this publication, we describe the rationale for the development of the Animal Model Quality Assessment tool, the questions used for the animal model assessment, and a high-level scoring system for the purpose of defining predictive translatability. Finally, we provide an example of a completed Animal Model Quality Assessment for the adoptive T-cell transfer model of colitis as a mouse model to mimic inflammatory bowel disease in humans.
Raloxifene prevents intracellular invasion of pathogenic bacteria through modulation of cell metabolic pathways
Authors: Chang JuOae , Kim Jihoon , Lee Wonsik
Published: February 2022

Background

Pathogenic bacteria can invade and survive inside phagocytic and non-phagocytic cells and use them as a sanctuary against antibiotics. Induction of various host protective mechanisms, including autophagy, can be a novel and effective method to combat intracellular bacteria. Recent studies report that raloxifene, a selective oestrogen receptor modulator, can induce cellular autophagy.

Objectives

To demonstrate the effect of raloxifene on intracellular invasion and proliferation of pathogenic bacteria and investigate raloxifene-induced metabolic changes in host cells.

Methods

Autophagic induction was determined by the extent of nuclear fragmentation and expression levels of the LC3B protein. Intracellular invasion of MRSA strains into A549 lung epithelial cells and invasion of Mycobacterium abscessus into RAW264.7 macrophages were assessed by invasion and proliferation assays. Changes in host cell metabolism were examined by transcriptomic profiling using RNA sequencing.

Results

Our data demonstrate increased autophagy in cells upon raloxifene treatment, which contributed to prevention of bacterial invasion and proliferation. Transcriptomic profiling of host cells revealed changes in cholesterol-related pathways and consequent increases in oxidative stress-related genes and in autophagic induction through the TRIM and GABA pathways.

Conclusions

Our results demonstrate raloxifene’s potential as a broad-spectrum antibacterial agent through autophagic induction in host cells and prevention of intracellular invasion and proliferation of pathogenic bacteria.
Youth Temperament Moderates Associations Between Parental Involvement and Pediatric Type 1 Diabetes Treatment Outcome
Authors: Yeo Anna J , Halpern Leslie F , Lin Betty , Riddick Linda , Sima Daniela , Wohlfahrt Kristine M , Jones Nancy
Published: February 2022

Objective

Both youth self-regulation and quality of parental involvement have been associated with blood glucose levels (HbA1c) of youth with type 1 diabetes mellitus (T1DM). However, it is unclear whether and how youth and parental factors interact in their relation to youth HbA1c. The differential susceptibility hypothesis proposes that youth with high negative affectivity (NA) and low effortful control (EC) may be more susceptible to the deleterious impact of lower quality parenting behaviors but also reap greater benefit from higher quality parenting behaviors. This study investigated whether youth temperament would moderate the link between diabetes-specific parental assistance (e.g., checking blood sugar) or support (e.g., encouraging, praising) and HbA1c among youth with T1DM.

Methods

Primary caregivers of youth with T1DM (N = 101; M age = 12.02, SD = 2.43) completed surveys on diabetes-specific parental involvement and youth temperament. Medical information (i.e., HbA1c) was obtained from chart review.

Results

Multiple regression analyses indicated that youth NA and EC significantly interacted with parental assistance, but not support. Specifically, higher parental assistance was associated with higher HbA1c among youth with high NA or high EC. High assistance was only linked to lower HbA1c for youth with low NA.

Conclusions

Results suggest that optimal levels of parental involvement related to better T1DM outcomes depend on youth’s NA or EC. Consistent with the goodness-of-fit framework, when parenting approaches match youth’s temperament, youth with T1DM may be better able to maintain lower HbA1c. Family interventions for pediatric T1DM management may take into consideration youth temperament.
Incarcerated umbilical hernia in a 22-month-old child
Authors: Saifee Jessica , Shindorf Mackenzie , Samara Omar , Bourland Steven , Somme Stig
Published: February 2022

Incarceration of an umbilical hernia (UH) rarely occurs in the pediatric population. They usually resolve spontaneously or are treated after the child turns 4–5 years old [1, 2]. Risk factors for incarceration have been identified, but little is understood about how incarceration of an UH occurs.
Ecological biomechanics of marine macrophytes
Authors: Koehl Mimi A R
Published: February 2022

Macroalgae and seagrasses in coastal habitats are exposed to turbulent water currents and waves that deform them and can rip them off the substratum, but that also transport essential water-borne substances to them and disperse their propagules and wastes. Field studies of the physical environment, ecological interactions, and life history strategies of marine macrophytes reveal which aspects of their biomechanical performance are important to their success in different types of natural habitats and enable us to design ecologically relevant laboratory experiments to study biomechanical function. Morphology and tissue mechanical properties determine the hydrodynamic forces on macrophytes and their fate when exposed to those forces, but different mechanical designs can perform well in the same biophysical habitat. There is a trade-off between maximizing photosynthesis and minimizing breakage, and some macrophytes change their morphology in response to environmental cues. Water flow in marine habitats varies on a wide range of temporal and spatial scales, so diverse flow microhabitats can occur at the same site. Likewise, the size, shape, and tissue material properties of macrophytes change as they grow and age, so it is important to understand the different physical challenges met by macrophytes throughout their lives.
The DUVET Survey: Resolved maps of star formation-driven outflows in a compact, starbursting disc galaxy
Authors: Reichardt Chu Bronwyn , Fisher Deanne B , Nielsen Nikole M , Chisholm John , Girard Marianne , Kacprzak Glenn G , Bolatto Alberto , Herrera-Camus Rodrigo , Sandstrom Karin , Li Miao , Rickards Vaught Ryan , McPherson Daniel K
Published: February 2022

We study star formation-driven outflows in a z ∼ 0.02 starbursting disc galaxy, IRAS08339+6517, using spatially resolved measurements from the Keck Cosmic Web Imager (KCWI). We develop a new method incorporating a multistep process to determine whether an outflow should be fit in each spaxel, and then subsequently decompose the emission line into multiple components. We detect outflows ranging in velocity, vout, from 100 to 600 km s−1 across a range of star formation rate surface densities, ΣSFR, from ∼0.01 to 10 M⊙ yr−1 kpc−2 in resolution elements of a few hundred parsec. Outflows are detected in ∼100 per cent of all spaxels within the half-light radius, and ∼70 per cent within r90, suggestive of a high covering fraction for this starbursting disc galaxy. Around 2/3 of the total outflowing mass originates from the star forming ring, which corresponds to ${\lt}10{{\ \rm per\ cent}}$ of the total area of the galaxy. We find that the relationship between vout and the ΣSFR, as well as between the mass loading factor, η, and the ΣSFR, are consistent with trends expected from energy-driven feedback models. We study the resolution effects on this relationship and find stronger correlations above a re-binned size-scale of ∼500 pc. Conversely, we do not find statistically significant consistency with the prediction from momentum-driven winds.
The Cosmic Mach Number as an environment measure for the underlying dark matter density field
Authors: Meriot Romain , Khochfar Sadegh , Oñorbe Jose , Smith Britton
Published: February 2022

Using cosmological dark matter (DM) only simulations of a (1.6 Gpc/h)3 volume from the Legacy simulation project, we calculate Cosmic Mach Numbers (CMN) and perform a theoretical investigation of their relation with halo properties and features of the density field to gauge their use as an measure of the environment. CMNs calculated on individual spheres show correlations with both the overdensity in a region and the density gradient in the direction of the bulk flow around that region. To reduce the scatter around the median of these correlations, we introduce a new measure, the rank ordered Cosmic Mach number ($\hat{\mathcal {M}}_g$), which shows a tight correlations with the overdensity $\delta =\frac{\rho -\bar{\rho }}{\bar{\rho }}$. Measures of the large-scale density gradient as well as other average properties of the halo population in a region show tight correlations with $\hat{\mathcal {M}}_g$ as well. Our results in this first empirical study suggest that $\hat{\mathcal {M}}_g$ is an excellent proxy for the underlying density field and hence environment that can circumvent reliance on number density counts in a region. For scales between 10 and $100 \, \mathrm{Mpc}\, h^{-1}$, Mach numbers calculated using DM haloes (> 1012 M⊙) that would typically host massive galaxies are consistent with theoretical predictions of the linear matter power spectrum at a level of $10{{\ \rm per\, cent}}$ due to non-linear effects of gravity. At redshifts z ≥ 3, these deviations disappear. We also quantify errors due to missing large-scale modes in simulations. Simulations of box size ≤1 Gpc h−1 typically predict CMNs 10–30 per cent too small on scales of ∼100 Mpc h−1.
Dissociative recombination and rotational transitions of D+2 in collisions with slow electrons
Authors: Epée Epée M D , Motapon O , Pop N , Iacob F , Roueff E , Schneider I F , Mezei J Zs
Published: February 2022

Rate coefficients for dissociative recombination and state-to-state rotational transitions of the D$_{2}^{+}$ ion induced by collisions with very low-energy electrons have been reported following our previous studies on HD+ and H$_{2}^{+}$. The same molecular structure data sets, excitations ($N_{i}^{+} \rightarrow$$N_{f}^{+}=N_{i}^{+}+2$ for $N_{i}^{+}=0$ to 10) and de-excitations ($N_{i}^{+}\rightarrow N_{f}^{+}=N_{i}^{+}-2$, for $N_{i}^{+}=2$ to 10) were used for collision energies ranging from 0.01 meV to 0.3 eV. Isotopic effects for dissociative recombination and rotational transitions of the vibrationally relaxed targets are presented.
Nested spheroidal figures of equilibrium – II. Generalization to layers
Authors: Huré J-M
Published: February 2022

We present a vectorial formalism to determine the approximate solutions to the problem of a composite body made of ${\cal L}$ homogeneous, rigidly rotating layers bounded by spheroidal surfaces. The method is based on the first-order expansion of the gravitational potential over confocal parameters, thereby generalizing the method described in Paper I for ${\cal L}=2$. For a given relative geometry of the ellipses and a given set of mass-density jumps at the interfaces, the sequence of rotation rates and interface pressures is obtained analytically by recursion. A wide range of equilibria result when layers rotate in an asynchronous manner, although configurations with a negative oblateness gradient are more favourable. In contrast, states of global rotation (all layers move at the same rate), found by solving a linear system of ${\cal L}-1$ equations, are much more constrained. In this case, we mathematically demonstrate that confocal and coelliptical configurations are not permitted. Approximate formula for small ellipticities are derived. These results reinforce and prolongate known results and classical theorems restricted to small elliptiticities. Comparisons with the numerical solutions computed from the Self-Consistent-Field method are successful.
The Three Hundred project: dissecting the Fundamental Plane of galaxy clusters up to z = 1
Authors: Díaz-García Luis A , Umetsu Keiichi , Rasia Elena , Cui Weiguang , Meneghetti Massimo
Published: February 2022

We perform a systematic study of the recently discovered Fundamental Plane of galaxy clusters (CFP) using ∼250 simulated clusters from The Three Hundred project, focusing on the stability of the plane against different temperature definitions and its dependence on the dynamical relaxation state of clusters. The CFP is characterized by $T\propto M_\mathrm{s}^\alpha \, r_\mathrm{s}^\beta$, defined with the gas temperature (T) and the characteristic halo scale radius and mass (rs and Ms) assuming a Navarro–Frenk–White halo description. We explore two definitions of weighted temperatures, namely mass-weighted and spectroscopic-like temperatures, in three radial ranges. The Three Hundred project clusters at z = 0 lie on a thin plane whose parameters (α, β) and dispersion (0.015–0.030 dex) depend on the gas temperature definition. The CFP for mass-weighted temperatures is closer to the virial equilibrium expectation (α = 1, β = −1) with a smaller dispersion. For gas temperatures measured within $500\ h^{-1}$ kpc, the resulting CFP deviates the most from the virial expectation and shifts towards the similarity solution for a secondary infall model (α = 1.5, β = −2). Independently of the temperature definition, we find that clusters at z = 1 and relaxed clusters form a CFP similar to the virial expectation, unlike disturbed clusters exhibiting stronger evolution. Only systems formed over the last 4 Gyr present a CFP that is closer to the similarity solution. All these findings are compatible with the CFP obtained for a Cluster Lensing And Supernova survey with Hubble subsample excluding the hottest clusters with TX > 12 keV.
MeqSilhouette v2: spectrally resolved polarimetric synthetic data generation for the event horizon telescope
Authors: Natarajan Iniyan , Deane Roger , Martí-Vidal Iván , Roelofs Freek , Janssen Michael , Wielgus Maciek , Blackburn Lindy , Blecher Tariq , Perkins Simon , Smirnov Oleg , Davelaar Jordy , Moscibrodzka Monika , Chael Andrew , Bouman Katherine L , Kim Jae-Young , Bernardi Gianni , van Bemmel Ilse , Falcke Heino , Özel Feryal , Psaltis Dimitrios
Published: February 2022

We present MeqSilhouette v2.0 (MeqSv2), a fully polarimetric, time-and frequency-resolved synthetic data generation software for simulating millimetre (mm) wavelength very long baseline interferometry (VLBI) observations with heterogeneous arrays. Synthetic data are a critical component in understanding real observations, testing calibration and imaging algorithms, and predicting performance metrics of existing or proposed sites. MeqSv2 applies physics-based instrumental and atmospheric signal corruptions constrained by empirically derived site and station parameters to the data. The new version is capable of applying instrumental polarization effects and various other spectrally resolved effects using the Radio Interferometry Measurement Equation (RIME) formalism and produces synthetic data compatible with calibration pipelines designed to process real data. We demonstrate the various corruption capabilities of MeqSv2 using different arrays, with a focus on the effect of complex bandpass gains on closure quantities for the EHT at 230 GHz. We validate the frequency-dependent polarization leakage implementation by performing polarization self-calibration of synthetic EHT data using PolSolve. We also note the potential applications for cm-wavelength VLBI array analysis and design and future directions.
Division site determination during asymmetric cell division in plants
Authors: Yi Peishan , Goshima Gohta
Published: February 2022

During development, both animals and plants exploit asymmetric cell division (ACD) to increase tissue complexity, a process that usually generates cells dissimilar in size, morphology, and fate. Plants lack the key regulators that control ACD in animals. Instead, plants have evolved two unique cytoskeletal structures to tackle this problem: the preprophase band (PPB) and phragmoplast. The assembly of the PPB and phragmoplast and their contributions to division plane orientation have been extensively studied. However, how the division plane is positioned off the cell center during asymmetric division is poorly understood. Over the past 20 years, emerging evidence points to a critical role for polarly localized membrane proteins in this process. Although many of these proteins are species- or cell type specific, and the molecular mechanism underlying division asymmetry is not fully understood, common features such as morphological changes in cells, cytoskeletal dynamics, and nuclear positioning have been observed. In this review, we provide updates on polarity establishment and nuclear positioning during ACD in plants. Together with previous findings about symmetrically dividing cells and the emerging roles of developmental cues, we aim to offer evolutionary insight into a common framework for asymmetric division-site determination and highlight directions for future work.
Higher Neck Pain Intensity and the Presence of Psychosocial Factors Are More Likely When Headache is Present after a Whiplash Injury: A Case-Control Study
Authors: Anarte-Lazo Ernesto , Bernal-Utrera Carlos , Montaño-Ocaña Juan , Falla Deborah , Rodriguez-Blanco Cleofas
Published: February 2022

Background

Several factors such as neck pain intensity, disability, anxiety, depression, female sex, or a previous history of headache are associated with post-whiplash headache. However, the possible role of psychosocial factors contributing to the presence of headache or worsening of headache after a whiplash trauma remains unclear. To address this gap in knowledge, there is the need to assess psychosocial factors concerning headache shortly after a whiplash injury.

Objective

To evaluate psychological features, pain and disability in people with acute whiplash associated disorders (WAD) and compare these features between those with and without headache.

Design

Case-control study.

Setting

A secondary care traumatology center.

Methods

Forty-seven people with acute WAD were recruited; 28 with headache, and 19 without. All participants completed self-reported questionnaires including Visual Analogue Scale (VAS) for neck pain intensity, the Neck Disability Index (NDI), Pain Catastrophizing Scale (PCS), Tampa Scale Kinesiophobia-11 (TSK-11), and State-Trait Anxiety Inventory.

Results

Neck pain intensity (P < .001), neck disability (P < 0.001), pain catastrophizing (P < .001), kinesiophobia (P < .001), and anxiety state (P = .007) and trait (P = .05) were higher in those with headache when compared to those without. In addition, high levels of neck pain (P = .025), moderate levels of neck disability (P < .001), moderate levels of pain catastrophizing (P = .015), and moderate (P = .002) and severe (P = .016) levels of kinesiophobia were related to the presence of headache.

Conclusions

The level of neck pain intensity and disability, kinesiophobia, catastrophizing, and anxiety were all greater in people with acute WAD who presented with a headache compared to those without headache.
The Quality and Efficiency of Public and Private Firms: Evidence from Ambulance Services
Authors: Knutsson Daniel , Tyrefors Björn
Published: February 2022

Economic theory predicts that outsourcing public services to private firms reduces costs, but the effect on quality is ambiguous. We explore quality differences between publicly and privately owned ambulances in Stockholm County, Sweden, a setting where patients are as good as randomly assigned to ambulances with different ownership status. We find that private ambulances reduce costs and perform better on contracted measures such as response time, but perform worse on noncontracted measures such as mortality. In fact, a patient has a 1.4% higher risk of death within three years if a private ambulance is dispatched (in aggregate, 420 more deaths each year). We also present evidence of the mechanism at work, suggesting that private firms cut costs at the expense of ambulance staff quality.
Modeling Pulsed Evolution and Time-Independent Variation Improves the Confidence Level of Ancestral and Hidden State Predictions
Authors: Gao Yingnan , Wu Martin
Published: February 2022

Ancestral state reconstruction is not only a fundamental tool for studying trait evolution, but also very useful for predicting the unknown trait values (hidden states) of extant species. A well-known problem in ancestral and hidden state predictions is that the uncertainty associated with predictions can be so large that predictions themselves are of little use. Therefore, for meaningful interpretation of predicted traits and hypothesis testing, it is prudent to accurately assess the uncertainty of the predictions. Commonly used constant-rate Brownian motion (BM) model fails to capture the complexity of tempo and mode of trait evolution in nature, making predictions under the BM model vulnerable to lack-of-fit errors from model misspecification. Using empirical data (mammalian body size and bacterial genome size), we show that the distribution of residual Z-scores under the BM model is neither homoscedastic nor normal as expected. Consequently, the 95% confidence intervals of predicted traits are so unreliable that the actual coverage probability ranges from 33% (strongly permissive) to 100% (strongly conservative). Alternative methods such as BayesTraits and StableTraits that allow variable rates in evolution improve the predictions but are computationally expensive. Here, we develop Reconstructing Ancestral State under Pulsed Evolution in R by Gaussian Decomposition (RasperGade), a method of ancestral and hidden state prediction that uses the Levy process to explicitly model gradual evolution, pulsed evolution, and time-independent variation. Using the same empirical data, we show that RasperGade outperforms both BayesTraits and StableTraits in providing reliable confidence estimates and is orders-of-magnitude faster. Our results suggest that, when predicting the ancestral and hidden states of continuous traits, the rate variation should always be assessed and the quality of confidence estimates should always be examined. [Bacterial genomic traits; model misspecification; trait evolution.]
Occurrence of Wheat Curl Mite and Mite-Vectored Viruses of Wheat in Colorado and Insights into the Wheat Virome
Authors: Albrecht Tessa , White Samantha , Layton Marylee , Stenglein Mark , Haley Scott , Nachappa Punya
Published: February 2022

The wheat curl mite (WCM) is a vector of three important wheat viruses in the U.S. Great Plains: wheat streak mosaic virus (WSMV), triticum mosaic virus (TriMV), and High Plains wheat mosaic virus (HPWMoV). This study was conducted to determine the current profile of WCM and WCM-transmitted viruses of wheat and their occurrence in Colorado, including novel wheat viruses via virome analysis. There was a high rate of virus incidence in symptomatic wheat samples collected in 2019 (95%) and 2020 (77%). Single infection of WSMV was most common in both years, followed by coinfection with WSMV + TriMV and WSMV + HPWMoV. Both type 1 and type 2 mite genotypes were found in Colorado. There was high genetic diversity of WSMV and HPWMoV isolates, whereas TriMV isolates showed minimal sequence variation. Analysis of WSMV isolates revealed novel virus variants, including one isolate from a variety trial, where severe disease symptoms were observed on wheat varieties carrying Wsm2, a known virus resistance locus. Virome analysis identified two to four sequence variants of all eight RNA segments of HPWMoV, which suggests co-occurrence of multiple genotypes within host populations and presence of a variant of HPWMoV. A possible novel virus in the family Tombusviridae and several mycoviruses were identified. Overall, the data presented here highlight the need to define the effect of novel WCM-transmitted virus variants on disease severity and the role of novel viruses.
Taxonomic Refinement of Xanthomonas arboricola
Authors: Zarei Sadegh , Taghavi S. Mohsen , Rahimi Touraj , Mafakheri Hamzeh , Potnis Neha , Koebnik Ralf , Fischer-Le Saux Marion , Pothier Joël F. , Palacio Bielsa Ana , Cubero Jaime , Portier Perrine , Jacques Marie-Agnes , Osdaghi Ebrahim
Published: February 2022

Xanthomonas arboricola comprises a number of economically important fruit tree pathogens classified within different pathovars. Dozens of nonpathogenic and taxonomically unvalidated strains are also designated as X. arboricola, leading to a complicated taxonomic status in the species. In this study, we have evaluated the whole-genome resources of all available Xanthomonas spp. strains designated as X. arboricola in the public databases to refine the members of the species based on DNA similarity indexes and core genome-based phylogeny. Our results show that, of the nine validly described pathovars within X. arboricola, pathotype strains of seven pathovars are taxonomically genuine, belonging to the core clade of the species regardless of their pathogenicity on the host of isolation (thus the validity of pathovar status). However, strains of X. arboricola pv. guizotiae and X. arboricola pv. populi do not belong to X. arboricola because of the low DNA similarities between the type strain of the species and the pathotype strains of these two pathovars. Thus, we propose to elevate the two pathovars to the rank of a species as X. guizotiae sp. nov. with the type strain CFBP 7408T and X. populina sp. nov. with the type strain CFBP 3123T. In addition, other mislabeled strains of X. arboricola were scattered within Xanthomonas spp. that belong to previously described species or represent novel species that await formal description.
Evidence-Based Prevention and Management of Pressure Injuries in Home Care: A Scoping Review
Authors: Karadağ Ayişe , Çakar Vildan
Published: February 2022

OBJECTIVE

To determine the presence of evidence-based practice protocols for the prevention and management of pressure injuries (PIs) in home care settings, whether the contents of existing protocols were based on current evidence, and adherence to these protocols.

DATA SOURCES

Comprehensive and structured literature searches were conducted using PubMed, Cochrane Library, CINAHL (Cumulative Index to Nursing and Allied Health Literature), PsycINFO, Ovid, Scopus, Web of Science, and Joanna Briggs Institute Evidence-Based Practice Database.

STUDY SELECTION

A literature search retrieved 2,929 articles. Investigators evaluated the titles, abstracts, and full texts of the articles retrieved from the literature search in accordance with the review questions and eligibility criteria. The authors included four studies in this scoping review.

DATA EXTRACTION

The researchers extracted details of the full-text articles, including author(s)/year of publication/country, aim(s), study population and sample size, study design, intervention type, outcomes, and key findings.

DATA SYNTHESIS

The four articles included in this scoping review are descriptive cross-sectional studies published between 2005 and 2010. Although the articles provided significant data on the quality of practices for the prevention and management of PIs in home care, no studies reported on the achievement of objective results.

CONCLUSIONS

The use of protocols for the prevention and management of PIs, including evidence-based interventions in home care, and adherence to existing protocols were low. Comprehensive observational and randomized controlled studies are necessary to improve evidence-based prevention and management of PIs in home care settings.
Using Augmented Reality for Intraoperative Guidance During Sacral Neuromodulation System Implantation
Authors: Freidin Dor , Zilka Nadav , Horesh Nir , Saukhat Olga , Ram Edward , Tejman-Yarden Shai
Published: February 2022

Objective:

The purpose of this study was to examine the feasibility of using augmented reality during lead placement for sacral nerve stimulation (SNS).

Methods:

The study was a prospective case series performed in a single tertiary center. Patients with fecal incontinence or urinary retention eligible for SNS according to the American society of colon and rectal surgeon’s guidelines were included. Each patient underwent a computerized tomography scan of the sacrum and pelvic floor before surgery; and a segmentation of the sacral bone, the skin, and three fiducial markers on the lower back was produced. Surgical planning included the design of an ideal virtual transmission tract leading to the S3 foramen using the most suitable location and needle trajectory for introducing the lead. During the surgical intervention, a needle was inserted into the S3 foramen using the aligned tract as visualized using the Microsoft HoloLens first generation head mounted unit.

Results:

Overall, 11 patients were included. Mean operative time was 43.8 minutes (range 25–81 minutes). All patients reported a significant reduction from the preoperative level of the mean postoperative Cleveland Clinic Incontinence Score (CCIS) assessed 2 weeks after the temporary SNS implant (CCIS preoperative 13.3, postoperative 8.5; CI –7.35 to –2.25; P < 0.01). The surgeons reported the imaging useful, allowing accurate and easier approach.

Conclusions:

Intraoperative augmented reality imaging for needle application during SNS appears to be feasible, practical, and may be useful in additional procedures.
Three-Dimensional Morphology and Configuration Analyses of the Craniovertebral Junction in Children with Hemifacial Microsomia
Authors: Xu Xi , Chen Xin , Zhao Shan-ba-ga , Jin Jing-Lu , Tang Xiao-Jun , Yin Lin , Liu Wei , Li Chuan , Feng Shi , Zhang Zhi-Yong
Published: February 2022

Study Design.

Observational and morphological study with three-dimensional (3D) computed tomography (CT) analysis.

Objective.

To discover the morphology and configuration deformities of craniovertebral junction (CVJ) and upper cervical spine in children with unilateral hemifacial microsomia (HFM). To determine whether there are specific HFM patients who are at higher risk of certain cervical vertebral anomaly.

Summary of Background Data.

The evaluation for cervical vertebrae anomaly in HFM children, especially in CVJ region, is underreported.

Methods.

Eighty-eight unilateral HFM children (64 males, 24 females) with four Pruzansky-Kaban types (I, Ila, Ilb, and III) underwent cranial and cervical CT scanning from skull to C5 in neutral position. The 3D morphology and configuration of the occipital condyle, atlas, and axis, etc. were evaluated on the presence of deformed detailed structures of CVJ region.

Results.

No C1 deformation was found in type I group. Six (14.3%) type Ila cases, seven (33.3%) type IIb cases, and six (37.5%) type Ill cases had lateral masses asymmetry of C1 (P 
< 0.05). Five (55.6%) type I cases, 17 (40.5%) type Ila cases, 12 (57.1%) type Ilb cases, and 10 (62.5%) type Ill cases had C2 anomaly (P > 0.05). The incidence rate of C1–C2 instability for four groups were 33.3% (type I), 33.3% (type IIa), 33.3% (type IIb), and 31.3% (type Ill), respectively (P > 0.05).

Conclusion.

For HFM children, the incidence of C1 deformation increased from type I to type Ill. The probability of C2 anomaly and C1–C2 instability in children with different types of HFM is nearly the same. The craniovertebral junction of every HFM child must be monitored carefully for C1–C2 instability before any surgical procedure to avoid atlantoaxial dislocation and spinal cord injury.

Level of Evidence: N/A
Comprehensive profiling of Lingzhihuang capsule by liquid chromatography coupled with mass spectrometry-based molecular networking and target prediction
Authors: Huang Mengliang , Yu Sijia , Shao Qing , Liu Hao , Wang Yingchao , Chen Hongzhang , Huang Yansheng , Wang Yi
Published: February 2022

Objective:

Lingzhihuang capsule (LZHC) is a natural product that consists of 10 commonly used medicinal plants, and it is used in traditional Chinese medicine to promote people's overall health. Previously, LZHC was successfully used as adjuvant therapy for treating patients with cancer. However, the chemical constituents of LZHC and their potential biological functions remain unclear. The aim of this study is to investigate the major bioactive compounds in LZHC and predict their pharmacological targets.

Methods:

The LZHC constituents were putatively identified by ultra-high performance liquid chromatography coupled with time-of-flight mass spectrometry combined with mass spectrometry-based molecular networking. The targets were predicted using SwissTargetPrediction software, and the associated gene ontology and Kyoto encyclopedia of genes and genomes pathways were analyzed using the Database for Annotation, Visualization, and Integrated Discovery. The mass spectrometry-based molecular network and compound-target-pathway network were constructed using Cytoscape 3.8.0 software.

Results:

We putatively identified 94 compounds of LZHC by mass spectrometry-based molecular networking, including triterpene (the main structural type) and other clusters (ie, flavonoids and organic acids). Our results suggested that multiple pivotal targets were regulated by LZHC, including tumor necrosis factor, nitric oxide synthase 2, glucocorticoid receptor, estrogen receptor, 3-oxo-5-alpha-steroid 4-dehydrogenase 2, prostaglandin e2 receptor ep4 subtype, estrogen receptor beta, phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform, mitogen-activated protein kinase 3, and rac-alpha serine, which are related to signal transduction, positive regulation of transcription from RNA polymerase II promoters, oxidation-reduction processes, inflammatory responses, and other biological processes. Functional annotation of those targets suggested that several signaling pathways may be regulated by LZHC, such as cancer-related proteoglycans, the PI3K-Akt-signaling pathway, and the cAMP-signaling pathway.

Conclusions:

Our findings reveal the chemical constituents of LZHC and provided scientific support for the efficacy of LZHC in terms of immune regulation, anti-aging, and tumor suppression.
Relationship Between COVID-19 Lockdown and Epidemiology of Neonatal Sepsis
Authors: Dutta Sourabh , Kumar Praveen , Paulpandian Rajarajan , Sajan Saini Shiv , Sreenivasan Priya , Mukhopadhyay Kanya , Sundaram Venkataseshan , Kumar Jogender , Ray Pallab
Published: February 2022

Background:

We compared the hospital-based epidemiology of neonatal sepsis after the coronavirus disease 2019 lockdown (LD) versus historical epochs and the LD period versus phases of unlocking.

Methods:

This retrospective cohort study was conducted in a level 3 neonatal unit. We compared neonates born in three 24-week periods—GroupLD: 22 March 2020 to 5 September 2020—the reference group, Grouppre-LD: 29 September 2019 to 14 March 2020 and Group temporally corresponding to LD in 2019 (corres-LD): 24 March 2019 to 7 September 2019. We also studied linear trends from LD phase 1.0 until Unlock 4.0. The key outcome was culture-positive sepsis.

Results:

There were 1622, 2744 and 2700 subjects in groupsLD,pre-LDandcorres-LD, respectively. The incidence of any culture-positive sepsis inpre-LDwas higher thanLD[odds ratio (95% CI) = 1.61 (1.02–2.56)]. This was mainly due to a statistically significant reduction inAcinetobacter baumanniisepsis, with incidence rate differences ofpre-LDversusLD[0.67 (95% CI: 0.37–0.97),P= 0.0001] andcorres-LDversusLD[0.40 (95% CI: 0.16–0.64),P= 0.0024]. Groupspre-LDandcorres-LDhad higher proportion of multi-drug resistant (MDR)/extreme drug resistance/pan drug resistance sepsis thanLD[77%, 77% and 44%, respectively (Pvalues of both groups vs.LD= 0.01)]. From LD 1.0 to unlock 4.0, there were fewer episodes of MDR sepsis (Plinear trends= 0.047). On multivariable analysis, grouppre-LD(vs. reference groupLD), male sex, birth weight and Apgar score independently predicted culture-positive sepsis.

Conclusions:

LD favorably impacted the epidemiology of neonatal sepsis in a hospital setting, with lessA. baumanniiand MDR sepsis, which persisted during unlocking.
A Qualitative Study on the Social Determinants of HIV Treatment Engagement Among Black Older Women Living With HIV in the Southeastern United States
Authors: Ojukwu Emmanuela , Cianelli Rosina , Villegas Rodriguez Natalia , De Oliveira Giovanna , Kalu Vivian
Published: February 2022

Black older women living with HIV (BOWLH) in the United States are disproportionately affected by HIV infection and poor treatment engagement rates, often caused by multiple social determinants of health. In this descriptive qualitative study, we interviewed 17 BOWLH to investigate the facilitators and barriers to HIV treatment engagement. Data were analyzed using the socioecological framework. Findings demonstrate the positive influences of supportive social networks, perceived benefits, HIV-related knowledge, raising HIV awareness in communities, and impact of HIV state laws. The highlighted barriers were mainly low income, substance use, HIV-related stigma, influence of stereotypes and assumptions about older women living with HIV, and health insurance. Religion, managing comorbidities, attitude toward, HIV disclosure, and caregiving roles had both positive and negative influences on engagement. These findings illuminate factors of HIV treatment engagement that might be culturally founded; disseminating these factors to health care professionals is a critical intervention to support this population.
Larger Volume and Higher Fat Content of the Pancreatic Head Are Predictive Factors for Postendoscopic Retrograde Cholangiopancreatography Pancreatitis
Authors: Shintani Shuhei , Inatomi Osamu , Bamba Shigeki , Takeda Yoshiya , Fujimoto Takehide , Ota Shinichi , Tsuji Yoshihisa , Kutsumi Hiromu , Watanabe Yoshiyuki , Andoh Akira
Published: February 2022

Objectives

Acute pancreatitis is the most critical complication of endoscopic retrograde cholangiopancreatography (ERCP). In this study, we investigated the association between the volume/fat content of the pancreatic head and the incidence of post-ERCP pancreatitis (PEP).

Methods

We retrospectively enrolled 157 patients who underwent ERCP. The volume and fat content of the pancreas were calculated by multislice computed tomographic imaging by using a volume analyzer. Multivariate analysis was performed to identify risk factors for PEP.

Results

The mean volumes of the whole pancreas and pancreatic head were significantly larger, and the fat content of the pancreatic head was significantly higher in the PEP group (P < 0.01). There were no significant differences in the mean volume and fat content of the pancreatic body and tail in the PEP group. Multivariate analysis revealed that the pancreatic guidewire placement (odds ratio [OR], 12.4; P < 0.01), pancreatic head volume (OR, 5.3; P < 0.01), and the pancreatic head fat content (OR, 4.8; P < 0.01) were independent risk factors for PEP.

Conclusions

The pancreatic head volume and fat content were independent predicting factors of PEP. Quantitative assessment of the pancreas may contribute to the prediction of PEP onset.