bluuebunny/crossref_metadata_2025 huggingface dataset:
Spherical winding and helicity
Authors: Xiao Daining , Prior Christopher B , Yeates Anthony R
Published: April 2023

In ideal magnetohydrodynamics, magnetic helicity is a conserved dynamical quantity and a topological invariant closely related to Gauss linking numbers. However, for open magnetic fields with non-zero boundary components, the latter geometrical interpretation is complicated by the fact that helicity varies with non-unique choices of a field’s vector potential or gauge. Evaluated in a particular gauge called the winding gauge, open-field helicity in Cartesian slab domains has been shown to be the average flux-weighted pairwise winding numbers of field lines, a measure constructed solely from field configurations that manifest its topological origin. In this paper, we derive the spherical analogue of the winding gauge and the corresponding winding interpretation of helicity, in which we formally define the concept of spherical winding of curves. Using a series of examples, we demonstrate novel properties of spherical winding and the validity of spherical winding helicity. We further argue for the canonical status of the winding gauge choice among all vector potentials for magnetic helicity by exhibiting equivalences between local coordinate changes and gauge transformations.
Achromatic polymer-dispersed liquid crystal lens with diffractive–refractive hybrid structure
Authors: Liang Binming , An Jing , Su Xin
Published: April 2023

The focal length of liquid crystal Fresnel lens is electrically controllable, but the disadvantage is the chromatic aberration is obvious. In this paper, the electrically controlled zoom characteristics of liquid crystal lens and the basic theory of Fresnel lens achromatic are analyzed, and a diffractive–refractive hybrid lens model made of polymer-dispersed liquid-crystal (PDLC) material is proposed. Fresnel liquid crystal lenses and PDLC hybrid lenses are tested with light at R (700.0 nm), G (546.1 nm) and B (435.8 nm) wavelengths, respectively. The simulation results show that the hybrid lens provides a greater range of adjustment of the focus position. After voltage modulation, the measured light with three different wavelengths have the same focal length, which means that the axial chromatic aberration is eliminated. In addition, with the elimination of axial chromatic aberration, the zoom range of the hybrid lens is doubled by further accurately controlling the electrode, which breaks through the limitation that the traditional liquid crystal lens can only work in monochromatic light spectrum.
Thermal/kinetic study of the formation mechanism of NbC-Fe composite layer on the surface of GCr15 prepared by hot pressure diffusion
Authors: Zhao Nana , Yao Teli , Wang Zihan , Shan Rui , Ren Congcong , Liu Heguang , Li Shujuan , Xu Yunhua , Cui Zhen
Published: April 2023

In this study, an NbC-Fe composite layer is in situ prepared on the surface of GCr15 bearing steel. The formation mechanism of the composite layer was investigated in terms of thermodynamics, dynamics, and crystal structure transformation processes during the in situ reaction. According to computational thermodynamics, the reaction at 1150 °C–1200 °C allows NbC, Fe3C, Cr3C2, Cr7C3, and Cr23C6 phases to spontaneously react and stabilize in the Fe-C-Nb-CR system. The functional relationship between the growth thickness, time, and temperature of the NbC-Fe composite layer was obtained experimentally and via computational dynamics. Particularly, the growth activation energy, Q, of the NbC-Fe composite layer was calculated to be 367.06 kJ mol−1. The combination of computational thermodynamic/kinetic research and experimental observation of crystal transformation data revealed that the formation mechanism of NbC in the NbC-Fe layer on the surface of GCr15 caused the C atoms in the bearing steel diffuse into the Nb plate and occupy the octahedral gap of the Nb unit cell to form NbC. In the formation mechanism of the NbC-Fe composite layer, C and Fe atoms partially migrated from the pearlite and diffused towards the direction of the Nb plate to form the NbC-Fe composite layer.
Phthonosand Misfortune
Authors: Eidinow Esther
Published: April 2023

In ancient Greek society, episodes of good fortune prompted expectations and obligations that fostered social networks of reciprocity. This chapter of the book argues that phthonos was an emotion that expressed a spectrum of negative responses to that system of reciprocity between mortals. Moreover, it suggests that this model can help to explain the phenomenon of divine phthonos, and explores in what ways this is different from its mortal counterpart. Finally, it examines the links between phthonos and occult aggression, using case studies from later periods that offer some first-person insights into these experiences.
Dependence and Vulnerability
Authors: Eidinow Esther
Published: April 2023

This chapter examines the likely position of female dependents in Athenian society in the aftermath of war. It presents the evidence for the status of and support provided for widows, orphans and girl children, and unmarried women, and considers possible sources of livelihood. Some might follow the armies, perhaps involved in food preparation, although it was more likely that many went along as personal attendants, entertainers, and sexual partners; others traded in the markets, took part in various crafts, or worked in the fields at agricultural tasks. Grave epigraphs show other professions were possible. Prostitution was also a possibility—and could be lucrative, but dangerous. Finally, some women sold ritual practices as a way of making a living.
epitope1D: accurate taxonomy-aware B-cell linear epitope prediction
Authors: da Silva Bruna Moreira , Ascher David B , Pires Douglas E V
Published: April 2023

The ability to identify B-cell epitopes is an essential step in vaccine design, immunodiagnostic tests and antibody production. Several computational approaches have been proposed to identify, from an antigen protein or peptide sequence, which residues are more likely to be part of an epitope, but have limited performance on relatively homogeneous data sets and lack interpretability, limiting biological insights that could otherwise be obtained. To address these limitations, we have developed epitope1D, an explainable machine learning method capable of accurately identifying linear B-cell epitopes, leveraging two new descriptors: a graph-based signature representation of protein sequences, based on our well-established Cutoff Scanning Matrix algorithm and Organism Ontology information. Our model achieved Areas Under the ROC curve of up to 0.935 on cross-validation and blind tests, demonstrating robust performance. A comprehensive comparison to alternative methods using distinct benchmark data sets was also employed, with our model outperforming state-of-the-art tools. epitope1D represents not only a significant advance in predictive performance, but also allows biologically meaningful features to be combined and used for model interpretation. epitope1D has been made available as a user-friendly web server interface and application programming interface at https://biosig.lab.uq.edu.au/epitope1d/.
Accurate and interpretable gene expression imputation on scRNA-seq data using IGSimpute
Authors: Xu Ke , Cheong ChinWang , Veldsman Werner P , Lyu Aiping , Cheung William K , Zhang Lu
Published: April 2023

Single-cell ribonucleic acid sequencing (scRNA-seq) enables the quantification of gene expression at the transcriptomic level with single-cell resolution, enhancing our understanding of cellular heterogeneity. However, the excessive missing values present in scRNA-seq data hinder downstream analysis. While numerous imputation methods have been proposed to recover scRNA-seq data, high imputation performance often comes with low or no interpretability. Here, we present IGSimpute, an accurate and interpretable imputation method for recovering missing values in scRNA-seq data with an interpretable instance-wise gene selection layer (GSL). IGSimpute outperforms 12 other state-of-the-art imputation methods on 13 out of 17 datasets from different scRNA-seq technologies with the lowest mean squared error as the chosen benchmark metric. We demonstrate that IGSimpute can give unbiased estimates of the missing values compared to other methods, regardless of whether the average gene expression values are small or large. Clustering results of imputed profiles show that IGSimpute offers statistically significant improvement over other imputation methods. By taking the heart-and-aorta and the limb muscle tissues as examples, we show that IGSimpute can also denoise gene expression profiles by removing outlier entries with unexpectedly high expression values via the instance-wise GSL. We also show that genes selected by the instance-wise GSL could indicate the age of B cells from bladder fat tissue of the Tabula Muris Senis atlas. IGSimpute can impute one million cells using 64 min, and thus applicable to large datasets.
Sars-escape network for escape prediction of SARS-COV-2
Authors: Singh Bist Prem , Tayara Hilal , To Chong Kil
Published: April 2023

Motivation

Viruses have coevolved with their hosts for over millions of years and learned to escape the host’s immune system. Although not all genetic changes in viruses are deleterious, some significant mutations lead to the escape of neutralizing antibodies and weaken the immune system, which increases infectivity and transmissibility, thereby impeding the development of antiviral drugs or vaccines. Accurate and reliable identification of viral escape mutational sequences could be a good indicator for therapeutic design. We developed a computational model that recognizes significant mutational sequences based on escape feature identification using natural language processing along with prior knowledge of experimentally validated escape mutants.

Results

Our machine learning-based computational approach can recognize the significant spike protein sequences of severe acute respiratory syndrome coronavirus 2 using sequence data alone. This modelling approach can be applied to other viruses, such as influenza, monkeypox and HIV using knowledge of escape mutants and relevant protein sequence datasets.

Availability

Complete source code and pre-trained models for escape prediction of severe acute respiratory syndrome coronavirus 2 protein sequences are available on Github at https://github.com/PremSinghBist/Sars-CoV-2-Escape-Model.git. The dataset is deposited to Zenodo at: doi: 10.5281/zenodo.7142638. The Python scripts are easy to run and customize as needed.

Contact

premsing212@jbnu.ac.kr
Non-human primate models for understanding the impact of the microbiome on pregnancy and the female reproductive tract
Authors: Hugon Anna Marie , Golos Thaddeus G
Published: April 2023

The microbiome has been shown, or implicated to be involved, in multiple facets of human health and disease, including not only gastrointestinal health but also metabolism, immunity, and neurology. Although the predominant focus of microbiome research has been on the gut, other microbial communities such as the vaginal or cervical microbiome are likely involved in physiological homeostasis. Emerging studies also aim to understand the role of different microbial niches, such as the endometrial or placental microbial communities, on the physiology and pathophysiology of reproduction, including their impact on reproductive success and the etiology of adverse pregnancy outcomes (APOs). The study of the microbiome during pregnancy, specifically how changes in maternal microbial communities can lead to dysfunction and disease, can advance the understanding of reproductive health and the etiology of APOs. In this review, we will discuss the current state of non-human primate (NHP) reproductive microbiome research, highlight the progress with NHP models of reproduction, and the diagnostic potential of microbial alterations in a clinical setting to promote pregnancy health. NHP reproductive biology studies have the potential to expand the knowledge and understanding of female reproductive tract microbial communities and host–microbe or microbe–microbe interactions associated with reproductive health through sequencing and analysis. Furthermore, in this review, we aim to demonstrate that macaques are uniquely suited as high-fidelity models of human female reproductive pathology.
SIAH1/CTR9 axis promotes the epithelial–mesenchymal transition of hepatocellular carcinoma
Authors: Liu Zhiyi , Luo Pengchao , Cao Kuan , Hu Qinghe , Hu Bin , Cui Licheng , Wang Xiaotian , Shi Hengliang , Zhang Bin , Wang Renhao
Published: April 2023

SIAH1 has been reported to participate in several human cancers, including hepatocellular carcinoma (HCC). However, the effect of SIAH1 on the epithelial–mesenchymal transition (EMT) has not been reported in HCC cells. Here, we discovered the inhibitory effect of SIAH1 on HCC cell migration and invasion, which was related with regulating EMT. Molecularly, a yeast two-hybrid experiment indicated that Cln Three Requiring 9 (CTR9) was a potential interacting protein of SIAH1, which was further verified by co-immunoprecipitation assays. Furthermore, SIAH1 inhibited the EMT of HCC cells through negatively regulating CTR9. Importantly, CTR9 was ubiquitinated and degraded by SIAH1 via the proteasome pathway in HCC cells. Additionally, it was showed that SIAH1 mainly mediated the K48-linked polyubiquitination on CTR9. Finally, the protein level of CTR9 was found to be inversely correlated with SIAH1 in human HCC tissues. Summed up all together, these findings reveal that SIAH1/CTR9 axis promotes the EMT of HCC cells and is a promising therapeutic target for HCC therapy.
The most hated tree in America: negative difference, the White imaginary, and the Bradford pear
Authors: Neville-Shepard Ryan , Kelly Casey Ryan
Published: April 2023

Against claims that we now live in a post-racial era, this article argues that panic over so-called “invasive species” illustrates how negative conceptions of difference are built into the White imaginary. We argue that the calls to exterminate the infamous Bradford pear tree across the US function as a kind of nanoracism, or what Achilles Mbembe defines as the organization of everyday affairs according to us–them logics that further justify overt racist practices. Performing a close reading of the discourse about the tree, we show how xenophobia and anti-Blackness lurk in a debate about non-human biota, specifically by normalizing inferential racist language that attacks difference, expressing fears of racial impurity, and calling for exterminating the Other.
(Hash)tagging intersection(ality): Black and Palestinian experiences on Twitter
Authors: Edwards Emily Lynell , Stephens David F
Published: April 2023

In this article, we examine how Twitter users discuss intersections of the Black American and Palestinian experience in 2021 through the lens of intersectionality. We explore two questions; how is intersectionality discussed and performed by Twitter users in relation to the Palestinian and Black experience against the backdrop of this particular crisis in Gaza? And how do users engage with the language of intersectionality to either reify, contradict, or complicate the intersection of the Palestinian and Black experiences on the platform? We find that intersectionality is mediated by elite users via branded communication, as well as invoked to highlight or deny the intersections of the Black and Palestinian experience by the most peripheral users on the platform.
Estimation of glomerular filtration rate in cardiorenal patients: a step forward
Authors: Quiroga Borja , Díez Javier
Published: April 2023

The progressive reduction in estimated glomerular filtration rate (eGFR) resulting in chronic kidney disease (CKD) is associated with increased risk of cardiovascular disease (CVD) (i.e., cardiorenal disease). Cardiorenal disease is associated with poor outcomes, mainly due to increased cardiovascular (CV) complications and CV death. Data from general population–based studies and studies of cohorts with CKD and/or CVD show that compared with creatinine-based eGFR, cystatin C–based eGFR and creatinine plus cystatin C–based eGFR detect higher risks of adverse CV outcomes and add predictive discrimination to current CVD risk scores. On the other hand, growing clinical evidence supports kidney and CV protective effects of sodium–glucose cotransporter-2 (SGLT2) inhibitors in cardiorenal patients. However, recent data suggest that some detrimental effects of SGLT2 inhibitors on skeletal muscle mass may lead to overestimation of creatinine-based eGFR and subsequent misinterpretation of associated CV risk in patients treated with these agents. Within this framework, we suggest the advisability of using cystatin C and/or creatinine plus cystatin C–based eGFR for routine clinical practice in cardiorenal patients to more accurately stratify CV risk and evaluate the kidney and CV protective effects of SGLT2 inhibitors. In this regard, we make a call to action to investigate the protective effects of these pharmacological agents using cystatin C–based eGFR.
Regional contributions to impaired myocardial mechanical function in heart failure with preserved ejection fraction
Authors: Biering-Sørensen Tor , Cikes Maja , Lassen Mats C H , Claggett Brian , Minamisawa Masatoshi , Santos Angela B S , Pieske-Kraigher Elisabeth , Shah Amil M , Zile Michael R , McMurray John J V , Solomon Scott D , Cheng Susan
Published: April 2023

Aims

Hypertensive heart disease (HHD) is recognized as a key clinical precursor to heart failure with preserved ejection fraction (HFPEF). However, pathophysiological transition from HHD to HFPEF is not well understood. We sought determine whether regional differences in impaired myocardial function may underlie the greater mechanical dysfunction seen in HFPEF compared to HHD.

Methods and results

We used standardized echocardiography to assess regional myocardial deformation in a cohort of n = 327 adults with preserved left ventricular (LV) ejection fraction (≥45%), including: n = 129 with HFPEF, n = 158 with HHD and no heart failure, and n = 40 normotensive controls. From detailed measurements of LV systolic strain performed in multiple views, we derived and then compared regional measures of basal, mid-ventricular, and apical longitudinal strains. In models adjusting for clinical covariates, basal and mid-ventricular LV myocardial deformation was more impaired in HHD than in controls (P ≤ 0.003), whereas apical deformation was more impaired in HFPEF than in HHD (P = 0.005). In multivariable-adjusted analyses, only apical strain remained independently associated with HFPEF vs. HHD status [odds ratio 1.18 (1.02–1.37), P = 0.030 per 1% decrease in apical strain]. Compared to other regional strains, apical longitudinal strain optimally differentiated HFPEF from HHD (area under the receiver operating curve: apical longitudinal strain = 0.67; mid-ventricular longitudinal strain = 0.59; basal longitudinal strain = 0.60).

Conclusion

We found that while apical mechanical function is preserved in HHD, it was impaired in HFPEF and may contribute to the transition from an asymptomatic heart disease to a symptomatic heart disease.
Comparative effectiveness of clopidogrel versus aspirin as a maintenance monotherapy 1 year after coronary artery bypass grafting
Authors: Kim Ji Seong , Kang Yoonjin , Sohn Suk Ho , Hwang Ho Young
Published: April 2023

OBJECTIVES

Data on the safety and efficacy of clopidogrel (CPD) monotherapy after coronary artery bypass grafting (CABG) are limited. We compared the clinical outcomes and graft patency rates during 4 years in CABG patients who maintained CPD or aspirin after 1 year of dual antiplatelet therapy (DAPT) use.

METHODS

A total of 671 patients who maintained 1-year DAPT after CABG with all grafts patent on one-year follow-up angiography and switched to single antiplatelet therapy (SAPT) using CPD (n = 272) or aspirin (n = 399) between January 2009 and December 2015 were enrolled. Propensity score matching analysis was used, and 227 pairs were matched in a 1:1 ratio. Overall mortality, cardiac mortality, and major adverse events, including all-cause mortality, acute myocardial infarction, coronary reintervention or reoperation, ischaemic stroke, and major bleeding, were compared. Graft patency was evaluated using graft angiography 5 years post-surgery.

RESULTS

Overall survival and the incidence of major adverse events during the 4-year follow-up did not differ significantly between the groups when un-matched (hazard ratio [HR], 95% confidence interval [CI]=1.24, 0.71 to 2.15, P = 0.46 and HR, 95% CI = 1.22, 0.77 to 1.92, P = 0.41, respectively) or matched (HR, 95% CI = 1.05, 0.55 to 2.01, P = 0.89 and HR, 95% CI = 1.01, 0.60 to 1.73, P = 0.96, respectively). In the postoperative 5-year graft angiography, new graft occlusion was found in 3.2% and 4.7% of patients and newly occurred graft occlusion rates of distal anastomoses were 1.2% and 1.6% in the CPD and aspirin groups, respectively, and were not statistically different between the 2 groups (P = 0.39 and 0.63, respectively). Changes of antiplatelet regimen were needed in 22.8% (91 of 399) of aspirin group and in 2.2% (6 of 272) of CPD group from the initiation of SAPT (P < 0.001).

CONCLUSIONS

In this series of patients undergoing CABG who received DAPT and remained stable for 1 year, SAPT maintenance with CPD or aspirin did not show any significant differences in 4-year outcomes such as all-cause mortality, major adverse events, and newly occurring graft occlusion. However, more patients taking aspirin required changes in antiplatelet regimens to other antiplatelet or anticoagulation therapies.
Cohort changes in the association between parental divorce and children’s education: A long-term perspective on the institutionalization hypothesis
Authors: Kalmijn Matthijs
Published: April 2023

The institutionalization hypothesis argues that in contexts where divorce is more common, its consequences will be less severe. An implication of this hypothesis is that the association between parental divorce and child outcomes will decline over time, parallel to the historical rise in divorce. Building on a handful of earlier tests of this idea, the current analysis provides a long-term cohort perspective with sufficient statistical power to detect possible trends. Data from 18 national surveys in the Netherlands were harmonized and pooled in order to obtain a large sample with sufficient numbers of children with divorced parents from a wide span of birth cohorts (Ntotal = 87,541, Ndivorced = 5,728). Using educational attainment as a dependent variable, and applying a set of relevant controls for key family background variables, there was no evidence that the association between parental divorce and education changed between 1930 and 1991. Multi-level models showed that there was no association between the prevalence of divorce and the magnitude of the parental divorce effect. The refutation of the institutionalization hypothesis for divorce is interpreted in terms of how the selection into divorce has changed, in combination with problems emerging in modern postdivorce relationships.
Dyslipidemia, inflammation, calcification, and adiposity in aortic stenosis: a genome-wide study
Authors: Yu Chen Hao , Dina Christian , Small Aeron M , Shaffer Christian M , Levinson Rebecca T , Helgadóttir Anna , Capoulade Romain , Munter Hans Markus , Martinsson Andreas , Cairns Benjamin J , Trudsø Linea C , Hoekstra Mary , Burr Hannah A , Marsh Thomas W , Damrauer Scott M , Dufresne Line , Le Scouarnec Solena , Messika-Zeitoun David , Ranatunga Dilrini K , Whitmer Rachel A , Bonnefond Amélie , Sveinbjornsson Garðar , Daníelsen Ragnar , Arnar David O , Thorgeirsson Gudmundur , Thorsteinsdottir Unnur , Gudbjartsson Daníel F , Hólm Hilma , Ghouse Jonas , Olesen Morten Salling , Christensen Alex H , Mikkelsen Susan , Jacobsen Rikke Louise , Dowsett Joseph , Pedersen Ole Birger Vesterager , Erikstrup Christian , Ostrowski Sisse R ,   Regeneron Genetics Center, O’Donnell Christopher J , Budoff Matthew J , Gudnason Vilmundur , Post Wendy S , Rotter Jerome I , Lathrop Mark , Bundgaard Henning , Johansson Bengt , Ljungberg Johan , Näslund Ulf , Le Tourneau Thierry , Smith J Gustav , Wells Quinn S , Söderberg Stefan , Stefánsson Kári , Schott Jean-Jacques , Rader Daniel J , Clarke Robert , Engert James C , Thanassoulis George
Published: April 2023

Aims

Although highly heritable, the genetic etiology of calcific aortic stenosis (AS) remains incompletely understood. The aim of this study was to discover novel genetic contributors to AS and to integrate functional, expression, and cross-phenotype data to identify mechanisms of AS.

Methods and results

A genome-wide meta-analysis of 11.6 million variants in 10 cohorts involving 653 867 European ancestry participants (13 765 cases) was performed. Seventeen loci were associated with AS at P ≤ 5 × 10−8, of which 15 replicated in an independent cohort of 90 828 participants (7111 cases), including CELSR2–SORT1, NLRP6, and SMC2. A genetic risk score comprised of the index variants was associated with AS [odds ratio (OR) per standard deviation, 1.31; 95% confidence interval (CI), 1.26–1.35; P = 2.7 × 10−51] and aortic valve calcium (OR per standard deviation, 1.22; 95% CI, 1.08–1.37; P = 1.4 × 10−3), after adjustment for known risk factors. A phenome-wide association study indicated multiple associations with coronary artery disease, apolipoprotein B, and triglycerides. Mendelian randomization supported a causal role for apolipoprotein B-containing lipoprotein particles in AS (OR per g/L of apolipoprotein B, 3.85; 95% CI, 2.90–5.12; P = 2.1 × 10−20) and replicated previous findings of causality for lipoprotein(a) (OR per natural logarithm, 1.20; 95% CI, 1.17–1.23; P = 4.8 × 10−73) and body mass index (OR per kg/m2, 1.07; 95% CI, 1.05–1.9; P = 1.9 × 10−12). Colocalization analyses using the GTEx database identified a role for differential expression of the genes LPA, SORT1, ACTR2, NOTCH4, IL6R, and FADS.

Conclusion

Dyslipidemia, inflammation, calcification, and adiposity play important roles in the etiology of AS, implicating novel treatments and prevention strategies.
Comprehensive review and evaluation of whole stand volume yield models for the aspen forest type in Minnesota, USA
Authors: Gifford Tyler S , Zobel John M , Hillard Scott C , Edgar Christopher B
Published: April 2023

Aspen (Populus spp.) exists as a forest type with circumboreal significance. In Minnesota, aspen is the most abundant and utilized timber species. Dating from 1929 to as recently as 2019, many whole stand volume yield models have been developed for the aspen forest type in Minnesota. With many model forms to choose from, this work sought to narrow down the best performing models across a myriad of forest conditions and locations. Data from recent cycles of the U.S. Forest Service, Forest Inventory and Analysis program were utilized for model fitting and assessment. Existing model forms were assessed, as well as 423 new model forms. Models were cross validated and compared with predictive accuracy statistics including root mean square error, mean absolute deviation and an agreement index (pseudo-R2). Analyses were conducted to evaluate model performance in relevant subsets, including: statewide, ecological section, age class and site class. To reflect model complexity and differences in available inventory data, models were also assessed by the number of required input variables. A newly postulated model form, the GZ model, provided improved accuracy across all subset scenarios, whereas a recently developed model form provided simplicity and applicability across many subsets. This work provides users of aspen whole stand volume yield models with a method to review model forms fit under a variety of conditions and select the most appropriate model.
Combining interpolated maximum wind gust speed and forest vulnerability for rapid post-storm mapping of potential forest damage areas in Finland
Authors: Laapas Mikko , Suvanto Susanne , Peltoniemi Mikko , Venäläinen Ari
Published: April 2023

In Finland, wind-induced forest damage is expected to increase in the future. Demand exists for timely and precise first-hand information about the main impact area of windstorms. Locating potential damage areas quickly is essential for effective operational planning of salvage loggings, aiming to reduce monetary losses of timber and risk for secondary damage caused by insects. This study presents an approach for mapping the potential damage areas immediately after a windstorm, by using high-resolution forest vulnerability data and information on the spatial distribution of maximum wind gust speed derived from weather station observations using kriging with external drift interpolation. The new method is evaluated by analyzing damage caused by nine major windstorms of the 2010s in Finland. Our results show that including roughness length information as an auxiliary variable in the interpolation improved the results and produced wind maps with more plausible structure and better separation between forested and non-forested land areas. The forest vulnerability data were most strongly linked to damage, whilst wind gust speed had weaker results. However, for future storms with unknown damage areas, we consider maximum wind gust speed still essential for defining the main impact area, whereas forest vulnerability data could then be used for more detailed damage predictions. Further advancements of wind interpolation approaches, preferably towards higher resolution and, if possible, based on a denser and more diverse observation network, is needed to fully exploit the potential of combined wind and forest vulnerability data. Albeit we recognize multiple uncertainties, room for improvements and benefits that additional data sources would bring, our study demonstrates a simple approach for rapid mapping of potential forest wind damage areas, which could be further developed into an operational tool.
Comparing mobile and terrestrial laser scanning for measuring and modelling tree stem taper
Authors: Stovall Atticus E L , MacFarlane David W , Crawford Debbie , Jovanovic Tom , Frank Jereme , Brack Cris
Published: April 2023

Measuring and modelling the shape of tree stems is a fundamental component of forest inventory systems for both commercial and biological purposes. The change in diameter of the stem along its length (a.k.a. 'taper') is one of the most important and widely used means of predicting tree stem volume. Until recently, the options for obtaining accurate estimates of stem taper and developing stem taper models have been limited to measurements of felled trees or the use of optical dendrometers on standing live trees. Here, we tested both a tripod-mounted terrestrial laser scanner (TLS; a Focus 3D 120 of FARO Technologies, Inc., Lake Mary, FL, USA), and a mobile laser scanner (MLS; the ZEB1 of the GeoSLAM Ltd, Nottingham, UK) to measure tree diameters at various heights along the stem of 20 destructively harvested broadleaf and needleleaf species using the outer hull modelling method, for the purpose of developing individual-tree and species-specific taper models. Laser scanner specifications were a major factor determining stem taper measurement accuracy. The longer-range, low beam divergence TLS could estimate stem diameter to an average of 15.7 m above ground (about 79 per cent of the canopy height), while the shorter-range high beam divergence MLS could estimate an average of 11.5 m above ground (about 45 per cent of the canopy height). Stem taper error increased with respect to height above ground, with the TLS providing more consistent and reliable diameter measurements (root mean square error (RMSE) = 1.93 cm; 9.57 per cent) compared with the MLS (RMSE = 2.59 cm; 12.84 per cent), but both methods were nearly unbiased. We attribute ~60 per cent of the uncertainty in stem measurements to laser beam diameter and point density, showing positive and negative correlations, respectively. MLS was unable to converge on the two tested taper models but was found to be an efficient means of easily sampling diameters at breast height (DBH) and reconstructing stem maps in simple forest stands with trees greater than ~10 cm DBH. TLS provided precision stem diameter measurements that allowed for the creation of similar taper models for three out of the four study species. Future work should focus on evaluating MLS systems with improved specifications (e.g. beam divergence and range), since these instruments will likely lead to dramatic improvements in reliable estimates of forest inventory parameters, in line with the current TLS technology.
Delineating regions of interest for mass spectrometry imaging by multimodally corroborated spatial segmentation
Authors: Guo Ang , Chen Zhiyu , Li Fang , Luo Qian
Published: April 2023

Mass spectrometry imaging (MSI), which localizes molecules in a tag-free, spatially resolved manner, is a powerful tool for the understanding of underlying biochemical mechanisms of biological phenomena. When analyzing MSI data, it is essential to delineate regions of interest (ROIs) that correspond to tissue areas of different anatomical or pathological labels. Spatial segmentation, obtained by clustering MSI pixels according to their mass spectral similarities, is a popular approach to automate ROI definition. However, how to select the number of clusters (#Clusters), which determines the granularity of segmentation, remains to be resolved, and an inappropriate #Clusters may lead to ROIs not biologically real. Here we report a multimodal fusion strategy to enable an objective and trustworthy selection of #Clusters by utilizing additional information from corresponding histology images. A deep learning–based algorithm is proposed to extract “histomorphological feature spectra” across an entire hematoxylin and eosin image. Clustering is then similarly performed to produce histology segmentation. Since ROIs originating from instrumental noise or artifacts would not be reproduced cross-modally, the consistency between histology and MSI segmentation becomes an effective measure of the biological validity of the results. So, #Clusters that maximize the consistency is deemed as most probable. We validated our strategy on mouse kidney and renal tumor specimens by producing multimodally corroborated ROIs that agreed excellently with ground truths. Downstream analysis based on the said ROIs revealed lipid molecules highly specific to tissue anatomy or pathology. Our work will greatly facilitate MSI-mediated spatial lipidomics, metabolomics, and proteomics research by providing intelligent software to automatically and reliably generate ROIs.
COVID–19 travel bans and the reactivation of colonial trauma in Africa
Authors: Naude Bianca
Published: April 2023

When the Omicron variant of the COVID–19 virus was identified in November 2021, western states responded by immediately imposing a travel ban on African countries in a bid to keep ‘the African virus’ out of their territories. Seen by some as a necessary step to protect western lives, the travel bans caused a visceral reliving among Africans of colonial-era experiences of shame, humiliation and degradation. We know that actors, during times of crisis, exaggerate identity borders between ‘us’ and ‘them’, and we can understand western reactions to the discovery of Omicron against this theoretical backdrop. What is not clear, however, is why the Omicron travel ban caused such a visceral reliving of a past trauma in the African collective. Supported by a qualitative analysis of news media, this research sets out to explain how travel bans imposed by western nations caused a re-traumatization of the African collective, arguing that narratives surrounding ‘Africa's Omicron virus’ are an extension of the ‘heart of darkness’ ideation that dominated imperial European discourse and practice. Deeper understanding of the many ways in which colonial subjugation persists today, the article argues, can help us better respond to similar future global crises.
Validation of the Antifungal National Antimicrobial Prescribing Survey (AF-NAPS) quality assessment tool
Authors: Khanina A , Douglas A P , Yeoh D K , So M , Abbotsford J , Spelman T , Kong D C M , Slavin M A , Thursky K A
Published: April 2023

Background

The Antifungal National Antimicrobial Prescribing Survey (AF-NAPS) was developed to undertake streamlined quality audits of antifungal prescribing. The validity and reliability of such tools is not characterized.

Objectives

To assess the validity and reliability of the AF-NAPS quality assessment tool.

Methods

Case vignettes describing antifungal prescribing were prepared. A steering group was assembled to determine gold-standard classifications for appropriateness and guideline compliance. Infectious diseases physicians, antimicrobial stewardship (AMS) and specialist pharmacists undertook a survey to classify appropriateness and guideline compliance of prescriptions utilizing the AF-NAPS tool. Validity was measured as accuracy, sensitivity and specificity compared with gold standard. Inter-rater reliability was measured using Fleiss’ kappa statistics. Assessors’ responses and comments were thematically analysed to determine reasons for incorrect classification.

Results

Twenty-eight clinicians assessed 59 antifungal prescriptions. Overall accuracy of appropriateness assessment was 77.0% (sensitivity 85.3%, specificity 68.0%). Highest accuracy was seen amongst specialist (81%) and AMS pharmacists (79%). Prescriptions with lowest accuracy were in the haematology setting (69%), use of echinocandins (73%), mould-active azoles (75%) and for prophylaxis (71%). Inter-rater reliability was fair overall (0.3906), with moderate reliability amongst specialist pharmacists (0.5304). Barriers to accurate classification were incorrect use of the appropriateness matrix, knowledge gaps and lack of guidelines for some indications.

Conclusions

The AF-NAPS is a valid tool, assisting assessors to correctly classify appropriate prescriptions more accurately than inappropriate prescriptions. Specialist and AMS pharmacists had similar performance, providing confidence that both can undertake AF-NAPS audits to a high standard. Identified reasons for incorrect classification will be targeted in the online tool and educational materials.
The antitrust victims of monopsony
Authors: Alderman Brianna L , Blair Roger D
Published: April 2023

The exercise of unlawful monopsony power by buyer cartels depresses both the price paid and the quantity purchased. Consequently, producer surplus and social welfare decline from competitive levels. There are six classes of antitrust victims, but only one has standing to sue for antitrust damages in the United States. The other five are neglected. We identify the neglected victims in this article. We also suggest some ways to expand the protection offered by section 4 of the Clayton Act.
Toxicity assessment of common acaricides and mineral oils on Anagyrus vladimiri, an effective biocontrol agent of citrus mealybug
Authors: Singh Shashwat , Protasov Alex , Kramer Reut Madar , Yaacobi Gal , Kaspi Roy
Published: April 2023

Chemical pesticides, while playing an important role in the suppression of insect pests, should be used in a manner that minimizes negative effects on natural enemies. The parasitoid, Anagyrus vladimiri Triapitsyn (Hymenoptera: Encyrtidae), plays an important role in the management of mealybug pests of citrus groves in the Mediterranean region. This study was conducted to evaluate the effect of commonly used acaricides (Spirodiclofen, Spirotetramat, Sulfur, Fenpyroximate, Abamectin) and mineral oils (Levanola, EOS, JMS, and Ultrapaz) on acute mortality of A. vladimiri. Toxicity was assessed in 4 cases: (i) direct spray application on adults, (ii) pesticide application on the mummified host, (iii) feeding with contaminated food, and (iv) contact with pesticide residue. The pesticide Abamectin, applied alone and with Levanola oil was highly toxic to adults in all bioassays, with the exception of direct spray application on the mummified host. Fenpyroximate was found to be highly toxic only when sprayed directly on adults, and sulfur was slightly harmful. Mineral oils were harmful when ingested with food; otherwise, they did not cause appreciable adult mortality. The findings of the present study suggest that all tested materials, with the exception of Abamectin and Fenpyroximate, are compatible with the survival of A. vladimiri. Direct ingestion of oils can, however, cause a degree of mortality. Given that indiscriminate use of these pesticides may affect the population ecology of A. vladimiri, they should be used with caution.
Molecular profiling and treatment pattern differences between intrahepatic and extrahepatic cholangiocarcinoma
Authors: Spencer Kristen , Pappas Leontios , Baiev Islam , Maurer Jordan , Bocobo Andrea Grace , Zhang Karen , Jain Apurva , De Armas Anaemy Danner , Reyes Stephanie , Le Tri Minh , Rahma Osama E , Stanton Jennifer , DeLeon Thomas T , Roth Marc , Peters Mary Linton B , Zhu Andrew X , Lennerz Jochen K , Iafrate A John , Boyhen Kylie , VanCott Christine , Roberts Lewis R , Lindsey Stacie , Horick Nora , Goff Laura Williams , Mody Kabir , Borad Mitesh J , Shroff Rachna T , Kelley Robin Kate , Javle Milind M , Goyal Lipika
Published: April 2023

Background

Treatment patterns for intrahepatic cholangiocarcinoma (ICC) and extrahepatic cholangiocarcinoma (ECC) differ, but limited studies exist comparing them. This study examines differences in molecular profiling rates and treatment patterns in these populations, focusing on use of adjuvant, liver-directed, targeted, and investigational therapies.

Methods

This multicenter collaboration included patients with ICC or ECC treated at 1 of 8 participating institutions. Retrospective data were collected on risk factors, pathology, treatments, and survival. Comparative statistical tests were 2-sided.

Results

Among 1039 patients screened, 847 patients met eligibility (ICC = 611, ECC = 236). Patients with ECC were more likely than those with ICC to present with early stage disease (53.8% vs 28.0%), undergo surgical resection (55.1% vs 29.8%), and receive adjuvant chemoradiation (36.5% vs 4.2%) (all P < .00001). However, they were less likely to undergo molecular profiling (50.3% vs 64.3%) or receive liver-directed therapy (17.9% vs 35.7%), targeted therapy (4.7% vs 18.9%), and clinical trial therapy (10.6% vs 24.8%) (all P < .001). In patients with recurrent ECC after surgery, the molecular profiling rate was 64.5%. Patients with advanced ECC had a shorter median overall survival than those with advanced ICC (11.8 vs 15.1 months; P < .001).

Conclusions

Patients with advanced ECC have low rates of molecular profiling, possibly in part because of insufficient tissue. They also have low rates of targeted therapy use and clinical trial enrollment. While these rates are higher in advanced ICC, the prognosis for both subtypes of cholangiocarcinoma remains poor, and a pressing need exists for new effective targeted therapies and broader access to clinical trials.
Chronic treatment with a combination of hepatocyte growth factor and JNK inhibitor ameliorates cavernosal veno-occlusive dysfunction: a rat model of cavernous nerve injury
Authors: Lee Junghoon , Son Hwancheol , Kim Soo Woong , Cho Min Chul
Published: April 2023

Background

Structural alterations of the penis, including cavernosal apoptosis and fibrosis, induce venous leakage into the corpus cavernosum or cavernosal veno-occlusive dysfunction, a key pathophysiology associated with erectile dysfunction after radical prostatectomy. We hypothesized that the effect of JNK inhibitors on reducing apoptosis and hepatocyte growth factor (HGF) on inducing tissue regeneration could be another treatment mechanism of erectile dysfunction after radical prostatectomy.

Aim

To investigate whether JNK inhibition combined with intracavernosal administration of HGF can completely preserve cavernosal veno-occlusive function (CVOF) in a rat model of erectile dysfunction induced via bilateral cavernosal nerve crush injury (CNCI).

Methods

A total of 42 male Sprague-Dawley rats were randomly assigned to sham control (group S), CNCI (group I), and CNCI treated with a combination of JNK inhibitor and HGF (group J + H) for 5 weeks after surgery.

Outcomes

Rats in each group were evaluated via dynamic infusion cavernosometry (DIC), caspase-3 activity assay, Masson trichrome staining, immunohistochemical staining of α-smooth muscle actin, and immunoblotting at 5 weeks after surgery.

Results

Regarding CVOF, group I showed decreased papaverine response, increased maintenance, and drop rates of DIC when compared with group S. Group J + H showed significant improvement in the 3 DIC parameters vs group I. No differences in the 3 DIC parameters were found between group J + H and group S. Regarding the structural integrity of the corpus cavernosum, group I showed increased caspase-3 activity, decreased smooth muscle (SM):collagen ratio, decreased SM content, decreased protein expression of PECAM-1, and decreased phosphorylation of c-Jun and c-Met. Group J + H showed significant attenuation in histologic and molecular derangement as compared with group I. There were no differences in caspase-3 activity, SM content, SM:collagen ratio, PECAM-1 protein expression, c-Jun phosphorylation, and c-Met phosphorylation between groups J + H and S.

Clinical Implications

Our results suggest that antiapoptotic and regenerative therapy for the corpus cavernosum is a potential mechanism of penile rehabilitation after radical prostatectomy.

Strengths and Limitations

This study provides evidence that combination treatment of JNK inhibitor and HGF preserves erectile function by restoring corporal SM and endothelium. However, additional human studies are needed to confirm the clinical effect.

Conclusion

Chronic treatment with JNK inhibitor and HGF may preserve CVOF to levels comparable to sham control by preserving the structural integrity of the corpus cavernosum and so represents a potential therapeutic option for preventing the development of cavernosal veno-occlusive dysfunction.
Real-world effectiveness of monkeypox vaccines: a systematic review
Authors: Xu Mingda , Liu Caifen , Du Zhanwei , Bai Yuan , Wang Zhen , Gao Chao
Published: April 2023

A systematic review was conducted to investigate and understand the real-world effectiveness of smallpox vaccines against mpox during 2022 outbreaks. The effectiveness of MVA-BN was estimated to be 87% [95% confidence interval (CI): 84–90%] for one-dose and 89% (95% CI: 78–100%) for two-dose vaccination. The next-generation vaccines are recommended for future preparedness.