bluuebunny/crossref_metadata_2025 huggingface dataset:
An open-source tool to assess the carbon footprint of research
Authors: Mariette Jérôme , Blanchard Odile , Berné Olivier , Aumont Olivier , Carrey Julian , Ligozat AnneLaure , Lellouch Emmanuel , Roche Philippe-Emmanuel , Guennebaud Gaël , Thanwerdas Joel , Bardou Philippe , Salin Gérald , Maigne Elise , Servan Sophie , Ben-Ari Tamara
Published: July 2022

The scrutiny over the carbon footprint of research and higher education has increased rapidly in the last few years. This has resulted in a series of publications providing various estimates of the carbon footprint of one or several research activities, principally at the scale of a university or a research center or, more recently, a field of research. The variety of tools or methodologies on which these estimates rely unfortunately prevents any aggregation or direct comparison. This is because carbon footprint assessments are very sensitive to key parameters (e.g., emission factors) or hypotheses (e.g., scopes). Hence, it is impossible to address fundamental questions such as: is the carbon footprint of research structurally different between disciplines? Are plane trips a major source of carbon emissions in academic research? Massive collection and curation of carbon footprint data, across a large array of research situations and disciplines, is hence an important, timely and necessary challenge to answer these questions. This paper presents a framework to collect and analyse large amounts of homogeneous research carbon emission data in a network of research entities at the national scale. It relies on an open-source web application, GES 1point5, designed to estimate the carbon footprint of a department, research lab or team in any country of the world. Importantly, GES 1point5 is also designed to aggregate all input data and corresponding GHG emissions estimates into a comprehensive database. GES 1point5 therefore enables (i) the identification of robust local or national determinants of the carbon footprint of research and (ii) the estimation of the carbon footprint of the entire research sector at national scale. A preliminary analysis of the carbon footprint of more than one hundred laboratories in France is presented to illustrate the potential of the framework. It shows that the average emissions are 479 t CO2e for a research lab and 3.6 t CO2e for an average lab member (respectively 404 and 3.1 t CO2e without accounting for the indirect radiative effects of aviation), with the current scope of GES 1point5. Availability and implementation: GES 1point5 is available online at http://labos1point5.org/ges-
1point5 and its source code can be downloaded from the GitLab platform at https://framagit.org/
labos1point5/l1p5-vuejs.
ColocQuiaL: a QTL-GWAS colocalization pipeline
Authors: Chen Brian Y , Bone William P , Lorenz Kim , Levin Michael , Ritchie Marylyn D , Voight Benjamin F
Published: July 2022

Identifying genomic features responsible for genome-wide association study (GWAS) signals has proven to be a difficult challenge; many researchers have turned to colocalization analysis of GWAS signals with expression quantitative trait loci (eQTL) and splicing quantitative trait loci (sQTL) to connect GWAS signals to candidate causal genes. The ColocQuiaL pipeline provides a framework to perform these colocalization analyses at scale across the genome and returns summary files and locus visualization plots to allow for detailed review of the results. As an example, we used ColocQuiaL to perform colocalization between a recent type 2 diabetes GWAS and Genotype-Tissue Expression (GTEx) v8 single-tissue eQTL and sQTL data.

Availability and implementation

ColocQuiaL is primarily written in R and is freely available on GitHub: https://github.com/bvoightlab/ColocQuiaL.
Best templates outperform homology models in predicting the impact of mutations on protein stability
Authors: Pak Marina A , Ivankov Dmitry N
Published: July 2022

Motivation

Prediction of protein stability change upon mutation (ΔΔG) is crucial for facilitating protein engineering and understanding of protein folding principles. Robust prediction of protein folding free energy change requires the knowledge of protein three-dimensional (3D) structure. In case, protein 3D structure is not available, one can predict the structure from protein sequence; however, the perspectives of ΔΔG predictions for predicted protein structures are unknown. The accuracy of using 3D structures of the best templates for the ΔΔG prediction is also unclear.

Results

To investigate these questions, we used a representative set of seven diverse and accurate publicly available tools (FoldX, Eris, Rosetta, DDGun, ACDC-NN, ThermoNet and DynaMut) for stability change prediction combined with AlphaFold or I-Tasser for protein 3D structure prediction. We found that best templates perform consistently better than (or similar to) homology models for all ΔΔG predictors. Our findings imply using the best template structure for the prediction of protein stability change upon mutation if the protein 3D structure is not available.

Availability and implementation

The data are available at https://github.com/ivankovlab/template-vs-model.

Supplementary information

Supplementary data are available at Bioinformatics online.
Combining CRISPR–Cas12a with terminal deoxynucleotidyl transferase dependent reporter elongation for pathogen detection using lateral flow test strips
Authors: Berghuis Nicole F , Mars-Groenendijk Roos , Busker Ruud W , Paauw Armand , van Leeuwen Hans C
Published: July 2022

CRISPR–Cas (CC)-based detection technologies have some exceptional features, which hold the promise of developing into the next-generation diagnostic platforms. One of these features is the ability to trigger non-specific single-stranded DNA/RNA cleavage activity after specific target recognition and Cas enzyme activation. This cleavage activity can be visualized either by single-stranded DNA/RNA fluorescence resonance energy transfer quenching reporters or via lateral flow strips, which separate and detect the cleaved reporters. In a previous study, we reported coupling CC-cleavage activity with the enzyme terminal deoxynucleotidyl transferase (TdT) that elongates cleaved ssDNA reporter fragments with dTTP nucleotides. These elongated poly(thymine) tails then act as scaffolds for the formation of copper nanoparticles which generate a bright fluorescent signal upon UV excitation. In the current study, we visualize the poly(thymine) tails on lateral flow strips, using different combinations of biotinylated or fluorescein-labeled nucleotides, various reporters, and capture oligos. One particular approach, using a fluorescein reporter, reached a target sensitivity of <1 pM and was named Cas activity assay on a strip and was tested using Bacillus anthracis genomic DNA.
Using the Theory of Family Boundary Ambiguity and Ambiguous Loss to Understand the Experiences of Foster Carers’ Own Children
Authors: Tatton Allison
Published: July 2022

In England, nearly three-quarters of looked after children are cared for in foster families. Despite this, relatively little is known about the experiences of foster carers’ children in families who foster. This study used narrative interviews to explore the experiences of twelve adults now aged eighteen to fifty-four years who had been brought up in such families. Their families had fostered for much or all of their childhood and growing up in a fostering family had had a considerable impact on them. Most participants viewed some of the fostered children as siblings and continued to do so into adulthood. The analysis used the theory of family boundary ambiguity and ambiguous loss to gain a deeper understanding of the participants’ experiences. The findings suggest that there is a need for much greater awareness of the issues that foster carers’ own children face. They also suggest that a change in how foster placements are supported needs to include a greater focus on the children of foster carers.
Cranial trepanation in pre-Columbian Peruvian cultures: was it an option to treat epilepsy?
Authors: Espino Poul H , Toro-Perez Juan E , Shkrum Stephanie , Burneo Jorge G
Published: July 2022

Cranial trepanation is the oldest known surgical procedure in the world, but why was it performed? By examining evidence from pre-Columbian Peruvian cultures—where trepanation was relatively common—Espino et al. critically evaluate whether trepanation was used as a treatment for epilepsy.
Ultra-Short-Course Antibiotics for Suspected Pneumonia With Preserved Oxygenation
Authors: Klompas Michael , McKenna Caroline , Ochoa Aileen , Ji Wenjing , Chen Tom , Young Jessica , Rhee Chanu ,   for the Prevention Epicenters Program, Centers for Disease Control and Prevention
Published: July 2022

Background

Suspected pneumonia is the most common indication for antibiotics in hospitalized patients but is frequently overdiagnosed. We explored whether normal oxygenation could be used as an indicator to support early discontinuation of antibiotics.

Methods

We retrospectively identified all patients started on antibiotics for pneumonia in 4 hospitals with oxygen saturations ≥95% on ambient air, May 2017–February 2021. We propensity-matched patients treated 1–2 days vs 5–8 days and compared hospital mortality and time to discharge using subdistribution hazard ratios (SHRs). Secondary outcomes included readmissions, 30-day mortality, Clostridioides difficile infections, hospital-free days, and antibiotic-free days.

Results

Among 39 752 patients treated for possible pneumonia, 10 012 had median oxygen saturations ≥95% without supplemental oxygen. Of these, 2871 were treated 1–2 days and 2891 for 5–8 days; 4478 patients were propensity-matched. Patients treated 1–2 vs 5–8 days had similar hospital mortality (2.1% vs 2.8%; SHR, 0.75 [95% confidence interval {CI}, .51–1.09]) but less time to discharge (6.1 vs 6.6 days; SHR, 1.13 [95% CI, 1.07–1.19]) and more 30-day hospital-free days (23.1 vs 22.7; mean difference, 0.44 [95% CI, .09–.78]). There were no significant differences in 30-day readmissions (16.0% vs 15.8%; odds ratio [OR], 1.01 [95% CI, .86–1.19]), 30-day mortality (4.6% vs 5.1%; OR, 0.91 [95% CI, .69–1.19]), or 90-day C. difficile infections (1.3% vs 0.8%; OR, 1.67 [95% CI, .94–2.99]).

Conclusions

One-quarter of hospitalized patients treated for pneumonia had oxygenation saturations ≥95% on ambient air. Outcomes were similar with 1–2 vs 5–8 days of antibiotics. Normal oxygenation levels may help identify candidates for early antibiotic discontinuation. Prospective trials are warranted.
Exercise-related major adverse cardiovascular events in asymptomatic recreational master athletes: a case series
Authors: Fruytier Lonneke A , van de Sande Danny AJP , Kemps Hareld MC
Published: July 2022

Background

In master athletes, atherosclerotic coronary artery disease (CAD) is the primary condition leading to major adverse cardiovascular events during sports. We report two cases of asymptomatic recreational athletes who suffered from an exercise-induced cardiovascular event.

Case summary

The first athlete is a 70-year-old male speed skater without known history of cardiovascular disease. He has no typical risk factors for CAD and denied preceding symptoms. During training at the speed skating rink, he suddenly experienced severe chest pain. Electrocardiogram (ECG) showed ST-segment elevation in the precordial leads. In the ambulance, an episode of ventricular fibrillation was converted to atrial fibrillation. Coronary angiography showed a thrombus in the left anterior descending (LAD) coronary artery, treated with a glycoprotein IIb/IIIa inhibitor intravenously.

The second athlete is a 59-year-old male endurance athlete who presented with chest pain during cycling. He had a history of cavotricuspid isthmus ablation and pulmonary vein isolation for paroxysmal atrial fibrillation and flutter but experienced no symptoms in the weeks prior to the event. He also had no risk factors for CAD. ECG showed ST-segment elevation in the inferior leads and reciprocal depression in V2–V4. Successful primary percutaneous intervention of the circumflex artery was performed.

Discussion

Limited data are available to guide recommendations for cardiovascular screening in master athletes. Since master athletes with CAD are often asymptomatic, more knowledge on the optimal pre-participation screening algorithm for identifying individuals at risk of adverse cardiac events is required.
Epigenetic mechanism of L-type calcium channel β-subunit downregulation in short QT human induced pluripotent stem cell-derived cardiomyocytes with CACNB2 mutation
Authors: Zhong Rujia , Zhang Feng , Yang Zhen , Li Yingrui , Xu Qiang , Lan Huan , Cyganek Lukas , El-Battrawy Ibrahim , Zhou Xiaobo , Akin Ibrahim , Borggrefe Martin
Published: July 2022

Aims

A loss-of-function mutation in L-type calcium (Ca2+) channel subunit gene CACNB2 has been reported to cause short QT syndrome subtype 5 (SQT5). However, the mechanism underlying the loss-of-function of the Ca2+ channel has not been clarified. In the present study, we aim to explore the DNA methylation mechanism of L-type Ca2+ channel downregulation in human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) of SQT5.

Methods and results

The hiPSC-CMs were generated from a healthy donor and a SQT5 patient carrying the CACNB2 variant c.1439C > T/p.S480L. The variant was genetically corrected using ribonucleoprotein-based CRISPR/Cas9 technique to obtain an isogenic control cell line. The action potential (AP) and Ca2+ current were measured by patch clamp. Protein expression levels were determined by western blotting. Dot blotting and bisulfite sequence were performed for epigenetic study. Our results showed that AP durations at 10% repolarization (APD10) and 50% repolarization (APD50) were significantly shortened in SQT5 cells and both the expression level of the β-subunit and channel current of L-type Ca2+ channel were reduced. Besides, an increased level of whole-genome DNA methylation and DNA methylation of CpG island in the promoter region of CACNB2 gene was detected. Overexpression of demethylation enzyme could rescue the decreased expression of CACNB2 and the L-type Ca2+ current.

Conclusion

In SQT5 hiPSC-CMs carrying the CACNB2-S480L variant, the decreased L-type Ca2+ current resulting from decreased CACNB2 protein expression was caused by enhanced methylation in the promoter region of the CACNB2 gene and upregulation of DNA methyltransferases might be one of the mechanisms.
Comprehensive comparison of stroke risk score performance: a systematic review and meta-analysis among 6 267 728 patients with atrial fibrillation
Authors: van der Endt Vera H W , Milders Jet , Penning de Vries Bas B L , Trines Serge A , Groenwold Rolf H H , Dekkers Olaf M , Trevisan Marco , Carrero Juan J , van Diepen Merel , Dekker Friedo W , de Jong Ype
Published: July 2022

Aims

Multiple risk scores to predict ischaemic stroke (IS) in patients with atrial fibrillation (AF) have been developed. This study aims to systematically review these scores, their validations and updates, assess their methodological quality, and calculate pooled estimates of the predictive performance.

Methods and results

We searched PubMed and Web of Science for studies developing, validating, or updating risk scores for IS in AF patients. Methodological quality was assessed using the Prediction model Risk Of Bias ASsessment Tool (PROBAST). To assess discrimination, pooled c-statistics were calculated using random-effects meta-analysis. We identified 19 scores, which were validated and updated once or more in 70 and 40 studies, respectively, including 329 validations and 76 updates—nearly all on the CHA2DS2-VASc and CHADS2. Pooled c-statistics were calculated among 6 267 728 patients and 359 373 events of IS. For the CHA2DS2-VASc and CHADS2, pooled c-statistics were 0.644 [95% confidence interval (CI) 0.635–0.653] and 0.658 (0.644–0.672), respectively. Better discriminatory abilities were found in the newer risk scores, with the modified-CHADS2 demonstrating the best discrimination [c-statistic 0.715 (0.674–0.754)]. Updates were found for the CHA2DS2-VASc and CHADS2 only, showing improved discrimination. Calibration was reasonable but available for only 17 studies. The PROBAST indicated a risk of methodological bias in all studies.

Conclusion

Nineteen risk scores and 76 updates are available to predict IS in patients with AF. The guideline-endorsed CHA2DS2-VASc shows inferior discriminative abilities compared with newer scores. Additional external validations and data on calibration are required before considering the newer scores in clinical practice.

Clinical trial registration

ID CRD4202161247 (PROSPERO).
Bacterial diversity and community structure shapes pederin polymorphism but lacks association with host genotype specificity in the rove beetle, Paederus fuscipes
Authors: Teoh Miao-Ching , Veera Singham G
Published: July 2022

Paederus beetles are notorious for their irritant haemolymph toxin pederin, which is synthesised by an unculturable bacterial symbiont, causing dermatitis when in contact with human skin. Pederin polymorphism is observed when (+) females carrying the toxin pederin and (−) females lacking this co-occur in natural populations. Despite reports detecting pederin polymorphism in several Paederina beetles, symbiont infection frequencies in their natural populations and the bacterial diversity differences underlying the polymorphism between these female types are understudied. Herein we report a high prevalence (>80%) of female Paederus fuscipes carrying bacterial ped genes in all six study populations. This finding suggests that selection pressure favouring pederin-producing females is crucial for survival in the natural environment. 16S rRNA metabarcoding analysis revealed significant dominance of the unculturable pederin-producing Pseudomonas-like bacterium (Gammaproteobacteria) in (+) females, consistent with previous studies. The microbial diversity of the (−) females revealed a significant abundance of Apibacter (Bacteroidia), previously undocumented, suggesting its importance in the functionality of (−) females. Predicted functions related to metabolisms are enriched in (−) females, suggesting fitness advantage possibilities in sustaining the population in the absence of predation. Further investigations on the possible genetic basis of the host genotype revealed no association of host mtDNA and pederin polymorphism in Pa. fuscipes.
Nitrite stress increases staphylococcal enterotoxin C transcription and triggers the SigB regulon
Authors: Etter Danai , Büchel Ramona , Patt Tabea , Biggel Michael , Tasara Taurai , Cernela Nicole , Stevens Marc J A , Johler Sophia
Published: July 2022

Staphylococcal food poisoning is a common food intoxication caused by staphylococcal enterotoxins. While growth of Staphylococcus aureus is not inhibited by the meat-curing agent nitrite, we hypothesize that nitrite has an influence on enterotoxin C (SEC) expression. We investigated the influence of 150 mg/l nitrite on SEC expression at mRNA and protein level in seven strains expressing different SEC variants. Additionally, regulatory knockout mutants (Δagr, ΔsarA, and ΔsigB) of high SEC producing strain SAI48 were investigated at mRNA level. Our findings suggest that nitrite effectively increases sec mRNA transcription, but the effects on SEC protein expression are less pronounced. While Δagr mutants exhibited lower sec mRNA transcription levels than wildtype strains, this response was not stress specific. ΔsigB mutants displayed a nitrite stress-specific response. Whole genome sequencing of the strains revealed a defective agr element in one strain (SAI3). In this strain, sec transcription and SEC protein synthesis was not affected by the mutation. Consequently, additional regulatory networks must be at play in SEC expression. Comparison of our findings about SEC with previous experiments on SEB and SED suggest that each SE can respond differently, and that the same stressor can trigger opposing responses in strains that express multiple toxins.
Systematic analysis of the roles of c-di-GMP signaling in Xanthomonas oryzae pv. oryzae virulence
Authors: Lin Yunuan , Mi Duo , Hou Yunyu , Lin Maojuan , Xie Qingbiao , Niu Xiaolei , Chen Yinhua , He Chaozu , Tao Jun , Li Chunxia
Published: July 2022

Cyclic di-guanosine monophosphate (c-di-GMP) is a ubiquitous second messenger, i.e. essential to bacterial adaptation to environments. Cellular c-di-GMP level is regulated by the diguanylate cyclases and the phosphodiesterases, and the signal transduction depends on its receptors. In Xanthomonas oryzae pv. oryzae strain PXO99A, 37 genes were predicted to encode GGDEF, EAL, GGDEF/EAL, HD-GYP, FleQ, MshE, PilZ, CuxR, Clp, and YajQ proteins that may be involved in c-di-GMP turnover or function as c-di-GMP receptors. Although the functions of some of these genes have been studied, but the rest have not been extensively studied. Here, we deleted these 37 genes from PXO99A and analyzed the virulence, motility, biofilm, and EPS production of these mutants. Our results show that most of these genes are required for PXO99A virulence, motility, biofilm formation, or exopolysaccharide production. Although some of them have been reported in previous studies, we found four novel genes (gedpX8, gdpX11, pliZX4, and yajQ) are implicated in X. oryzae pv. oryzae virulence. Our data demonstrate that c-di-GMP signaling is vital for X. oryzae pv. oryzae virulence and some virulence-related factors production, but there is no positive correlation between them in most cases. Taken together, our systematic research provides a new light to understand the c-di-GMP signaling network in X. oryzae pv. oryzae.
A chromosome-level reference genome of a Convolvulaceae species Ipomoea cairica
Authors: Jiang Fan , Wang Sen , Wang Hengchao , Wang Anqi , Xu Dong , Liu Hangwei , Yang Boyuan , Yuan Lihua , Lei Lihong , Chen Rong , Li Weihua , Fan Wei
Published: July 2022

Ipomoea cairica is a perennial creeper that has been widely introduced as a garden ornamental across tropical, subtropical, and temperate regions. Because it grows extremely fast and spreads easily, it has been listed as an invasive species in many countries. Here, we constructed the chromosome-level reference genome of Ipomoea cairica by Pacific Biosciences HiFi and Hi-C sequencing, with the assembly size of 733.0 Mb, the contig N50 of 43.8 Mb, the scaffold N50 of 45.7 Mb, and the Benchmarking Universal Single-Copy Orthologs complete rate of 98.0%. Hi-C scaffolding assigned 97.9% of the contigs to 15 pseudo-chromosomes. Telomeric repeat analysis reveals that 7 of the 15 pseudo-chromosomes are gapless and telomere to telomere. The transposable element content of Ipomoea cairica is 73.4%, obviously higher than that of other Ipomoea species. A total of 38,115 protein-coding genes were predicted, with the Benchmarking Universal Single-Copy Orthologs complete rate of 98.5%, comparable to that of the genome assembly, and 92.6% of genes were functional annotated. In addition, we identified 3,039 tRNA genes and 2,403 rRNA genes in the assembled genome. Phylogenetic analysis showed that Ipomoea cairica formed a clade with Ipomoea aquatica, and they diverged from each other 8.1 million years ago. Through comparative genome analysis, we reconfirmed that a whole genome triplication event occurred specific to Convolvulaceae family and in the ancestor of the genus Ipomoea and Cuscuta. This high-quality reference genome of Ipomoea cairica will greatly facilitate the studies on the molecular mechanisms of its rapid growth and invasiveness.
Biases in Retrospective Perceptions of Changes in Well-Being Associated With Aging Attitudes
Authors: Hess Thomas M , Park Jeongsoo , Fung Helene H , Rothermund Klaus
Published: July 2022

Objectives

Aging attitudes have important consequences on functioning in later life. A critical question concerns whether such attitudes may bias perceptions of one’s own aging, with potentially negative effects on important outcomes.

Methods

Using data from adults aged 30–85 years in Germany (n = 623), Hong Kong (n = 317), and the United States (n = 313), we examined the impact of age and aging attitudes on accuracy of perceptions of change in well-being over 5 years in different domains of functioning.

Results

Across contexts, comparisons revealed good correspondence between retrospective reports and actual change. However, older adults and those with negative attitudes retrospectively reported less positive change over this period. Inconsistent with expectations, attitudes did not consistently bias accuracy of retrospective reports over cultures and domains of functioning, nor did age have a consistent moderating effect on the impact of attitudes on accuracy.

Discussion

The results highlight the complex relationship between various personal characteristics and perceptions of change in well-being, as well as the potentially insidious effects of attitudes on the accuracy of these perceptions.
Tectonic evolution of the Liupan Shan fold-and-thrust belt, NE Tibetan Plateau during the late Cenozoic: numerical simulations
Authors: Zhou Shuhong , Hu Caibo , Zhang Kai-Jun , Orellana-Rovirosa Felipe , Shi Yaolin
Published: July 2022

The propagation of Tibetan Plateau high-elevation towards the Asian interior remains poorly understood. We conduct a series of 2-D viscoelastic plastic finite element models addressing the development of the Liupan Shan fold-and-thrust belt with multiple detachments in the NE Tibetan Plateau. We focus on the spatio–temporal relations of the Liupan Shan fold-and-thrust belt and dynamic mechanisms of growth in the NE margin of Tibetan Plateau during the late Cenozoic. Our models, consisting of a seismically-constrained two-layer-crust (of variable thicknesses) plus lithospheric mantle consider tectonic horizontal contraction and the influence of elastoplastic materials, including Model 1 (only the upper crust is elastoplastic), Model 2 (both the upper crust and the middle part of the lower crust are elastoplastic) and Model 3 (the whole lithosphere is elastoplastic). The results show that Model 1 can only reflect the properties of shallow detachment layer. Models 2 and 3 can better reflect the properties of multidetachment layers and approximately represent the process of fold-and-thrust belt formation and evolution; thus suggesting the importance of plastic rheology in the deep crust. In addition, Model 3 suggests that the pre-existing fault near the Moho below Liupan Shan is activated during the evolution process of ∼8 Ma. In summary, the results embody that the initiation and evolution of the fold-and-thrust belt depend on detachment structures: the deep and shallow detachments control the evolution of surface deformation and fold-and-thrust belt altogether. The simulated surface deformation is generally consistent with actual surface elevation distribution. Moreover, the growth of the Liupan Shan range may represent an expansion of the NE Tibetan Plateau toward the Ordos basin vicinity. Additionally, the tectonically driven uplift of Liupan Shan area supports the general crustal shortening tectonic mechanism of the Tibetan Plateau.
The C4 protein of tomato yellow leaf curl Sardinia virus primes drought tolerance in tomato through morphological adjustments
Authors: Pagliarani Chiara , Moine Amedeo , Chitarra Walter , Nerva Luca , Catoni Marco , Tavazza Raffaela , Matić Slavica , Vallino Marta , Secchi Francesca , Noris Emanuela
Published: July 2022

Viruses can interfere with the ability of plants to overcome abiotic stresses, indicating the existence of common molecular networks that regulate stress responses. A begomovirus causing the tomato yellow leaf curl disease was recently shown to enhance heat tolerance in tomato and drought tolerance in tomato and Nicotiana benthamiana and experimental evidence suggested that the virus-encoded protein C4 is the main trigger of drought responses. However, the physiological and molecular events underlying C4-induced drought tolerance need further elucidation. In this study, transgenic tomato plants expressing the tomato yellow leaf curl Sardinia virus (TYLCSV) C4 protein were subjected to severe drought stress, followed by recovery. Morphometric parameters, water potential, gas exchanges, and hormone contents in leaves were measured, in combination with molecular analysis of candidate genes involved in stress response and hormone metabolism. Collected data proved that the expression of TYLCSV C4 positively affected the ability of transgenic plants to tolerate water stress, by delaying the onset of stress-related features, improving the plant water use efficiency and facilitating a rapid post-rehydration recovery. In addition, we demonstrated that specific anatomical and hydraulic traits, rather than biochemical signals, are the keynote of the C4-associated stress resilience. Our results provide novel insights into the biology underpinning drought tolerance in TYLCSV C4-expressing tomato plants, paving the way for further deepening the mechanism through which such proteins tune the plant-virus interaction.
Modular regulation of floral traits by aPRE1homolog inMimulus verbenaceus: implications for the role of pleiotropy in floral integration
Authors: Chen Hongfei , Xiao Zheng , Ding Baoqing , Diggle Pamela K , Yuan Yao-Wu
Published: July 2022

Floral traits often show correlated variation within and among species. For species with fused petals, strong correlations among corolla tube, stamen, and pistil length are particularly prevalent, and these three traits are considered an intra-floral functional module. Pleiotropy has long been implicated in such modular integration of floral traits, but empirical evidence based on actual gene function is scarce. We tested the role of pleiotropy in the expression of intra-floral modularity in the monkeyflower species Mimulus verbenaceus by transgenic manipulation of a homolog of Arabidopsis PRE1. Downregulation of MvPRE1 by RNA interference resulted in simultaneous decreases in the lengths of corolla tube, petal lobe, stamen, and pistil, but little change in calyx and leaf lengths or organ width. Overexpression of MvPRE1 caused increased corolla tube and stamen lengths, with little effect on other floral traits. Our results suggest that genes like MvPRE1 can indeed regulate multiple floral traits in a functional module but meanwhile have little effect on other modules, and that pleiotropic effects of these genes may have played an important role in the evolution of floral integration and intra-floral modularity.
Hospitalization Experiences and Post-traumatic Stress in Inflammatory Bowel Disease: Opportunities for Change
Authors: Taft Tiffany H , McGarva Josie , Omprakash Tina A , Tomasino Kathryn , Pandit Anjali , Mutlu Ece A , Hanauer Stephen B
Published: July 2022

Introduction

Medical trauma related to IBD (IBD-PTS) affects approximately 25% of patients and is associated with poor outcomes. Prior studies identify common hospitalization experiences as potentially traumatic but have not measured risk relationships for the development of IBD-PTS. We aim to investigate what aspects of hospitalizations may increase the chance of medical trauma and IBD-PTS development.

Methods

Adult patients with IBD enrolled in the IBD Partners database were recruited. Study specific questionnaires included PTSD checklist, 5th edition (PCL-5), patient experience questionnaire, and items about the patient’s most stressful hospitalization and nonhospital sources of medical trauma. Established criteria for the PCL-5 identified significant IBD-PTS symptoms (re-experiencing, avoidance, mood change, hyperarousal, global diagnosis). Select disease and treatment information was obtained from the main IBD Partners dataset. Univariate and multivariate statistics evaluated the relationships between hospitalization data and IBD-PTS.

Results

There were 639 participants with at least 1 hospitalization for IBD included. Approximately two-thirds had Crohn’s disease; most were White, non-Hispanic, female, middle-aged, and reported their IBD as being in remission. Forty percent of patients stated a hospitalization was a source of IBD-PTS. Frequent anxiety while hospitalized increased the odds of IBD-PTS 2 to 4 times; similar relationships existed for pain/pain control. Higher quality communication, information, and listening skills reduced the odds of IBD-PTS, albeit marginally.

Conclusions

Patients with IBD consistently cite hospitalizations as potential sources of medical trauma. Poorly managed anxiety and pain demonstrate the greatest chance for IBD-PTS development. Gender and racial/ethnic differences emerged for these risks. Positive interactions with the medical team may help mitigate in-hospital IBD-PTS development.
Complete resolution of paraneoplastic syndrome of inappropriate antidiuretic hormone secretion following thymic small-cell carcinoma thoracoscopic resection
Authors: Hemmati Pouya , Cassivi Stephen D
Published: July 2022

Thymic neuroendocrine tumours are rare anterior mediastinal neoplasms often associated with paraneoplastic syndromes. A patient presented with intractable hyponatraemia and a DOTATATE-avid mediastinal mass. Following medical optimization, she underwent thoracoscopic thymectomy with en bloc thymic small-cell carcinoma resection. Her symptoms resolved and her sodium levels normalized. In localized disease, curative-intent, minimally invasive thymic neuroendocrine tumour resection is safe and effective following preoperative staging and paraneoplastic syndrome management.
Risk factors for early adverse outcomes after bovine jugular vein conduit implantation: influence of oversized conduit on the outcomes
Authors: Kim Dong-Hee , Kwon Young Kern , Choi Eun Seok , Kwon Bo Sang , Park Chun Soo , Yun Tae-Jin
Published: July 2022

OBJECTIVES

We investigated potential risk factors for early failure of bovine jugular vein conduit (Contegra®) implantation for right ventricular outflow tract (RVOT) reconstruction.

METHODS

A single-centre retrospective review of 115 consecutive patients (54 males) who underwent RVOT reconstruction with Contegra between 2016 and 2019 was performed. Overall survival, explantation-free survival and freedom from significant RVOT lesions (valve regurgitation ≥ moderate or flow velocity ≥3.5 m/s) were investigated.

RESULTS

Median age, body weight and Contegra diameter were 10.3 months [interquartile range (IQR) 5.7–26.9 months], 7.8 kg (IQR 6.3–12.4 kg) and 14 mm (IQR 12–16 mm), respectively. During the median follow-up duration of 25.1 months, there were 7 deaths, 34 significant RVOT lesions, 10 endocarditis episodes and 15 explantations. Overall survival and explantation-free survival at 3 years were 94.8% and 78.4%, respectively. Significant RVOT lesions (n = 34) comprised 20 stenoses, 8 regurgitations and 6 combined lesions. Freedom from significant RVOT lesions at 3 years was 62.6%. Cox regression identified higher indexed Contegra size (Contegra diameter/body weight, mm/kg) as the only risk factor for decreased time to explantation or death (hazard ratio 2.32, P < 0.001) and time to significant RVOT lesions development (hazard ratio 2.75, P < 0.001). The cut-off value of indexed Contegra size for significant RVOT lesions at 12 months was 1.905 mm/kg (sensitivity, 0.75; specificity, 0.78; area under the curve, 0.82).

CONCLUSIONS

Outcomes of RVOT reconstruction using Contegra were acceptable. However, oversized Contegra should be avoided when possible.

IRB APPROVAL DATE

26 October 2020.

IRB REGISTRATION NUMBER

S2020-2505-0001
Ex vivo evaluation of the Ozaki procedure in comparison with the native aortic valve and prosthetic valves
Authors: Saisho Hiroyuki , Scharfschwerdt Michael , Schaller Tim , Sadat Najla , Aboud Anas , Ensminger Stephan , Fujita Buntaro
Published: July 2022

OBJECTIVES

We investigated the hydrodynamic performance and cusp kinematics of the Ozaki neocuspidized aortic valve in comparison with the native aortic and prosthetic valves in an ex vivo study.

METHODS

Native aortic valves of swine hearts were replaced by aortic valve substitutes, and their hydrodynamic performance (effective orifice area and mean pressure gradient) was evaluated in a mock circulation under defined conditions. The following aortic valve substitutes were investigated: native aortic valve, Ozaki valve, Perimount Magna Ease, Trifecta and St. Jude Medical Masters. All prosthetic valves had a labelled size of 21 mm.

RESULTS

The Ozaki valve and native aortic valve showed a similar and significantly larger orifice area than all investigated prosthetic valves particularly at high flow rates. There was no significant difference between the Ozaki valve and the native aortic valve. The native aortic valve and Ozaki valve showed a similar increase in orifice area with increasing flow through the valve while prosthetic valves showed a markedly weaker increase. Similarly, the native and Ozaki valve showed a similar increase in mPG with forward flow which was weaker than prosthetic valves. Cusp kinematics were similar between the native and Ozaki valve, whilst prosthetic valves were clearly distinguishable from them.

CONCLUSIONS

The Ozaki procedure showed excellent hydrodynamic performance compared to prosthetic valves and showed similar cusp motion characteristics to the native aortic valve. Our results suggest that the Ozaki neocuspidized valve behaves physiologically in many aspects, which may contribute to beneficial clinical outcomes.
Aripiprazole vs Risperidone Head-to-Head Effectiveness in First-Episode Non-Affective-Psychosis: A 3-Month Randomized, Flexible-Dose, Open-Label Clinical Trial
Authors: Garrido-Sánchez Lucía , Gómez-Revuelta Marcos , Ortiz-García de la Foz Víctor , Pelayo-Terán José María , Juncal-Ruiz María , Ruiz-Veguilla Miguel , Mayoral-Van Son Jacqueline , Ayesa-Arriola Rosa , Vázquez-Bourgon Javier , Crespo-Facorro Benedicto
Published: July 2022

Background

Antipsychotic choice for the acute phase of a first episode of psychosis (FEP) is of the utmost importance since it may influence long-term outcome. However, head-to-head comparisons between second-generation antipsychotics remain scarce. The aim of this study was to compare the effectiveness in the short term of aripiprazole and risperidone after FEP outbreak.

Methods

From February 2011 to October 2018, a prospective, randomized, open-label study was undertaken. Two hundred-sixty-six first-episode drug-naïve patients were randomly assigned to aripiprazole (n = 136) or risperidone (n = 130) and followed-up for 12 weeks. The primary effectiveness measure was all-cause treatment discontinuation. In addition, an analysis based on intention-to-treat principle was conducted to assess clinical efficacy.

Results

The overall dropout rate at 12 weeks was small (6.39%). Effectiveness measures were similar between treatment arms as treatment discontinuation rates (χ 2 = 0,409; P = .522), and mean time to all-cause discontinuation (log rank χ 2 = −1.009; P = .316) showed no statistically significant differences. Despite no statistically significant differences between groups regarding clinical efficacy, aripiprazole required higher chlorpromazine equivalent dosage (χ 2 = 2.160; P = .032) and extended mean time (W = 8183.5; P = .008) to reach clinical response. Sex-related adverse events and rigidity were more frequent in the risperidone group, whereas sialorrhea was on the aripiprazole group.

Conclusions

No differences regarding effectiveness were found between aripiprazole and risperidone for the short-phase treatment of FEP. Despite the importance of efficacy during this phase, differences in side effect profiles and patient’s preferences are essential factors that may lead clinical decisions for these patients.

Clinicaltrials.gov

NCT02532491. Effectiveness of Second-Generation Antipsychotics in First Episode Psychosis Patients: 1-year Follow-up (PAFIP3_1Y).
A second-order accurate numerical scheme for a time-fractional Fokker–Planck equation
Authors: Mustapha Kassem , Knio Omar M , Le Maître Olivier P
Published: July 2022

A second-order accurate time-stepping scheme for solving a time-fractional Fokker–Planck equation of order $\alpha \in (0, 1)$, with a general driving force, is investigated. A stability bound for the semidiscrete solution is obtained for $\alpha \in (1/2,1)$ via a novel and concise approach. Our stability estimate is $\alpha $-robust in the sense that it remains valid in the limiting case where $\alpha $ approaches $1$ (when the model reduces to the classical Fokker–Planck equation), a limit that presents practical importance. Concerning the error analysis, we obtain an optimal second-order accurate estimate for $\alpha \in (1/2,1)$. A time-graded mesh is used to compensate for the singular behavior of the continuous solution near the origin. The time-stepping scheme scheme is associated with a standard spatial Galerkin finite element discretization to numerically support our theoretical contributions. We employ the resulting fully discrete computable numerical scheme to perform some numerical tests. These tests suggest that the imposed time-graded meshes assumption could be further relaxed, and we observe second-order accuracy even for the case $\alpha \in (0,1/2]$, that is, outside the range covered by the theory.
From the Myth ofSelf-Governmentto the Rise ofHoloptism: Another Genealogy of Liberal Governmentality
Authors: Jacob Théo
Published: July 2022

A long-standing critique of liberalism is that it is both amoral and anti-communitarian. Bound to the totemic figures of the Law and the Market, the “liberal art of governing” is unable to conceive of social regulations outside this twin rational framework. However, the 1990s saw the international dissemination of State managerial reform—embodied by the slogan “doing better with less”—where entrepreneurial practices coexist with participatory and decentralizing policies. In the context of State redeployment, an emerging strategy is evolving as economic neoliberalism merges with cooperative liberalism inspired by the American myth of self-government. By establishing a genealogy for this other side of liberal governmentality, this paper demonstrates how contemporary neo-progressivism emphasizes “holoptic” technologies. By encouraging a “proactive citizenship” through moral and community coercion, holoptic technologies can provide new resources to resurgent authoritarianism. Thus, the study of governmentality within the field of international political sociology should take into account a power architecture that is based on the local scale and implemented by States in a context of convergence of global political orders.
New Xyleborine (Coleoptera: Curculionidae: Scolytinae) Genus With an Afrotropical-Neotropical Distribution
Authors: Osborn Rachel K , Smith Sarah M , Cognato Anthony I
Published: July 2022

Plant-associated arthropods have been shown to cross large oceanic distances on floating plant material and to establish themselves on distant landmasses. Xyleborini (Coleoptera: Curculionidae: Scolytinae) ambrosia beetles occur in forests worldwide and are likely capable of long range dispersal. In less than 20 million years, this group dispersed from Asia to tropical regions of Africa and South America. The phylogeny, taxonomy, and biogeography of one Xyleborus species group which occurs on both continents are reviewed for this study. Based on a well-resolved molecular phylogeny resulting from parsimony, likelihood, and Bayesian analyses of four gene loci, we describe a new monophyletic genus, Xenoxylebora Osborn, Smith & Cognato, gen. nov., for this bicontinental Xyleborus species group with seven Afrotropical and six Neotropical species. Six new species are described: Xenoxylebora pilosa Osborn, Smith & Cognato, sp. nov. from Africa, and Xenoxylebora addenda Osborn, Smith & Cognato, sp. nov., Xenoxylebora calculosa Osborn, Smith & Cognato, sp. nov., Xenoxylebora hystricosa Osborn, Smith & Cognato, sp. nov., Xenoxylebora serrata Osborn, Smith & Cognato, sp. nov., and Xenoxylebora sulcata Osborn, Smith & Cognato, sp. nov., from South America. Seven new combinations from Xyleborus are proposed: Xenoxylebora caudata (Schedl 1957) comb. nov., Xenoxylebora collarti (Eggers 1932) comb. nov., Xenoxylebora perdiligens (Schedl 1937) comb. nov., Xenoxylebora sphenos (Sampson 1912) comb. nov., Xenoxylebora subcrenulata (Eggers 1932) comb. nov., and Xenoxylebora syzygii (Nunberg 1959) comb. nov. from Africa, and Xenoxylebora neosphenos (Schedl 1976) comb. nov. from South America. One new synonym is proposed: Xenoxylebora sphenos (Sampson 1912) = Xyleborus tenellusSchedl 1957 syn. nov. Descriptions, diagnoses, images, and a key to the identification of all 13 species are provided. The sequence of colonization between Africa and South America is uncertain for Xenoxylebora. Prevailing ocean currents and predominant locality patterns observed for other organisms suggest an African Xenoxylebora origin. However, the phylogeny, biogeographical analyses, and a calibrated divergence time suggest a possible South American origin for African Xenoxylebora (2.3 Ma, 95% HDP 4.5–0.6 Ma), which is supported by the occurrence of ocean counter currents between the continents and evidence of dispersal from South America to Africa among some plant and arthropod taxa.
When Do Diplomatic Protests Boomerang? Foreign Protests against US Arms Sales and Domestic Public Support in Taiwan
Authors: Kagotani Koji , Wu Wen-Chin
Published: July 2022

Diplomatic protests convey one government's displeasure with the policies of another government. Yet, public support for their own government's policies can be influenced by the actions of others, so diplomatic protests have the potential to increase domestic support for the policy within the target country. A rally-’round-the-flag effect has been found to be associated with wars, crises, and sanctions. Here, we assess the existence of such an effect in relation to diplomatic protests by foreign governments. Using a survey experiment, we assess the impact of foreign government protests—specifically protests by China—against US arms sales to Taiwan on public support for Taiwan's government and its policies. We find that who lodges the protest, whether it is an adversary or a supporter, is more important than the language of the protest itself. We argue that diplomatic protests create a dilemma—lodging complaints about the behavior of other governments can increase public support for those very policies in the target country.
Combining Computational and Archival Methods to Study International Organizations: Refugees and the International Labour Organization, 1919–2015
Authors: Allen William L , Easton-Calabria Evan
Published: July 2022

Researchers studying international organizations have access to growing and varied archives due to digitization efforts. While developments in computational methods confer efficiency gains for examining these materials at scale, they raise concerns about their validity when applied to interpretive tasks in historical settings. In response, we present a general and flexible workflow that uses simple computational techniques from linguistics to enhance archival researchers’ interpretive skills and sensitivity to historical contexts. These techniques also identify patterns that can serve as evidence of causal mechanisms when embedded within strong research designs and theoretical expectations. Then, we demonstrate our mixed-method approach by applying it to a dataset of International Labour Organization’s (ILO) annual reports spanning ninety-three years. Examining the ILO's engagement with refugees as described in these documents, we identify key moments during which refugees have been particularly salient for this organization, and the emergence of new issues on its high-level policy agenda.