bluuebunny/crossref_metadata_2025 huggingface dataset:
Development and validation of a model for predicting mortality in patients with hip fracture
Authors: Hjelholt Thomas J , Johnsen Søren P , Brynningsen Peter K , Knudsen Jakob S , Prieto-Alhambra Daniel , Pedersen Alma B
Published: October 2021

Objective

to develop a user-friendly prediction tool of 1-year mortality for patients with hip fracture, in order to guide clinicians and patients on appropriate targeted preventive measures.

Design

population-based cohort study from 2011 to 2017 using nationwide data from the Danish Hip Fracture Registry.

Subjects

a total of 28,791 patients age 65 and above undergoing surgery for a first-time hip fracture.

Methods

patient-related prognostic factors at the time of admission were assessed as potential predictors: Nursing home residency, comorbidity (Charlson Comorbidity Index [CCI] Score), frailty (Hospital Frailty Risk Score), basic mobility (Cumulated Ambulation Score), atrial fibrillation, fracture type, body mass index (BMI), age and sex. Association with 1-year mortality examined by determining the cumulative incidence, applying univariable logistic regression and assessing discrimination (area under the receiver operating characteristics curve [AUROC]). The final model (logistic regression) was utilised on a development cohort (70% of patients). Discrimination and calibration were assessed on the validation cohort (remaining 30% of patients).

Results

all predictors showed an association with 1-year mortality, but discrimination was moderate. The final model included nursing home residency, CCI Score, Cumulated Ambulation Score, BMI and age. It had an acceptable discrimination (AUROC 0.74) and calibration, and predicted 1-year mortality risk spanning from 5 to 91% depending on the combination of predictors in the individual patient.

Conclusions

using information obtainable at the time of admission, 1-year mortality among patients with hip fracture can be predicted. We present a user-friendly chart for daily clinical practice and provide new insight regarding the interplay between prognostic factors.
The association between the inflammatory response following surgery and post-operative delirium in older oncological patients: a prospective cohort study
Authors: Brattinga Baukje , Plas Matthijs , Spikman Jacoba M , Rutgers Abraham , de Haan Jacco J , Absalom Anthony R , van der Wal-Huisman Hanneke , de Bock Geertruida H , van Leeuwen Barbara L
Published: October 2021

Introduction

Post-operative delirium (POD) is associated with increased morbidity and mortality rates in older patients. Neuroinflammation, the activation of the intrinsic immune system of the brain, seems to be one of the mechanisms behind the development of POD. The aim of this study was to explore the association between the perioperative inflammatory response and the development of POD in a cohort of older oncological patients in need for surgery.

Methods

In this prospective cohort study, patients 65 years and older in need for oncologic surgery were included. Inflammatory markers C-reactive protein (CRP), interleukin-1 beta (IL-1β), IL-6, IL10 and Neutrophil gelatinase-associated lipocalin (NGAL) were measured in plasma samples pre- and post-operatively. Delirium Observation Screening Scale (DOS) was used as screening instrument for POD in the first week after surgery. In case of positive screening, diagnosis of POD was assessed by a clinician.

Results

Between 2010 and 2016, plasma samples of 311 patients with median age of 72 years (range 65–89) were collected. A total of 38 (12%) patients developed POD in the first week after surgery. The perioperative increase in plasma levels of IL-10 and NGAL were associated with POD in multivariate logistic regression analysis (OR 1.33 [1.09–1.63] P = 0.005 and OR 1.30 [1.03–1.64], P = 0.026, respectively). The biomarkers CRP, IL-1β and IL-6 were not significantly associated with POD.

Conclusions

Increased surgery-evoked inflammatory responses of IL-10 and NGAL are associated with the development of POD in older oncological patients. The outcomes of this study contribute to understanding the aetiology of neuroinflammation and the development of POD.
ORT: a workflow linking genome-scale metabolic models with reactive transport codes
Authors: Rubinstein Rebecca L , Borton Mikayla A , Zhou Haiyan , Shaffer Michael , Hoyt David W , Stegen James , Henry Christopher S , Wrighton Kelly C , Versteeg Roelof
Published: October 2021

Motivation

Nutrient and contaminant behavior in the subsurface are governed by multiple coupled hydrobiogeochemical processes which occur across different temporal and spatial scales. Accurate description of macroscopic system behavior requires accounting for the effects of microscopic and especially microbial processes. Microbial processes mediate precipitation and dissolution and change aqueous geochemistry, all of which impacts macroscopic system behavior. As ‘omics data describing microbial processes is increasingly affordable and available, novel methods for using this data quickly and effectively for improved ecosystem models are needed.

Results

We propose a workflow (‘Omics to Reactive Transport—ORT) for utilizing metagenomic and environmental data to describe the effect of microbiological processes in macroscopic reactive transport models. This workflow utilizes and couples two open-source software packages: KBase (a software platform for systems biology) and PFLOTRAN (a reactive transport modeling code). We describe the architecture of ORT and demonstrate an implementation using metagenomic and geochemical data from a river system. Our demonstration uses microbiological drivers of nitrification and denitrification to predict nitrogen cycling patterns which agree with those provided with generalized stoichiometries. While our example uses data from a single measurement, our workflow can be applied to spatiotemporal metagenomic datasets to allow for iterative coupling between KBase and PFLOTRAN.

Availability and implementation

Interactive models available at https://pflotranmodeling.paf.subsurfaceinsights.com/pflotran-simple-model/. Microbiological data available at NCBI via BioProject ID PRJNA576070. ORT Python code available at https://github.com/subsurfaceinsights/ort-kbase-to-pflotran. KBase narrative available at https://narrative.kbase.us/narrative/71260 or static narrative (no login required) at https://kbase.us/n/71260/258.

Supplementary information

Supplementary data are available at Bioinformatics online.
A Novel Image Thresholding Method Combining Entropy With Parzen Window Estimation
Authors: Xiong Fusong , Zhang Jian , Ling Yun , Zhang Zhiqiang
Published: October 2021

Image thresholding is an important and efficient image segmentation technique, which is crucial and essential for image analysis and computer vision. In this paper, we proposed a new image thresholding method based on entropy and parzen window (PW) estimation. First, the probability of each gray-level distribution is approximate by using the PW estimation. Second, by combining the obtained probability information with entropic information of the foreground and background, a new objective function is created. At last, the ideal threshold value is obtained by optimizing the objective function. By comparing with some classical thresholding methods, such as inter class variance method (OTSU), minimum error thresholding method (MET), Kapur’s entropy based method (KAPUR) and the recent methods that take spatial information into consideration (2D-D histogram method, GLLV histogram method and Gabor histogram method), the proposed method, experiment on 10 images (one synthetic image, four nondestructive testing images and five real-world images), presents a better performance on the accuracy, robustness and visual effect of segmentation.
Modelling the impact of social distancing and targeted vaccination on the spread of COVID-19 through a real city-scale contact network
Authors: Hartnett Gavin S , Parker Edward , Gulden Timothy R , Vardavas Raffaele , Kravitz David
Published: October 2021

We use mobile device data to construct empirical interpersonal physical contact networks in the city of Portland, Oregon, both before and after social distancing measures were enacted during the COVID-19 pandemic. These networks reveal how social distancing measures and the public’s reaction to the incipient pandemic affected the connectivity patterns within the city. We find that as the pandemic developed there was a substantial decrease in the number of individuals with many contacts. We further study the impact of these different network topologies on the spread of COVID-19 by simulating an SEIR epidemic model over these networks and find that the reduced connectivity greatly suppressed the epidemic. We then investigate how the epidemic responds when part of the population is vaccinated, and we compare two vaccination distribution strategies, both with and without social distancing. Our main result is that the heavy-tailed degree distribution of the contact networks causes a targeted vaccination strategy that prioritizes high-contact individuals to reduce the number of cases far more effectively than a strategy that vaccinates individuals at random. Combining both targeted vaccination and social distancing leads to the greatest reduction in cases, and we also find that the marginal benefit of a targeted strategy as compared to a random strategy exceeds the marginal benefit of social distancing for reducing the number of cases. These results have important implications for ongoing vaccine distribution efforts worldwide.
Personalised Medicine with IL-23 Blockers: Myth or Reality?
Authors: Gottlieb Zoë S , Sands Bruce E
Published: October 2021

Background and Aims

The medical management of inflammatory bowel disease [IBD] has become increasingly targeted, through the identification of specific immune mediators involved in its pathogenesis. IL-23 is an inflammatory cytokine involved in both innate and adaptive immunity, which has been identified as a therapeutic target in Crohn’s disease [CD] and ulcerative colitis [UC] through its upstream inhibition of the T helper 17 [Th17] pathway. We sought to review available data on the efficacy of IL-23 inhibitors in the treatment of IBD and the potential for clinical and molecular predictors of response to facilitate a personalised medicine approach with these agents.

Methods

We reviewed and summarised available clinical trial data on the use of the IL-23 inhibitors risankizumab, brazikumab, mirikizumab, and guselkumab in the treatment of IBD, as well as the evidence from studies of these agents in IBD and other immune-mediated conditions which might inform prediction of response to IL-23 inhibition.

Results

Early clinical trials have demonstrated promising results following both induction and maintenance therapy with IL-23 inhibitors in CD and UC. Pre- and post-treatment levels of IL-22 and post-treatment levels of IL-17 have been identified as potential molecular predictors of response to therapy, in several studies. No significant clinical predictors of response have been identified thus far.

Conclusions

IL-23 antagonism is a promising therapeutic approach in IBD. Further exploration of molecular and clinical predictors of response may identify patients most likely to benefit from these medications.
Monitoring of physical activity promotion in children and adolescents in the EU: current status and future perspectives
Authors: Marzi Isabel , Tcymbal Antonina , Gelius Peter , Abu-Omar Karim , Reimers Anne K , Whiting Stephen , Wickramasinghe Kremlin
Published: October 2021

Background

Policy action is required to address physical inactivity in boys and girls. This action can be supported by international data collection, comparisons and sharing of good practices. Thus, this study aims to present and discuss the ongoing monitoring of physical activity (PA) indicators in children and adolescents in the 28 EU Member States.

Methods

Data on PA recommendations, PA prevalence, physical education (PE) and PA promotion programs for children and adolescents were provided by governments in a joint EU/WHO survey on the implementation status of the EU Council Recommendation on Health-Enhancing Physical Activity (HEPA) across Sectors.

Results

In 23 countries, national recommendations on PA are available. Detailed PA prevalence data among children and adolescents was available in 27 countries, in most cases separately for sex/gender and age groups. The total amount of PE lessons in schools differed greatly between countries and lessons were predominantly mandatory. After-school HEPA promotion programs were mostly implemented in EU Member States (78.6%), followed by active school breaks (57.1%), active travel to school (57.1%) and active breaks during school lessons (53.6%).

Conclusions

This study summarizes the monitoring of PA indicators among children and adolescents in all EU Member States by providing a comprehensive overview of the status of PA promotion and monitoring across the region. Based on our findings, it could be concluded that the current EU monitoring system on PA promotion should be adapted to provide evidence that can inform future policy development.
Genome-Wide Allele-Specific Expression in Obligately AsexualDaphnia pulexand the Implications for the Genetic Basis of Asexuality
Authors: Ye Zhiqiang , Jiang Xiaoqian , Pfrender Michael E , Lynch Michael
Published: October 2021

Although obligately asexual lineages are thought to experience selective disadvantages associated with reduced efficiency of fixing beneficial mutations and purging deleterious mutations, such lineages are phylogenetically and geographically widespread. However, despite several genome-wide association studies, little is known about the genetic elements underlying the origin of obligate asexuality and how they spread. Because many obligately asexual lineages have hybrid origins, it has been suggested that asexuality is caused by the unbalanced expression of alleles from the hybridizing species. Here, we investigate this idea by identifying genes with allele-specific expression (ASE) in a Daphnia pulex population, in which obligate parthenogens (OP) and cyclical parthenogens (CP) coexist, with the OP clones having been originally derived from hybridization between CP D. pulex and its sister species, Daphnia pulicaria. OP D. pulex have significantly more ASE genes (ASEGs) than do CP D. pulex. Whole-genomic comparison of OP and CP clones revealed ∼15,000 OP-specific markers and 42 consistent ASEGs enriched in marker-defined regions. Ten of the 42 ASEGs have alleles coding for different protein sequences, suggesting functional differences between the products of the two parental alleles. At least three of these ten genes appear to be directly involved in meiosis-related processes, for example, RanBP2 can cause abnormal chromosome segregation in anaphase I, and the presence of Wee1 in immature oocytes leads to failure to enter meiosis II. These results provide a guide for future molecular resolution of the genetic basis of the transition to ameiotic parthenogenesis.
Inter-annual and decadal variability of Calanus finmarchicus and C. hyperboreus in Subarctic waters north of Iceland 1990–2020
Authors: Gislason Astthor , Gudmundsson Kristinn , Olafsdottir Solveig R , Petursdottir Hildur
Published: October 2021

This study compares inter-annual dynamics of the two biomass dominant copepods in the Iceland Sea, the North Atlantic species Calanus finmarchicus and the Arctic C. hyperboreus, in an era of relatively low temperatures in the beginning of the study period (1990-1995) and higher temperatures thereafter. Samples were collected annually in May along a cross-shore transect of eight stations. The long-term variability in abundance of the two Calanus species was analysed in relation to hydrography, nutrients and phytoplankton dynamics, and large-scale climatic changes in the North Atlantic Ocean. Sea surface temperatures showed an increasing trend from the beginning to the end of the time series for all stations. From the end of the 1990s, C. finmarchicusshowed an increasing trend at the outermost station, whereas C. hyperboreus generally showed a decreasing trend along the whole transect from the mid-2000s. For both species, temperature was the single most important environmental factor explaining variance in abundance, however with opposite effects for the Arctic (C. hyperboreus) and the Atlantic (C. finmarchicus) species. It is hypothesized that warming north of Iceland may lead to increase of C. finmarchicus abundance through increased recruitment and advection, and decreased C. hyperboreus abundance. The change in species composition may in turn influence upper trophic levels, e.g. the capelin, the region’s main planktivorous fish.
Impact of early quantitative morbidity on 1-year outcomes in coronary artery bypass graft surgery
Authors: Hébert Mélanie , Lamy André , Noiseux Nicolas , Stevens Louis-Mathieu ,   the CORONARY Investigators
Published: October 2021

OBJECTIVES

We applied the Clavien-Dindo Complications Classification (CDCC) and the Comprehensive Complication Index (CCI) to the CORONARY trial to assess whether quantitative early morbidity affects outcomes at 1 year.

METHODS

All postoperative hospitalization and 30-day follow-up complications were assigned a CDCC grade. CCI were calculated for all patients (n = 4752). Kaplan–Meier analysis examined 1-year mortality and 1-year co-primary outcome (i.e. death, non-fatal stroke, non-fatal myocardial infarction, new-onset renal failure requiring dialysis or repeat coronary revascularization) by CDCC grade. Multivariable logistic regression evaluated the predictive value of CCI for both outcomes.

RESULTS

For off-pump and on-pump coronary artery bypass graft surgery, median CDCC were 1 [interquartile range: 0, 2] and 2 [1, 2] (P < 0.001), while median CCI were 8.7 [0, 22.6] and 20.9 [8.7, 29.6], respectively (P < 0.001). In on-pump, there were more grade I and grade II complications, particularly grade I and II transfusions (P < 0.001) and grade I acute kidney injury (P = 0.039), and more grade IVa respiratory failures (P = 0.047). Patients with ≥IIIa complications had greater cumulative 1-year mortality (P < 0.001). The median CCI was 8.7 [0, 22.6] in patients who survived and 22.6 [8.7, 44.3] in patients who died at 1 year (P < 0.001). The CCI remained an independent risk factor for 1-year mortality and 1-year co-primary outcome after multivariable adjustment (P < 0.001).

CONCLUSIONS

On-pump coronary artery bypass graft surgery had a greater number of complications in the early postoperative period, likely driven by transfusions, respiratory outcomes and acute kidney injury. This affects 1-year outcomes. Similar analyses have not yet been used to compare both techniques and could prove useful to quantify procedural morbidity.

Clinical trial registration

https://www.clinicaltrials.gov/ct2/show/NCT00463294; Unique Identifier: NCT00463294.
A new interval efficiency measure in data envelopment analysis based on efficiency potential
Authors: Lozano Sebastián , Khezri Somayeh
Published: October 2021

This study proposes a new approach for evaluating the efficiency of decision-making units (DMUs) with interval data. We define a potential-based measure of efficiency (PBM), analogous with the concepts of the vector field and the potential function in Physics that projects the DMUs onto the best and the worst frontiers defined by the best and the worst values of the inputs and outputs of the DMUs. This contrasts with the standard and arguably unfair approach that benchmarks the best performance of a DMU against the worst performance of all other DMUs or the worst performance of a DMU against the best performance of all other DMUs. We argue that it is more sensible to assume that all the DMUs perform at their best or at their worst. Then, in this way, a narrower efficiency interval is determined for each DMU. We show how to derive a numerical efficiency, and hence, how to rank DMUs from the efficiency interval. Our methodology is illustrated using a dataset that relates to the performance of the branches of an insurance company in Iran. We compare our methodology with other existing methods from the literature.
Infinite Energy Quasi-Periodic Solutions to Nonlinear Schrödinger Equations on ℝ
Authors: Wang W-M
Published: October 2021

We present a set of smooth infinite energy global solutions (without spatial symmetry) to the non-integrable, nonlinear Schrödinger equations on $\mathbb R$. These solutions are space-time quasi-periodic with two frequencies each. Previous results [3, 4], and the generalization [32], are quasi-periodic in time, but periodic in space. This paper generalizes J. Bourgain’s [5] semi-algebraic set method to analyze nonlinear PDEs, in the non-compact space quasi-periodic setting on $\mathbb R$.
Integral Representation and Supports of Functionals on Lipschitz Spaces
Authors: Aliaga Ramón J , Pernecká Eva
Published: October 2021

We analyze the relationship between Borel measures and continuous linear functionals on the space $\textrm{Lip}_0(M)$ of Lipschitz functions on a complete metric space $M$. In particular, we describe continuous functionals arising from measures and vice versa. In the case of weak$^\ast $ continuous functionals, that is, members of the Lipschitz-free space $\mathcal{F}(M)$, measures on $M$ are considered. For the general case, we show that the appropriate setting is rather the uniform (or Samuel) compactification of $M$ and that it is consistent with the treatment of $\mathcal{F}(M)$. This setting also allows us to give a definition of support for all elements of $\textrm{Lip}_0(M)^\ast $ with similar properties to those in $\mathcal{F}(M)$, and we show that it coincides with the support of the representing measure when such a measure exists. We deduce that the members of $\textrm{Lip}_0(M)^\ast $ that can be expressed as the difference of two positive functionals admit a Jordan-like decomposition into a positive and a negative part.
Anti-dsDNA Testing Specificity for Systemic Lupus Erythematosus: A Systematic Review
Authors: Orme Michelle E , Voreck Anja , Aksouh Redha , Schreurs Marco W J
Published: October 2021

Background

Autoantibody specificity in autoimmune diseases is variable due to each patient’s individual spectrum of autoantibodies and the inherent differences between detection methods and tests. Since false-positive results have downstream consequences, we conducted a comprehensive assessment of anti-double stranded DNA (anti-dsDNA) specificity from published studies of systemic lupus erythematosus (SLE).

Methods

A systematic review (MEDLINE, Embase, Cochrane Central Register of Controlled Trials, and Database of Abstracts of Reviews of Effects) identified cross-sectional or case-control studies published January 2004 to August 2019, reporting anti-dsDNA test accuracy data in SLE. Study quality was assessed using Quality Assessment Tool for Diagnostic Accuracy Studies, version 2. A meta-analysis was conducted to estimate specificity by test method or named test where feasible.

Results

Thirty studies were included covering 43 different tests. The Crithidia luciliae indirect immunofluorescence test (CLIFT) and fluorescence enzyme immunoassay methods are likely to be ≥ 90% specific (Euroimmun 97.8% (95% CI 96.2%–98.7%) 4 studies; EliA 94.7% (95% CI 91.7%–96.7%), 6 studies; CLIFT 98.7% (95% CI 96.7%–99.5%), 8 studies/7 tests]. For other test methods, specificity was not fully demonstrated to be ≥ 90% and/or the control group included healthy patients possibly overestimating specificity. More studies are required for NOVA Lite [96.0% (95% CI 87.2%–98.9%), 5 studies], chemiluminescence immunoassays [92.3% (95% CI 83.6%–96.6%), 6 studies/4 tests], multiplex immunoassays [89.3% (95% CI 86.1%–91.8%), 4 studies/2 tests], and Farr fluorescent immunoassays (no estimate, 2 studies). Specificity data reported for Farr radioimmunoassays [93.8% (95% CI 85.4–97.5%), 11 studies, 9 tests] and enzyme-linked immunosorbent assays [93.4% (95% CI 89.9%–95.7%), 15 studies/16 tests] lacked consistency.

Conclusion

Anti-dsDNA testing shows considerable variation in test specificity, with potential impact on the management of SLE patients. This review may help laboratory specialists and clinicians choose and interpret the appropriate anti-dsDNA test for their setting.
Prioritizing Design Process over Design Outcomes to Address Non-Indigenous Engagement with Indigenous Knowledge Systems in Design Practice
Authors: Kelly Meghan
Published: October 2021

This article will discuss non-Indigenous designer engagement with Indigenous knowledge systems and the tensions that surround these areas of design practice historically. Scholarly literature demonstrates the way in which a Eurocentric design sensibility dominates design discourse and how, more recently, the discourse has shifted to first, the decolonization of design and the recognition of Indigenous design without influence or input from non-Indigenous participation and secondly, a process of collaboration which recognizes Indigenous led, Indigenous determined outcomes. Examining the argument of ‘whiteness’ which explains that non-Indigenous and Indigenous collaboration will demonstrate colonial power structures, this article will refer to the International Indigenous Design Charter, a document created to address this tension and guide designers on best practice protocols when working with Indigenous knowledge systems in professional design practice. The International Charter offers a way to restore historical narratives and leads us to understand that attention should move away from design outcomes to one where there is a focus on the design process. This would ensure self-determination and empowerment of Indigenous communities and will challenge the dominance of Eurocentric design sensibilities by providing the opportunity for new voices in the evaluation of design.
Analysis of Genetic Diversity of Banana Weevils (Cosmopolites sordidus) (Coleoptera: Curculionidae) Using Transcriptome-Derived Simple Sequence Repeat Markers
Authors: Milton Ali , Muhanguzi Dennis , Male Allan , Kajubi Ali , Buah Stephen , Kubiriba Jerome , Tumuhimbise Robooni
Published: October 2021

The banana weevil, Cosmopolites sordidus (Germar) (Coleoptera: Curculionidae) is an economically important insect pest of bananas. It causes up to 100% yield losses and substantial lifespan reduction in bananas. Advances in genomics, proteomics, and sequencing technologies have provided powerful pathways to genotyping disastrous pests such as C. sordidus. However, such technologies are often not available to the majority of rural subtropical African banana growers and pest control managers. This study was therefore motivated by the need to create cheap and easily accessible C. sordidus genotyping methods that could be deployed by banana pest control managers to the benefit of C. sordidus control programs in the tropics where such advanced technologies are not readily accessible. We used an in-house C. sordidus transcriptome from the an-ongoing study from which we mined an array of simple sequence repeat (SSR) markers. Of these, six highly polymorphic transcriptome-derived SSR markers were used to successfully genotype within and among banana weevil population genetic diversity of 12 C. sordidus populations collected from four banana-growing agro-ecological zones (AEZs) in Uganda. The developed transcriptome-derived SSR markers can be used by researchers in population genetics for characterization of the C. sordidus and identification of new genes that are linked to traits of particular interest. The significant genetic diversity revealed in C. sordidus provides pertinent information for integrated pest management strategies.
Assessing the risk of resistance to cationic biocides incorporating realism-based and biophysical approaches
Authors: Fox Laura J , Kelly Paul P , Humphreys Gavin J , Waigh Thomas A , Lu Jian R , McBain Andrew J
Published: October 2021

The control of microorganisms is a key objective in disease prevention and in medical, industrial, domestic, and food-production environments. Whilst the effectiveness of biocides in these contexts is well-evidenced, debate continues about the resistance risks associated with their use. This has driven an increased regulatory burden, which in turn could result in a reduction of both the deployment of current biocides and the development of new compounds and formulas. Efforts to balance risk and benefit are therefore of critical importance and should be underpinned by realistic methods and a multi-disciplinary approach, and through objective and critical analyses of the literature. The current literature on this topic can be difficult to navigate. Much of the evidence for potential issues of resistance generation by biocides is based on either correlation analysis of isolated bacteria, where reports of treatment failure are generally uncommon, or laboratory studies that do not necessarily represent real biocide applications. This is complicated by inconsistencies in the definition of the term resistance. Similar uncertainties also apply to cross-resistance between biocides and antibiotics. Risk assessment studies that can better inform practice are required. The resulting knowledge can be utilised by multiple stakeholders including those tasked with new product development, regulatory authorities, clinical practitioners, and the public. This review considers current evidence for resistance and cross-resistance and outlines efforts to increase realism in risk assessment. This is done in the background of the discussion of the mode of application of biocides and the demonstrable benefits as well as the potential risks.
Arai Shōgo and His Global Civil War, circa 1885
Authors: Ghadimi Amin
Published: October 2021

This article explores the historical relationship between terrorism and global thought through the case of Arai Shōgo, a commoner from Tochigi, Japan. Arai was chief of operations in the 1885 Osaka Incident, a failed plot among Japanese democratic radicals to travel to Korea, detonate explosives, topple the Korean government, incite war with China, resist European imperialism, and invigorate the democratic movement back in Japan. By examining Arai’s intellectual life as well as his geopolitical and local context, the article suggests that the rise of public political terrorism in East Asia not only signaled but also resulted from the crisis of intellectual globalization in the 1880s, in which terrorism marked the historical origins of the phenomenon of global civil war.
An ecological perspective on water shedding from leaves
Authors: Lenz Anne-Kristin , Bauer Ulrike , Ruxton Graeme D
Published: October 2021

Water shedding from leaves is a complex process depending on multiple leaf traits interacting with rain, wind, and air humidity, and with the entire plant and surrounding vegetation. Here, we synthesize current knowledge of the physics of water shedding with implications for plant physiology and ecology. We argue that the drop retention angle is a more meaningful parameter to characterize the water-shedding capacity of leaves than the commonly measured static contact angle. The understanding of the mechanics of water shedding is largely derived from laboratory experiments on artificial rather than natural surfaces, often on individual aspects such as surface wettability or drop impacts. In contrast, field studies attempting to identify the adaptive value of leaf traits linked to water shedding are largely correlative in nature, with inconclusive results. We make a strong case for taking the hypothesis-driven experimental approach of biomechanical laboratory studies into a real-world field setting to gain a comprehensive understanding of leaf water shedding in a whole-plant ecological and evolutionary context.
‘We can’t read it all’: Theorizing a hermeneutics for large-scale data in the humanities with a case study in stylometry
Authors: Ringler Hannah
Published: October 2021

Computational methods often produce large amounts of data about texts, which create theoretical and practical challenges for textual interpretation. How can we make claims about texts, when we cannot read every text or analyze every piece of data produced? This article draws on rhetorical and literary theories of textual interpretation to develop a hermeneutical theory for gaining insight about texts with large amounts of computational data. It proposes that computational data about texts can be thought of as analytical lenses that make certain textual features salient. Analysts can read texts with these lenses, and argue for interpretations by arguing for how the analyses of many pieces of data support a particular understanding of text(s). By focusing on validating an understanding of the corpus rather than explaining every piece of data, we allow space for close reading by the human reader, focus our contributions on the humanistic insight we can gain from our corpora, and make it possible to glean insight in a way that is feasible for the limited human reader while still having strategies to argue for (or against) certain interpretations. This theory is demonstrated with an analysis of academic writing using stylometry methods, by offering a view of knowledge-making processes in the disciplines through a close analysis of function words.
The management of membranous nephropathy—an update
Authors: Caravaca-Fontán Fernando , Fernández-Juárez Gema M , Floege Jürgen , Goumenos Dimitrios , Kronbichler Andreas , Turkmen Kultigin , van Kooten Cees , Frangou Eleni , Stevens Kate I , Segelmark Mårten , Tesar Vladimir , Anders Hans-Joachim , Bruchfeld Annette
Published: October 2021

In recent decades, several important advances have taken place in the understanding of the pathogenesis underlying membranous nephropathy (MN) that have sparked renewed interest in its management. Four landmark trials in MN and a fifth clinical trial—which was a pilot study—have been published in recent years. The results from some of these trials have had a significant impact on the recommendations included in the 2021 Kidney Disease: Improving Global Outcomes (KDIGO) Guideline for the Management of Glomerular Diseases, representing a significant step forward compared with the previous guideline in several aspects, including diagnosis, disease monitoring and treatment strategies. However, considering the rapidly evolving advances in the knowledge of MN and the recent publication of the STARMEN and RI-CYCLO trials, several recommendations contained in the guideline warrant updates. This article provides a perspective of the Immunonephrology Working Group of the European Renal Association regarding the management of MN in native kidneys of adult patients.
Guazia, the earliest ovule without cupule but with unique integumentary lobes
Authors: Wang De-Ming , Liu Le , Zhou Yi , Qin Min , Meng Mei-Cen , Guo Yun , Xue Jin-Zhuang
Published: October 2021

The earliest ovules in the Late Devonian (Famennian) are surrounded by a cupule that is involved in both protection and pollination, and generally have free integumentary lobes. Here we report a new taxon from the Famennian of China, Guazia dongzhiensis gen. et sp. nov. The terminally borne ovule is apparently acupulate (without cupule) and has four radially arranged wing-like integumentary lobes that are extensively fused, and folded lengthwise and inwards. Guazia provides evidence that not all Devonian seeds possess a cupule and it increases their diversity in integumentary lobes. This genus also suggests that the integuments develop new functions, probably including wind dispersal at the expense of the cupules.
Governing evidence use in the nutrition policy process: evidence and lessons from the 2020 Canada food guide
Authors: Weldon Isaac , Parkhurst Justin
Published: October 2021

Nutrition guideline development is traditionally seen as a mechanism by which evidence is used to inform policy decisions. However, applying evidence in policy is a decidedly complex and politically embedded process, with no single universally agreed-upon body of evidence on which to base decisions, and multiple social concerns to address. Rather than simply calling for “evidence-based policy,” an alternative is to look at the governing features of the evidence use system and reflect on what constitutes improved evidence use from a range of explicitly identified normative concerns. This study evaluated the use of evidence within the Canada Food Guide policy process by applying concepts of the “good governance of evidence” – an approach that incorporates multiple normative principles of scientific and democratic best practice to consider the structure and functioning of evidence advisory systems. The findings indicated that institutionalizing a process for evidence use grounded in democratic and scientific principles can improve evidence use in nutrition policy making.
Dietary modulation of large extracellular vesicles: the good and the bad for human health
Authors: Monfoulet Laurent-Emmanuel , Martinez Maria Carmen
Published: October 2021

Extracellular vesicles (EVs) encompassing nanovesicles derived from the endosome system and generated by plasmatic membrane shedding are of increasing interest in view of their ability to sustain cell-to-cell communication and the possibility that they could be used as surrogate biomarkers of healthy and unhealthy trajectories. Nutritional strategies have been developed to preserve health, and the impact of these strategies on circulating EVs is arousing growing interest. Data available from published studies are now sufficient for a first integration to better understand the role of EVs in the relationship between diet and health. Thus, this review focuses on human intervention studies investigating the impact of diet or its components on circulating EVs. Because of analytical bias, only large EVs have been assessed so far. The analysis highlights that poor-quality diets with elevated fat and sugar content increase levels of circulating large EVs, and these can be partly counteracted by healthy food or some food micronutrients and bioactive compounds. However, knowledge of the content and the biological functions of these diet-induced EVs is still missing. It is important to address these aspects in new research in order to state if EVs are mediators of the effects of diet on health.
Archiving Faith: Record-Keeping and Catholic Community Formation in Eighteenth-Century Mesopotamia
Authors: Parker Lucy , Maxton Rosie
Published: October 2021

This article investigates the archiving practices of a little-known group of Catholics in the Ottoman Empire, the Diyarbakır Chaldeans, in the late seventeenth and eighteenth centuries. It argues for a flexible definition of archives, based not on traditional characteristics such as links to a defined institutional repository, but on their purpose of community formation. The loose institutional structure of the Chaldean Church resulted in an unconventional archive, which never had one physical centre and consisted largely of liturgical manuscripts; nonetheless, it recorded recognizably archival material and gained cohesion from the overlapping circles of families, scribes and churches involved in its production, as well as from systematic innovations in scribal practices. The Diyarbakır Chaldean archive not only reflected the distinctive form of the community but also contributed to creating and reshaping it. By recording social ties, it kept these obligations alive for decades and generated ongoing commitments. It also imagined the community on an illusory level, occluding tensions and troubles in order to preserve an idealized image of a church united under pious leadership. This dispersed, mobile archive thus was intimately connected to community formation and contributed to the survival of the Chaldean Church in a time of immense difficulty.
Respiratory and C4-photosynthetic NAD-malic enzyme coexist in bundle sheath cell mitochondria and evolved via association of differentially adapted subunits
Authors: Hüdig Meike , Tronconi Marcos A , Zubimendi Juan P , Sage Tammy L , Poschmann Gereon , Bickel David , Gohlke Holger , Maurino Veronica G
Published: October 2021

In plant mitochondria, nicotinamide adenine dinucleotide-malic enzyme (NAD-ME) has a housekeeping function in malate respiration. In different plant lineages, NAD-ME was independently co-opted in C4 photosynthesis. In the C4 Cleome species, Gynandropsis gynandra and Cleome angustifolia, all NAD-ME genes (NAD-MEα, NAD-MEβ1, and NAD-MEβ2) were affected by C4 evolution and are expressed at higher levels than their orthologs in the C3 species Tarenaya hassleriana. In T. hassleriana, the NAD-ME housekeeping function is performed by two heteromers, NAD-MEα/β1 and NAD-MEα/β2, with similar biochemical properties. In both C4 species, this role is restricted to NAD-MEα/β2. In the C4 species, NAD-MEα/β1 is exclusively present in the leaves, where it accounts for most of the enzymatic activity. Gynandropsis gynandra NAD-MEα/β1 (GgNAD-MEα/β1) exhibits high catalytic efficiency and is differentially activated by the C4 intermediate aspartate, confirming its role as the C4-decarboxylase. During C4 evolution, NAD-MEβ1 lost its catalytic activity; its contribution to the enzymatic activity results from a stabilizing effect on the associated α-subunit and the acquisition of regulatory properties. We conclude that in bundle sheath cell mitochondria of C4 species, the functions of NAD-ME as C4 photosynthetic decarboxylase and as a housekeeping enzyme coexist and are performed by isoforms that combine the same α-subunit with differentially adapted β-subunits.
Protease-stable DARPins as promising oral therapeutics
Authors: Simeon Rudo A , Zeng Yu , Chonira Vikas , Aguirre Andrea Martinez , Lasagna Mauricio , Baloh Marko , Sorg Joseph A , Tommos Cecilia , Chen Zhilei
Published: October 2021

Clostridioides difficile is an enteric bacterium whose exotoxins, TcdA and TcdB, inactivate small GTPases within the host cells, leading to bloody diarrhea. In prior work, our group engineered a panel of potent TcdB-neutralizing designed ankyrin repeat proteins (DARPin) as oral therapeutics against C. difficile infection. However, all these DARPins are highly susceptible to digestion by gut-resident proteases, i.e. trypsin and chymotrypsin. Close evaluation of the protein sequence revealed a large abundance of positively charged and aromatic residues in the DARPin scaffold. In this study, we significantly improved the protease stability of one of the DARPins, 1.4E, via protein engineering. Unlike 1.4E, whose anti-TcdB EC50 increased >83-fold after 1-hour incubation with trypsin (1 mg/ml) or chymotrypsin (0.5 mg/ml), the best progenies—T10-2 and T10b—exhibit similar anti-TcdB potency as their parent in PBS regardless of protease treatment. The superior protease stability of T10-2 and T10b is attributed to the removal of nearly all positively charged and aromatic residues except those directly engaged in target binding. Furthermore, T10-2 was found to retain significant toxin-neutralization ability in ex vivo cecum fluid and can be easily detected in mouse fecal samples upon oral administration. Both T10-2 and T10b enjoy a high thermo- and chemo-stability and can be expressed very efficiently in Escherichia coli (>100 mg/l in shaker flasks). We believe that, in additional to their potential as oral therapeutics against C. difficile infection, T10-2 and T10b can also serve as a new generation DARPin scaffold with superior protease stability.
Standard model gauge fields localized on non-Abelian vortices in six dimensions
Authors: Arai Masato , Blaschke Filip , Eto Minoru , Kawaguchi Masaki , Sakai Norisuke
Published: October 2021

A brane-world SU(5) grand unified theory model with global non-Abelian vortices is constructed in six-dimensional spacetime. We find a solution with a vortex associated to SU(3) separated from another vortex associated to SU(2). This 3–2 split configuration achieves a geometric Higgs mechanism for SU(5) → SU(3) × SU(2) × U(1) symmetry breaking. A simple deformation potential induces a domain wall between non-Abelian vortices, leading to a linear confining potential. The confinement stabilizes the vortex separation moduli, and ensures the vorticities of the SU(3) and SU(2) groups are identical. This dictates the equality of the numbers of fermion zero modes in the fundamental representation of SU(3) (quarks) and SU(2) (leptons), leading to quark/lepton generations. The standard model massless gauge fields are localized on the non-Abelian vortices thanks to a field-dependent gauge kinetic function. We perform fluctuation analysis with an appropriate gauge fixing and obtain a four-dimensional effective Lagrangian of unbroken and broken gauge fields at quadratic order. We find that SU(3) × SU(2) × U(1) gauge fields are localized on the vortices and exactly massless. Complications in analyzing the spectra of gauge fields with the nontrivial gauge kinetic function are neatly worked out by a vector-analysis-like method.
Central Bank Swap Lines: Evidence on the Effects of the Lender of Last Resort
Authors: Bahaj Saleem , Reis Ricardo
Published: October 2021

Theory predicts that central-bank lending programs put ceilings on private domestic lending rates, reduce ex post financing risk, and encourage ex ante investment. This article shows that with global banks and integrated financial markets, but domestic central banks, then lending of last resort can be achieved using swap lines. Through them, a source central bank provides source-currency credit to recipient-country banks using the recipient central bank as the monitor and as the bearer of the credit risk. In theory, the swap lines should put a ceiling on deviations from covered interest parity, lower average ex post bank borrowing costs, and increase ex ante inflows from recipient-country banks into privately issued assets denominated in the source-country’s currency. Empirically, these three predictions are tested using variation in the terms of the swap line over time, variation in the central banks that have access to the swap line, variation in the days of the week in which the swap line is open, variation in the exposure of different securities to foreign investment, and variation in banks’ exposure to dollar funding risk. The evidence suggests that the international lender of last resort is very effective.
One-year renal outcome in lupus nephritis patients with acute kidney injury: a nomogram model
Authors: Sun Fangfang , Wang Huijing , Zhang Danting , Han Fei , Ye Shuang
Published: October 2021

Objective

To develop a short-term renal outcome prediction model for acute kidney injury (AKI) in patients with LN.

Methods

Two lupus AKI cohorts from two independent centres during 2013–2019 were included: a derivation cohort from a rheumatology centre and a validation cohort from a nephrology centre. Clinical characteristics and renal histologic features were obtained. The outcome measurement was the recovery of kidney function within 12 months. Lasso regression was used for feature selection. Prediction models with or without pathology were built and a nomogram was plotted. Model evaluation including calibration curve and decision curve analysis was performed.

Results

A total of 130 patients were included in the derivation cohort and 96 patients in the validation cohort, of which 82 and 73 patients received a renal biopsy, respectively. The prognostic nomogram model without pathology included determinants of SLE duration, days from AKI onset to treatment and baseline creatinine level [C-index 0.85 (95% CI 0.78, 0.91) and 0.79 (95% CI 0.70, 0.88) for the two cohorts]. A combination of histologic tubulointerstitial (TI) fibrosis in the nomogram gave an incremental predictive performance (C-index 0.93 vs 0.85; P = 0.039) in the derivation cohort but failed to improve the performance in the validation cohort (C-index 0.81 vs 0.79; P = 0.78). Decision curve analysis suggested clinical benefit of the prediction models.

Conclusion

The predictive nomogram models might facilitate more accurate management for lupus patients with AKI.