bluuebunny/crossref_metadata_2025 huggingface dataset:
Chromosome-level genome assembly of an endangered plant Prunus mongolica using PacBio and Hi-C technologies
Authors: Zhu Qiang , Wang Yali , Yao Ning , Ni Xilu , Wang Cuiping , Wang Meng , Zhang Lei , Liang Wenyu
Published: May 2023

Prunus mongolica is an ecologically and economically important xerophytic tree native to Northwest China. Here, we report a high-quality, chromosome-level P. mongolica genome assembly integrating PacBio high-fidelity sequencing and Hi-C technology. The assembled genome was 233.17 Mb in size, with 98.89% assigned to eight pseudochromosomes. The genome had contig and scaffold N50s of 24.33 Mb and 26.54 Mb, respectively, a BUSCO completeness score of 98.76%, and CEGMA indicated that 98.47% of the assembled genome was reliably annotated. The genome contained a total of 88.54 Mb (37.97%) of repetitive sequences and 23,798 protein-coding genes. We found that P. mongolica experienced two whole-genome duplications, with the most recent event occurring ~3.57 million years ago. Phylogenetic and chromosome syntenic analyses revealed that P. mongolica was closely related to P. persica and P. dulcis. Furthermore, we identified a number of candidate genes involved in drought tolerance and fatty acid biosynthesis. These candidate genes are likely to prove useful in studies of drought tolerance and fatty acid biosynthesis in P. mongolica, and will provide important genetic resources for molecular breeding and improvement experiments in Prunus species. This high-quality reference genome will also accelerate the study of the adaptation of xerophytic plants to drought.
Identification of Evolutionary Trajectories Shared across Human Betacoronaviruses
Authors: Escalera-Zamudio Marina , Kosakovsky Pond Sergei L , Martínez de la Viña Natalia , Gutiérrez Bernardo , Inward Rhys P D , Thézé Julien , van Dorp Lucy , Castelán-Sánchez Hugo G , Bowden Thomas A , Pybus Oliver G , Hulswit Ruben J G
Published: May 2023

Comparing the evolution of distantly related viruses can provide insights into common adaptive processes related to shared ecological niches. Phylogenetic approaches, coupled with other molecular evolution tools, can help identify mutations informative on adaptation, although the structural contextualization of these to functional sites of proteins may help gain insight into their biological properties. Two zoonotic betacoronaviruses capable of sustained human-to-human transmission have caused pandemics in recent times (SARS-CoV-1 and SARS-CoV-2), although a third virus (MERS-CoV) is responsible for sporadic outbreaks linked to animal infections. Moreover, two other betacoronaviruses have circulated endemically in humans for decades (HKU1 and OC43). To search for evidence of adaptive convergence between established and emerging betacoronaviruses capable of sustained human-to-human transmission (HKU1, OC43, SARS-CoV-1, and SARS-CoV-2), we developed a methodological pipeline to classify shared nonsynonymous mutations as putatively denoting homoplasy (repeated mutations that do not share direct common ancestry) or stepwise evolution (sequential mutations leading towards a novel genotype). In parallel, we look for evidence of positive selection and draw upon protein structure data to identify potential biological implications. We find 30 candidate mutations, from which 4 (codon sites 18121 [nsp14/residue 28], 21623 [spike/21], 21635 [spike/25], and 23948 [spike/796]; SARS-CoV-2 genome numbering) further display evolution under positive selection and proximity to functional protein regions. Our findings shed light on potential mechanisms underlying betacoronavirus adaptation to the human host and pinpoint common mutational pathways that may occur during establishment of human endemicity.
Neighborhood Social Cohesion and Loneliness in Mid- and Later Life: Are Benefits Contingent on Race/Ethnicity or Neighborhood Disorder?
Authors: Massihzadegan Setarreh , Stokes Jeffrey E
Published: May 2023

Objectives

Connections between social integration and health throughout the life span are well established, including at the neighborhood level and among older adults. Less explored is how pathways between neighborhood social cohesion and well-being may differ by race/ethnicity or by neighborhood disorder. This study investigates whether perceived neighborhood social cohesion is associated with loneliness in adults aged 50 and older, and whether this association is moderated by race/ethnicity or perceived neighborhood disorder.

Methods

We used pooled cross-sectional data from the 2016 and 2018 waves of the Health and Retirement Study and respondents to the Leave-behind Questionnaire age 50 and older, living in the community (N = 10,713). Data were analyzed using multivariate ordinary least squares regression.

Results

Perceived social cohesion was negatively associated with loneliness (B = −0.13, p < .001); however, this effect was strongest among White respondents, and significantly weaker for respondents who were Black (B = 0.02, p < .05), Hispanic (B = 0.03, p < .05), or of another race/ethnicity (B = 0.03, p < .05). Further, neighborhood disorder moderated the association between social cohesion and loneliness (B = 0.02, p < .001), reducing the strength of relationship for those in areas of high disorder. Inclusion of this interaction also attenuated the interaction between neighborhood cohesion and race for Black older adults.

Discussion

Findings show that neighborhood social cohesion matters for midlife and older adults’ loneliness, but that this relationship varies by race/ethnicity and neighborhood disorder. As such, neighborhood racial/ethnic makeup and both social and objective neighborhood characteristics should be considered when designing interventions to reduce loneliness.
Trait Loss in Evolution: What Cavefish Have Taught Us about Mechanisms Underlying Eye Regression
Authors: Sifuentes-Romero Itzel , Aviles Ari M , Carter Joseph L , Chan-Pong Allen , Clarke Anik , Crotty Patrick , Engstrom David , Meka Pranav , Perez Alexandra , Perez Riley , Phelan Christine , Sharrard Taylor , Smirnova Maria I , Wade Amanda J , Kowalko Johanna E
Published: May 2023

Synopsis

Reduction or complete loss of traits is a common occurrence throughout evolutionary history. In spite of this, numerous questions remain about why and how trait loss has occurred. Cave animals are an excellent system in which these questions can be answered, as multiple traits, including eyes and pigmentation, have been repeatedly reduced or lost across populations of cave species. This review focuses on how the blind Mexican cavefish, Astyanax mexicanus, has been used as a model system for examining the developmental, genetic, and evolutionary mechanisms that underlie eye regression in cave animals. We focus on multiple aspects of how eye regression evolved in A. mexicanus, including the developmental and genetic pathways that contribute to eye regression, the effects of the evolution of eye regression on other traits that have also evolved in A. mexicanus, and the evolutionary forces contributing to eye regression. We also discuss what is known about the repeated evolution of eye regression, both across populations of A. mexicanus cavefish and across cave animals more generally. Finally, we offer perspectives on how cavefish can be used in the future to further elucidate mechanisms underlying trait loss using tools and resources that have recently become available.
Common Interests Without Common Expertise: Reflections on Early-career Experiences in Cross-Disciplinary Research
Authors: Chan Kit Yu Karen , Wheeler Jeanette D
Published: May 2023

Synopsis

Cross-disciplinary research enables us to tackle complex problems that require expertise from different fields. Such collaborations involve researchers who have different perspectives, communication styles, and knowledge bases, and can produce results far greater than the sum of their parts. However, in an era of increasing scientific specialization, there exist many barriers for students and early-career researchers (ECRs) interested in training and undertaking interdisciplinary research endeavors. This perspective examines the challenges that students and ECRs perceive and experience in cross-disciplinary work and proposes pathways to create more inclusive and welcoming research environments. This work emerges from a National Science Foundation (NSF)-funded workshop held during the Society for Integrative and Comparative Biology (SICB) Annual Meeting in January 2023 in Austin, TX. The workshop brought together seasoned interdisciplinary scientists with undergraduate and graduate students to identify and discuss perceived challenges through small group discussions and experience sharing. Through summarizing a range of student concerns about embarking on careers as interdisciplinary scientists and identifying ways to dismantle institutional and lab management-level barriers, we aim to promote an inclusive and collaborative problem-solving environment for scientists of all experience levels.
Sex Without Sexes: Can the Cost of Finding a Mate Explain Diversity in Fungal Mating Systems?
Authors: James Timothy Y
Published: May 2023

Synopsis

Eukaryotes have evolved myriad ways of uniting gametes during sexual reproduction. A repeated pattern is the convergent evolution of a mating system with the fusion of larger gametes with smaller gametes (anisogamy) from that of fusion between morphologically identical gametes (isogamy). In anisogamous species, sexes are defined as individuals that produce only one gamete type. Although sexes abound throughout Eukarya, in fungi there are no biological sexes, because even in anisogamous species, individuals are hermaphroditic and produce both gamete types. For this reason, the term mating types is preferred over sexes, and, thus defined, only individuals of differing mating types can mate (homoallelic incompatibility). In anisogamous fungal species, there is scant evidence that there are more than two mating types, and this may be linked to genetic constraints, such as the use of mating types to determine the inheritance of cytoplasmic genomes. However, the mushroom fungi (Agaricomycetes) stand out as having both large numbers of mating types within a species, which will allow nearly all individuals to be compatible with each other, and reciprocal exchange of nuclei during mating, which will avoid cytoplasmic mixing and cyto-nuclear conflicts. Although the limitation of mating types to two in most fungi is consistent with the cyto-nuclear conflicts model, there are many facets of the Agaricomycete life cycle that also suggest they will demand a high outbreeding efficiency. Specifically, they are mostly obligately sexual and outcrossing, inhabit complex competitive niches, and display broadcast spore dispersal. Subsequently, the Agaricomycete individual pays a high cost to being choosy when encountering a mate. Here, I discuss the costs of mate finding and choice and demonstrate how most fungi have multiple ways of reducing these costs, which can explain why mating types are mostly limited to two per species. Nevertheless, it is perplexing that fungi have not evolved multiple mating types on more occasions nor evolved sexes. The few exceptions to these rules suggest that it is dictated by both molecular and evolutionary constraints.
Implementation of integrated ecosystem assessments in the International Council for the Exploration of the Sea—conceptualizations, practice, and progress
Authors: Clay Patricia M , Ferretti Johanna , Bailey Jennifer L , Goti Leyre , Dankel Dorothy J , Santurtun Marina , Fuller Jessica , Linke Sebastian , Schmidt Jörn , Nielsen Kåre Nolde , Goldsborough David , Groeneveld Rolf , Fraga Ana Rita , Elegbede Isa , Röckmann Christine
Published: May 2023

With increasing activities of multiple sectors in marine spaces, management of marine social–ecological systems requires more holistic approaches. Adopting such an approach, however, presents difficult institutional and disciplinary challenges. Here, we use the International Council for the Exploration of the Sea (ICES) as a case study on the implementation of ecosystem-based management (EBM) and integrated ecosystem assessments (IEAs). ICES includes EBM and IEAs in its Science Priorities and established IEA Working Groups (WGs) to carry out regional IEAs. But to what degree does this IEA WG work follow best practices? We examine policy documents, academic literature, and interview data from chairs of all IEA WGs. Results indicate mixed success. All groups acknowledge the holistic goals of IEA, and many use the IEA model as laid out by Levin et al. However, we found a significant variation in the degree to which the full model is applied. We identified two primary areas for improvement: (1) integration of social and economic issues and (2) involvement of stakeholders. We offer examples of how WGs have been making progress towards full IEAs, discuss how ICES can further support this transition, and suggest lessons with respect to the adoption of EBM and IEAs more broadly.
Effects of Mask Reuse on the Oropharyngeal, Skin, and Mask Microbiome
Authors: Merenstein Carter , Fitzgerald Ayannah S , Khatib Layla A , Graham-Wooten Jevon , Bushman Frederic D , Collman Ronald G
Published: May 2023

Background

Face masks have been critical in the coronavirus disease 2019 (COVID-19) pandemic, but supplies were sometimes limited and disposable masks contribute greatly to environmental waste. Studies suggest that filtration capacity is retained with repeated use, and surveys indicate many people reuse surgical masks. However, the impact of mask reuse on the host is understudied.

Methods

We applied 16S rRNA gene sequencing to investigate the bacterial microbiome of the facial skin and oropharynx of individuals randomized to wearing fresh surgical masks daily versus masks reused for 1 week.

Results

Compared to daily fresh masks, reuse was associated with increased richness (number of taxa) of the skin microbiome and trend towards greater diversity, but no difference in the oropharyngeal microbiome. Used masks had either skin-dominant or oropharynx-dominant bacterial sequences, and reused masks had >100-fold higher bacterial content but no change in composition compared to those used for 1 day.

Conclusions

One week of mask reuse increased the number of low-abundance taxa on the face but did not impact the upper respiratory microbiome. Thus, face mask reuse has little impact on the host microbiome, although whether minor changes to the skin microbiome might relate to reported skin sequelae of masking (maskne) remains to be determined.
Antibiotic prescription patterns during last days of hospitalized patients with advanced cancer: the role of palliative care consultation
Authors: Kim Jeong-Han , Yoo Shin Hye , Keam Bhumsuk , Heo Dae Seog
Published: May 2023

Objectives

Issues regarding antibiotic use in end-of-life patients with advanced cancer present a challenging ethical dilemma in academic referral centres. This study aimed to investigate the role of palliative care consultation on antibiotic prescription patterns among hospitalized patients with advanced cancer during their last days of life.

Methods

This retrospective cohort study included adult patients with metastatic solid cancer admitted to a tertiary referral hospital for at least 4 days and subsequently died and who were given antibiotics 4 days before death between January 2018 and December 2021. Patients were divided into palliative care consultation (PC) and non-consultation (non-PC) groups. The outcomes were the proportion of patients who received antibiotic combination treatment, antibiotic escalation and antibiotic de-escalation within 3 days of death. Propensity score analysis with the inverse probability of the treatment weighting method was used to compare the outcomes.

Results

Among the 1177 patients enrolled, 476 (40.4%) received palliative care consultation and 701 (59.6%) did not. The PC group received considerably less antibiotic combination treatment (49.0% versus 61.1%, adjusted OR: 0.69, 95% CI: 0.53–0.90, P = 0.006) and antibiotic escalation (15.8% versus 34.8%, adjusted OR: 0.41, 95% CI: 0.30–0.57, P < 0.001) than the non-PC group. Additionally, the PC group reported significantly higher antibiotic de-escalation (30.7% versus 17.4%, adjusted OR: 1.74, 95% CI: 1.28–2.36, P < 0.001).

Conclusion

Receiving palliative care consultation may minimize aggressive antibiotic prescription patterns in the last days of patients with advanced cancer in an academic referral centre setting.
Novel hyperthermoacidic archaeal enzymes for removal of thermophilic biofilms from stainless steel
Authors: Nam Yurina , Barnebey Adam , Kim Hayoung K , Yannone Steven M , Flint Steve
Published: May 2023

Aims

To test the efficacy of novel hot/acid hyperthermoacidic enzyme treatments on the removal of thermophilic spore-forming biofilms from stainless steel surfaces.

Methods and results

The present study measured the efficacy of hyperthermoacidic enzymes (protease, amylase, and endoglucanase) that are optimally active at low pH (≈3.0) and high temperatures (≈80°C) at removing thermophilic bacilli biofilms from stainless steel (SS) surfaces. Plate counts, spore counts, impedance microbiology, as well as epifluorescence microscopy, and scanning electron microscopy (SEM) were used to evaluate the cleaning and sanitation of biofilms grown in a continuous flow biofilm reactor. Previously unavailable hyperthermoacidic amylase, protease, and the combination of amylase and protease were tested on Anoxybacillus flavithermus and Bacillus licheniformis, and endoglucanase was tested on Geobacillus stearothermophilus. In all cases, the heated acidic enzymatic treatments significantly reduced biofilm cells and their sheltering extracellular polymeric substances (EPS).

Conclusions

Hyperthermoacidic enzymes and the associated heated acid conditions are effective at removing biofilms of thermophilic bacteria from SS surfaces that contaminate dairy plants.
Azimuthal seismic reflection characteristics with quality factor Q in viscoelastic horizontal transverse isotropic media
Authors: Xi Yijun , Yin Xingyao
Published: May 2023

In seismic exploration, a precise description of the seismic reflection property is critical for reservoir prediction and fluid identification. In the study of seismic wave transmission effects, taking into account both the viscoelastic and anisotropic properties of a medium is compatible with the features of the earth. Moreover, it is advantageous to the characterization of complicated reservoirs. According to the elastic medium foundation and the imaginary component with quality factor Q, seismic reflection properties of viscoelastic media are described in the complex domain. The complex wave number is expressed by phase velocity and Q. The attenuation angle is introduced when the complex wave number is represented by a propagation vector and an attenuation vector. The exact velocity and polarization direction of a viscoelastic medium are expressed using a complex stiffness matrix incorporating Q matrix elements. The quasi-Zoeppritz equation for viscoelastic horizontal transverse isotropic (VHTI) media is derived by using boundary conditions based on the wave function of viscoelastic media. The numerical simulation of reflectivity reveals that the reflection coefficient in a viscoelastic medium is clearly different from that of an elastic medium. Moreover, the difference in reflection coefficient in various orientations has distinct characteristics.
Outcome trajectory estimation for optimal dynamic treatment regimes with repeated measures
Authors: Zhang Yuan , Vock David M , Patrick Megan E , Finestack Lizbeth H , Murray Thomas A
Published: May 2023

In recent sequential multiple assignment randomized trials, outcomes were assessed multiple times to evaluate longer-term impacts of the dynamic treatment regimes (DTRs). Q-learning requires a scalar response to identify the optimal DTR. Inverse probability weighting may be used to estimate the optimal outcome trajectory, but it is inefficient, susceptible to model mis-specification, and unable to characterize how treatment effects manifest over time. We propose modified Q-learning with generalized estimating equations to address these limitations and apply it to the M-bridge trial, which evaluates adaptive interventions to prevent problematic drinking among college freshmen. Simulation studies demonstrate our proposed method improves efficiency and robustness.
Plant protoplasts in the age of synthetic biology
Authors: Reyna-Llorens Ivan , Ferro-Costa Miquel , Burgess Steven J
Published: May 2023

Protoplasts, which are plant cells with their cell walls removed, have been used for decades in plant research and have been instrumental in genetic transformation and the study of various aspects of plant physiology and genetics. With the advent of synthetic biology, these individualized plant cells are fundamental to accelerate the ‘design–build–test–learn’ cycle, which is relatively slow in plant research. Despite their potential, challenges remain in expanding the use of protoplasts in synthetic biology. The capacity of individual protoplasts to hybridize to form new varieties, and to regenerate from single cells, creating individuals with new features is underexplored. The main objective of this review is to discuss the use of protoplasts in plant synthetic biology and to highlight the challenges to exploiting protoplast technologies in this new ‘age of synthetic biology’.
Artificial intelligence and clinical decision support: clinicians’ perspectives on trust, trustworthiness, and liability
Authors: Jones Caroline , Thornton James , Wyatt Jeremy C
Published: May 2023

Artificial intelligence (AI) could revolutionise health care, potentially improving clinician decision making and patient safety, and reducing the impact of workforce shortages. However, policymakers and regulators have concerns over whether AI and clinical decision support systems (CDSSs) are trusted by stakeholders, and indeed whether they are worthy of trust. Yet, what is meant by trust and trustworthiness is often implicit, and it may not be clear who or what is being trusted. We address these lacunae, focusing largely on the perspective(s) of clinicians on trust and trustworthiness in AI and CDSSs. Empirical studies suggest that clinicians’ concerns about their use include the accuracy of advice given and potential legal liability if harm to a patient occurs. Onora O’Neill’s conceptualisation of trust and trustworthiness provides the framework for our analysis, generating a productive understanding of clinicians’ reported trust issues. Through unpacking these concepts, we gain greater clarity over the meaning ascribed to them by stakeholders; delimit the extent to which stakeholders are talking at cross purposes; and promote the continued utility of trust and trustworthiness as useful concepts in current debates around the use of AI and CDSSs.
Fullerenes in the circumstellar medium of Herbig Ae/Be stars: insights from the Spitzer mid-infrared spectral catalog
Authors: Arun R , Mathew Blesson , Manoj P , Maheswar G , Shridharan B , Kartha Sreeja S , Narang Mayank
Published: May 2023

This study presents the largest mid-infrared spectral catalogue of Herbig Ae/Be stars to date, containing the Spitzer Infrared Spectrograph spectra of 126 stars. Based on the catalogue analysis, two prominent infrared vibrational modes of C60 bands at 17.4 and 18.9 μm are detected in the spectra of nine sources, while 7.0 μm feature is identified in the spectra of HD 319896. The spectral index analysis and the comparison of the known sources with C60 features indicated that there exist two different types of emission classes among the sample of stars. The infrared spectra of six Herbig Ae/Be stars in this study resemble that of reflection nebulae, and their association with previously known reflection nebulae is confirmed. In the case of three Herbig Ae/Be stars, we report the tentative evidence of C60 emission features originating from the circumstellar disc or nearby diffused emission region. The detection fraction of C60 in the total HAeBe star sample is ∼7 per cent, whereas the detection fraction is 30 per cent for HAeBe stars associated with nebulosity. In the catalog, C60 is exclusively present in the circumstellar regions of B type Herbig Ae/Be stars, with no evidence of its presence detected in stars with later spectral types. The present study has increased the number of young stellar objects and reflection nebulae detected with C60 multifold, which can help in understanding the excitation and formation pathway of the species.
The shape of dark matter haloes: results from weak lensing in the ultraviolet near-infrared optical Northern survey (UNIONS)
Authors: Robison Bailey , Hudson Michael J , Cuillandre Jean-Charles , Erben Thomas , Fabbro Sébastien , Gavazzi Raphaël , Guinot Axel , Gwyn Stephen , Hildebrandt Hendrik , Kilbinger Martin , McConnachie Alan , Miller Lance , Spitzer Isaac , van Waerbeke Ludovic
Published: May 2023

Cold dark matter haloes are expected to be triaxial and so appear elliptical in projection. We use weak gravitational lensing from the Canada–France Imaging Survey (CFIS) component of the Ultraviolet Near-Infrared Optical Northern Survey (UNIONS) to measure the ellipticity of the dark matter haloes around Luminous Red Galaxies (LRGs) from the Sloan Digital Sky Survey Data Release 7 (DR7) and from the CMASS and LOWZ samples of the Baryon Oscillation Spectroscopic Survey (BOSS), assuming their major axes are aligned with the stellar light. We find that DR7 LRGs with masses M ∼ 2.7 × 1013 M⊙ h−1 have halo ellipticities e = 0.46 ± 0.10. Expressed as a fraction of the galaxy's ellipticity, we find fh = 2.2 ± 0.6. For BOSS LRGs, the detection is of marginal significance: e = 0.20 ± 0.10 and fh = 0.7 ± 0.7. These results are in agreement with other measurements of halo ellipticity from weak lensing and, taken together with previous results, suggest an increase in halo ellipticity of 0.10 ± 0.06 per decade in halo mass. This trend agrees with the predictions from hydrodynamical simulations, which find that at higher halo masses, not only do dark matter haloes become more elliptical, but that the misalignment between the major axis of the stellar light in the central galaxy and that of the dark matter decreases.
Multifrequency analysis of the radio emission from a post-merger galaxy CGCG 292-057
Authors: Misra Arpita , Jamrozy Marek , Weżgowiec Marek
Published: May 2023

Galaxies exhibiting a specific large-scale extended radio emission, such as X-shaped radio galaxies, belong to a rare class of winged radio galaxies. The morphological evolution of these radio sources is explained using several theoretical models, including galaxy mergers. However, such a direct link between a perturbed radio morphology and a galaxy merger remains observationally sparse. Here, we investigate a unique radio galaxy J1159+5820, whose host CGCG 292-057 displays the optical signature of a post-merger system with a distinct tidal tail feature, and an X-shaped radio morphology accompanied by an additional pair of inner lobes. We observed the target on a wide range of radio frequencies ranging from 147 to 4959 MHz, using dedicated GMRT and VLA observations, and supplemented it with publicly available survey data for broad-band radio analysis. Particle injection models were fitted to radio spectra of lobes and different parts of the wings. Spectral ageing analysis performed on the lobes and the wings favours a fast jet realignment model with a reorientation time-scale of a few million years. We present our results and discuss the possible mechanisms for the formation of the radio morphology.
The five types of glomerulonephritis classified by pathogenesis, activity and chronicity (GN-AC)
Authors: Romagnani Paola , Kitching A Richard , Leung Nelson , Anders Hans-Joachim
Published: May 2023

Glomerulonephritis (GN) is a diverse group of immune-mediated disorders. Currently, GN is classified largely by histological patterns that are difficult to understand and teach, and most importantly, do not indicate treatment choices. Indeed, altered systemic immunity is the primary pathogenic process and the key therapeutic target in GN. Here, we apply a conceptual framework of immune-mediated disorders to GN guided by immunopathogenesis and hence immunophenotyping: (i) infection-related GN require pathogen identification and control; (ii) autoimmunity-related GN, defined by presence of autoantibodies and (iii) alloimmunity-related GN in transplant recipients both require the suppression of adaptive immunity in lymphoid organs and bone marrow; (iv) autoinflammation-related GN, e.g. inborn errors of immunity diagnosed by genetic testing, requires suppression of single cytokine or complement pathways; and (v) Monoclonal gammopathy-related GN requires B or plasma cell clone-directed therapy. A new GN classification should include disease category, immunological activity to tailor the use of the increasing number of immunomodulatory drugs, and chronicity to trigger standard chronic kidney disease care including the evolving spectrum of cardio-renoprotective drugs. Certain biomarkers allow diagnosis and the assessment of immunological activity and disease chronicity without kidney biopsy. The use of these five GN categories and a therapy-focused GN classification is likely to overcome some of the existing hurdles in GN research, management and teaching by reflecting disease pathogenesis and guiding the therapeutic approach.
CKD therapy to improve outcomes of immune-mediated glomerular diseases
Authors: Anders Hans-Joachim , Fernandez-Juarez Gema M , Vaglio Augusto , Romagnani Paola , Floege Jürgen
Published: May 2023

The management of immunoglobulin A nephropathy, membranous nephropathy, lupus nephritis, anti-neutrophil cytoplasmic antibody–associated vasculitis, C3 glomerulonephritis, autoimmune podocytopathies and other immune-mediated glomerular disorders is focused on two major treatment goals, preventing overall mortality and the loss of kidney function. Since minimizing irreversible kidney damage best serves both goals, the management of immune-mediated kidney disorders must focus on the two central pathomechanisms of kidney function decline, i.e., controlling the underlying immune disease process (e.g. with immunotherapies) and controlling the non-immune mechanisms of chronic kidney disease (CKD) progression. Here we review the pathophysiology of these non-immune mechanisms of CKD progression and discuss non-drug and drug interventions to attenuate CKD progression in immune-mediated kidney disorders. Non-pharmacological interventions include reducing salt intake, normalizing body weight, avoiding superimposed kidney injuries, smoking cessation and regular physical activity. Approved drug interventions include inhibitors of the renin–angiotensin–aldosterone system and sodium–glucose cotransporter-2. Numerous additional drugs to improve CKD care are currently being tested in clinical trials. Here we discuss how and when to use these drugs in the different clinical scenarios of immune-mediated kidney diseases.
Complement inhibitors for kidney disease
Authors: Wooden Benjamin , Tarragon Blanca , Navarro-Torres Mariela , Bomback Andrew S
Published: May 2023

A refined understanding of the role of complement in the pathogenesis of glomerular and other kidney diseases has, over the past two decades, been matched by the development of novel, complement-targeting therapies. As we increasingly recognize the important role that complement activation across all three pathways—classical, lectin and alternative—plays in glomerular lesions both rare (e.g. C3 glomerulopathy) and common (e.g. immunoglobulin A nephropathy), we can identify avenues for precise, targeted approaches to modifying the natural history of these kidney diseases. In this review, we survey the evidence on using complement inhibition from the earliest, small-scale studies focusing on C5-targeting agents to more recent, large, multicenter, randomized trials utilizing complement blockade higher up in the complement pathway at the level of C3. We conclude by examining where the field of complement targeting therapy may be headed in light of these studies.
Preventing infections in immunocompromised patients with kidney diseases: vaccines and antimicrobial prophylaxis
Authors: Windpessl Martin , Kostopoulou Myrto , Conway Richard , Berke Ilay , Bruchfeld Annette , Soler Maria Jose , Sester Martina , Kronbichler Andreas
Published: May 2023

The coronavirus disease 2019 (COVID-19) pandemic revealed that our understanding of infectious complications and strategies to mitigate severe infections in patients with glomerular diseases is limited. Beyond COVID-19, there are several infections that specifically impact care of patients receiving immunosuppressive measures. This review will provide an overview of six different infectious complications frequently encountered in patients with glomerular diseases, and will focus on recent achievements in terms of vaccine developments and understanding of the use of specific antimicrobial prophylaxis. These include influenza virus, Streptococcus pneumoniae, reactivation of a chronic or past infection with hepatitis B virus in cases receiving B-cell depletion, reactivation of cytomegalovirus, and cases of Pneumocystis jirovecii pneumonia in patients with anti-neutrophil cytoplasmic antibody–associated vasculitis. Varicella zoster virus infections are particularly frequent in patients with systemic lupus erythematosus and an inactivated vaccine is available to use as an alternative to the attenuated vaccine in patients receiving immunosuppressants. As with COVID-19 vaccines, vaccine responses are generally impaired in older patients, and after recent administration of B-cell depleting agents, and high doses of mycophenolate mofetil and other immunosuppressants. Strategies to curb infectious complications are manifold and will be outlined in this review.
Maher Zain
Authors: Othman Khairiah
Published: May 2023

Maher Zain is a popular Lebanese Swedish R&B singer, songwriter, and music producer well known for his Islamic message songs. He caused a worldwide sensation when he emerged with his debut album Thank You Allah in 2009 which went to quadruple platinum in Indonesia (4 million copies sold) and quintuple platinum in Malaysia (five million copies sold). Although Maher Zain is now well known for his signature hip but pious Islamic R&B songs, that was not the case earlier. He had a passion for music at a young age but did not pursue music until after he finished his aeronautical engineering degree in university. Initially, Maher Zain with Nadir Khayat (also known as RedOne) worked as music producers for artists such as Kat DeLuna and Lady Gaga in New York. Although it was an exciting time working with big-name artists, Maher Zain felt that something was not quite right. Thus, on a trip back to Sweden in 2009, he reconnected with his spiritual Muslim roots and felt at peace and contented. He signed up with Awakening Records in 2009 and set out to reinvent himself as a singer and a songwriter but also to identify himself as a trifecta of being a Muslim, an Arab, and a Westerner and to try and fuse these elements together into one. Thus, when he released his debut album Thank you Allah, it was an unmistakable pop style series of songs with an R&B influence and traditional Islamic songs (nasheed) with Western musical instruments and arrangements. His subsequent albums Forgive Me in 2012 and One in 2016 went quadruple platinum (4 million copies sold) and double platinum (2 million copies sold) respectively in Malaysia. His presence as a singer is very much felt in social media, such as on YouTube, where his videos have hundreds of millions of views. To connect with his fans around the world, Zain has released versions of his songs not only in English and Arabic, but also in other languages such as Indonesian, Malay, French, Urdu, and Turkish. Zain has also toured extensively around the world, extending his appeal. His songs have been analyzed by scholars for their messages and linguistic aspects. His popularity is said to have strongly influenced the political landscape of the Arab world especially during the Arab Spring uprising. Zain has also used his popularity to be actively involved in charity works, including as an active supporter for the United Nations High Commission for Refugees (UNHCR) and performing in more than one hundred charity concerts across thirty-five countries.
History of Ancient Israelite Religion
Authors: Hess Richard
Published: May 2023

Israelite religion refers to the evidence and interpretation of the religious life and practice of ancient Israel. The period includes third and second millennia bce precursors to the Israelites as well as their first appearance in the land of Israel in the late second millennium and continuing to the Babylonian destruction of Jerusalem and exile of Israelite people in 586 bce. The study of Israelite Religion was closely tied with the study of Old Testament theology. Archaeological discoveries of the nineteenth century and critical approaches to the Hebrew Bible led to the separation of Israelite Religion from theology and to its examination in terms of historical developments of the Israelite people and their beliefs and practices. Ancient Near Eastern texts, especially from Assyria, established connections between Israelite belief, as found in biblical traditions, and the wider cultural context. This was further developed by the discovery of archival sources from the second millennium among West Semitic sites at Mari, Alalakh, Ugarit, and Emar. While Mari attested to personal names and clan religious practices such as those found in Genesis 12–37, Ugarit revealed myths of deities and accounts of their activities that had biblical parallels. Later discoveries from Emar provided evidence of cultic activities and celebrations similar to those found in priestly and ritual texts of Israel such as the book of Leviticus. Cultic finds of early standing stones (Hebrew mazzebah, pl. mazzebot) contributed to identifying a religious presence in the region millennia before Israel emerged. The early and unique cult site at Mt. Ebal paralleled that of the people’s first extra-biblical mention in the Egyptian Merneptah stele (c. 1209 bce). Iron Age temple sites such as Dan and Arad contributed to understanding Israelite practice as well as the tri-partite Jerusalem temple of 1 Kings 5–8 ascribed to Solomon. For the latter, important parallels were located to the north, especially at ‘Ain Dara’ and Tell Tayinat. Perhaps most significant in the study of this topic was the discovery and 1980s publication of Kuntillet ‘Ajrud, what was likely a caravansary in the northeast Sinai, with religious dedicatory inscriptions from c. 800 bce. Written in Hebrew and related dialects these texts bear witness to a belief by some that Israel’s chief or only deity Yahweh had a consort, Asherah/Asherata. More than any single discovery, this revolutionized the study of Israel’s religion. Many now concluded that Israelite faith during the Monarchy did not include belief of a sole deity.
Upāya
Authors: Schroeder Jeff
Published: May 2023

Upāya is a Sanskrit term meaning “means” or “strategem.” In a Buddhist context, upāya generally carries connotations of upāya-kauśalya (Pāli: upāya-kosalla), or “skill in means.” In English, upāya (T. thabs, Ch. fāngbiàn, K. pangp’yŏn, J. hōben) and upāya-kauśalya have also been translated as “skillful means,” “expedient means,” “appropriate means,” “skill in liberative technique,” “tactical skill,” and “adaptability.” Barely attested in the Pāli Canon, the term takes on great importance in Mahayana sutras (e.g. the Prajñāpāramitā, Queen Śrīmālā, Lotus, Vimalakīrti, Nirvana, and Flower Ornament sutras) and in commentaries by Asaṅga, Śāntideva, Candrakīrti, and others. The term has a wide semantic range. Most commonly, it refers to the Buddha’s skillful adaptation of his teaching methods to specific audiences or to a buddha or bodhisattva’s skillful transgression of moral principles for the sake of benefiting others. Closely related to the doctrine of the two truths (satyadvaya), the notion of upāya has served as a basis for doctrinal classification systems in which lesser teachings are deemed provisional upāya that prepare people for higher truths. Buddhists and Buddhist studies scholars have disagreed over whether use of upāya is restricted only to buddhas and advanced bodhisattvas or is employable by all; how upāyic and non-upāyic teachings or actions can be distinguished; whether all Buddhist teachings ought to be defined as upāya; whether upāya is a Mahayana innovation or a feature of Buddhism since its founding; and whether morally transgressive acts of upāya can be ethically justified. Upāya has also been an important theme in East Asian folklore, literature, and theater.
Brazil and Africa
Authors: da Silva Carlos
Published: May 2023

This article is centered on the connections between Africa and Brazil during the era of the slave trade. Luso-Brazilian vessels transported as many as five million enslaved African men and women, which corresponds roughly to 40 percent of all captives shipped to the Americas. In Brazil, enslaved and freed Africans recreated ethnic, political, and cultural communities, but political and religious events in Africa continued to play an important role in shaping patterns of slave resistance. Throughout this period, a multiracial crew formed by traders of different ethnicities and legal status (enslaved, freed, and free) circulated across the Atlantic. Politically speaking, African and Luso-Brazilian authorities on both sides of the Atlantic engaged in diplomatic exchanges in order to guarantee the operation of the slave trade beginning in the middle of the eighteenth century. These diplomatic actions intensified in the first decades of the nineteenth century in the context of British measures to abolish the transatlantic slave trade. The bilateral approach expressed in some works listed in this bibliography challenges the Triangular model, very influential in English-speaking historiography, placing the connections between Brazil and Africa in the South Atlantic at the center. The article covers mostly the eighteenth and the nineteenth centuries, although a few (very important) works stress the formation of these links as early as the sixteenth and seventeenth centuries. The discovery of mining regions intensified the trade in enslaved Africans to Brazil in the eighteenth century as well as the commercial activities on the African coast, particularly in places such as the Bight of Benin and Angola. In this period the active participation of African freedmen can be observed in the business of slaving, and their role increased in the nineteenth century with the high demand for African labor due to the expansion of sugar and coffee plantations. But numerous freedmen and freedwomen returned to Africa to escape political and religious persecution, especially after the 1835 Muslim uprising in Bahia. Many others established Atlantic communities in West Africa. Brazilian historiography is well represented in the list due to the growth of the Brazilian production regarding Brazil-Africa links since 2000. The Bahian-based research group Escravidão e Invenção da Liberdade has been one of the most prominent in examining the connections between Brazil and West Africa in the eighteenth and nineteenth centuries.
Berbice in the Atlantic World
Authors: Kars Marjoleine
Published: May 2023

Berbice was a small colony in northeastern South America. Along with Suriname, Essequibo, and Demerara, Berbice was colonized by the Dutch. The four contiguous colonies were located on the so-called Wild Coast, the area between the Orinoco and Amazon Rivers. Berbice, Demerara, and Essequibo were captured by the British in 1803. The were ceded by the Dutch to the British in 1814 and collectively became British Guiana in 1831. At independence in 1966, the country became known as Guyana. Berbice was first colonized in 1627, some 70 miles up the Berbice River as a private patroonship, or hereditary fief, granted by the Dutch West India Company to Abraham van Pere, a merchant from the province of Zeeland. Aided by Native Arawak (Lokono) and Caribs (Kali’na), colonists initially focused on Native trade and farming tobacco. Over time the Van Peres developed a few sugar plantations worked by enslaved Africans and Amerindians. In the 1670s, Amerindians and enslaved Africans rose in rebellion against the Dutch, who used divide-and-conquer tactics to pull apart the coalition and enlist powerful Natives on their side. With Native help, a tiny European minority managed to make chattel slavery of Africans a viable enterprise. Early in the eighteenth century, the Van Pere family sold the colony to a group of investors in Amsterdam who formed the Society of Berbice. The “Company,” as it was known, henceforth ran the colony. Under its government, Berbice grew rapidly, though it remained small and underdeveloped. Plantations, strung along the Berbice River and its tributary, the Canje River, focused on growing coffee, cotton, and cacao. Only on “company plantations” did enslaved people grow sugar. On the eve of a massive slave rebellion that began in 1763 and lasted more than a year, Berbice counted at most 350 Europeans and 4,500 to 5,000 enslaved Africans spread over 135 plantations. The rebellion devastated the colony, which only continued thanks to massive loans from the Dutch government, which the Company never repaid. Tired of bailing out private companies, the Dutch government took over management of the Wild Coast colonies in 1795. After the British takeover, Berbice briefly thrived. While the historiography of Suriname is well developed, we still know little about the other three Wild Coast colonies, though change is in the air. Attracted by rich and unexplored records, historians have begun to study the nature of Dutch colonialism in the area, the history of African-descended people in Berbice, and Dutch-Native relations. Much work remains to be done.
Relational Pedagogies in Early Childhood Education
Authors: Papatheodorou Theodora
Published: May 2023

Relationships are crucial throughout life and transcend temporal, geographical, cultural, and discipline boundaries. Aristotle recognized that humans are social beings, while the African philosophy of Ubuntu posits that humans exist in relation to and because of others. Research from brain development, during the last fifty years, has also demonstrated and asserted the importance of relationships for the child’s development and well-being. Indeed, relationships are at the heart of early childhood care and education curricula and practices and well-ingrained in the consciousness of early years educators. While philosophical and cultural notions of existence in the world converse with evidence from neuroscience about child development, the field of early years education is at an early stage to conceptualizing the relational dimension of pedagogy. It was in the early 2000s that relationships started to be explored from a pedagogical perspective and the term relational pedagogy emerged in the field of early childhood education. Notable early publications include J. Brownlee’s article “Teacher Education Students’ Epistemological Beliefs: Developing a Relational Model of Teaching” (2004) and J. Brownlee and D. Berthelson’s article “Developing Relational Epistemology through Relational Pedagogy: New Ways of Thinking about Personal Epistemology in Teacher Education” (2008). The edited volume by T. Papatheodorou and J. Moyles, Learning Together: Exploring Relational Pedagogy (2009), also offers a compilation of research and reflective papers exploring relational pedagogy. This annotated bibliography provides an evidence base for relational pedagogy as it has evolved from early 2000s to present time. It is organized under four main sections to include (i) theoretical and conceptual papers, (ii) empirical research papers, (iii) publications which provide practice guidance, and (iv) unexplored areas of study relevant to relational pedagogy. This annotated bibliography was supported by Bogdan Dragomir, who conducted initial literature searches, and the anonymous reviewers, who provided initial constructive feedback.