bluuebunny/crossref_metadata_2025 huggingface dataset:
Progress towards adopting low-carbon agriculture on peatlands for sustainable development in Indonesia
Authors: Fawzi N I , Nabillah R , Suwardi  , Mulyanto B , Palunggono H B
Published: March 2024

Indonesia, progressing towards sustainable development, faces the complex task of transitioning to low-carbon agriculture in peatlands, an essential part of broader sustainable objectives. Under the Paris Agreement, it targets a conditional 41% emission reduction, focusing on minimizing emissions from peat decomposition and fires within agricultural practices in peatlands. This paper explores the complexities and progress of low-carbon agriculture in peatlands, underscoring its significance in the larger sustainable development agenda. Our study reveals that current strategies to reduce carbon emissions in peatlands aim at restoring their natural waterlogged conditions. Yet, progress is hindered mainly due to an inadequate understanding of greenhouse gas emissions from peatlands and overlooking their unique features, which leads to overestimated emissions from agricultural use. For improved strategies, it’s important to analyze successful existing sustainable practices and enhance understanding of peatland ecology. Techniques like the “Water Management Trinity,” implemented since 1986, and eco-management emphasize the importance of using permanent water gates to maintain water levels optimal for both peat preservation and crop production. Over time, these practices modify peatland attributes, making emissions comparable to those from mineral soil, thus rendering low-carbon agriculture attainable. It’s vital for stakeholders to assess emissions with updated data, incorporating detailed information on peatland characteristics and emissions. The journey towards low-carbon agriculture in Indonesia’s peatlands is a complex endeavor necessitating the amalgamation of scientific research, sustainable practices, and socio-economic development. Adopting a holistic approach can strike a balance between agricultural productivity, peatland conservation, and climate change mitigation, fulfilling sustainable development goals in Indonesia and globally.
Determinants of Livable Houses in Magelang Regency for Households with Stunted Children under Five Years of Age
Authors: Putri R F , Giyarsih S R , Prastiwi D , Nurcahyo E H , Stiyaningsih H , Amanah N , Yusnandar
Published: March 2024

Stunting in children under five years of age is a nutritional issue that many countries, including Indonesia, have yet to successfully address. According to Basic Health Research or Riset Kesehatan Dasar (Riskesdas) data from 2018, Magelang Regency has the second highest prevalence of stunted children under five in Jawa Tengah Province, at 37.9 percent. Environmental factors such as the availability of healthy and livable houses have an influence on this level. The purpose of this study is to examine the relationship between the availability of livable houses and the prevalence of stunted children under five in Magelang Regency, as well as the factors that influence the issue. The data used in the study were obtained from interviews conducted in 2019 and 2023, as well as data from Statistics Indonesia (BPS). The research employed descriptive analysis combined with inferential analysis using binary logistic regression to achieve the objectives of the study. The findings reveal that livable houses in Magelang Regency had a negative relationship with households with incidences of stunted children under five years old. Regional classification, waste management sites, sanitation constraints, perceptions of waste handling, and the head of the household’s (KRT) field of business were significant determinants of the availability of livable houses.
The Paradox of Farmers in Response Agricultural Land Conversion to National Strategic Development Policies in Central Java
Authors: Utami B W , Hariadi S S , Raya A B
Published: March 2024

The pros and cons of developing infrastructure, including transportation infrastructure, in a country known as an agricultural country will certainly involve and possibly sacrifice several parties. The development causes a dilemma for the affected parties. Klaten Regency is one of the areas in Central Java where the Yogyakarta-Solo toll road would be built. This article investigates some farmers affected by toll road construction in Klaten Regency to present the dilemma they felt using an approach to the level of achievement of farmers’ feelings towards this policy. The results of the research show the following achievement levels: (1) farmers felt sad about the land conversion due to the toll road construction project policy, (2) farmers were happy about the land acquisition compensation appraisal, and (3) farmers were sad about the decision to sell the land.
Pro-Environmental Tourism: Lessons Learned from Adventure, Wellness and Eco-tourism in Padusan Village, Mojokerto, East Java
Authors: Insani N , Ridhoi R , Hidajat H G , A’rachman F R , Darmendra I P Y , Ardiyanti R N , Veronica A
Published: March 2024

In the aftermath of Covid-19, nature tourism has gained significant traction in Indonesia. Padusan Village in Mojokerto Regency, East Java, stands out as a prime example. Nestled at the foot of Mount Welirang and bordering a lush forest, the village offers a unique blend of adventure, wellness, and ecotourism experiences. This research aims to: 1) Catalog the diverse adventure, wellness, and eco-tourism activities available in Padusan village, and 2) Highlight tourism practices that can foster pro-environmental behaviour industry-wide. A qualitative case study methodology was adopted. Data was gathered through on-site observations and in-depth interviews. Thematic analysis was the primary tool for data interpretation, with triangulation ensuring data accuracy. Preliminary findings underscore the village’s effective use of its natural hot springs and sustainable forest resources. More importantly, the nature-centric tourism in Padusan Village not only offers rejuvenation but also nudges tourists towards environmentally responsible behaviours. This study underscores the potential of nature tourism in shaping sustainable practices in the broader tourism industry.
Black Young Adult Superwomen in the Face of Gendered Racial Microaggressions: Contextualizing Challenges With Acceptance and Avoidance and Emotional Eating
Authors: Volpe Vanessa V , Collins Abbey N , Ross Julia M , Ellis Katrina R , Lewis Jioni A , Ladd Brianna A , Fitzpatrick Stephanie L
Published: March 2024

Background

Black young adult women (ages 18–35) are at disproportionate risk for obesity and emotional eating. Emotional eating interventions target psychological flexibility, such as reducing experiential avoidance and increasing acceptance of food-related thoughts. Yet Black women face gendered racism, and some endorse roles that reduce psychological flexibility, such as the superwoman schema role. Culturally centered stress and coping has often been overlooked, leading to an incomplete understanding of processes that engender emotional eating and the implications for appropriate and effective interventions for Black young adult women.

Purpose

We investigated direct and indirect pathways of associations between stress from gendered racial microaggressions to emotional eating through the endorsement of superwoman schema and two aspects of psychological flexibility.

Methods

Black young adult women (N = 504; Mage = 24.72; 75.2% African American; 98.4% cisgender) participated in an online survey wherein they reported demographics, stress from gendered racial microaggressions, superwoman schema, experiential avoidance, acceptance of food-related thoughts, and emotional eating. Path analysis was conducted to examine direct and indirect effects.

Results

Results provided evidence for indirect associations between more stress from gendered racial microaggressions and more emotional eating. More stress was associated with greater endorsement of the superwoman schema which was associated with more experiential avoidance and less acceptance of food-related thoughts, which were each associated with more emotional eating.

Conclusions

Endorsement of superwoman schema and concomitant avoidance and less acceptance may be one way that gendered racial stress propels emotional eating. Future research could test intervention components that disrupt this path.
Knowledge and the Aesthetics of Nature
Authors: Vice Samantha
Published: March 2024

Conceptualism in natural aesthetics takes knowledge of natural objects to be necessary for their appropriate appreciation. Concentrating on animals, I explore a particular version of conceptualism – functionalism – in light of debates about the effects of cognition on perception - so-called ‘cognitive penetration of perception.’ I establish the claims about cognitive penetration to which functionalism is committed, and assess the implications of its assumptions for the normative claim that functional appreciation is most appropriate to nature. I argue that functionalism has not yet provided strong reasons for thinking that knowledge affects perception in the relevant ways, and in ways required by its normative claims.
Analysis of 10-year income trends for pharmacists and other select health professionals
Authors: Chisholm-Burns Marie A , Spivey Christina A
Published: March 2024

Purpose

To evaluate income trends among pharmacists and other select health professions (dentists, nurse practitioners, registered nurses, and physicians) in the US for the 10-year period of 2012 to 2021, with special attention given to the first 2 years of the COVID-19 pandemic (2020 and 2021).

Methods

A retrospective analysis was conducted of 2012 to 2021 income data for select health professions, collected from the American Community Survey. Univariate time series analysis was conducted using exponential smoothing to examine income patterns over the 10-year study period and forecast income for the next 5-year period (2022 to 2026) for each health profession. Additionally, time series regression models were constructed for each health profession. Descriptive statistics (mean percent change in income and SD) were calculated for each health profession for the prepandemic era (2012 to 2019) and the first 2 years of the pandemic (2020 and 2021).

Results

Goodness-of-fit statistics for each forecast model indicate highly accurate forecasts. The model for each health profession indicates a significant positive trajectory in income (P < 0.001), although pharmacists are projected to have a lower rate of income growth among the 5 health professions for the next 5-year period, 2022 to 2026. During the first 2 years of the pandemic, pharmacists had the lowest mean percent change in income (mean, 2.0%; SD, 2.0%) among the 5 health professions.

Conclusion

Growth in pharmacist income is projected to lag behind that in other health professions in the near future. Individual-, organization-, and profession-level strategies may facilitate opportunities for income growth among pharmacists.
A possible pattern in the evolution of male meiotic cytokinesis in angiosperms
Authors: Hu Mingli , Ren Zhanhong , Rong Ning , Bai Mei , Wu Hong , Yang Ming
Published: March 2024

Evolution of cellular characteristics is a fundamental aspect of evolutionary biology, but knowledge about evolution at the cellular level is very limited. In particular, whether a certain intracellular characteristic evolved in angiosperms, and what significance of such evolution is to angiosperms, if it exists, are important and yet unanswered questions. We have found that bidirectional cytokinesis occurs or likely occurs in male meiosis in extant basal and near-basal angiosperm lineages, which differs from the unidirectional cytokinesis in male meiosis in monocots and eudicots. This pattern of cytokinesis in angiosperms seems to align with the distribution pattern of angiosperms with the lineages basal to monocots and eudicots living in tropical, subtropical or temperate environments and monocots and eudicots in an expanded range of environments including tropical, subtropical, temperate, subarctic and arctic environments. These two cytokinetic modes seem to result from two phragmoplast types, respectively. A phragmoplast in the bidirectional cytokinesis dynamically associates with the leading edge of a growing cell plate whereas a phragmoplast in the unidirectional cytokinesis is localized to an entire division plane. The large assembly of microtubules in the phragmoplast in unidirectional cytokinesis may be indicative of increased microtubule stability compared with that of the small microtubule assembly in the phragmoplast in bidirectional cytokinesis. Microtubules could conceivably increase their stability from evolutionary changes in tubulins and/or microtubule-associated proteins. Microtubules are very sensitive to low temperatures, which should be a reason for plants to be sensitive to low temperatures. If monocots and eudicots have more stable microtubules than other angiosperms, they will be expected to deal with low temperatures better than other angiosperms. Future investigations into the male meiotic cytokinetic directions, microtubule stability at low temperatures, and proteins affecting microtubule stability in more species may shed light on how plants evolved to inhabit cold environments.
Phylogenetics, character evolution, and historical biogeography of the Neotropical genus Besleria (Gesneriaceae)
Authors: Ferreira Gabriel E , Clark John L , Clavijo Laura , Zuluaga Alejandro , Chautems Alain , Hopkins Michael J G , Araujo Andrea O , Perret Mathieu
Published: March 2024

Besleria, a genus of perennial herbs, shrubs, or small trees growing in the understorey of rainforests, is one of the largest genera of neotropical Gesneriaceae, with over 165 species. Despite the ecological importance and ubiquity of Besleria in rainforest ecosystems, taxonomic and evolutionary studies of Besleria are limited. Here, we generated a phylogenetic analysis of Besleria using four nuclear and chloroplast DNA regions (ITS, matK, rps16, and trnL-trnF) covering more than 50% of the recognized species, along with two secondary calibration points to infer divergence times. Our results support the monophyly of Besleria and allowed us to revise the infrageneric classification and biogeographical history of the genus. We identified five major clades that do not correspond to sections or subsections in previous classifications. These clades are well circumscribed geographically but remain difficult to characterize using previously hypothesized morphological characters. Biogeographical reconstructions indicate an origin in the northern Andes during the Middle Miocene (ca. 15 Mya). The current distribution patterns of this plant group have been significantly shaped by geological and climatic events, particularly Andean uplift and the formation of the Panama Isthmus.
Species delimitation and taxonomic revision of the Ptilagrostis dichotoma species complex (Poaceae) based on statistical morphological variations
Authors: Zhang Xie-Yong , Chen Wen-Li
Published: March 2024

Statistical morphological variations at the population level serve as a robust foundation for species delimitation and taxonomic treatment. We employed this approach to investigate species delimitation within the Ptilagrostis dichotoma species complex (Poaceae), which is characterized by open panicles. While three species have been described, the boundaries between these species and the morphological distributions of all taxonomic traits remain unclear. In this study, we examined the geographical variability of 19 morphological traits based on at least six individuals from each of the 28 populations across the entire distributional range of the species complex. Our statistical analyses identified five distinct phenotypic clusters with specific geographical preferences. Three of these clusters corresponded to the previously described species, while the remaining two clusters represented previously undescribed species. Furthermore, our findings highlight several traits, such as basal leaf scabrosity, panicle branch pulvinae, and glume length, which exhibit distinct gaps between phenotypic units and prove highly valuable for species delimitation. Finally, two new species are described and a key is provided to differentiate the five species. This morphological revision establishes a basis for future studies on species boundaries and divergences of the complex based on other evidence.
Andean uplift, climatic events, and rainforest bridges determined the spatiotemporal evolution of the cumaru and tonka beans (Dipterygeae: Leguminosae)
Authors: Carvalho Catarina S , Lima Haroldo C , Lemes Maristerra R , Cardoso Domingos
Published: March 2024

Historical climatic and geological events are largely known to have impacted biome evolution across the Neotropics and their associated rich biodiversity. However, a clear understanding of dispersal and biome shifts between neotropical biomes over time is still lacking for many ecologically important plant clades. We investigated the timing and ancestral species movements within the early branching papilionoid legume Dipterygeae lineage of neotropical tree species, some of which are among the most ecologically dominant across Amazonian rainforests and Brazilian savannas, to understand how dispersal and evolutionary trajectories in biome predilection have led to their modern distribution. We also estimated the evolution of fruit types and discuss their potential roles in the colonization of non-Amazonian rainforest habitats. To address these questions, we used one nuclear (ITS/5.8S) and two plastid (matK and trnL intron) DNA regions of the Dipterygeae clade to estimate divergence times with a Bayesian relaxed-clock approach, ancestral area distribution, and evolutionary shifts in biome and morphological traits. All currently recognized species of this clade were sampled, covering its full geographical range. Dipterygeae originated in the Amazonia during the Middle Eocene, where it has undergone a long history of in situ diversification, particularly over the last 15 Myr. Dispersal events into the rainforests of the Brazilian Coastal Atlantic Forest and Chocó + Central America, the fire-prone savannas of the Cerrado, and the Caatinga seasonally dry tropical forest occurred independently. Most lineages ecologically associated with rainforests are dispersed by animals (zoochory), whereas shifts to open habitats generally coincide with wind dispersal (anemochory). Our study highlights the significance of geological events, climatic factors, and shifts in fruit type as crucial contributors to the diversification of Dipterygeae.
APP antisense oligonucleotides reduce amyloid-β aggregation and rescue endolysosomal dysfunction in Alzheimer’s disease
Authors: Hung Christy , Fertan Emre , Livesey Frederick J , Klenerman David , Patani Rickie
Published: March 2024

APP gene dosage is strongly associated with Alzheimer’s disease (AD) pathogenesis. Genomic duplication of the APP locus leads to autosomal dominant early-onset AD. Individuals with Down syndrome (trisomy of chromosome 21) harbour three copies of the APP gene and invariably develop progressive AD with highly characteristic neuropathological features.

Restoring expression of APP to the equivalent of that of two gene copies, or lower, is a rational therapeutic strategy, as it would restore physiological levels of neuronal APP protein without the potentially deleterious consequences of inadvertently inducing loss of APP function.

Here we find that antisense oligonucleotides (ASOs) targeting APP are an effective approach to reduce APP protein levels and rescue endolysosome and autophagy dysfunction in APP duplication and Trisomy 21 human induced pluripotent stem cell (hiPSC)-derived cortical neurons. Importantly, using ultrasensitive single-aggregate imaging techniques, we show that APP targeting ASOs significantly reduce both intracellular and extracellular amyloid-β-containing aggregates.

Our results highlight the potential of APP ASOs as a therapeutic approach for forms of AD caused by duplication of the APP gene, including monogenic AD and AD related to Down syndrome.
Photoluminescence of 3- and 4-coordinate platinum(0) phosphine complexes
Authors: Mizumoto Yoji , Murao Mio , Yamazaki Yasuomi , Tsubomura Taro
Published: March 2024

Six platinum complexes bearing monodentate phosphine ligands were prepared and their structures and photophysical properties examined. The complexes were photoluminescent in the solid state, with a maximum quantum yield of 72%. The tris(phosphine) platinum complexes displayed more red-shifted emissions than the tetrakis complexes. The nature of the emissive excited states is discussed based on the results of density functional theory and time-dependent density functional theory calculations.
Dermatology clinic attendance rates: does the content of an SMS reminder make a difference?
Authors: Damani Namiz , Saffar Nawar , Yesudian Paul D
Published: March 2024

This is a study assessing the impact of SMS reminders on ‘did not attend’ rates, including the effect of an attempt to ‘nudge’ patients by highlighting the financial burden to the NHS of a missed appointment in an effort to motivate them to attend their outpatient clinic appointment.
Lower Insulin Sensitivity Through 36 Months of Life With in Utero HIV and Antiretroviral Exposure in Botswana: Results From the Tshilo Dikotla Study
Authors: Jao Jennifer , Bonner Lauren B , Dobinda Katrina , Powis Kathleen M , Sun Shan , Legbedze Justine , Mmasa Keolebogile N , Makhema Joseph , Mmalane Mompati , Kgole Samuel , Masasa Gosego , Moyo Sikhulile , Gerschenson Mariana , Mohammed Terence , Abrams Elaine J , Kurland Irwin J , Geffner Mitchell E
Published: March 2024

Background

There are little data on changes in insulin sensitivity during the first few years of life following in utero human immunodeficiency virus (HIV) and antiretroviral (ARV) exposure.

Methods

The Tshilo Dikotla study enrolled pregnant persons with HIV (PWH) (receiving tenofovir/emtricitabine or lamivudine plus dolutegravir or efavirenz) and pregnant individuals without HIV, as well as their liveborn children. Newborns were randomized to receive either zidovudine (AZT) or nevirapine (NVP) postnatal prophylaxis. Homeostasis Model Assessment for Insulin Resistance (HOMA-IR) was assessed at birth and 1, 18, 24, and 36 months of life. We fit linear mixed-effects models to evaluate the association between in utero HIV/ARV exposure and average HOMA-IR from birth through 36 months of life, adjusting for confounders.

Results

A total of 419 children were included (287 with in utero HIV/ARV exposure and uninfected [CHEU] and 132 without in utero HIV/ARV exposure [CHUU]). CHEU were born to older women (29.6 vs 25.3 years of age) with higher gravidity (3 vs 1). HOMA-IR was persistently higher in CHEU versus CHUU in adjusted analyses (mean difference of 0.07 in log10 HOMA-IR, P = .02) from birth through 36 months of life. Among CHEU, no differences in HOMA-IR were observed from birth through 36 months by in utero ARV exposure status or between AZT and NVP infant prophylaxis arms.

Conclusions

In utero HIV/ARV exposure was associated with lower insulin sensitivity throughout the first 36 months of life, indicating persistent early life metabolic disturbances which may raise concern for poorer metabolic health later in life.
Risk factors for long-term mortality after acute aortic dissection—results of the German registry for acute aortic dissection type a long-term follow-up
Authors: Böning Andreas , Kretzer John-Arved , Arif Rawa , Etz Christian D , Pöling Jochen , Rylski Bartosz , Czerny Martin , Brickwedel Jens , Peterss Sven , Holubec Tomas , Jawny Philipp , Krueger Tobias , Feißt Manuel ,   for the GERAADA Study Group
Published: March 2024

OBJECTIVES

Several short-term analyses from German Registry for Acute Aortic Dissection Type A (GERAADA) have been published. This study investigated whether short-term risk factors are transferable to the long-term prognosis of patients.

METHODS

Thirty-three centres with 2686 patients participated in the long-term follow-up. A total of 1164 patients died, 1063 survived and 459 were lost to follow-up during the follow-up timeframe (mean duration: 10.2 years). Long-term mortality of the cohort was compared with an age-stratified, German population.

RESULTS

One, 5 and 10 years after initial surgery, the survival of the GERAADA patient cohort was 71.4%, 63.4% and 51%, respectively. Without the early deaths (90-day mortality 25.4%), survival was calculated after 1, 5 and 10 years: 95.6%, 83.5% and 68.3%. Higher age, longer extracorporeal circulation time, shorter perioperative ventilation time and postoperative neurologic deficits were predictive of long-term prognosis. In an age-divided landmark analysis, the mortality of aortic dissection surgery survivors was found to be similar to that of the general German population. If patients are sorted in risk groups according to the GERAADA score, long-term survival differs between the risk groups.

CONCLUSIONS

If patients have survived an acute postoperative period of 90 days, life expectancy comparable to that of the general German population can be assumed in lower- and medium-risk patients. Whether the GERAADA score can provide valuable insights into the long-term prognosis of patients undergoing surgery for acute aortic dissection type A is still unclear.
Large-scale plasma proteomics in the UK Biobank modestly improves prediction of major cardiovascular events in a population without previous cardiovascular disease
Authors: Royer Patrick , Björnson Elias , Adiels Martin , Josefson Rebecca , Hagberg Eva , Gummesson Anders , Bergström Göran
Published: March 2024

Aims

Improved identification of individuals at high risk of developing cardiovascular disease would enable targeted interventions and potentially lead to reductions in mortality and morbidity. Our aim was to determine whether use of large-scale proteomics improves prediction of cardiovascular events beyond traditional risk factors (TRFs).

Methods and results

Using proximity extension assays, 2919 plasma proteins were measured in 38 380 participants of the UK Biobank. Both data- and literature-based feature selection and trained models using extreme gradient boosting machine learning were used to predict risk of major cardiovascular events (MACEs: fatal and non-fatal myocardial infarction, stroke, and coronary artery revascularization) during a 10-year follow-up. Area under the curve (AUC) and net reclassification index (NRI) were used to evaluate the additive value of selected protein panels to MACE prediction by Systematic COronary Risk Evaluation 2 (SCORE2) or the 10 TRFs used in SCORE2. SCORE2 and SCORE2 refitted to UK Biobank data predicted MACE with AUCs of 0.740 and 0.749, respectively. Data-driven selection identified 114 proteins of greatest relevance for prediction. Prediction of MACE was not improved by using these proteins alone (AUC of 0.758) but was significantly improved by combining these proteins with SCORE2 or the 10 TRFs (AUC = 0.771, P < 001, NRI = 0.140, and AUC = 0.767, P = 0.03, NRI 0.053, respectively). Literature-based protein selection (113 proteins from five previous studies) also improved risk prediction beyond TRFs while a random selection of 114 proteins did not.

Conclusion

Large-scale plasma proteomics with data-driven and literature-based protein selection modestly improves prediction of future MACE beyond TRFs.
Mechanism-based therapy of non-cardiac syncope: a practical guide
Authors: Brignole Michele , Rivasi Giulia , Fedorowski Artur
Published: March 2024

The term non-cardiac syncope includes all forms of syncope, in which primary intrinsic cardiac mechanism and non-syncopal transient loss of consciousness can be ruled out. Reflex syncope and orthostatic hypotension are the most frequent aetiologies of non-cardiac syncope. As no specific therapy is effective for all types of non-cardiac syncope, identifying the underlying haemodynamic mechanism is the essential prerequisite for an effective personalized therapy and prevention of syncope recurrences. Indeed, choice of appropriate therapy and its efficacy are largely determined by the syncope mechanism rather than its aetiology and clinical presentation. The two main haemodynamic phenomena leading to non-cardiac syncope include either profound hypotension or extrinsic asystole/pronounced bradycardia, corresponding to two different haemodynamic syncope phenotypes, the hypotensive and bradycardic phenotypes. The choice of therapy—aimed at counteracting hypotension or bradycardia—depends on the given phenotype. Discontinuation of blood pressure–lowering drugs, elastic garments, and blood pressure–elevating agents such as fludrocortisone and midodrine are the most effective therapies in patients with hypotensive phenotype. Cardiac pacing, cardioneuroablation, and drugs preventing bradycardia such as theophylline are the most effective therapies in patients with bradycardic phenotype of extrinsic cause.
Data integration strategies for whole-cell modeling
Authors: Tummler Katja , Klipp Edda
Published: March 2024

Data makes the world go round—and high quality data is a prerequisite for precise models, especially for whole-cell models (WCM). Data for WCM must be reusable, contain information about the exact experimental background, and should—in its entirety—cover all relevant processes in the cell. Here, we review basic requirements to data for WCM and strategies how to combine them. As a species-specific resource, we introduce the Yeast Cell Model Data Base (YCMDB) to illustrate requirements and solutions. We discuss recent standards for data as well as for computational models including the modeling process as data to be reported. We outline strategies for constructions of WCM despite their inherent complexity.
Identification of Parthenogenesis-Inducing Effector Proteins in Wolbachia
Authors: Fricke Laura C , Lindsey Amelia R I
Published: March 2024

Bacteria in the genus Wolbachia have evolved numerous strategies to manipulate arthropod sex, including the conversion of would-be male offspring to asexually reproducing females. This so-called “parthenogenesis induction” phenotype can be found in a number of Wolbachia strains that infect arthropods with haplodiploid sex determination systems, including parasitoid wasps. Despite the discovery of microbe-mediated parthenogenesis more than 30 yr ago, the underlying genetic mechanisms have remained elusive. We used a suite of genomic, computational, and molecular tools to identify and characterize two proteins that are uniquely found in parthenogenesis-inducing Wolbachia and have strong signatures of host-associated bacterial effector proteins. These putative parthenogenesis-inducing proteins have structural homology to eukaryotic protein domains including nucleoporins, the key insect sex determining factor Transformer, and a eukaryotic-like serine–threonine kinase with leucine-rich repeats. Furthermore, these proteins significantly impact eukaryotic cell biology in the model Saccharomyces cerevisiae. We suggest that these proteins are parthenogenesis-inducing factors and our results indicate that this would be made possible by a novel mechanism of bacterial-host interaction.
Fixation times of de novo and standing beneficial variants in subdivided populations
Authors: Sudbrack Vitor , Mullon Charles
Published: March 2024

The rate at which beneficial alleles fix in a population depends on the probability of and time to fixation of such alleles. Both of these quantities can be significantly impacted by population subdivision and limited gene flow. Here, we investigate how limited dispersal influences the rate of fixation of beneficial de novo mutations, as well as fixation time from standing genetic variation. We investigate this for a population structured according to the island model of dispersal allowing us to use the diffusion approximation, which we complement with simulations. We find that fixation may take on average fewer generations under limited dispersal than under panmixia when selection is moderate. This is especially the case if adaptation occurs from de novo recessive mutations, and dispersal is not too limited (such that approximately FST<0.2). The reason is that mildly limited dispersal leads to only a moderate increase in effective population size (which slows down fixation), but is sufficient to cause a relative excess of homozygosity due to inbreeding, thereby exposing rare recessive alleles to selection (which accelerates fixation). We also explore the effect of metapopulation dynamics through local extinction followed by recolonization, finding that such dynamics always accelerate fixation from standing genetic variation, while de novo mutations show faster fixation interspersed with longer waiting times. Finally, we discuss the implications of our results for the detection of sweeps, suggesting that limited dispersal mitigates the expected differences between the genetic signatures of sweeps involving recessive and dominant alleles.
Exploring salt tolerance mechanisms using machine learning for transcriptomic insights: case study in Spartina alterniflora
Authors: Huang Zhangping , Chen Shoukun , He Kunhui , Yu Tingxi , Fu Junjie , Gao Shang , Li Huihui
Published: March 2024

Salt stress poses a significant threat to global cereal crop production, emphasizing the need for a comprehensive understanding of salt tolerance mechanisms. Accurate functional annotations of differentially expressed genes are crucial for gaining insights into the salt tolerance mechanism. The challenge of predicting gene functions in under-studied species, especially when excluding infrequent GO terms, persists. Therefore, we proposed the use of NetGO 3.0, a machine learning-based annotation method that does not rely on homology information between species, to predict the functions of differentially expressed genes under salt stress. Spartina alterniflora, a halophyte with salt glands, exhibits remarkable salt tolerance, making it an excellent candidate for in-depth transcriptomic analysis. However, current research on the S. alterniflora transcriptome under salt stress is limited. In this study we used S. alterniflora as an example to investigate its transcriptional responses to various salt concentrations, with a focus on understanding its salt tolerance mechanisms. Transcriptomic analysis revealed substantial changes impacting key pathways, such as gene transcription, ion transport, and ROS metabolism. Notably, we identified a member of the SWEET gene family in S. alterniflora, SA_12G129900.m1, showing convergent selection with the rice ortholog SWEET15. Additionally, our genome-wide analyses explored alternative splicing responses to salt stress, providing insights into the parallel functions of alternative splicing and transcriptional regulation in enhancing salt tolerance in S. alterniflora. Surprisingly, there was minimal overlap between differentially expressed and differentially spliced genes following salt exposure. This innovative approach, combining transcriptomic analysis with machine learning-based annotation, avoids the reliance on homology information and facilitates the discovery of unknown gene functions, and is applicable across all sequenced species.
In patients supported with peripheral veno-arterial extracorporeal membrane oxygenation, what factors are associated with the development of spinal cord ischaemia?
Authors: Zhu Alison , Tan Charis , Chard Richard , Orr Yishay
Published: March 2024

A best evidence topic in cardiac surgery was written according to a structured protocol. The question addressed was ‘in patients supported with peripheral veno-arterial extracorporeal membrane oxygenation, what factors are associated with the development of spinal cord ischaemia’? Altogether, more than 22 papers were found using the reported search, of which 10 represented the best evidence to answer the clinical question. The authors, journal, date and country of publication, patient group studied, study type, relevant outcomes and results of these papers are tabulated. Of the 28 patients reported by included studies, the thoracic spinal cord was most commonly affected. Twenty patients (71%) survived to hospital discharge and 7 (25%) were reported to have neurological recovery. Potential confounders included coronary angiography, cardiac arrest requiring chest compressions and concomitant intra-aortic balloon pump. Consequently, all papers highlighted the likely multifactorial aetiology of spinal cord infarction in these patients. We propose that close neurological observation, particularly in patients who have received chest compressions, and management of potential aetiological factors is crucial to aid in timely diagnosis and potential prevention of this rare complication. Limiting sedation and neuromuscular blockade to enable neurologic assessment of the lower limbs may allow more timely diagnosis.
Evaluation of 5 Polymerase Chain Reaction Assays for the Detection of Mpox Virus
Authors: Fattouh Ramzi , Boissinot Karel , Jeong Esther , Mendlowitz Andrew B , Sjaarda Calvin P , Wong Henry , Kozak Robert , Sheth Prameet M , Matukas Larissa M
Published: March 2024

Background

In 2022, the global dissemination of mpox virus (MPXV) outside endemic regions prompted the expansion of diagnostic testing worldwide. This study assesses the performance characteristics of 5 real-time polymerase chain reaction (PCR) assays in detecting MPXV during the 2022 outbreak.

Methods

Clinical specimens collected from patients across Ontario, Canada, were tested on the following assays: RealStar Orthopoxyvirus PCR and FlexStar Monkeypox virus PCR (Altona Diagnostics), Novaplex MPXV (Seegene), VIASURE Monkeypox virus Real Time PCR Reagents (CerTest Biotec), and a laboratory-developed test. Positive percent agreement (PPA), negative percent agreement (NPA), relative limit of detection (LOD), and precision were evaluated and MPXV lineages were determined using an amplicon-based whole-genome sequencing (WGS) assay.

Results

Swabs were collected from various anatomic sites (65 positive and 30 negative). All assays demonstrated 100% NPA (95% confidence interval, 88.4%/88.1%–100.0%), with PPA ranging from 92.2% (82.7%–97.4%) to 96.9% (89.3%–99.6%). LOD and precision were comparable across assays, with coefficient of variations <3%. WGS analysis identified 6 lineages, all belonging to subclade IIb.

Conclusions

The assays exhibited excellent PPA, NPA, LOD, and precision. Ongoing performance monitoring is essential to detect assay escape mutants and ensure universal detection of evolving MPXV strains.
Comparative Diagnostic Utility of SARS-CoV-2 Rapid Antigen and Molecular Testing in a Community Setting
Authors: Kim Ashley E , Bennett Julia C , Luiten Kyle , O’Hanlon Jessica A , Wolf Caitlin R , Magedson Ariana , Han Peter D , Acker Zack , Regelbrugge Lani , McCaffrey Kathryn M , Stone Jeremey , Reinhart David , Capodanno Benjamin J , Morse Stephen S , Bedford Trevor , Englund Janet A , Boeckh Michael , Starita Lea M , Uyeki Timothy M , Carone Marco , Weil Ana , Chu Helen Y
Published: March 2024

Background

SARS-CoV-2 antigen-detection rapid diagnostic tests (Ag-RDTs) have become widely utilized but longitudinal characterization of their community-based performance remains incompletely understood.

Methods

This prospective longitudinal study at a large public university in Seattle, WA utilized remote enrollment, online surveys, and self-collected nasal swab specimens to evaluate Ag-RDT performance against real-time reverse transcription polymerase chain reaction (rRT-PCR) in the context of SARS-CoV-2 Omicron. Ag-RDT sensitivity and specificity within 1 day of rRT-PCR were evaluated by symptom status throughout the illness episode and Orf1b cycle threshold (Ct).

Results

From February to December 2022, 5757 participants reported 17 572 Ag-RDT results and completed 12 674 rRT-PCR tests, of which 995 (7.9%) were rRT-PCR positive. Overall sensitivity and specificity were 53.0% (95% confidence interval [CI], 49.6%–56.4%) and 98.8% (95% CI, 98.5%–99.0%), respectively. Sensitivity was comparatively higher for Ag-RDTs used 1 day after rRT-PCR (69.0%), 4–7 days after symptom onset (70.1%), and Orf1b Ct ≤20 (82.7%). Serial Ag-RDT sensitivity increased with repeat testing ≥2 (68.5%) and ≥4 (75.8%) days after an initial Ag-RDT-negative result.

Conclusions

Ag-RDT performance varied by clinical characteristics and temporal testing patterns. Our findings support recommendations for serial testing following an initial Ag-RDT-negative result, especially among recently symptomatic persons or those at high risk for SARS-CoV-2 infection.
Sect, Sectarian, Sectarianism: The Birth, Death, and Resurrection of an Analytical Category in the Study of Western Religions
Authors: Moss Yonatan
Published: March 2024

This article charts the changing uses of the interconnected terms sect, sectarian, sectarianist, and sectarianism in the academic study of Judaism, Christianity, and Islam. Following a review of the term sect’s early roots in Greco-Roman antiquity and its distinctly Christian transformation, three main steps are analyzed in the genealogy of the category in modern scholarship: (1) deployments by Weber and his early followers; (2) an influential sociological turn in the latter half of the twentieth century; and (3) a sharp decline in the years around the turn of the century in the popularity of sect as a category, followed by a redefinition of its derivative terms (sectarian, etc.) in recent years. Toward the end of the article, lessons are drawn from this genealogy for the future use of the category within scholarship.
Maternal diabetes and fracture risk in offspring: a population-based analysis
Authors: Shah Viral N , Leslie William D , Lautatzis Maria-Elena , Liu Kun , Prior Heather J , Wicklow Brandy
Published: March 2024

Factors affecting intrauterine environment exerts influence on skeletal health and fracture risk in later life. Diabetes during pregnancy is known to influence birth weight and is associated with fetal overgrowth. However, the effects of maternal diabetes on fracture risk in offspring is unknown. This study was aimed to evaluate the association between maternal diabetes and fracture risk in offspring. Using population-based administrative health data for Manitoba, Canada, we identified deliveries complicated by gestational diabetes and type 2 diabetes between April 1, 1980, and March 31, 2020. The cohort was followed for a median of 15.8 yr. The primary outcome was any incident fracture in offspring. Secondary outcomes were long bone upper extremity fracture, long bone lower extremity fracture, vertebral fracture, and any non-trauma fractures. Cox proportional hazard regression models were used to estimate fracture risk in offspring by maternal diabetes status adjusted for relevant covariates. Of the 585 176 deliveries, 26 397 offspring were born to women with diabetes (3.0% gestational diabetes and 1.5% type 2 diabetes), and 558 779 were born to women without diabetes. The adjusted risk for any fracture was 7% (hazard ratio, 1.07; 95% CI, 2.7–11.5%) higher in the offspring of mothers with diabetes than offspring of mothers without diabetes. Types of fractures were similar between the 2 groups with a predominance of long bone upper extremity fractures. In conclusion, maternal diabetes was associated with a modest increase in fracture risk in offspring. Longitudinal prospective studies are needed to understand intrauterine and postnatal factors that may influence fracture risk in the offspring of mothers with diabetes.
Observation of key phenological stages of hemlock woolly adelgid (Hemiptera: Adelgidae): using citizen science as a tool to inform research and management
Authors: Dietschler Nicholas J , Bittner Tonya D , Lefebvre Marshall Bigler , Schmidt Jasmine , Jubb Carrie S , James Aryanna , Salom Scott M , Whitmore Mark C
Published: March 2024

Increasing efficiency of data gathering at the landscape scale on the growing number of pests and pathogens threatening forests worldwide has potential to improve management outcomes. Citizen science is expanding, with growing support and utility in environmental and conservation fields. We present a case study showing how citizen science observations can be used to inform research and management of a devastating forest pest. Hemlock woolly adelgid, Adelges tsugae Annand (Hemiptera: Adelgidae), was introduced to eastern North America, leading to decline and mortality of eastern [Tsuga canadensis (L.) Carrière] (Pinales: Pinaceae) and Carolina hemlock (Tsuga caroliniana Engelmann) trees. Management activities, most notably biological control, rely on observations of A. tsugae phenology to inform the timing of releases and monitoring surveys of their highly synchronized specialist predators. In this article, we outline a citizen science program and report phenological observations on A. tsugae. Additionally, we report data comparing A. tsugae estivation break in Virginia (VA) and New York (NY) State, revealing that estivation break is synchronized between NY and VA. This observation is supported by 6 years of citizen scientist observations, showing similar patterns throughout NY, with egg laying shown to be much more variable than estivation break.
Food and time: dietary plasticity of different sources of a generalist insect herbivore
Authors: Hernandez Katherine , Bowers M Deane
Published: March 2024

Painted lady butterflies (Vanessa cardui L., Nymphalidae) are generalist herbivores and serve as a model system across several fields of biology. While it has been demonstrated that V. cardui caterpillars can develop on different host plants, much of this work has been done on commercially sourced caterpillars, which could limit our understanding of wild V. cardui populations. In this study, we sought to explore possible differences in how commercial and wild V. cardui caterpillars may respond to feeding on different host plants, and subsequently, how their diet impacts immune response and survival. Here, we analyzed performance, survival, and immune response of wild and commercially sourced V. cardui caterpillars over several generations on diets that consisted of either 1 of 4 different host plant species or a mixed diet including all 4 species. Qualitatively, we observed that wild larvae had a better larval performance and hemocyte counts compared to the commercial larvae. The results demonstrate that both wild and commercially sourced caterpillars grew and survived best on the same diet treatments (mallow, narrowleaf plantain, and a mixed diet) during development across generations. Immune responses showed similar patterns across host plants between wild and commercial populations, with individuals showing lowered immune responses on dandelion and lupine and higher ones on mallow, plantain and the mixed diet; although the relative rankings on those 3 diets varied. Survival also demonstrated similar patterns, in that individuals reared on dandelion and lupine had the lowest survival.