bluuebunny/crossref_metadata_2025 huggingface dataset:
Prostate cancer and liquid biopsies: Clinical applications and challenges
Authors: Urabe Fumihiko , Sumiyoshi Takayuki , Tashiro Kojiro , Goto Takayuki , Kimura Takahiro , Kobayashi Takashi
Published: March 2024

Liquid biopsy has emerged as a valuable and minimally invasive tool for real‐time detection of clinically actionable abnormalities across various cancer types. Its applicability is particularly compelling in the realm of prostate cancer, where novel therapeutic agents, including those targeting DNA repair systems, are under development. Despite these advancements, challenges persist in effectively screening for prostate cancer, enhancing risk stratification, and determining optimal approaches for treating advanced disease. Consequently, there is a pressing need for improved biomarkers to aid clinicians in decision‐making within these contexts. Cell‐free DNA and extracellular vesicle analysis have demonstrated promise in diagnosis, prognostication, assessment of treatment responses, and identification of emerging mechanisms of resistance. Nevertheless, obstacles must be addressed before liquid biopsies can be integrated into routine clinical practice. These challenges encompass preanalytical considerations such as sample collection and storage, methods of extracellular vesicle isolation and enrichment, and the need for enhanced interpretation of generated sequencing data. This review provides a comprehensive overview of current clinical opportunities in managing prostate cancer through blood‐based liquid biopsy, highlighting the progress made, and acknowledging the challenges that remain. Additionally, we discuss the next steps required for the effective implementation of liquid biopsies in guiding personalized treatment strategies for prostate cancer.
SfREPAT38, a pathogen response gene (REPAT), is involved in immune response of Spodoptera frugiperda larvae through mediating Toll signalling pathway
Authors: Wang Yuxue , Mbiza Natasha Isabel Tanatsiwa , Liu Ting , Wang Yi , Zhang Yi , Luo Xincheng , Chu Longyan , Li Jianping , Yang Yazhen , Wang Xiangping , Zhang Jianmin , Yu Yonghao
Published: March 2024

REPAT (response to pathogen) is an immune‐associated gene family that plays important roles in insect immune response to pathogens. Although nine REPAT genes have been identified in Spodoptera frugiperda (Lepidoptera: Noctuidae) currently, their functions and mechanisms in the immune response to pathogens still remain unclear. Therefore, SfREPAT38, a pathogen response gene (REPAT) of S. frugiperda, was characterised and its function was analysed. The results showed that SfREPAT38 contains a signal peptide and a transcription activator MBF2 (multi‐protein bridging factor 2) domain. Quantitative real‐time polymerase chain reaction analysis showed that SfREPAT38 was highly expressed in the sixth‐instar larvae (L6) and was the highest in expression in the midgut of L6. We found that the expression of SfREPAT38 could be activated by challenge with four microbial pathogens (Bacillus thuringiensis, Metarhizium anisopliae, Spodoptera exigua nuclearpolyhedrosis and Escherichia coli), except 12 h after E. coli infection. Furthermore, the SfREPAT38 expression levels significantly decreased at 24, 48 and 72 h after SfREPAT38 dsRNA injection or feeding. Feeding with SfREPAT38 dsRNA significantly decreased the weight gain of S. frugiperda, and continuous feeding led to the death of S. frugiperda larvae from the fourth day. Moreover, SfREPAT38 dsRNA injection resulted in a significant decrease of weight gain on the fifth day. Silencing SfREPAT38 gene down‐regulated the expression levels of immune genes belonging to the Toll pathway, including SPZ, Myd88, DIF, Cactus, Pell and Toll18W. After treatment with SfREPAT38 dsRNA, S. frugiperda became extremely sensitive to the B. thuringiensis infection, and the survival rate dramatically increased, with 100% mortality by the eighth day. The weight of S. frugiperda larvae was also significantly lower than that of the control groups from the second day onwards. In addition, the genes involved in the Toll signalling pathway and a few antibacterial peptide related genes were down‐regulated after treatment. These results showed that SfREPAT38 is involved in the immune response of S. frugiperda larvae through mediating Toll signalling pathway.
Halo‐hydromorphism alters nitrogen fertilization responses of tall wheatgrass pastures: Capture and use of resources, tiller dynamics and forage production
Authors: Fina Federico , Bertram Nicolás , Gatti María Laura , Di Bella Carla E. , Grimoldi Agustín A. , Berone Germán D.
Published: March 2024

Halo‐hydromorphism limits productivity in approximately 100 million hectares worldwide. Tall wheatgrass (Thinopyrum ponticum) is a species widely used in these environments for its seeding potential, being the addition of nitrogen a considered technological tool to increase forage quality and production. The objective of the study was to determine the impact of nitrogen fertilization on the capture and use of resources (radiation, water and nitrogen) in a cool season perennial sward growing in contrasting halo‐hydromorphic conditions. Cultivated pastures from three independent sites were used. Sites were described according to the degree of halo‐hydromorphism using soil salinity and water table attributes (salinity and depth) as environmental indicators: low HHM site [electrical conductivity (EC1:2.5) 0.97 dS/m; water table salinity 2.03 dS/m; depth 85 cm], intermediate HHM site (EC1:2.5 3.86 dS/m; water table salinity 7.40 dS/m; depth 134 cm) and high HHM site (EC1:2.5 4.49 dS/m; water table salinity 7.85 dS/m; depth 31 cm). At each site, a late spring regrowth (~750°Cd) was studied by applying two treatments (n = 5): without (N0) and nitrogen fertilization (N150; 150 kg/ha of nitrogen in the form of urea). The response of tall wheatgrass to nitrogen fertilization in halo‐hydromorphic conditions depends on soil salinity and water table attributes. N150 treatments production was twice as high as in N0 in low HHM and intermediate HHM environments (from 1750 to 3500 kgDM/ha and from 1080 to 1985 kgDM/ha, respectively). Meanwhile, in high HHM conditions, forage production was only 40% higher when nitrogen was added (from 625 to 870 kgDM/ha). In low HHM the higher N150 production was related to tiller density and size, whereas in intermediate HHM and high HHM was linked only to tiller size. In N150 treatments, the nitrogen nutrition index was negatively affected with the increase in HHM conditions (0.77, 0.62 and 0.55 for low HHM, intermediate HHM and high HHM, respectively). Instead, nitrogen nutrition index of N0 was similar in all the environments (~0.42). In N150, forage production capacity analysed in terms of radiation and water use efficiency (RUE and WUE, respectively) was similar in low HHM and intermediate HHM environments (RUE ~0.81 gDM/Mj and WUE ~13 kgDM/mm). These findings emphasize the importance of conducting analyses based on resource use and capture to understand productive responses to the increase in growth‐limiting factors. Furthermore, they contribute to the identification of environments suitable for nitrogen fertilization.
Systolic and diastolic blood pressure time in target range and cardiovascular outcomes in patients with hypertension and pre‐frailty or frailty status
Authors: Zhu Jiajia , Yang Kun , Liu Wenxian
Published: March 2024

In patients with hypertension and pre‐frailty or frailty, the influence of systolic (SBP) and diastolic blood pressure (DBP) time in target range (TTR) on clinical outcomes is unclear. Thus, we conducted a post hoc analysis of the Systolic Blood Pressure Intervention Trial (SPRINT). Classifying 4208 participants into frail and non‐frail groups using a frailty index, the study calculated blood pressure time in target range (BP‐TTR) for the first three months using the Rosendaal method. The primary endpoint included a composite of nonfatal myocardial infarction (MI), acute coronary syndromes, stroke, acute decompensated heart failure (ADHF), and cardiovascular death. Relationships between BP‐TTR and outcomes were analyzed using Kaplan‐Meier curves, Cox models, and restricted cubic spline curves, with subgroup analysis for further insights. In a median follow‐up of 3.17 years, primary outcomes occurred in 6.7% of participants. Kaplan‐Meier analysis showed that a lower systolic blood pressure time in target range (SBP‐TTR) (0%–25%) correlated with an increased cumulative incidence of the primary outcome (p < .001), nonfatal MI (P = .021), stroke (P = .004), and cardiovascular death (P = .002). A higher SBP‐TTR (75%–<100%) was linked to a reduced risk of these outcomes. The restricted cubic spline (RCS) curve revealed a linear association between SBP‐TTR and the primary outcome (non‐linear P = .704). Similar patterns were observed for diastolic blood pressure time in target range (DBP‐TTR). Subgroup analysis showed that the protective effect of higher SBP‐TTR was less pronounced at low DBP‐TTR levels (P for interaction = .023). In conclusion, this study highlights the importance of maintaining BP within the target range to mitigate cardiovascular risks in this population.
Identification of fish specimens of the Tocantins River, Brazil, using DNA barcoding
Authors: Lima Renato Corrêia , de Lima Sabrina Rufino , Rocha Marcelo Salles , dos Anjos Hélio Daniel Beltrão , Dantas Yasmin Catarina Alves , Benites Ignácio Davi Navegante , Queiroz Cleonilde da Conceição Silva , Fraga Elmary da Costa , Batista Jacqueline da Silva
Published: March 2024

The fish fauna of the Tocantins River possesses many endemic species; however, it is little studied in molecular terms and is quite threatened by the construction of several hydroelectric dams. Therefore, the objective of this study was to identify the ichthyofauna of the Tocantins River using DNA barcoding. For this, collections were carried out in five points of this river, which resulted in the capture of 725 individuals from which partial sequences of the cytochrome oxidase subunit I (COI) gene were obtained for genetic analysis. A total of 443 haplotypes were recovered with the mean intraspecific K2P genetic distance of 1.82%. Altogether, 138 species were identified based on morphological criteria, which was a quantity that was much lower than that indicated by the four molecular methods (assemble species by automatic partitioning [ASAP], barcode index number [BIN], generalized mixed Yule coalescent (GMYC), and Bayesian Poisson tree processes [bPTP]) through which 152–157 molecular entities were identified. In all, 41 unique BINs were obtained based on the data generated in the BOLDSystems platform. According to the result indicated by ASAP (species delimitation approach considered the most appropriate in the present study), there was an increase of 17 molecular entities (12.32%), when compared to the number of species identified through their morphological criteria, as it can show cryptic diversity, candidates for new species, and misidentifications. There were 21 incongruities indicated between the different identification approaches for species. Therefore, it is suggested that these taxonomic problems be cautiously evaluated by experts to solve such taxonomic issues.
The effectiveness of non‐pharmacological interventions on reducing pain in patients undergoing bone marrow aspiration and biopsy: A systematic review and meta‐analysis of randomized controlled trials
Authors: Li Chengyang , Zhang Xiao , Zhuang Xueting , Zhang Kun , Huang Qiyuan , Ge Song , Wu Yong , Hu Rong
Published: March 2024

Background

Patients often consider bone marrow aspiration and biopsy to be one of the most painful medical procedures. The effectiveness of non‐pharmacological interventions to reduce pain during bone marrow aspiration and biopsy remains unclear.

Aim

To synthesize existing evidence regarding the effectiveness of non‐pharmacological interventions in mitigating procedural pain among patients undergoing bone marrow aspiration and biopsy.

Design

A systematic review and meta‐analysis of randomized controlled trials.

Methods

Six electronic databases, including PubMed, EMBASE, CINAHL, PsycINFO, Cochrane Library and Web of Science were searched from inception to July 15, 2023. The risk of bias was assessed using the Cochrane Risk of Bias Tool Version 2.0. Meta‐analysis was conducted using STATA 16. The certainty of the evidence was assessed by the GRADE approach.

Results

This meta‐analysis included 18 studies derived from 17 articles involving a total of 1017 participants. The pooled results revealed statistically significant pain reduction effects using distraction (SMD: −.845, 95% CI: −1.344 to −.346, p < .001), powered bone marrow biopsy system (SMD: −.266, 95% CI: −.529 to −.003, p = .048), and acupoint stimulation (SMD: −1.016, 95% CI: −1.995 to −.037, p = .042) among patients undergoing bone marrow aspiration and biopsy. However, the pooled results on hypnosis (SMD: −1.228, 95% CI: −4.091 to 1.515, p = .368) showed no significant impact on pain reduction. Additionally, the pooled results for distraction did not demonstrate a significant effect on operative anxiety (MD: −2.942, 95% CI: −7.650 to 1.767, p = .221).

Conclusions

Distraction, powered bone marrow biopsy system and acupoint stimulation are effective in reducing pain among patients undergoing bone marrow aspiration and biopsy.

Patient or Public Contribution

Not applicable.

Relevance to Clinical Practice

This meta‐analysis highlights the effectiveness of distraction, powered bone marrow biopsy system and acupoint stimulation for reducing pain in patients undergoing bone marrow biopsy. Healthcare professionals should consider integrating these interventions into pain management practices for these patients.

Registration

(PROSPERO): CRD42023422854.
Nursing practices to optimise rheumatic fever prevention in a high‐risk country: An integrative review
Authors: Murray Ruby , Mowat Rebecca , Foster Mandie Jane , Blamires Julie
Published: March 2024

Background

New Zealand is one of the last high‐income countries in the world experiencing significant rates of rheumatic fever. Nurses play a crucial role in rheumatic fever prevention; however, little is understood as to how nurses can best achieve this.

Aim

To explore nursing practices that optimise rheumatic fever prevention.

Design

An integrative review.

Methods

Four electronic databases (CINAHL, SCOPUS, Medline via, and Ovid) were searched for peer‐reviewed empirical articles published from 2013 to 2023. Grey literature (guidelines/reports) was also sourced. Critical appraisal was applied using the Mixed‐Methods Appraisal Tools and the Joanna Briggs Critical Appraisal checklist. Qualitative Research in Psychology, 3(2), 77–101, thematic analysis method was used to generate themes.

Results

Seven research articles and three national reports were included. Four themes—in‐depth nursing knowledge and improving prophylaxis adherence, cultural competency, and therapeutic nurse–patient relationships—were found.

Conclusion

While nursing knowledge and ways to improve injection adherence are essential, being culturally receptive and developing therapeutic relationships are equally important. Without strong and trusting relationships, it is difficult to deliver care required for prevention success.

Implications to care

When working with vulnerable populations it is important to be culturally receptive in all interactions with patients and their families.

Impact

New Zealand has high rates of rheumatic fever, especially among vulnerable populations such as Pacific Islanders and Māori. Nurses are often frontline primary care providers who, when skilled with the right tools, can help reduce the prevalence of this disease.

Reporting method

The Preferred Reporting Items for Systematic Reviews and Meta‐Analysis flow chart.

Patient or public contribution

No Patient or Public Contribution was required for this research.
Diversity in singlehood experiences: Testing an attachment theory model of sub‐groups of singles
Authors: Pepping Christopher A. , Girme Yuthika U. , Cronin Timothy J. , MacDonald Geoff
Published: March 2024

Objective

Relationship science has developed several theories to explain how and why people enter and maintain satisfying relationships. Less is known about why some people remain single, despite increasing rates of singlehood throughout the world. Using one of the most widely studied and robust theories—attachment theory—we aim to identify distinct sub‐groups of singles and examine whether these sub‐groups differ in their experience of singlehood and psychosocial outcomes.

Method

Across two studies of single adults (Ns = 482 and 400), we used latent profile analysis (LPA) to identify distinct sub‐groups of singles.

Results

Both studies revealed four distinct profiles consistent with attachment theory: (1) secure; (2) anxious; (3) avoidant; and (4) fearful‐avoidant. Furthermore, the four sub‐groups of singles differed in theoretically distinct ways in their experience of singlehood and on indicators of psychosocial well‐being.

Conclusions

These findings suggest that singles are a heterogeneous group of individuals that can be meaningfully differentiated based on individual differences in attachment security.
Assessment of COVID‐19 Messaging Strategies to Increase Testing for Students With Intellectual and Developmental Disabilities
Authors: Walsh Tyler J , Kalb Luther G , Gemmell Michael , Liu Jingxia , Caburnay Charlene A , Gurnett Christina A , Newland Jason G ,   the COMPASS‐T Study Group
Published: March 2024

Background

Students with intellectual and developmental disabilities (IDD) were disproportionately impacted by the COVID‐19 pandemic. This study's goal was to assess the effectiveness of 2 messaging strategies on participation in SARS‐CoV‐2 weekly testing.

Methods

Cluster randomized trials were conducted at 2 school systems, the special school district (SSD) and Kennedy Krieger Institute (Kennedy) to assess messaging strategies, general versus enhanced, to increase weekly screening for SARS‐CoV‐2. Testing was offered to staff and students from November 23, 2020 to May 26, 2022. The primary outcomes were percentage of students and staff consented weekly and percentage of study participants who had a test performed weekly. Generalized estimating equation models were utilized to evaluate the primary outcomes.

Results

Increases in enrollment and testing occurred during study start up, the beginning of school years, and following surges in both systems. No statistical difference was observed in the primary outcomes between schools receiving standard versus enhanced messaging.

Implications for School Health Policy, Practice, and Equity

Frequent and consistent communication is vital for families and staff. Weekly screening testing within schools is possible and highlighted the importance of utilizing equitable protocols to provide important testing to students with IDD.

Conclusion

Enhanced messaging strategies did not increase the number of participants enrolled or the percentage of enrolled participants being tested on a weekly basis.
Summary survey on publishing contract in the OAPI space
Authors: Ngombé Yvon Laurier
Published: March 2024

The OAPI member states constitute a space for the harmonization of copyright in Africa. This harmonization is yet to be completed, as attested by the conventional rules relating to the publishing contract. In addition, investigating about the publishing contract in the OAPI space requires an examination of both the text of the Bangui Agreement and that of the national laws of the 17 member states. Some differences must be pointed out keeping in mind the question of possible conflict of laws.
Distribution of Aspergillus species and prevalence of azole resistance in clinical and environmental samples from a Spanish hospital during a three‐year study period
Authors: Lucio Jose , Alcazar‐Fuoli Laura , Gil Horacio , Cano‐Pascual Samuel , Hernandez‐Egido Sara , Cuetara Maria Soledad , Mellado Emilia
Published: March 2024

Background

Surveillance studies are crucial for updating trends in Aspergillus species and antifungal susceptibility information.

Objectives

Determine the Aspergillus species distribution and azole resistance prevalence during this 3‐year prospective surveillance study in a Spanish hospital.

Materials and Methods

Three hundred thirty‐five Aspergillus spp. clinical and environmental isolates were collected during a 3‐year study. All isolates were screened for azole resistance using an agar‐based screening method and resistance was confirmed by EUCAST antifungal susceptibility testing. The azole resistance mechanism was confirmed by sequencing the cyp51A gene and its promoter. All Aspergillus fumigatus strains were genotyped using TRESPERG analysis.

Results

Aspergillus fumigatus was the predominant species recovered with a total of 174 strains (51.94%). The rest of Aspergillus spp. were less frequent: Aspergillus niger (14.93%), Aspergillus terreus (9.55%), Aspergillus flavus (8.36%), Aspergillus nidulans (5.37%) and Aspergillus lentulus (3.28%), among other Aspergillus species (6.57%). TRESPERG analysis showed 99 different genotypes, with 72.73% of the strains being represented as a single genotype. Some genotypes were common among clinical and environmental A. fumigatus azole‐susceptible strains, even when isolated months apart. We describe the occurrence of two azole‐resistant A. fumigatus strains, one clinical and another environmental, that were genotypically different and did not share genotypes with any of the azole‐susceptible strains.

Conclusions

Aspergillus fumigatus strains showed a very diverse population although several genotypes were shared among clinical and environmental strains. The isolation of azole‐resistant strains from both settings suggest that an efficient analysis of clinical and environmental sources must be done to detect azole resistance in A. fumigatus.
The dynamics and outcomes of AKI progression during the COVID‐19 pandemic
Authors: Ratnayake Aruni , Sarnowski Alexander , Sinclair Fiona , Annear Nicholas M. P. , Banerjee Debasish , Chis Ster Irina
Published: March 2024

Purpose

Acute kidney injury (AKI) associated with COVID‐19 is associated with poor prognosis. This study assessed the hitherto uninvestigated impact of COVID‐19 on the progression and clinical outcomes of patients with AKI.

Methods

Data from 576 patients with AKI admitted between 13/3/20 and 13/5/20 were studied. Increasingly complex analyses, from logistic regressions to competing‐risk and multi‐state models, have revealed insights into AKI progression dynamics associated with PCR‐confirmed COVID‐19 acquisition and death. Meta‐analyses of case fatality ratios among patients with AKI were also conducted.

Results

The overall case‐fatality ratio was 0.33 [95% CI (0.20–0.36)]; higher in COVID‐19 positive (COVID+) patients 0.52 [95% CI (0.46–0.58)] than in their negative (COVID‐) counterparts 0.16 [95% CI (0.12–0.20)]. In AKI Stage‐3 patients, that was 0.71 [95% CI (0.64–0.79)] among COVID+ patients with 45% dead within 14 days and 0.35 [95% CI (0.25–0.44)] in the COVID‐ group and 28% died within 14 days. Among patients diagnosed with AKI Stage‐1 within 24 h, the probability of progression to AKI Stage‐3 on day 7 post admission was 0.22 [95% CI (0.17–0.27)] among COVID+ patients, and 0.06 [95% CI (0.03, 0.09)] among those who tested negative. The probability of discharge by day 7 was 0.71 [95% CI (0.66, 0.75)] in COVID‐ patients, and 0.27 [95% CI (0.21, 0.32)] in COVID+ patients. By day 14, in AKI Stage‐3 COVID+ patients, that was 0.35 [95% CI (0.25, 0.44)] with little change by day 10, that is, 0.38 [95% CI (0.29, 0.47)].

Conclusion

These results are consistent with either a rapid progression in severity, prolonged hospital care, or high case fatality ratio among AKI Stage‐3 patients, significantly exacerbated by COVID‐19 infection.

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Microbial responses to stress cryptically alter natural selection on plants
Authors: Bolin Lana G. , Lau Jennifer A.
Published: March 2024

Microbial communities can rapidly respond to stress, meaning plants may encounter altered soil microbial communities in stressful environments. These altered microbial communities may then affect natural selection on plants. Because stress can cause lasting changes to microbial communities, microbes may also cause legacy effects on plant selection that persist even after the stress ceases.

To explore how microbial responses to stress and persistent microbial legacy effects of stress affect natural selection, we grew Chamaecrista fasciculata plants in stressful (salt, herbicide, or herbivory) or nonstressful conditions with microbes that had experienced each of these environments in the previous generation.

Microbial community responses to stress generally counteracted the effects of stress itself on plant selection, thereby weakening the strength of stress as a selective agent. Microbial legacy effects of stress altered plant selection in nonstressful environments, suggesting that stress‐induced changes to microbes may continue to affect selection after stress is lifted.

These results suggest that soil microbes may play a cryptic role in plant adaptation to stress, potentially reducing the strength of stress as a selective agent and altering the evolutionary trajectory of plant populations.
Aerobic methane production in Scots pine shoots is independent of drought or photosynthesis
Authors: Tenhovirta Salla A. M. , Kohl Lukas , Koskinen Markku , Polvinen Tatu , Salmon Yann , Paljakka Teemu , Pihlatie Mari
Published: March 2024

Shoot‐level emissions of aerobically produced methane (CH4) may be an overlooked source of tree‐derived CH4, but insufficient understanding of the interactions between their environmental and physiological drivers still prevents the reliable upscaling of canopy CH4 fluxes.

We utilised a novel automated chamber system to continuously measure CH4 fluxes from the shoots of Pinus sylvestris (Scots pine) saplings under drought to investigate how canopy CH4 fluxes respond to the drought‐induced alterations in their physiological processes and to isolate the shoot‐level production of CH4 from soil‐derived transport and photosynthesis.

We found that aerobic CH4 emissions are not affected by the drought‐induced stress, changes in physiological processes, or decrease in photosynthesis. Instead, these emissions vary on short temporal scales with environmental drivers such as temperature, suggesting that they result from abiotic degradation of plant compounds.

Our study shows that aerobic CH4 emissions from foliage are distinct from photosynthesis‐related processes. Thus, instead of photosynthesis rates, it is more reliable to construct regional and global estimates for the aerobic CH4 emission based on regional differences in foliage biomass and climate, also accounting for short‐term variations of weather variables such as air temperature and solar radiation.
Toward unveiling transcriptome dynamics and regulatory modules at the maternal/filial interface of developing maize kernel
Authors: He Juan , Wang Jincang , Zhang Zhiyong
Published: March 2024

The basal region of maize (Zea mays) kernels, which includes the pedicel, placenta‐chalazal, and basal endosperm transfer layers, serves as the maternal/filial interface for nutrient transfer from the mother plant to the developing seed. However, transcriptome dynamics of this maternal/filial interface remain largely unexplored. To address this gap, we conducted high‐temporal‐resolution RNA sequencing of the basal and upper kernel regions between 4 and 32 days after pollination and deeply analyzed transcriptome dynamics of the maternal/filial interface. Utilizing 790 specifically and highly expressed genes in the basal region, we performed the gene ontology (GO) term and weighted gene co‐expression network analyses. In the early‐stage basal region, we identified five MADS‐box transcription factors (TFs) as hubs. Their homologs have been demonstrated as pivotal regulators at the maternal/filial interface of rice or Arabidopsis, suggesting their potential roles in maize kernel development. In the filling‐stage basal region, numerous GO terms associated with transcriptional regulation and transporters are significantly enriched. Furthermore, we investigated the molecular function of three hub TFs. Through genome‐wide DNA affinity purification sequencing combined with promoter transactivation assays, we suggested that these three TFs act as regulators of 10 basal‐specific transporter genes involved in the transfer of sugars, amino acids, and ions. This study provides insights into transcriptomic dynamic and regulatory modules of the maternal/filial interface. In the future, genetic investigation of these hub regulators must advance our understanding of maternal/filial interface development and function.
Hyperbolicity in non‐metric cubical small‐cancellation
Authors: Arenas Macarena , Jankiewicz Kasia , Wise Daniel T.
Published: March 2024

Given a non‐positively curved cube complex , we prove that the quotient of defined by a cubical presentation satisfying sufficient non‐metric cubical small‐cancellation conditions is hyperbolic provided that is hyperbolic. This generalises the fact that finitely presented classical small‐cancellation groups are hyperbolic.
Arctic sea ice–air interactions weaken El Niño–Southern Oscillation
Authors: Deng Jiechun , Dai Aiguo
Published: March 2024

El Niño–Southern Oscillation (ENSO) over the tropical Pacific can affect Arctic climate, but whether it can be influenced by the Arctic is unclear. Using model simulations, we show that Arctic sea ice–air interactions weaken ENSO by about 12 to 17%. The northern North Pacific Ocean warms due to increased absorption of solar radiation under such interactions. The warming excites an anomalous tropospheric Rossby wave propagating equatorward into the tropical Pacific to strengthen cross-equator winds and deepen the thermocline. These mean changes dampen ENSO amplitude via weakened thermocline and zonal advective feedbacks. Observed historical changes from 1921–1960 (with strong sea ice–air interactions) to 1971–2000 (with weak interactions) are qualitatively consistent with the model results. Our findings suggest that Arctic sea ice–air interactions affect both the mean state and variability in the tropical Pacific, and imply increased ENSO amplitude as Arctic sea ice and its interactions with the atmosphere diminish under anthropogenic warming.
Generative emulation of weather forecast ensembles with diffusion models
Authors: Li Lizao , Carver Robert , Lopez-Gomez Ignacio , Sha Fei , Anderson John
Published: March 2024

Uncertainty quantification is crucial to decision-making. A prominent example is probabilistic forecasting in numerical weather prediction. The dominant approach to representing uncertainty in weather forecasting is to generate an ensemble of forecasts by running physics-based simulations under different conditions, which is a computationally costly process. We propose to amortize the computational cost by emulating these forecasts with deep generative diffusion models learned from historical data. The learned models are highly scalable with respect to high-performance computing accelerators and can sample thousands of realistic weather forecasts at low cost. When designed to emulate operational ensemble forecasts, the generated ones are similar to physics-based ensembles in statistical properties and predictive skill. When designed to correct biases present in the operational forecasting system, the generated ensembles show improved probabilistic forecast metrics. They are more reliable and forecast probabilities of extreme weather events more accurately. While we focus on weather forecasting, this methodology may enable creating large climate projection ensembles for climate risk assessment.
Cargo selective vesicle tethering: The structural basis for binding of specific cargo proteins by the Golgi tether component TBC1D23
Authors: Cattin-Ortolá Jérôme , Kaufman Jonathan G. G. , Gillingham Alison K. , Wagstaff Jane L. , Peak-Chew Sew-Yeu , Stevens Tim J. , Boulanger Jérôme , Owen David J. , Munro Sean
Published: March 2024

The Golgi-localized golgins golgin-97 and golgin-245 capture transport vesicles arriving from endosomes via the protein TBC1D23. The amino-terminal domain of TBC1D23 binds to the golgins, and the carboxyl-terminal domain of TBC1D23 captures the vesicles, but how it recognizes specific vesicles was unclear. A search for binding partners of the carboxyl-terminal domain unexpectedly revealed direct binding to carboxypeptidase D and syntaxin-16, known cargo proteins of the captured vesicles. Binding is via a threonine-leucine-tyrosine (TLY) sequence present in both proteins next to an acidic cluster. A crystal structure reveals how this acidic TLY motif binds to TBC1D23. An acidic TLY motif is also present in the tails of other endosome-to-Golgi cargo, and these also bind TBC1D23. Structure-guided mutations in the carboxyl-terminal domain that disrupt motif binding in vitro also block vesicle capture in vivo. Thus, TBC1D23 attached to golgin-97 and golgin-245 captures vesicles by a previously undescribed mechanism: the recognition of a motif shared by cargo proteins carried by the vesicle.
Let’s talk posters: a novel role-playing activity to prepare undergraduate researchers for poster presentations
Authors: Dillon Meghan , Gerstman Julia , Scarcella Alexandria , Mantz Meghan , Kleeschulte Courtney , Light Caitlin J.
Published: March 2024

Calls to increase undergraduate involvement in research have led to a significant increase in student participation via course-based undergraduate research experiences (CUREs). These CUREs provide students an authentic research experience, which often involves dissemination of research by public speaking. For instance, the First-year Research Immersion (FRI) program at Binghamton University is a three-semester CURE sequence that prepares students for scientific research and effective communication of their findings. After one semester of research, students from the FRI program are tasked with presenting their research to hundreds of faculty members, staff, friends, and family at the annual FRI poster session. However, our students, and undergraduates in general, report high anxiety and fear around public speaking such as this. To better prepare our students for public speaking at a research poster session, we developed a workshop that includes a novel role-play activity to mimic a fast-paced poster session or conference in order to address students' fears and increase confidence levels. The role-play activity gives students iterative practice such that they are prepared for the realities of a poster session including variation of poster attendees. During the activity, students switch roles between presenter and audience member. In the role of an audience member, students are given Pokèmon-like role-playing cards that explain the traits and abilities of various types of poster-goers that students might come across (faculty in and out of discipline, staff, family, friends, etc.). Students improvise and enact their card-assigned role as they engage with their classmates who are practicing their poster presentations. To assess student outcomes, students were given three surveys: pre-activity, post-activity, and post-poster presentation. Immediately following the activity, 64% of students reported the highest level of confidence, and following the poster session, 93% of students reported extreme confidence in their poster presentation abilities. These data show that this role-play activity can help address student confidence and better prepare students to communicate their research.
Bacillus subtilis
stress-associated mutagenesis and developmental DNA repair
Authors: Pedraza-Reyes Mario , Abundiz-Yañez Karen , Rangel-Mendoza Alejandra , Martínez Lissett E. , Barajas-Ornelas Rocío C. , Cuéllar-Cruz Mayra , Leyva-Sánchez Hilda C. , Ayala-García Víctor M. , Valenzuela-García Luz I. , Robleto Eduardo A.
Published: March 2024

SUMMARY

The metabolic conditions that prevail during bacterial growth have evolved with the faithful operation of repair systems that recognize and eliminate DNA lesions caused by intracellular and exogenous agents. This idea is supported by the low rate of spontaneous mutations (10
−9
) that occur in replicating cells, maintaining genome integrity. In contrast, when growth and/or replication cease, bacteria frequently process DNA lesions in an error-prone manner. DNA repairs provide cells with the tools needed for maintaining homeostasis during stressful conditions and depend on the developmental context in which repair events occur. Thus, different physiological scenarios can be anticipated. In nutritionally stressed bacteria, different components of the base excision repair pathway may process damaged DNA in an error-prone approach, promoting genetic variability. Interestingly, suppressing the mismatch repair machinery and activating specific DNA glycosylases promote stationary-phase mutations. Current evidence also suggests that in resting cells, coupling repair processes to actively transcribed genes may promote multiple genetic transactions that are advantageous for stressed cells. DNA repair during sporulation is of interest as a model to understand how transcriptional processes influence the formation of mutations in conditions where replication is halted. Current reports indicate that transcriptional coupling repair-dependent and -independent processes operate in differentiating cells to process spontaneous and induced DNA damage and that error-prone synthesis of DNA is involved in these events. These and other noncanonical ways of DNA repair that contribute to mutagenesis, survival, and evolution are reviewed in this manuscript.
Perrault syndrome: The Way Forward After Genetic Counselling?
Authors: Kapil Ishan , Anand Rohit , Padhi Phalguni
Published: March 2024

A female, term neonate, born via vaginal delivery to a G5P1D1A3 hypothyroid mother with a history of an elder sibling being homozygous forHSD17B4mutation, diagnosed while working up his progressive neurological disorder and succumbing to the same. The family screening revealed that both parents were heterozygous carriers of the same mutation in the geneHSD17B4. After genetic counselling, amniocentesis revealed the fetus to be having homozygosity for the same mutation. In view of precious pregnancy, normal antenatal scans and investigations, the pregnancy was continued, and baby was born with a birth weight of 2.65 kg and had a smooth perinatal transition. Parents were counselled regarding the course of the illness, possible complications and the need for regular follow-up. Ultrasound of the abdomen, pelvis and head was normal in the neonatal period. She was vaccinated as per the national schedule and gaining weight normally.
‘You just don’t feel like your work goes recognised’: healthcare worker experiences of tension related to public discourse around the COVID-19 pandemic
Authors: Timmins George Thomas , Bandini Julia I , Ahluwalia Sangeeta C , Bialas Armenda , Meredith Lisa S , Gidengil Courtney
Published: March 2024

Objectives

To understand the impact of public discourse and reaction around the COVID-19 pandemic on healthcare worker (HCW) experiences and well-being caring for patients with COVID-19.

Methods

We conducted 60 min in-depth interviews with 11 physicians and 12 nurses who were providing care to patients with COVID-19 in acute care settings at two health systems in the Western USA. Interviews were conducted in Spring-Summer 2022 using a semi-structured interview protocol that guided respondents through different stages of the pandemic.

Results

Three themes emerged from the data around providing care in the unique social context of the COVID-19 pandemic including: (1) public polarisation and disagreement with science; (2) feelings of hope and optimism during the pandemic and (3) the compounded strain of providing care within this unique social context of the pandemic.

Conclusions

To prepare for future pandemics, improved public health communications and social-emotional supports for HCWs are critical to ameliorate the physical and emotional impacts related to the social context of modern US pandemic response.
Spherically symmetric teleparallel geometries
Authors: Coley A. A. , Landry A. , van den Hoogen R. J. , McNutt D. D.
Published: March 2024

We are interested in the development of spherically symmetric geometries inF(T) teleparallel gravity which are of physical importance. We first express the general forms for the spherically symmetric frame and the zero curvature, metric compatible, spin connection. We then analyse the antisymmetric field equations (the solutions of which split into two cases, which we subsequently consider separately), and derive and analyse the resulting symmetric field equations. In order to further study the applications of spherically symmetric teleparallel models, we study 3 subcases in which there is an additional affine symmetry so that the resulting field equations reduce to a system of ordinary differential equations. First, we study static spherical symmetric geometries and solve the antisymmetric field equations and subsequently derive the full set of symmetric field equations. In particular, we investigate vacuum spacetimes and obtain a number of new solutions. Second, we consider an additional affine frame symmetry in order to expand the affine frame symmetry group to that of a spatially homogeneous Kantowski–Sachs geometry. Third, we study the special case of spherical symmetry with an additional fourth similarity affine vector.
Abax: Extracting Mathematical Formulas from Chart Images Using Spatial Pixel Information
Authors: Alexiou Michail S. , Bourbakis Nikolaos G.
Published: March 2024

Current state-of-the-art techniques in 2D chart analysis primarily emphasize the recognition of textual information as a means of comprehending and summarizing chart contents. However, the effective analysis and understanding of information embedded in chart images depends on accurate reverse-engineering of the behavior of depicted variables. In this paper, we propose a methodology, named Abax, as an initial study for recognizing and approximating the mathematical functions that describe the behavior of variables illustrated in chart images, particularly those containing curves. Abax is focused on approximating the values of function parameters using spatial pixel information derived from the identified keypoints of each curve. Qualitative results of the described method are presented as a proof of concept, demonstrating accurate extraction of information from fives types of functions: linear, polynomial, asymptotic, sinusoidal and arbitrary.
Molecular Epidemiology of SARS-CoV-2 within Accra Metropolis Postlockdown
Authors: Aboagye Frank T. , Annison Lawrence , Hackman Henry Kwadwo , Acquah Maame E. , Ashong Yvonne , Owusu-Frimpong Isaac , Egyam Bill C. , Annison Sharon , Osei-Adjei George , Antwi-Baffour Samuel
Published: March 2024

Introduction. Currently, sequencing has been the only tool for the identification of circulating severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants. However, it is known to be an expensive and laborious approach involving high technical expertise. Considering the reduced adherence to preventive measures postlockdown in Accra, this study presents an alternative method that leverages polymerase chain reaction (PCR) to identify circulating SARS-CoV-2 variants in the Accra Metropolis postlockdown. Methods. This prospective cross-sectional study was conducted between July and December 2022. Nasopharyngeal samples were collected from 268 consenting participants. Samples were subjected to nucleic acid extraction and followed by real-time polymerase chain reaction for the detection and quantification of SARS-CoV-2 RNA. SARS-CoV-2 positive samples were subsequently subjected to variant identification using rapid PCR. Findings. The prevalence of SARS-CoV-2 within the Accra Metropolis was 30.2%. The majority of the SARS-CoV-2 infection was diagnosed in females, participants aged 41–50 years, and symptomatic participants. Participants aged ≤10 years and females recorded the highest viral load while participants aged 41–50 years recorded the highest number of infections. The SARS-CoV-2 variants detected were Alpha (64.2%), Delta (22.2%), and Omicron (13.6%). Predictors of SARS-CoV-2 infection identified were chills, cough, headache, body weakness, sore throat, and dyspnoea in order of decreasing association with SARS-CoV-2 infection. There was a strong association between symptom status, gender, age, and SARS-CoV-2 infection. Conclusion. There was a high prevalence of SARS-CoV-2 within the Accra Metropolis postlockdown within the sampling period. The Alpha variant of SARS-CoV-2 is the predominant circulating variant, and persons presenting with symptoms are most likely to be diagnosed with COVID-19. Children aged ≤10 years serve as a reservoir for infection transmission.
Approximate Controllability and Ulam Stability for Second-Order Impulsive Integrodifferential Evolution Equations with State-Dependent Delay
Authors: Bensalem Abdelhamid , Salim Abdelkrim , Benchohra Mouffak , N’Guérékata Gaston
Published: March 2024

In this paper, we shall establish sufficient conditions for the existence, approximate controllability, and Ulam–Hyers–Rassias stability of solutions for impulsive integrodifferential equations of second order with state-dependent delay using the resolvent operator theory, the approximating technique, Picard operators, and the theory of fixed point with measures of noncompactness. An example is presented to illustrate the efficiency of the result obtained.
Modification of the Clarke and Wright Algorithm with a Dynamic Savings Matrix
Authors: Fikejz Jan , Brázdová Markéta , Jánošíková Ľudmila
Published: March 2024

The goods collection and delivery process often relates to distribution logistics problems. The task is to deliver goods from warehouses to customers under specific circumstances. Efforts to optimize the process are largely aimed at reducing overall costs of goods transportation. Among the prominent algorithms for solving the basic type of the delivery (or collection) problem, which includes a single depot and a homogeneous vehicle fleet, is the algorithm developed by Clarke and Wright in 1964. This algorithm minimizes transportation costs by maximizing the savings achieved through merging multiple routes into one. This paper primarily aims to solve the pickup and delivery problem where the goods must be delivered and empty packaging collected in a single process. The request of a customer can be routed from the depot or from another customer. Similarly, the destination of the request may be the depot or another customer. Unlike the original version of the Clarke and Wright algorithm, the initial routes are created to satisfy delivery orders, and therefore, the same customer can occur in multiple routes. Consequently, a situation may arise in which two routes containing one or more common vertices must be combined during the calculation. Furthermore, these vertices need not be the outermost vertices of the routes. This situation cannot be addressed by using the original version of the Clarke and Wright algorithm, and that is why we propose its modification. Merging routes through inner vertices means that the cost savings depend on the configurations of the routes, and therefore, they cannot be calculated a priori. Instead, the dynamic savings matrix must be used.