bluuebunny/crossref_metadata_2025 huggingface dataset:
From whole bodies to single cells: A guide to transcriptomic approaches for ecology and evolutionary biology
Authors: Hoedjes Katja M. , Grath Sonja , Posnien Nico , Ritchie Michael G. , Schlötterer Christian , Abbott Jessica K. , Almudi Isabel , Coronado‐Zamora Marta , Durmaz Mitchell Esra , Flatt Thomas , Fricke Claudia , Glaser‐Schmitt Amanda , González Josefa , Holman Luke , Kankare Maaria , Lenhart Benedict , Orengo Dorcas J. , Snook Rhonda R. , Yılmaz Vera M. , Yusuf Leeban
Published: June 2024

RNA sequencing (RNAseq) methodology has experienced a burst of technological developments in the last decade, which has opened up opportunities for studying the mechanisms of adaptation to environmental factors at both the organismal and cellular level. Selecting the most suitable experimental approach for specific research questions and model systems can, however, be a challenge and researchers in ecology and evolution are commonly faced with the choice of whether to study gene expression variation in whole bodies, specific tissues, and/or single cells. A wide range of sometimes polarised opinions exists over which approach is best. Here, we highlight the advantages and disadvantages of each of these approaches to provide a guide to help researchers make informed decisions and maximise the power of their study. Using illustrative examples of various ecological and evolutionary research questions, we guide the readers through the different RNAseq approaches and help them identify the most suitable design for their own projects.
The proteome of Nicotiana benthamiana is shaped by extensive protein processing
Authors: Zheng Kaijie , Lyu Joy C. , Thomas Emma L. , Schuster Mariana , Sanguankiattichai Nattapong , Ninck Sabrina , Kaschani Farnusch , Kaiser Markus , van der Hoorn Renier A. L.
Published: June 2024

Processing by proteases irreversibly regulates the fate of plant proteins and hampers the production of recombinant proteins in plants, yet only few processing events have been described in agroinfiltrated Nicotiana benthamiana, which has emerged as the main transient protein expression platform in plant science and molecular pharming.

Here, we used in‐gel digests and mass spectrometry to monitor the migration and topography of 5040 plant proteins within a protein gel. By plotting the peptides over the gel slices, we generated peptographs that reveal where which part of each protein was detected within the protein gel.

These data uncovered that 60% of the detected proteins have proteoforms that migrate at lower than predicted molecular weights, implicating extensive proteolytic processing. This analysis confirms the proteolytic removal and degradation of autoinhibitory prodomains of most but not all proteases, and revealed differential processing within pectinemethylesterase and lipase families. This analysis also uncovered intricate processing of glycosidases and uncovered that ectodomain shedding might be common for a diverse range of receptor‐like kinases. Transient expression of double‐tagged candidate proteins confirmed processing events in vivo.

This large proteomic dataset implicates an elaborate proteolytic machinery shaping the proteome of N. benthamiana.
Public Employees' whistleblowing intention: Explanation by an adapted theory of planned behavior
Authors: Zhang Yahong , Hung Wan‐Ju , Dong Hsiang‐Kai , Chen Don‐Yun
Published: June 2024

Public employees' whistleblowing is an effective anti‐corruption means because they can provide rigorous evidence of wrongdoing in public organizations. However, whistleblowing may cause risks to the individuals and their organization, which discourage them from reporting. While the topic has been understudied, a few studies have adopted the theory of planned behavior (TPB) from psychology to gain insights into whistleblowing. However, these studies have overlooked the unique characteristics of the public sector and the contextual factors surrounding whistleblowing. Our research aims to fill this gap by incorporating these missing elements into the theoretical framework and thus developing an adapted TPB. Using survey data from Taiwan, this study provides empirical evidence to support the adapted TPB in explaining the intention of public employees to blow the whistle.

Chinese Abstract

由公務人員本身來舉報不法事件, 被視為是一種相當有效的反貪腐手段, 因為他們通常能夠提供這些不當行為的有力證據。然而, 舉報不法事件卻可能會對公務人員個人或其單位帶來風險, 也因此往往成為其最終選擇沉默的主要原因。雖然過去已有一些研究採取「計劃行為理論 (TPB)」來探討此一主題, 但這些研究卻沒有考量公部門獨有的特性及環境系絡對舉報行為的影響。本研究希望能夠整合這些過去被遺漏的要素, 並且發展出更適合公部門的理論框架。本研究使用臺灣文官調查 (TGBS) 所蒐集的資料, 進行實證分析並用更完整的 TPB 模型來解釋公職人員舉報不法的行為意圖。.
Journey through the spectacular landscape of melanocortin 1 receptor
Authors: Upadhyay P. R. , Swope V. B. , Starner R. J. , Koikov L. , Abdel‐Malek Z. A.
Published: June 2024

The physiological role of α‐melanocyte stimulating hormone in regulating integumental pigmentation of many vertebrate species has been recognized since the 1960's. However, its physiological significance for human pigmentation remained enigmatic until the 1990's. α‐Melanocyte stimulating hormone and related melanocortins are synthesized locally in the skin, primarily by keratinocytes, in addition to the pituitary gland, and therefore act as paracrine factors for melanocytes. Human melanocytes express the melanocortin 1 receptor, which recognizes α‐melanocyte stimulating hormone and the related adrenocorticotropic hormone as agonists. This review summarizes the current knowledge of the pleotropic effects of the activated melanocortin 1 receptor that maintain human melanocyte homeostasis by regulating melanogenesis and the response to environmental stressors, mainly solar radiation. Certain allelic variants of the melanocortin 1 receptor gene are associated with specific pigmentary phenotypes in various human populations. Variants associated with red hair phenotype compromise the function of the encoded receptor. Activation of the human melanocortin 1 receptor regulates eumelanin synthesis and enhances DNA damage response of melanocytes to solar radiation and oxidative stressors. We describe how synthetic selective melanocortin 1 receptor agonists can be efficacious as sunless tanning agents, for treatment of vitiligo and photosensitivity disorders, and for prevention of skin cancer, including melanoma.
‘It's all there in the language’—a conversation with Garrett Stewart
Authors: LaRocca David
Published: June 2024

What does a famed literary theorist have to say about the interaction between ‘literature’ and ‘philosophy’? Well, if he's Garrett Stewart, the celebrated agent of pyrotechnic style in the service of durable insights across disparate disciplines and media, then we have much reason to lean in and listen. Stewart is the author of 20 books that range with uncanny competency across Victorian narrative, contemporary American fiction, written auralities, poetics and prose stylistics, cinematic evolution from silver oxide to screen pixel, book art, scenes of reading in painting, and most recently, the vocal drama of Barbra Streisand. The distances between his disciplinary terrains are as vast as his close readings of them are coordinated and trenchant. Here, sitting down before a shared conversational canvas, Stewart fields questions from David LaRocca, who asks how he, if he, thinks about the program of literature and philosophy. LaRocca, editor of the recent Attention Spans: Garrett Stewart, a Reader (Bloomsbury, 2024) and the forthcoming Bandwidths: Reading Across Media with Garrett Stewart (Bloomsbury), tracks the urgency of our moment—in which literature and philosophy are independently besieged and yet may concede little rapprochement. Where does philosophy happen in literature (a philosopher's question) is turned around by Stewart such that we see literature conjuring philosophy at the level of the sentence. We are not peering ‘in’ so much as looking ‘at’ the art of literature teaching philosophy through refined reading and the analytical inquest of the syllable and the sayable. Anyone who works at the fraught fissure of these realms will benefit from the ways Stewart makes literature and philosophy sensible to one another—even as he productively unsettles the terms and conditions of their affiliation.
The effect of motivational interviewing on quality of life and self‐efficacy behaviors of individuals with chronic illness: A meta‐analysis study
Authors: Uzun Sevda , Gürhan Nermin
Published: June 2024

Objective

This study aims to reveal the effect of the motivational interviewing on the quality of life and self‐efficacy behaviors of individuals with chronic diseases.

Material‐method

For this meta‐analysis study, PubMed, Web of Science, EBSCOhost, Google Scholar, and YÖK Theses databases were searched in January–May 2021 without year limitation. As a result, 38 studies were included in the study: 23 for the quality of life variable, and 21 for the self‐efficacy behaviors variable (in 6 studies, both variables were examined together). The data were synthesized with meta‐analysis and narrative methods. The total sample size of the studies is 25,425.

Results

This meta‐analysis study showed that the motivational interviewing applied to individuals with chronic diseases changed their quality of life (SMD: 0.296, %95 CI: 0.054–0.537, Z = 2.402, p = .016, I2 = %95). The type of chronic disease, measurement tool, sample group, disease group, age range, and whether the motivational interviewer was a nurse or not changed the effect size of the motivational interviewing on the quality of life. The self‐efficacy score average of the experimental group to which motivational interviewing was applied was statistically similar to that of the control group (SMD: 0.141, %95 CI: −0.065, 0.347; Z = 1.346, p = .178, I2 = %87).

Conclusions

As a result of the meta‐analysis, it was determined that the use of motivational interviewing increased the quality of life level of individuals with chronic diseases. However, it is thought that more research is needed because some studies were conducted with small sample size and prepost test design. The results of the study may provide guidance on the interventions to be used in improving the quality of life of individuals with chronic diseases.
Enhancing drought tolerance in chilli pepper through AdDjSKI‐mediated modulation of ABA sensitivity, photosynthetic preservation, and ROS scavenging
Authors: Bulle Mallesham , Venkatapuram Ajay Kumar , Rahman Md. Mezanur , Attia Kotab A. , Mohammed Arif Ahmed , Abbagani Sadanandam , Kirti P. B.
Published: June 2024

Drought stress threatens the productivity of numerous crops, including chilli pepper (Capsicum annuum). DnaJ proteins are known to play a protective role against a wide range of abiotic stresses. This study investigates the regulatory mechanism of the chloroplast‐targeted chaperone protein AdDjSKI, derived from wild peanut (Arachis diogoi), in enhancing drought tolerance in chilli peppers. Overexpressing AdDjSKI in chilli plants increased chlorophyll content, reflected in the maximal photochemical efficiency of photosystem II (PSII) (Fv/Fm) compared with untransformed control (UC) plants. This enhancement coincided with the upregulated expression of PSII‐related genes. Our subsequent investigations revealed that transgenic chilli pepper plants expressing AdDjSKI showed reduced accumulation of superoxide and hydrogen peroxide and, consequently, lower malondialdehyde levels and decreased relative electrolyte leakage percentage compared with UC plants. The mitigation of ROS‐mediated oxidative damage was facilitated by heightened activities of antioxidant enzymes, including superoxide dismutase, catalase, ascorbate peroxidase, and peroxidase, coinciding with the upregulation of the expression of associated antioxidant genes. Additionally, our observations revealed that the ectopic expression of the AdDjSKI protein in chilli pepper plants resulted in diminished ABA sensitivity, consequently promoting seed germination in comparison with UC plants under different concentrations of ABA. All of these collectively contributed to enhancing drought tolerance in transgenic chilli plants with improved root systems when compared with UC plants. Overall, our study highlights AdDjSKI as a promising biotechnological solution for enhancing drought tolerance in chilli peppers, addressing the growing global demand for this economically valuable crop.
Neighborhood‐level racialized socioeconomic deprivation and contraceptive use in the United States, 2011–2019
Authors: Cartwright Alice F. , Wallace Maeve , Su Jessica , Curtis Siân , Angeles Gustavo , Speizer Ilene S.
Published: June 2024

Introduction

The social and structural environments where people live are understudied in contraceptive research. We assessed if neighborhood measures of racialized socioeconomic deprivation are associated with contraceptive use in the United States.

Methods

We used restricted geographic data from four waves of the National Survey of Family Growth (2011–2019) limited to non‐pregnant women ages 15–44 who had sex in the last 12 months. We characterized respondent neighborhoods (census tracts) with the Index of Concentration at the Extremes (ICE), a measure of spatial social polarization, into areas of concentrated privilege (predominantly white residents living on high incomes) and deprivation (predominantly people of color living on low incomes). We used multivariable binary and multinomial logistic regression with year fixed effects to estimate adjusted associations between ICE tertile and contraceptive use and method type. We also assessed for an interactive effect of ICE and health insurance type.

Results

Of the 14,396 respondents, 88.4% in neighborhoods of concentrated deprivation used any contraception, compared to 92.7% in the most privileged neighborhoods. In adjusted models, the predicted probability of using any contraception in neighborhoods of concentrated deprivation was 2.8 percentage points lower than in neighborhoods of concentrated privilege, 5.0 percentage points higher for barrier/coital dependent methods, and 4.3 percentage points lower for short‐acting methods. Those with Medicaid were less likely to use any contraception than those with private insurance irrespective of neighborhood classification.

Conclusions

This study highlights the salience of structural factors for contraceptive use and the need for continued examination of structural oppressions to inform health policy.
Origin of the H1N1 (Russian influenza) pandemic of 1977—A risk assessment using the modified Grunow–Finke tool (mGFT)
Authors: Kalyar Fatema , Chen Xin , Chughtai Abrar Ahmad , MacIntyre Chandini Raina
Published: June 2024

In 1977, the Soviet Union (Union of Soviet Socialist Republics [USSR]) notified the World Health Organization (WHO) about an outbreak of H1N1 influenza, which later spread to many countries. The H1N1 strain of 1977 reappeared after being absent from the world for over 20 years. This pandemic simultaneously spread to several cities in the USSR and China. Many theories have been postulated to account for the emergence of this pandemic, including natural and unnatural origins. The purpose of this study was to use the modified Grunow–Finke risk assessment tool (modified Grunow‐Finke tool [mGFT]) to investigate the origin of the 1977 H1N1 pandemic. Data was collected from WHO archives and published documents. The assessment of the pandemic's origin involved the utilization of a modified version of the original Grunow–Finke risk assessment tool (GFT). Using the mGFT, the final score was 37 out of 60 points (probability: 62%), indicating a high likelihood that the Russian influenza pandemic of 1977 was of unnatural origin. Several variables supported this finding, including the sudden re‐emergence of a previously extinct strain, a genetic signature of laboratory modification for vaccine development, and unusual epidemiology. Inter‐rater reliability was moderate to high. By applying the mGFT to the 1977 Russian influenza pandemic, we established a high probability that this pandemic was of unnatural origin. Although this is not definitive, it is consistent with the possibility that it originated from an incompletely attenuated live influenza vaccine. The mGFT is a useful risk analysis tool to evaluate the origin of epidemics.
Through Thick and Thin: Gesture and Speech Remain as an Integrated System in Atypical Development
Authors: Demir‐Lira Ö. Ece , Göksun Tilbe
Published: June 2024

Gesture and speech are tightly linked and form a single system in typical development. In this review, we ask whether and how the role of gesture and relations between speech and gesture vary in atypical development by focusing on two groups of children: those with peri‐ or prenatal unilateral brain injury (children with BI) and preterm born (PT) children. We describe the gestures of children with BI and PT children and the relations between gesture and speech, as well as highlight various cognitive and motor antecedents of the speech‐gesture link observed in these populations. We then examine possible factors contributing to the variability in gesture production of these atypically developing children. Last, we discuss the potential role of seeing others’ gestures, particularly those of parents, in mediating the predictive relationships between early gestures and upcoming changes in speech. We end the review by charting new areas for future research that will help us better understand the robust roles of gestures for typical and atypically‐developing child populations.
Money matters: The association between blood donation rates and healthcare system quality across 171 countries
Authors: Hoorn Lieke C. , Graf Caroline , Merz Eva‐Maria
Published: June 2024

Background

Worldwide, insufficient blood donations cause blood shortages that jeopardize vital medical treatments for patients. Blood donation rates vary widely across countries, yet the determinants of this variation remain poorly understood. This study aims to illuminate the role of the institutional context in which blood donation is embedded by examining the link between country‐level blood donation rates and healthcare system quality.

Study Design and Methods

The study employed a cross‐sectional design using data on blood donation rates from 171 countries from the 2021 WHO Global Status Report on Blood Safety and Availability and three healthcare quality indicators (i.e., Healthcare Access and Quality [HAQ] Index, life expectancy, and health expenditures). The pre‐registered hypotheses are tested using multiple linear regression. Robustness checks control for confounding factors.

Results

HAQ Index and health expenditures are positively associated with blood donation rates, whereas life expectancy is not related to blood donation when controlling for confounds. Health expenditures display the most robust association with blood donations, even when controlling for confounding factors, and when comparing countries within the same continent.

Conclusion

Higher healthcare system quality in terms of HAQ Index and higher healthcare expenditures are related to higher blood donation rates. The finding that healthcare expenditures are most consistently related to blood donation rates indicates that policymakers should consider prioritizing financial support for the healthcare system, including blood‐collecting institutions. More broadly, a better understanding of the role of contextual factors for blood donation may be needed to increase blood availability worldwide.
Intradural‐extramedullary inflammatory pseudotumour of the cervical spinal cord of a dog
Authors: Reyes Henry Mendo , Fiorentino Erica , Matiasek Kaspar , Menchetti Marika
Published: June 2024

An 8‐year‐old mixed‐breed dog was presented with cervical hyperesthesia, tetraparesis, and mild proprioceptive ataxia in all four limbs. 3 Tesla MRI showed a dorsal compressive intradural‐extramedullary mass at the level of C1–C2, isointense to the gray matter with a hypointense ventral core on T2 weighted images (WI), isointense on T1WI, with a strong and homogeneous contrast enhancement. A C1–C2 partial dorsal laminectomy was performed, and the lesion was removed en bloc. The histopathological and immunohistochemical analysis defined the diagnosis of inflammatory pseudotumor.
Sex disparities of human neuromuscular decline in older humans
Authors: Guo Yuxiao , Jones Eleanor J. , Smart Thomas F. , Altheyab Abdulmajeed , Gamage Nishadi , Stashuk Daniel W. , Piasecki Jessica , Phillips Bethan E. , Atherton Philip J. , Piasecki Mathew
Published: June 2024

Females typically live longer than males but, paradoxically, spend a greater number of later years in poorer health. The neuromuscular system is a critical component of the progression to frailty, and motor unit (MU) characteristics differ by sex in healthy young individuals and may adapt to ageing in a sex‐specific manner due to divergent hormonal profiles. The purpose of this study was to investigate sex differences in vastus lateralis (VL) MU structure and function in early to late elderly humans. Intramuscular electromyography signals from 50 healthy older adults (M/F: 26/24) were collected from VL during standardized submaximal contractions and decomposed to quantify MU characteristics. Muscle size and neuromuscular performance were also measured. Females had higher MU firing rate (FR) than males (P = 0.025), with no difference in MU structure or neuromuscular junction transmission (NMJ) instability. All MU characteristics increased from low‐ to mid‐level contractions (P < 0.05) without sex × level interactions. Females had smaller cross‐sectional area of VL, lower strength and poorer force steadiness (P < 0.05). From early to late elderly, both sexes showed decreased neuromuscular function (P < 0.05) without sex‐specific patterns. Higher VL MUFRs at normalized contraction levels previously observed in young are also apparent in old individuals, with no sex‐based difference of estimates of MU structure or NMJ transmission instability. From early to late elderly, the deterioration of neuromuscular function and MU characteristics did not differ between sexes, yet function was consistently greater in males. These parallel trajectories underscore the lower initial level for older females and may offer insights into identifying critical intervention periods.

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Key points

Females generally exhibit an extended lifespan when compared to males, yet this is accompanied by a poorer healthspan and higher rates of frailty.

In healthy young people, motor unit firing rate (MUFR) at normalized contraction intensities is widely reported to be higher in females than in age‐matched males.

Here we show in 50 people that older females have higher MUFR than older males with little difference in other MU parameters. The trajectory of decline from early to late elderly does not differ between sexes, yet function is consistently lower in females.

These findings highlight distinguishable sex disparities in some MU characteristics and neuromuscular function, and suggest early interventions are needed for females to prevent functional deterioration to reduce the ageing health–sex paradox.
Numerical Investigation of the Impact of the Rectangular Nozzle Aspect Ratio on Liquid Jet in Crossflow
Authors: Shao Meng , He Zhixia , Wang Qian
Published: June 2024

High-fidelity simulation is conducted to investigate liquid jet in crossflow, specifically regarding the rectangular nozzle. The influence of aspect ratio (AR) of nozzles on the atomization characteristics of liquid column in the process of primary breakup is explored by the analysis of the flow structure of crossflow and liquid column. The aspect ratio is ranging from 1 to 8. The results indicate that as the increase of aspect ratio, the disturbance of crossflow to the liquid on the sides is weakened. While the thickness of liquid column also gradually decreases, which enables smaller disturbances to promote droplet shedding. Therefore, surface breakup first weakens and then strengthens. In the column breakup process, the increase of aspect ratio causes crossflow to become the main factor affecting column breakup, and the influence of air pressure gradually weakens. This indicates a shift in the mechanism of surface instability from “Rayleigh–Taylor” (R–T) instability to “Kelvin–Helmholtz” (K–H) instability.
“En el buen camino”: Colaboración entre maestros e investigadores para la implementación del aprendizaje cooperativo en la educación física de educación primaria
Authors: Arumí-Prat Joan , Torres-Cladera Gemma , Pla-Campas Gil
Published: June 2024

Propósito: Dada la dificultad existente en la implementación de los Modelo Basado en la Práctica (MBP) en la educación física (EF) expresada en la literatura, se presenta un estudio sobre la aplicación del Aprendizaje Cooperativo (AC) en la EF de primaria. Método: Un equipo investigador trans-institucional (escuela-universidad) experto en AC, supervisó y desarrolló un análisis temático narrativo de caso único a partir de los relatos autoetnográficos creativos, pero no ficticios, de una maestra de EF de 5° curso. Resultados: Se presentan cinco relatos no ficcionales que narran en crudo eventos significativos de cada una de las condiciones básicas de la AC. Discusión/Conclusión: La investigación evidencia el valor de las narrativas como motor de reflexión educativa que contribuye a mostrar la complejidad en la aplicación del AC en un aula y a disminuir la brecha existente entre la teoría de los MBP y su aplicación práctica.
The Fungal Kingdom: diverse and essential roles in earth's ecosystem
Authors: Buckley Merry
Published: June 2024

There's more to fungi than just mushrooms. Fungi are the cause of scores of life-threatening diseases, they are the earth's best degraders of organic matter, and they are proving to be more useful to science and manufacturing every year. They come in many forms, ranging from single-celled yeasts on the order of ~10 ÌM to mushrooms the size of dinner plates to thin, powdery coatings of mold. Despite the diversity that science has revealed about fungi and their myriad roles in health, ecology, and industry, much about these organisms remains a mystery. The American Academy of Microbiology convened a colloquium November 2–4, 2007, in Tucson, Arizona, to discuss fungi, the current state of research in fungal biology (mycology), and the gaps in our understanding of this important group of organisms. Experts in mycology, medicine, plant pathogens, genetics/genomics, ecology, and other areas developed specific recommendations for advancing fungal research.
Antagonism of epidermal growth factor receptor signaling favors hepatitis E virus life cycle
Authors: Woytinek Kathrin , Glitscher Mirco , Hildt Eberhard
Published: June 2024

Hepatitis E virus (HEV) poses a global threat, which currently remains understudied in terms of host interactions. Epidermal growth factor receptor (EGFR) plays multifaceted roles in viral pathogenesis, impacting host-cell entry, viral replication, and host-defense modulation. On the one hand, EGFR signaling emerged as a major driver in innate immunity; on the other hand, a crosstalk between HEV and EGFR requires deeper analysis. We therefore aimed to dissect the receptor’s involvement in the HEV life cycle. In persistently HEV-infected cells, the EGFR amount is decreased alongside with enhanced receptor internalization. As compared with the control ligand-induced EGFR, activation revealed an early receptor internalization and degradation in HEV-replicating cells, resulting in a notable EGFR signaling delay. Interestingly, inhibition or silencing of EGFR increased viral replication, extracellular and intracellular viral transcripts, and released infectious particles. The pro-viral impact of EGFR inhibition was attributed to (i) impaired expression of interferon-stimulated genes, (ii) activation of the autophagosomal system, (iii) virus-induced inhibition of lysosomal acidification, and (iv) a decrease of the cellular cholesterol level.

IMPORTANCE

This study identifies epidermal growth factor receptor (EGFR) as a novel host factor affecting hepatitis E virus (HEV): EGFR downregulation promotes viral replication, release, and evasion from the innate immune response. The discovery that EGFR inhibition favors viral spread is particularly concerning for HEV patients undergoing EGFR inhibitor treatment.
Bacterial cell volume regulation and the importance of cyclic di-AMP
Authors: Foster Alexander J. , van den Noort Marco , Poolman Bert
Published: June 2024

Nucleotide-derived second messengers are present in all domains of life. In prokaryotes, most of their functionality is associated with general lifestyle and metabolic adaptations, often in response to environmental fluctuations of physical parameters. In the last two decades, cyclic di-AMP has emerged as an important signaling nucleotide in many prokaryotic lineages, including Firmicutes, Actinobacteria, and Cyanobacteria. Its importance is highlighted by the fact that both the lack and overproduction of cyclic di-AMP affect viability of prokaryotes that utilize cyclic di-AMP, and that it generates a strong innate immune response in eukaryotes. In bacteria that produce the second messenger, most molecular targets of cyclic di-AMP are associated with cell volume control. Besides, other evidence links the second messenger to cell wall remodeling, DNA damage repair, sporulation, central metabolism, and the regulation of glycogen turnover. In this review, we take a biochemical, quantitative approach to address the main cellular processes that are directly regulated by cyclic di-AMP and show that these processes are very connected and require regulation of a similar set of proteins to which cyclic di-AMP binds. Altogether, we argue that cyclic di-AMP is a master regulator of cell volume and that other cellular processes can be connected with cyclic di-AMP through this core function. We further highlight important directions in which the cyclic di-AMP field has to develop to gain a full understanding of the cyclic di-AMP signaling network and why some processes are regulated, while others are not.
An ancillary care policy in a vaccine trial conducted in a resource-constrained setting: evaluation and policy recommendations
Authors: Lemey Gwen , Larivière Ynke , Osang'ir Bernard Isekah , Zola Trésor , Kimbulu Primo , Milolo Solange , Danoff Engbu , Tchuma Yves , Maketa Vivi , Mitashi Patrick , Ravinetto Raffaella , Van Damme Pierre , Van geertruyden Jean-Pierre , Muhindo-Mavoko Hypolite
Published: June 2024

Introduction

Clear guidelines to implement ancillary care (AC) in clinical trials conducted in resource-constrained settings are lacking. Here, we evaluate an AC policy developed for a vaccine trial in the Democratic Republic of the Congo and formulate policy recommendations.

Methods

To evaluate the AC policy, we performed a longitudinal cohort study, nested in an open-label, single-centre, randomised Ebola vaccine trial conducted among healthcare personnel. Participants’ demographic information, residence distance to the study site and details on the financial and/or medical support provided for any (serious) adverse events ((S)AE) were combined and analysed. To assess the feasibility of the AC policy, an expenditure analysis of the costs related to AC support outcomes was performed.

Results

Enrolment in this evaluation study started on 29 November 2021. The study lasted 11 months and included 655 participants from the Ebola vaccine trial. In total, 393 participants used the AC policy, mostly for AE management (703 AE and 94 SAE) via medication provided by the study pharmacy (75.3%). Men had a 35.2% (95% CI 4.0% to 56.6%) lower likelihood of reporting AE compared with women. Likewise, this was 32.3% lower (95% CI 5.8% to 51.4%) for facility-based compared with community-based healthcare providers. The daily AE reporting was 78.8% lower during the passive vs the active trial stage, and 97.4% lower during unscheduled vs scheduled visits (p<0.001). Participants living further than 10 km from the trial site more frequently reported the travel distance as a reason for not using the policy (p<0.04). In practice, only 1.1% of the operational trial budget was used for AC policy support.

Conclusion

The trial design, study population and local health system impacted the use of the AC policy. Nonetheless, the AC policy implementation in this remote and resource-constrained setting was feasible, had negligible budgetary implications and contributed to participants’ healthcare options and well-being.
Herpes zoster vaccine and the risk of stroke: a population-based cohort study using linked data from the Clinical Practice Research Datalink
Authors: Richardson Kathryn , Loke Yoon Kong , McDonald Helen I , Parretti Helen Mary , Marra Fawziah
Published: June 2024

Background

Studies report herpes zoster associated with short-term stroke risk, but it is unclear whether herpes zoster vaccine reduces stroke risk.

Methods

We performed cohort studies using Clinical Practice Research Datalink Aurum linked to hospital admission, mortality and deprivation data. We included 678 110 adults aged 70–80 years receiving a live attenuated herpes zoster vaccination between 1 September 2013 and 31 December 2019. We conducted three comparisons to a historical unvaccinated cohort, an active comparator and a self-controlled case series (SCCS). The historical cohort comprised 678 110 matched unvaccinated adults between 2007 and 2012. The active comparator comprised 653 373 adults receiving an influenza vaccination between 2013 and 2019 meeting herpes zoster vaccine eligibility. Cox regression was used to estimate HRs for stroke in the subsequent 5 years adjusted for measured confounders, in the vaccinated compared with comparator cohorts. Secondary outcomes included stroke/transient ischaemic attack and myocardial infarction. The SCCS included incident strokes 12 months before or after herpes zoster vaccination to address healthy vaccinee bias.

Results

We recorded 16 281 and 30 430 incident strokes among vaccinated and unvaccinated historical patients, over a median of 2.7 and 5.0 years follow-up, respectively. The adjusted HR for stroke for herpes zoster vaccination compared with unvaccinated historical patients was 0.84 (95% CI 0.82 to 0.86) and to influenza-vaccinated patients was 0.88 (0.85 to 0.89). However, stroke incidence rates were lower in the herpes zoster-vaccinated group prevaccination compared with both comparator cohorts. The SCCS found no association between herpes zoster vaccination and stroke 30–119 days later.

Conclusions

Despite our cohort study, with extensive confounder adjustment and an influenza vaccination active comparator, finding herpes zoster vaccination associated with 12%–16% reduced stroke rates, additional analyses suggested this was largely explained by healthy vaccinee bias. Our study illustrates the importance of robust sensitivity analyses and testing the suitability of causal inference tools for observational vaccine studies.
Drug repositioning identifies histone deacetylase inhibitors that promote innate immunity in non-tuberculous mycobacterial infection
Authors: Rodriguez-Carlos Adrián , Raúl Anguita , Jacobo-Delgado Yolanda M. , Serrano Carmen Judith , Santos-Mena Alan , De Jesus-Gonzalez Luis Adrian , Boix Ester , Rivas-Santiago Bruno
Published: June 2024

Non-tuberculosis infections in immunocompromised patients represent a cause for concern, given the increased risks of infection, and limited treatments available. Herein, we report that molecules for binding to the catalytic site of histone deacetylase (HDAC) inhibit its activity, thus increasing the innate immune response against environmental mycobacteria. The action of HDAC inhibitors (iHDACs) was explored in a model of type II pneumocytes and macrophages infection by Mycobacterium aurum. The results show that the use of 1,3-diphenylurea increases the expression of the TLR-4 in M. aurum infected MDMs, as well as the production of defb4, IL-1β, IL-12, and IL-6. Moreover, we observed that aminoacetanilide upregulates the expression of TLR-4 together with TLR-9, defb4, CAMP, RNase 6, RNase 7, IL-1β, IL-12, and IL-6 in T2P. Results conclude that the tested iHDACs selectively modulate the expression of cytokines and antimicrobial peptides that are associated with reduction of non-tuberculous mycobacteria infection.
Search for baryon junctions in photonuclear processes and isobar collisions at RHIC
Authors: Lewis Nicole , Lv Wendi , Ross Mason Alexander , Tsang Chun Yuen , Brandenburg James Daniel , Lin Zi-Wei , Ma Rongrong , Tang Zebo , Tribedy Prithwish , Xu Zhangbu
Published: June 2024

During the early development of quantum chromodynamics, it was proposed that baryon number could be carried by a non-perturbative Y-shaped topology of gluon fields, called the gluon junction, rather than by the valence quarks as in the QCD standard model. A puzzling feature of ultra-relativistic nucleus-nucleus collisions is the apparent substantial baryon excess in the mid-rapidity region that could not be adequately accounted for in most conventional models of quark and diquark transport. The transport of baryonic gluon junctions is predicted to lead to a characteristic exponential distribution of net-baryon density with rapidity and could resolve the puzzle. In this context we point out that the rapidity density of net-baryons near mid-rapidity indeed follows an exponential distribution with a slope of $$-0.61\pm 0.03$$

-
0.61
±
0.03

as a function of beam rapidity in the existing global data from A+A collisions at AGS, SPS and RHIC energies. To further test if quarks or gluon junctions carry the baryon quantum number, we propose to study the absolute magnitude of the baryon vs. charge stopping in isobar collisions at RHIC. We also argue that semi-inclusive photon-induced processes ($$\gamma +p$$

γ
+
p

/A) at RHIC kinematics provide an opportunity to search for the signatures of the baryon junction and to shed light onto the mechanisms of observed baryon excess in the mid-rapidity region in ultra-relativistic nucleus-nucleus collisions. Such measurements can be further validated in A+A collisions at the LHC and $$e+p$$

e
+
p

/A collisions at the EIC.
From pole parameters to line shapes and branching ratios
Authors: Heuser L. A. , Chanturia G. , Guo F.-K. , Hanhart C. , Hoferichter M. , Kubis B.
Published: June 2024

Resonances are uniquely characterized by their complex pole locations and the corresponding residues. In practice, however, resonances are typically identified experimentally as structures in invariant mass distributions, with branching fractions of resonances determined as ratios of count rates. To make contact between these quantities it is necessary to connect line shapes and resonance parameters. In this work we propose such a connection and illustrate the formalism with detailed studies of the $$\rho (770)$$

ρ
(
770
)

and $$f_0(500)$$

f
0

(
500
)

resonances. Based on the line shapes inferred from the resonance parameters along these lines, expressions for partial widths and branching ratios are derived and compared to other approaches in the literature.
$$M_W$$ in string derived Z$$^\prime $$ models
Authors: Faraggi Alon E. , Goodsell Mark D.
Published: June 2024

We introduce a phenomenological model for a string-derived $$Z^\prime $$

Z
′

scenario, and study its predictions for the mass of the W boson. In the process, we compare it to collider constraints for both pair-produced particles, Higgs boson properties, and $$Z^\prime $$

Z
′

searches. We also describe the implementation of new tools in the scanning code BSMArt.
Using computational fluid dynamic for evaluation of rupture risk of micro cerebral aneurysms in the growth process: Hemodynamic analysis
Authors: Shiryanpoor Iman , Kheiri Amir , Gerdroodbary M. Barzegar , Valipour Peiman , Moradi Rasoul
Published: June 2024

The significance of the hemodynamic analysis in the growth process of the micro saccular intracranial aneurysm is undeniable. This study has investigated the change of hemodynamic factors in the evolution process of the saccular aneurysm. The main goal is to estimate the rupture risk of aneurysm in the growth process. The numerical method is applied for the investigation of the hemodynamic factors in the evolution process of the saccular intracranial aneurysms. Wall shear stress, pressure and Oscillatory index are analyzed in this research. Two scale-down models and one scale-up geometry of the saccular aneurysm are studied in this paper. Presented results disclosed that mean wall shear stress increases more than two times when the intracranial aneurysm scale is 1/4 original size.
Casimir energy for Lorentz-violating scalar field with helical boundary condition in d spatial dimensions
Authors: Valuyan M. A.
Published: June 2024

Delving into spring-like helical configurations, such as DNA within our cells, motivates physicists to inquire about the effects of such structures in the realm of quantum field theory, specifically unraveling their manifestation of effectiveness in Casimir energy. To explore this, we initiated our investigation with the Casimir effect and proceeded to calculate the Casimir energy, along with its thermal and radiative corrections, for massive and massless Lorentz-violating scalar fields across (d+1)-dimensional spacetime. Adhering to the principle that the renormalization program should be consistent with the boundary conditions applied to the quantum fields was paramount. Accordingly, one-loop correction to the Casimir energy for both massive and massless scalar fields under helical boundary conditions by employing a position-dependent counterterm was performed. Our results, spanning across spatial dimensions, exhibited convergence and coherence with established physical grounds. Additionally, we presented the Casimir energy density using graphical plots for systems featuring time-like and space-like Lorentz violations across all spatial dimensions, followed by a comprehensive discussion of the obtained results.
Fuzzy Partitioned Discrete-event System and Its Decentralized Supervisory Control
Authors: Singh Shailendra , Tiwari S. P. , Choudhary Narayan , Abolpour Kh.
Published: June 2024

This work uses the idea of a fuzzy partitioned automaton to examine a fuzzy partitioned discrete-event system and associated decentralized supervisory control theory. We will specifically look at the notion of a fuzzy partitioned automaton and how it may be used to simulate the aforementioned system. In addition, we investigate the decentralized fuzzy supervisory control theory for a fuzzy partitioned discrete-event system and look at the conditions for its existence.
Molecular Dynamic Simulations of Dual Inhibitors for AChE and BChE; Theoretical and Experimental Approaches
Authors: Raza Muhammad Asam , Arif Maimoona , Farwa Umme , Sandhu Zeshan Ali , Ashraf Adnan , Bahyoune Nouhaila , Nashre-ul-Islam Swah Mohd. , Almutairi Tahani Mazyad , Bouissane Latifa
Published: June 2024

The aim of the study is to design and synthesize thiazolidinone derivatives having therapeutic potential using PABA as a core component. The characterization of thiazolidinones MS1–MS6 was carried out using different spectroscopic techniques before being subjected to DFT studies to calculate various parameters such as HOMO/LUMO energy gaps and global chemical properties. Thiazolidinones MS1–MS6 were screened to evaluate their in vitro enzyme inhibition potential. In addition to experimental work, theoretical approaches were used as supporting components to design the enzyme inhibitors. In-silico ADMET and docking studies were performed to check the therapeutic properties of thiazolidinone derivatives. The enzyme inhibition potential predicted that MS1–MS6 have potential to inhibit AChE and BChE. The highest activity was depicted by MS4 with a percentage inhibition of 81.7 ± 1.1% against AChE. The molecular dynamic simulation was run for MS4 showing a similar activity on enzyme compared to the standard inhibitor. Both experimental and theoretical assessments suggested the therapeutic importance of the thiazolidinone derivatives MS1–MS6. In-depth studies are ongoing to complete therapeutic probing in terms of toxicity and chemical uses.
Developing Predictive Models and Early Warning Systems for Invading Pathogens: Wheat Rusts
Authors: Gilligan Christopher A.
Published: June 2024

Innovations in aerobiological and epidemiological modeling are enabling the development of powerful techniques to infer connectivity networks for transboundary pathogens in ways that were not previously possible. The innovations are supported by improved access to historical and near real-time highly resolved weather data, multi-country disease surveillance data, and enhanced computing power. Using wheat rusts as an exemplar, we introduce a flexible modeling framework to identify characteristic pathways for long-distance spore dispersal within countries and beyond national borders. We show how the models are used for near real-time early warning systems to support smallholder farmers in East Africa and South Asia. Wheat rust pathogens are ideal exemplars because they continue to pose threats to food security, especially in regions of the world where resources for control are limited. The risks are exacerbated by the rapid appearance and spread of new pathogenic strains, prodigious spore production, and long-distance dispersal for transboundary and pandemic spread.
Analysis of Lithium-ion Batteries through Electrochemical Impedance Spectroscopy Modeling
Authors: Teki Vamsee Krishna , Kasi Jahnavi , Chidurala Saiprakash , Priyadarshini Subhashree , Joga S. Ramana Kumar , Maharana Manoj Kumar , Panigrahi Chinmoy Kumar
Published: June 2024

Electrochemical impedance spectroscopy (EIS) is a very effective methodology employed in the evaluation of performance and degradation mechanisms associated with lithium-ion batteries. In order to comprehend the complex electrochemical processes taking place within these energy storage devices, reliable and effective diagnostic tools are required due to the constant improvements in battery technology. EIS methodology has gained prominence as a very effective non-destructive method for examining the electrochemical characteristics of batteries. This technique offers significant contributions by providing useful insights into the internal operations of batteries. The main objective of this study is to create an electrical equivalent circuit model of a lithium-ion battery based on physics, and then use EIS to comprehend the electrical behavior and impedance of the battery to evaluate its performance under various operating scenarios. We seek to identify the critical elements influencing the battery’s capacity, performance, and lifespan by capturing the intricate interaction of EIS. The results of this research are going to enhance the understanding of battery behavior and supporting the design as a more reliable and efficient energy storage systems for a wide range of applications, from portable electronic devices to electric vehicles and renewable energy integration.