bluuebunny/crossref_metadata_2025 huggingface dataset:
Periodontitis and thyroid function: A bidirectional Mendelian randomization study
Authors: Gao Yan , Huang Donghai , Liu Yong , Qiu Yuanzheng , Lu Shanhong
Published: January 2024

Background and Objective

Previous studies suggest interaction between periodontitis and thyroid function, while the causality has not yet been established. We applied the Mendelian randomization (MR) method to assess bidirectional causal association between periodontitis and thyroid‐related traits, including free thyroxine (FT4), thyroid stimulating hormone (TSH), hypothyroidism, hyperthyroidism and autoimmune thyroid disease (AITD).

Methods

Genetic instruments were extracted from large‐scale genome‐wide association studies on normal‐range FT4 (N = 49 269) and TSH (N = 54 288) levels, TSH in full range (N = 119 715); hypothyroidism (discovery/replication cohorts: N = 53 423/334 316), hyperthyroidism (discovery/replication cohorts: N = 51 823/257 552), AITD (N = 755 406) and periodontitis (N = 45 563). Here, the inverse variance weighted (IVW) method was applied as the primary analysis, and robustness of results were assessed by several pleiotropic‐robust methods. Results were adjusted for Bonferroni correction thresholds with significant p < .004 (0.05/13) and suggestive p between .004 and .05.

Results

The IVW analysis revealed a suggestively causal linkage between genetic predisposition to periodontitis and the increased risk of hypothyroidism (discovery cohort: odds ratio [OR] = 1.24, 95% confidence interval [CI] = 1.05–1.46, p = .012; replication cohort: OR = 1.06, 95% CI = 1.01–1.11, p = .011). No evidence was found for supporting the impact of periodontitis on hyperthyroidism and AITD risks (associated p ≥ .209), as well as thyroid‐related traits on periodontitis risk (associated p ≥ .105). These findings were robust and consistent through sensitivity analysis with other MR models.

Conclusion

This bidirectional MR reveals periodontitis should not be attributed to variations in thyroid function but it has potential causal effect on hypothyroidism risk, which provides a better understanding of the relationship between periodontitis and thyroid function, and potential evidence for the clinical intervention of hypothyroidism. Further investigations are warranted to elucidate the nature and underlying mechanisms of this finding.
A guided tour through the qualitative research city
Authors: Wieland Andreas , Tate Wendy L. , Yan Tingting
Published: January 2024

This article argues for the expansion of qualitative research approaches in supply chain management (SCM). By comparing mainstream qualitative approaches to popular Parisian landmarks, it argues that just as tourists can miss the city's essence by visiting only famous sites, SCM researchers limit their understanding by relying solely on conventional approaches. It emphasizes that, much like exploring lesser‐known parts of a city, incorporating diverse qualitative approaches can enrich SCM research. Highlighting the dominance of realist and positivist approaches, the article calls for greater inclusion of nominalist and anti‐positivist approaches. It introduces different “buildings” of qualitative research (grounded theory, interpretive research, sensemaking, sociomateriality, actor–network theory, ethnography, action research, discourse analysis, narrative research, and historical research), each offering unique insights into SCM. The article argues that embracing these diverse approaches can lead to a deeper understanding of complex global supply chain phenomena and encourage innovative theoretical development, thereby broadening the scope and impact of the discipline.
Toddlers’ Verb‐Marking Errors Are Predicted by the Relative Frequency of Uninflected Sequences in Well‐Formed Child‐Directed Speech: A Preregistered Corpus Analysis
Authors: Sawyer Hannah , Bannard Colin , Pine Julian
Published: January 2024

Verb‐marking errors such as she play football and daddy singing are a hallmark feature of English‐speaking children's speech. We investigated the proposal that these errors are input‐driven errors of commission arising from the high relative frequency of subject + unmarked verb sequences in well‐formed child‐directed speech. We tested this proposal via a preregistered corpus analysis and asked at what level the effects occur: Is it the relative frequency of specific subject + unmarked verb sequences in the input that is important, or is it simply that verbs become entrenched, such that their frequency of appearance with any third person singular subject accounts for errors? We found that the best predictor of children's verb‐marking errors is the relative frequency of unmarked forms of specific subject + verb sequences. Our results supported the proposal that children's apparent omissions of certain grammatical morphemes are in fact input‐driven errors of commission and provided insight into the mechanisms by which this occurs.
Biobjective optimization for railway alignment fine‐grained designs with parallel existing railways
Authors: Gao Yan , Zhang Tianlong , Zhu Caiyiyi , Yang Shusheng , Schonfeld Paul , Zou Kai , Zhang Jialing , Zhu Ying , Wang Ping , He Qing
Published: January 2024

Urban high‐speed railway construction is complex due to limited land resources, high population density, and potential construction risks, especially when new tracks are parallelly aligned to operational railways. Addressing a gap in current literature on fine optimization of manual alignment in such scenarios, this paper introduces a biobjective approximate fine‐grained optimization model for railway alignments (BA‐FORA). Utilizing an approximate dynamic programming (ADP) method, BA‐FORA effectively searches the feasible region to approach a global optimum, overcoming the dimensionality challenges inherent in standard dynamic programming (DP). This paper presents a biobjective optimization framework that takes into account both construction cost and construction risk adjacent to existing operating railways (CRAEOR), offering a method for the fine‐grained design of new railways adjacent to existing railways. Finally, the proposed BA‐FORA framework is applied to practical cases, demonstrating its superior optimization performance. The findings indicate that the BA‐FORA model can autonomously investigate and enhance railway alignment. It generates cost‐effective and low‐risk solutions exceeding manual efforts, ensuring alignment constraint compliance.
News from ‘black belt’ masters of symbiosis
Authors: Grube Martin , Balestrini Raffaella
Published: January 2024

This article is a Commentary on Chrismas et al. (2024), 241: 2243–2257.
Metabolite‐based genome‐wide association studies enable the dissection of the genetic bases of flavonoids, betaine and spermidine in wolfberry (Lycium)
Authors: Zhao Jianhua , Xu Yuhui , Li Haoxia , An Wei , Yin Yue , Wang Bin , Wang Liping , Wang Bi , Duan Linyuan , Ren Xiaoyue , Liang Xiaojie , Wang Yajun , Wan Ru , Huang Ting , Zhang Bo , Li Yanlong , Luo Jie , Cao Youlong
Published: January 2024

Wolfberry is a plant with medicinal and food values. However, its bioactive ingredients and the corresponding genetic bases have not been determined. Here, we de novo generated a chromosome‐level genome assembly for wolfberry, yielding a genome sequence of ~1.77 Gb with contig N50 of 50.55 Mb and 39 224 predicted gene models. A variation map, using 307 re‐sequenced accessions, was called based on this genome assembly. Furthermore, the fruit metabolome of these accessions was profiled using 563 annotated metabolites, which separated Lycium barbarum L. and non‐L. barbarum L. The flavonoids, coumarins, alkaloids and nicotinic acid contents were higher in the former than in the latter. A metabolite‐based genome‐wide association study mapped 156 164 significant single nucleotide polymorphisms corresponding to 340 metabolites. This included 19 219 unique lead single nucleotide polymorphisms in 1517 significant association loci, of which three metabolites, flavonoids, betaine and spermidine, were highlighted. Two candidate genes, LbUGT (evm.TU.chr07.2692) and LbCHS (evm.TU.chr07.2738), with non‐synonymous mutations, were associated with the flavonoids content. LbCHS is a structural gene that interacts with a nearby MYB transcription factor (evm.TU.chr07.2726) both in L. barbarum and L. ruthenicum. Thus, these three genes might be involved in the biosynthesis/metabolism of flavonoids. LbSSADH (evm.TU.chr09.627) was identified as possibly participating in betaine biosynthesis/metabolism. Four lycibarbarspermidines (E–G and O) were identified, and only the lycibarbarspermidines O content was higher in L. barbarum varieties than in non‐L. barbarum varieties. The evm.TU.chr07.2680 gene associated with lycibarbarspermidines O was annotated as an acetyl‐CoA‐benzylalcohol acetyltransferase, suggesting that it is a candidate gene for spermidine biosynthesis. These results provide novel insights into the specific metabolite profile of non‐L. barbarum L. and the genetic bases of flavonoids, betaine and spermidine biosynthesis/metabolism.
FIONA1‐mediated mRNA m6A methylation regulates the response of Arabidopsis to salt stress
Authors: Cai Jing , Hu Jianzhong , Xu Tao , Kang Hunseung
Published: January 2024

N6‐methyladenosine (m6A) is an mRNA modification widely found in eukaryotes and plays a crucial role in plant development and stress responses. FIONA1 (FIO1) is a recently identified m6A methyltransferase that regulates Arabidopsis (Arabidopsis thaliana) floral transition; however, its role in stress response remains unknown. In this study, we demonstrate that FIO1‐mediated m6A methylation plays a vital role in salt stress response in Arabidopsis. The loss‐of‐function fio1 mutant was sensitive to salt stress. Importantly, the complementation lines expressing the wild‐type FIO1 exhibited the wild‐type phenotype, whereas the complementation lines expressing the mutant FIO1m, in which two critical amino acid residues essential for methyltransferase activity were mutated, did not recover the wild‐type phenotype under salt stress, indicating that the salt sensitivity is associated with FIO1 methyltransferase activity. Furthermore, FIO1‐mediated m6A methylation regulated ROS production and affected the transcript level of several salt stress‐responsive genes via modulating their mRNA stability in an m6A‐dependent manner in response to salt stress. Importantly, FIO1 is associated with salt stress response by specifically targeting and differentially modulating several salt stress‐responsive genes compared with other m6A writer. Collectively, our findings highlight the molecular mechanism of FIO1‐mediated m6A methylation in the salt stress adaptation.
Real‐time generation of spherical panoramic video using an omnidirectional multi‐camera system
Authors: Gao Jiongli , Wu Jun , Huang Mingyi , Xu Gang
Published: January 2024

This paper presents a novel method for real‐time generation of seamless spherical panoramic videos from an omnidirectional multi‐camera system (OMS). Firstly, a multi‐view video alignment model called spherical projection constrained thin‐plate spline (SP‐TPS) was established and estimated using an approximately symmetrical seam‐line, maintaining the structure inconsistency around the seam‐line. Then, a look‐up table was designed to support real‐time processing of video re‐projection, video dodging and seam‐line updates. In the table, the overlapping areas in OMS multi‐view videos, the seam‐lines between spherical panoramas and OMS multi‐view videos and the pixel coordinate mapping relationship between spherical panoramas and OMS multi‐view videos were pre‐stored as a whole. Finally, a spherical panoramic video was outputted in real‐time through look‐up table computation under an ordinary GPU processor. The experiments were conducted on multi‐view video taken by “1 + 4” and “1 + 7” OMS, respectively. Experimental results demonstrate that compared with four state‐of‐the‐art methods reported in the literature and two bits of commercial software for video stitching, the proposed method excels in eliminating visual artefacts and demonstrates superior adaptability to scenes with varying depths of field. Assuming that OMS is not movable in the scene, this method can generate seamless spherical panoramic videos with a resolution of 8 K in real time, which is of great value to the surveillance field.
Knowability paradox, decidability solution?
Authors: Knowles William Bondi
Published: January 2024

Fitch's knowability paradox shows that for each unknown truth there is also an unknowable truth, a result which has been thought both odd in itself and at odds with views which impose epistemic constraints on truth and/or meaningfulness. Here a solution is considered which has received little attention in the debate but which carries prima facie plausibility. The decidability solution is to accept that Fitch sentences are unknowably true but deny the significance of this on the grounds that Fitch sentences are nevertheless decidable. The decidability solution is particularly attractive for those whose primary concern is an epistemic constraint on meaningfulness (‘verificationists’). For those whose main concern is truth (‘anti‐realists’), the situation is more complex: Melia takes the solution to exonerate anti‐realism completely; Williamson sees it as completely irrelevant. The truth lies between these two extremes: there is one broad anti‐realist commitment to which the solution does not apply, but there is also one, the “fundamental tenet” of anti‐realism according to Dummett, to which it does.
Estimation of direct and maternal covariance along with genetic and phenotypic trends of reproduction traits in Murrah buffalo
Authors: Sharma Smriti , Dhaka Surender Singh , Patil Chandrashekhar Santosh , Rathi Pallavi
Published: January 2024

The research utilized data from 662 Murrah buffaloes meticulously recorded over 24 years (1996–2019) from historical pedigree sheets maintained at the buffalo farm of the Department of Livestock Production and Management (LPM) at Lala Lajpat Rai University of Veterinary and Animal Sciences (LUVAS), Hisar. A series of six univariate animal models were employed to calculate estimates of (co)variance components and heritability for first lactation reproduction traits. Among these models, Model 2 was identified as the best fit for age at first calving (AFC) and calving interval (CI), while Model 1 proved optimal for service period (SP) and conception rate (CR). The heritability estimates for AFC, SP, CR and CI across the models were ranged between 0.11 and 0.32, 0.01 and 0.03, 0.05 and 0.06, and 0.01 and 0.06, respectively. Maternal effects (m2) were observed in AFC and CI, ranging from 0.10 to 0.20 and 0.01 to 0.03, respectively. Across all three traits, there was a consistent negative genetic correlation (−0.75 to −0.92) between direct additive and maternal effects. The breeding values for AFC, SP, CR and CI varied within specific ranges from −32.85 to 44.33 days, −15.61 to 28.42 days, −7.41 to 6.48% and −20.64 to 35.79 days, respectively. Significantly, Spearman's rank correlation analysis revealed highly significant relationships (p < .01) between the breeding values of different models, indicating strong and consistent associations within these traits. These findings underscore the stable and reliable connections observed within the breeding values for these essential reproductive traits across the various models used in the study. The majority of reproductive traits showed favourable negative trends, indicating a positive outcome. A decrease in AFC, SP and CI suggests an extended economic life for the animals. Additionally, the upward trends in CR reflect positive indications of effective management practices and skilled operational procedures.
Labor supply responses to rainfall shocks
Authors: Maitra Pushkar , Tagat Anirudh
Published: January 2024

Agricultural production in developing countries is heavily rainfall dependent. Any unexpected variation in rainfall can affect the welfare of households. Using unit record data from India, this paper shows that households can insure against agricultural productivity (rainfall) shocks. Evidence suggests that they do so by varying the time allocation of individual members to different activities, particularly to regular wage work and human capital accumulation. There is a gender‐differentiated aspect to this response. Rainfall shocks adversely affect women's human capital accumulation. While there is no evidence that households use participation in NREGS to insure against rainfall shocks, the availability of NREGS helps reduce the impact of rainfall shocks on human capital accumulation.
A longitudinal interpretative phenomenological analysis study of athletes' lived experiences in elite disc golf competitions
Authors: Furre Runar , Johansen B. T. , Knight C. J. , Mosewich A. D. , Solstad B. E.
Published: January 2024

Gaining the inside perspective of an elite athlete throughout the competitive season provides a unique approach to understand the lived experience during multiple competitive events. The purpose of the present study was to investigate how elite disc golf athletes perceive and interpret their experiences of performing during various training and competitive events over the course of an elite disc golf season. Two elite disc golf athletes, one man and one woman, were recruited using homogeneous purposive sampling. The participants were interviewed three times and observed during three competitive events, as well as before and after a training session. A longitudinal interpretative phenomenological analysis (LIPA) was adopted to capture temporal and dynamic changes of the participants' lived experiences. The findings illustrated the athletes' personal experiences of performing during competitive disc golf events, with both athletes' experiences of competition changing during the season. Their competitive experiences appear to relate to the meaning disc golf has for the athletes, which in this study had both an experiential and existential level of meaning over time. Such a finding illustrates the importance of honoring athletes' unique experiences in making sense of their performances during an elite disc golf season. Taking the time to understand athletes' perceptions of their personal experiences appear important in attempting to understand their sense‐making of their hot cognition before, during, and after competitions.
Comparison of intradermal and serum testing for environmental allergen‐specific immunoglobulin E determination in a laboratory colony of cats with naturally acquired atopic syndrome
Authors: Lefrançois Julie , Otis Colombe , Moreau Maxim , Visser Marike , Bessey Lauren , Gonzales Andrea , Pelletier Jean‐Pierre , Martel‐Pelletier Johanne , Troncy Eric , Sauvé Frédéric
Published: January 2024

Background

Allergen testing is used to select antigens included in the desensitisation vaccine. Intradermal skin test (IDT) is the gold standard in cats, yet allergen‐specific immunoglobulin (Ig)E serological testing (ASIS) is often used. Feline data are lacking regarding the agreement between IDT and ASIS results.

Hypothesis/Objectives

The first objective of the study was to establish a colony of cats with naturally acquired feline atopic syndrome (FAS). Further objectives were to define their hypersensitivity disorder to detail the allergen tests results, and to assess similarity between the allergen tests.

Animals

Thirty‐five cats with FAS and 10 control cats.

Materials and Methods

Enrolled cats went through a five phase‐screening and quarantine process before joining the colony. An elimination diet trial was performed on all FAS cats. ASIS and IDT were consecutively performed on all cats under sedation.

Results

Reactions to 34 allergens were compiled for the 45 cats. Global sensitivity and specificity of ASIS were 34.7% and 78.9%, respectively. Only flea (ICC = 0.26, p = 0.040) and Dermatophagoides pteronyssinus (ICC = 0.48, p < 0.001) allergens had a significant intraclass correlation (weak agreement). Two FAS cats had negative tests including one cat with a concomitant food allergy.

Conclusions and Clinical Relevance

This study depicts the first reported colony of cats with naturally acquired FAS. This is the first feline study to compare and show the poor agreement between allergen tests with a panel of 34 allergens. This colony also harbours two cats with FAS with negative allergen tests. These may represent the first described cats with an intrinsic form of atopic syndrome.
Truth and Suffering
Authors: Beer Paulo
Published: January 2024

Although truth occupies a central position in philosophy and the philosophy of science, there is much debate about its actual role in scientific practice. Truth and Suffering explores different conceptions of truth and their profound influence on our understanding and approach to suffering. By discussing how different definitions of truth shape distinct ways of producing knowledge, the analysis prompts reflection on the impact of knowledge production on people’s lives. Drawing on the work of authors from psychoanalysis and the philosophy of science, this book challenges dominant mental health paradigms, particularly the hegemony of biologic psychiatry. It resists attempts to naturalise symptoms and emphasises the need for ethical and political factors to be consistently taken into account when addressing suffering. Offering a clear and original approach to an important and complex debate, Truth and Suffering is of interest not only to specialist readers in a variety of fields, ranging from philosophy of science to psychoanalysis, but also provides an introduction to newcomers interested in these discussions.
An approximate solution of singularly perturbed problem on uniform mesh
Authors: Arslan Derya , Çelik Ercan
Published: January 2024

In this study, we obtain approximate solution for singularly perturbed problem of differential equation having two integral boundary conditions. With this purpose, we propose a new finite difference scheme. First, we construct this exponentially difference scheme on a uniform mesh using the finite difference method. We use the quasilinearization method and the interpolating quadrature formulas to establish the numerical scheme. Then, as a result of the error analysis, we show that the method under study is convergent in the first order. Consequently, theoretical findings are supported by numerical results obtained with an example. Approximate solutions curves are compared on the chart to provide concrete indication. The maximum errors and convergence rates obtained are given on the table for different varepsilon  and N values.
Parametric Vibration and Combined Resonance of a Bending-Torsional Coupled Turbine Blade With a Preset Angle
Authors: Ren Yuankai , Lu Jianwei , Deng Gaoming , Zhou Dinghua
Published: January 2024

The parametric vibration and combined resonance of a turbine blade with a preset angle subjected to the combined effect of parametric and forced excitation were investigated. The blade was modeled as a rotating beam considering the effects of centrifugal, gyroscopic, and bending-torsion coupling. The instability region of the corresponding linear system with parametric excitation was analyzed using Floquet theory, and the effect of blade parameters on this region was discussed. Notably, the parametric vibration of the torsional degree-of-freedom (DOF) caused by parametric excitation of the bending degree-of-freedom has been found. The results show that the size and position of the parameter resonance region are affected by the blade aspect ratio and preset angle, respectively. Furthermore, the multiscale method was employed to solve the blade equation under the combined action of parametric and forced excitation to study the combined resonance caused by forced excitation and gyroscopic items. The effect of blade parameters and excitation characteristics on regions of combined resonance were investigated. The phenomenon of heteroclinic bifurcation was observed due to changes in the excitation frequency, and the harmonic components that accompanied the bifurcation changed. Specifically, a multiperiod response dominated by the excitation frequency and subharmonic components shifted to a single-period response dominated by subharmonic components. This study provides a theoretical explanation for the nonsynchronous resonance of blades and the subharmonic signals in blade vibration and guides blade parameter design, especially for wind turbines.
The Exercise Right for Active Ageing Study: Participation in Community-Based Exercise Classes by Older Australians During the COVID-19 Pandemic
Authors: Ekegren Christina L. , Ayton Darshini , Skouteris Helen , Soh Sze-Ee
Published: January 2024

The aim of this study was to determine factors associated with participation of community-dwelling older Australians (≥65 years) in the Exercise Right for Active Ageing program, consisting of 12 low- to moderate-intensity group exercise classes, delivered weekly, in person or online, by accredited exercise scientists and physiologists across Australia. Out of 6,949 participants recruited, 6,626 (95%) attended one or more classes and were included in the primary analysis, and 49% of participants attended all 12 classes. Factors associated with higher class attendance included participation in yoga/flexibility/mobility classes, attendance at a free trial class (adjusted incidence rate ratio [95% confidence interval]: 1.05 [1.03, 1.08]), and attending online classes (1.19 [1.11, 1.26]). Factors associated with lower class attendance included state of residence, living in inner regional areas (0.95 [0.93, 0.98]), and having two or more comorbidities (0.97 [0.95, 0.99]). High class attendance suggests that the Exercise Right for Active Ageing program was well received by older Australians, particularly in states less impacted by COVID-19 lockdowns.
Associations Between Changes in 24-Hour Movement Behaviors in Children and Adolescents During the COVID-19 Pandemic: A Systematic Review and Mediation-Based Meta-Analysis
Authors: Neville Ross D. , Hopkins William G. , McArthur Brae Anne , Draper Catherine E. , Madigan Sheri
Published: January 2024

Background: Although 24-hour movement behaviors are known to be interconnected, limited knowledge exists about whether change in one behavior during the COVID-19 pandemic (eg, increased screen time) was associated with change in another (eg, reduced physical activity or sleep). This review estimates mediational associations between changes in children’s physical activity, screen time, and sleep during the COVID-19 pandemic. Methods: We included studies published between January 1, 2020 and June 27, 2022, in the PubMed/MEDLINE, Embase, PsycINFO, SPORTDiscus, and Web of Science databases. Summary data were extracted from included studies and analyzed with random-effects meta-regression. Results: This review included 26 studies representing 18,959 children across 18 mid-high-income countries (53% male; mean age, 11.5 [2.9] y). There was very good evidence of decreased total daily physical activity (factor change, 0.62; 90% CI, 0.47–0.81) and strong evidence of increased screen time (1.56; 90% CI, 1.38–1.77). There was very good evidence of decreased moderate to vigorous physical activity (0.75; 90% CI, 0.62–0.90) and weak evidence of increased sleep (1.02; 90% CI, 1.00–1.04). Mediational analysis revealed strong evidence that most of the reduction in total daily physical activity from before, to during, the pandemic was associated with increased screen time (0.53; 90% CI, 0.42–0.67). We observed no further mediational associations. Conclusion: Increased reliance on and use of screen-based devices during the COVID-19 pandemic can be linked with reduced child and adolescent physical activity. This finding links COVID-related restrictions to potential displacement effects within child and adolescent 24-hour movement behavior.
The Dropout From Youth Sport Crisis: Not as Simple as It Appears
Authors: Battaglia Anthony , Kerr Gretchen , Tamminen Katherine
Published: January 2024

Given the documented benefits associated with organized sport and thus the assumption that youth who leave sport are losing out on developmental benefits, dropout has been predominantly framed as a crisis to be solved. Throughout this paper we aimed to challenge the overarching narrative of youth dropout from organized sport as a negative outcome only by highlighting the complexity of youth sport experiences and participation patterns. First, we highlight the lack of conceptual clarity regarding the term “dropout” and question its relevance for describing youth’s sport experiences. Next, we discuss how declines in organized sport participation may reflect developmentally appropriate transitions in sport and broader physical activity for youth and across the life span. Finally, we suggest that, at times, disengagement may be a positive and protective outcome for youth when the sport environment is harmful. Recommendations for future research and practice are provided to advance the understanding of youth sport experiences and participation patterns.
A new ROS response factor YvmB protects
Bacillus licheniformis
against oxidative stress under adverse environment
Authors: He Penghui , Hu Shiying , Zhang Yongjia , Xiang Zhengwei , Zhang Zheng , Wang Dong , Chen Shouwen
Published: January 2024

Bacillus
spp., a class of aerobic bacteria, is widely used as a biocontrol microbe in the world. However, the reactive oxygen species (ROS) will accumulate once the aerobic bacteria are exposed to environmental stresses, which can decrease cell activity or lead to cell death. Hydroxyl radical (·OH), the strongest oxide in the ROS, can damage DNA directly, which is generated through Fenton Reaction by H
2
O
2
and free iron. Here, we proved that the synthesis of pulcherriminic acid (PA), an iron chelator produced by
Bacillus
spp., could reduce DNA damage to protect cells from oxidative stress by sequestrating excess free iron, which enhanced the cell survival rates in stressful conditions (salt, antibiotic, and high temperature). It was worth noting that the synthesis of PA was found to be increased under oxidative stress. Thus, we demonstrated that the YvmB, a direct negative regulator of PA synthesis cluster
yvmC-cypX
, could be oxidized at cysteine residue (C57) to form a dimer losing the DNA-binding activity, which led to an improvement in PA production. Collectively, our findings highlight that YvmB senses ROS to regulate PA synthesis is one of the evolved proactive defense systems in bacteria against adverse environments.

IMPORTANCE

Under environment stress, the electron transfer chain will be perturbed resulting in the accumulation of H
2
O
2
and rapidly transform to ·OH through Fenton Reaction. How do bacteria deal with oxidative stress? At present, several iron chelators have been reported to decrease the ·OH generation by sequestrating iron, while how bacteria control the synthesis of iron chelators to resist oxidative stress is still unclear. Our study found that the synthesis of iron chelator PA is induced by reactive oxygen species (ROS), which means that the synthesis of iron chelator is a proactive defense mechanism against environment stress. Importantly, YvmB is the first response factor found to protect cells by reducing the ROS generation, which present a new perspective in antioxidation studies.
Seasonal influenza viruses decay more rapidly at intermediate humidity in droplets containing saliva compared to respiratory mucus
Authors: Rockey Nicole C. , Le Sage Valerie , Marr Linsey C. , Lakdawala Seema S.
Published: January 2024

Expulsions of virus-laden aerosols or droplets from the oral and nasal cavities of an infected host are an important source of onward respiratory virus transmission. However, the presence of infectious influenza virus in the oral cavity during infection has not been widely considered, and thus, little work has explored the environmental persistence of influenza virus in oral cavity expulsions. Using the ferret model, we detected infectious virus in the nasal and oral cavities, suggesting that the virus can be expelled into the environment from both anatomical sites. We also assessed the stability of two influenza A viruses (H1N1 and H3N2) in droplets of human saliva or respiratory mucus over a range of relative humidities. We observed that influenza virus infectivity decays rapidly in saliva droplets at intermediate relative humidity, while viruses in airway surface liquid droplets retain infectivity. Virus inactivation was not associated with bulk protein content, salt content, or droplet drying time. Instead, we found that saliva droplets exhibited distinct inactivation kinetics during the wet and dry phases at intermediate relative humidity, and droplet residue morphology may lead to the elevated first-order inactivation rate observed during the dry phase. Additionally, distinct differences in crystalline structure and nanobead localization were observed between saliva and airway surface liquid droplets. Together, our work demonstrates that different respiratory fluids exhibit unique virus persistence profiles and suggests that influenza viruses expelled from the oral cavity may contribute to virus transmission in low- and high-humidity environments.

IMPORTANCE

Determining how long viruses persist in the environment is important for mitigating transmission risk. Expelled infectious droplets and aerosols are composed of respiratory fluids, including saliva and complex mucus mixtures, but how well influenza viruses survive in such fluids is largely unknown. Here, we find that infectious influenza virus is present in the oral cavity of infected ferrets, suggesting that saliva-containing expulsions can play a role in onward transmission. Additionally, influenza virus in droplets composed of saliva degrades more rapidly than virus within respiratory mucus. Droplet composition impacts the crystalline structure and virus localization in dried droplets. These results suggest that viruses from distinct sites in the respiratory tract could have variable persistence in the environment, which will impact viral transmission fitness.
IFN-λ3 is induced by
Leishmania donovani
and can inhibit parasite growth in cell line models but not in the mouse model, while it shows a significant association with leishmaniasis in humans
Authors: De Manjarika , Sukla Soumi , Bharatiya Seema , Keshri Sagar , Roy Debarati Guha , Roy Sutopa , Dutta Debrupa , Saha Shriya , Ejazi Sarfaraz Ahmad , Ravichandiran V. , Ali Nahid , Chatterjee Mitali , Chinnaswamy Sreedhar
Published: January 2024

The intracellular protozoan parasite
Leishmania donovani
causes debilitating human diseases that involve visceral and dermal manifestations. Type 3 interferons (IFNs), also referred to as lambda IFNs (IFNL, IFN-L, or IFN-λ), are known to play protective roles against intracellular pathogens at the epithelial surfaces. Herein, we show that
L. donovani
induces IFN-λ3 in human as well as mouse cell line-derived macrophages. Interestingly, IFN-λ3 treatment significantly decreased parasite load in infected cells
,
mainly by increasing reactive oxygen species production. Microscopic examination showed that IFN-λ3 inhibited uptake but not replication, while the phagocytic ability of the cells was not affected. This was confirmed by experiments that showed that IFN-λ3 could decrease parasite load only when added to the medium at earlier time points, either during or soon after parasite uptake, but had no effect on parasite load when added at 24 h post-infection, suggesting that an early event during parasite uptake was targeted. Furthermore, the parasites could overcome the inhibitory effect of IFN-λ3, which was added at earlier time points, within 2-3 days post-infection. BALB/c mice treated with IFN-λ3 before infection led to a significant increase in expression of IL-4 and ARG1 post-infection in the spleen and liver, respectively, and to different pathological changes, especially in the liver, but not to changes in parasite load. Treatment with IFN-λ3 during infection did not decrease the parasite load in the spleen either. However, IFN-λ3 was significantly increased in the sera of visceral leishmaniasis patients, and the IFNL genetic variant rs12979860 was significantly associated with susceptibility to leishmaniasis.
Second site reversion of HIV-1 envelope protein baseplate mutations maps to the matrix protein
Authors: Alfadhli Ayna , Romanaggi CeAnn , Barklis Robin Lid , Barklis Eric
Published: January 2024

How HIV-1 Env trimers assemble into virus particles remains incompletely understood. In restrictive cells, viral incorporation of Env is dependent on the Env CT and on the MA protein, which assembles lattices composed of hexamers of trimers in immature and mature viruses. Recent evidence indicates that CT assembles trimeric baseplate structures that require membrane-proximal residues to interface with trimeric transmembrane domains and C-terminal helices in the CT. We found that mutations of these membrane-proximal residues impaired replication in restrictive cells. This defect was countered by a MA mutation that does not localize to any obvious interprotein regions but was only inefficiently suppressed by a MA mutation that stabilizes MA trimers and has been shown to suppress other CT-dependent Env defects. Our results suggest that efficient suppression of baseplate mutations involves stabilization of MA inter-trimer contacts and/or direct MA-CT associations. These observations shed new light on how Env assembles into virions.
c-Jun signaling during initial HSV-1 infection modulates latency to enhance later reactivation in addition to directly promoting the progression to full reactivation
Authors: Dochnal Sara A. , Whitford Abigail L. , Francois Alison K. , Krakowiak Patryk A. , Cuddy Sean , Cliffe Anna R.
Published: January 2024

The molecular mechanisms that regulate the reactivation of herpes simplex virus-1 (HSV-1) from latent infection are unknown. The host transcription and pioneer factor c-Jun is the main target of the JNK cell stress pathway that is known to be important in exit of HSV from latency. Surprisingly, we found that c-Jun does not act with JNK during exit from latency but instead promotes the transition to full reactivation. Moreover, c-Jun and enhanced neuronal stress during initial neuronal infection promoted a more reactivation-competent form of HSV-1 latency. c-Jun, therefore, functions at multiple stages during HSV-1 latent infection of neurons to promote reactivation. Importantly, this study contributes to a growing body of evidence that
de novo
HSV-1 infection conditions can modulate latent infection and impact future reactivation events, raising important questions on the clinical impact of stress during initial HSV-1 acquisition on future reactivation events and consequences.
SARS-CoV-2 spike glycosylation affects function and neutralization sensitivity
Authors: Zhang Fengwen , Schmidt Fabian , Muecksch Frauke , Wang Zijun , Gazumyan Anna , Nussenzweig Michel C. , Gaebler Christian , Caskey Marina , Hatziioannou Theodora , Bieniasz Paul D.
Published: January 2024

The attachment of glycans to the spike proteins of viruses during their synthesis and movement through the secretory pathway can affect their properties. This study shows that the glycans attached to the severe acute respiratory syndrome coronavirus-2 spike protein enable its movement to the cell surface and incorporation into virus particles. Certain glycans, including one that is attached to asparagine 343 in the receptor-binding domain of the spike protein, can also affect virus neutralization by antibodies. This glycan can increase or decrease sensitivity to individual antibodies, likely through direct effects on antibody epitopes and modulation of spike conformation. However, the overall effect of the glycan in the context of the polyclonal mixture of antibodies in convalescent serum is to reduce neutralization sensitivity. Overall, this study highlights the complex effects of glycosylation on spike protein function and immune evasion.
Candida auris
detected in the oral cavity of a dog in Kansas
Authors: White Theodore C. , Esquivel Brooke D. , Rouse Salcido Elisa M. , Schweiker Allison M. , dos Santos Amanda R. , Gade Lalitha , Petro Erin , KuKanich Butch , KuKanich Kate S.
Published: January 2024

Candida auris
is an emerging fungal infection of humans and is particularly problematic because it is multi-drug resistant and difficult to treat. It is also known to be spread from person to person by contact and can remain on surfaces for long periods of time. In this report, a dog in a shelter in Kansas is found to be colonized with
Candida auris
. This is the first study to document the presence of
Candida auris
on a pet, the first to document
C. auris
presence on a non-human mammal in the United States, and the first to report an isolate of
C. auris
within the state of Kansas. The presence of
C. auris
in a pet dog raises the possibility of zoonotic transmission from pets to human or vice versa.
Distinct structural motifs are necessary for targeting and import of Tim17 in
Trypanosoma brucei
mitochondrion
Authors: Darden Chauncey , Donkor Joseph E. , Korolkova Olga , Barozai Muhammad Younas Khan , Chaudhuri Minu
Published: January 2024

Nuclear-encoded mitochondrial proteins are correctly translocated to their proper sub-mitochondrial destination using location-specific mitochondrial targeting signals and via multi-protein import machineries (translocases) in the outer and inner mitochondrial membranes (TOM and TIMs, respectively). However, targeting signals of multi-pass Tims are less defined. Here, we report the characterization of the targeting signals of
Trypanosoma brucei
Tim17 (TbTim17), an essential component of the most divergent TIM complex. TbTim17 possesses a characteristic secondary structure including four predicted transmembrane (TM) domains in the center with hydrophilic N- and C-termini. After examining mitochondrial localization of various deletion and site-directed mutants of TbTim17 in
T. brucei
using subcellular fractionation and confocal microscopy, we located at least two internal targeting signals (ITS): (i) within TM1 (31–50 AAs) and (ii) TM4 + loop 3 (120–136 AAs). Both signals are required for proper targeting and integration of TbTim17 in the membrane. Furthermore, a positively charged residue (K
122
) is critical for mitochondrial localization of TbTim17. This is the first report of characterizing the ITS for a multipass inner membrane protein in a divergent eukaryote, like
T. brucei
.

IMPORTANCE

African trypanosomiasis (AT) is a deadly disease in human and domestic animals, caused by the parasitic protozoan
Trypanosoma brucei
. Therefore, AT is not only a concern for human health but also for economic development in the vast area of sub-Saharan Africa.
T. brucei
possesses a single mitochondrion per cell that imports hundreds of nuclear-encoded mitochondrial proteins for its functions.
T. brucei
Tim17 (TbTim17), an essential component of the TbTIM17 complex, is a nuclear-encoded protein; thus, it is necessary to be imported from the cytosol to form the TbTIM17 complex. Here, we demonstrated that the internal targeting signals within the transmembrane 1 (TM1) and TM4 with loop 3, and residue K122 are required collectively for import and integration of TbTim17 in the
T. brucei
mitochondrion. This information could be utilized to block TbTim17 function and parasite growth.
Genome sequencing unveils
bla
KPC-2
-harboring plasmids as drivers of enhanced resistance and virulence in nosocomial
Klebsiella pneumoniae
Authors: Han Xinhong , Zhou Junxin , Yu Lifei , Shao Lina , Cai Shiqi , Hu Huangdu , Shi Qiucheng , Wang Zhengan , Hua Xiaoting , Jiang Yan , Yu Yunsong
Published: January 2024

This study is based on a CRKP screening program between patients and ward environments in an intensive care unit, describing the pKPC-2 (
bla
KPC-2
-harboring plasmids) population structure and evolutionary characteristics in clinical settings. Long-read sequencing was performed in genetically closely related strains, enabling the high-resolution analysis of evolution pathway between or within pKPC-2 subgroups. We revealed the extremely high rates of multicopy antibiotic resistance genes (ARGs) in clinical settings and its effect on resistance profile toward novel β-lactam/β-lactamase inhibitor combinations, which belongs to the last line treatment choices toward CRKP infection. A novel hybrid pKPC-2 carrying CRKP with enhanced resistance and virulence level was captured during its clonal spread between patients and ward environment. These evidences highlight the threat of pKPC-2 to CRKP treatment and control. Thus, surveillance and timely disinfection in clinical settings should be practiced to prevent transmission of CRKP carrying threatful pKPC-2. And rational use of antibiotics should be called for to prevent inducing of pKPC-2 evolution, especially the multicopy ARGs.
High-precision U-Pb geochronology links magmatism in the Southwestern Laurentia large igneous province and Midcontinent Rift
Authors: Mohr M.T. , Schmitz M.D. , Swanson-Hysell N.L. , Karlstrom K.E. , Macdonald F.A. , Holland M.E. , Zhang Y. , Anderson N.S.
Published: January 2024

The Southwestern Laurentia large igneous province (SWLLIP) comprises voluminous, widespread ca 1.1 Ga magmatism in the southwestern United States and northern Mexico. The timing and tempo of SWLLIP magmatism and its relationship to other late Mesoproterozoic igneous provinces have been unclear due to difficulties in dating mafic rocks at high precision. New precise U-Pb zircon dates for comagmatic felsic segregations within mafic rocks reveal distinct magmatic episodes at ca. 1098 Ma (represented by massive sills in Death Valley, California, the Grand Canyon, and central Arizona) and ca. 1083 Ma (represented by the Cardenas Basalts in the Grand Canyon and a sill in the Dead Mountains, California). The ca. 1098 Ma magmatic pulse was short-lived, lasting 0.25−0.24+0.67 m.y., and voluminous and widespread, evidenced by the ≥100 m sills in Death Valley, the Grand Canyon, and central Arizona, consistent with decompression melting of an upwelling mantle plume. The ca. 1083 Ma magmatism may have been generated by a secondary plume pulse or post-plume lithosphere extension.

The ca. 1098 Ma pulse of magmatism in southwestern Laurentia occurred ~2 m.y. prior to an anomalous renewal of voluminous melt generation in the Midcontinent Rift of central Laurentia that is recorded by the ca. 1096 Ma Duluth Complex layered mafic intrusions. Rates of lateral plume spread predicted by mantle plume lubrication theory support a model where a plume derived from the deep mantle impinged near southwestern Laurentia, then spread to thinned Midcontinent Rift lithosphere over ~2 m.y. to elevate mantle temperatures and generate melt. This geodynamic hypothesis reconciles the close temporal relationships between voluminous magmatism across Laurentia and provides an explanation for that anomalous renewal of high magmatic flux within the protracted magmatic history of the Midcontinent Rift.