bluuebunny/crossref_metadata_2025 huggingface dataset:
The characteristics of T‐cell receptor repertoire in relation to systemic immune response of patients with ischemic stroke
Authors: Zong Yan , Liu Yuanyuan , Wang Junyang , Rastegar‐Kashkooli Yousef , Fu Peiji , Chen Shuai , Zhang Qianlin , Huang Maosen , Wang Junmin , Zhang Jiewen , Wang Jian , Jiang Chao
Published: October 2024

T lymphocytes play a vital role in the immune‐inflammatory response following a stroke. However, the specific mechanisms behind the contrasting functions of T cells in the brain and peripheral tissues after a stroke remain unclear and require further investigation. T‐cell receptors (TCRs) are essential in controlling how T lymphocytes develop and become active. This study aims to gain a deeper understanding of the biological function of T lymphocytes by analyzing the TCR repertoire in patients who have experienced an acute ischemic stroke (AIS). High‐throughput TCR sequencing was conducted on peripheral blood samples from 25 AIS patients and 10 healthy controls. We compared the percentage of T cells and the characteristics of the TCR repertoire, specifically focusing on the recombination of V(D)J gene fragments and the diversity of the complementarity determining region 3 (CDR3) of the Vβ gene. Additionally, this study analyzed the potential biological significance of the skewed TCR repertoire in AIS patients. In patients with AIS, the proportion of circulating lymphocytes (LY%) decreased while the systemic immune‐inflammatory index (SII) increased compared to healthy controls. The average number of TCR read pairs decreased, corresponding with the presence of lymphopenia. However, the recombination of V(D)J gene fragments, the number of CDR3 clonotypes, and the diversity of CDR3 was elevated in the peripheral blood of AIS patients. Furthermore, the increased number of CDR3 amino acid or nucleotide clonotypes was negatively correlated with neurologic deficits but positively correlated with AIS patients' systemic immune condition and functional outcomes. Our findings suggest that both immunosuppression and enhanced antigen‐specific T‐cell response may exist in the periphery of the AIS patients. Further investigation into the mechanisms underlying these opposing changes may lead to the discovery of novel targets to reverse immunosuppression or mitigate the detrimental effects of T cells in the lesioned brain of AIS patients.

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John Schulenberg as a developmental scholar and mentor: Personal reflections
Authors: Maggs Jennifer L.
Published: October 2024

John Schulenberg has had significant impact on developmental science. His conceptual writing and empirical research, grounded in developmental contextualism, emphasized the critical role that developmental transitions play in shaping health risks, especially substance use, across the life course. Schulenberg's integration of developmental concepts with large‐scale epidemiological studies, particularly through his leadership in the Monitoring the Future study, provides key insights into how significant life changes—such as school transitions, employment, and relationships—interact to influence well‐being across adolescence and early adulthood. He was a fierce advocate for adolescence and young adulthood being critical phases of life, deserving of focused attention and support. John was also a devoted mentor to the next generation of developmental scientists. This commentary reflects on John Schulenberg's legacy, highlighting five of his foundational concepts (developmental tasks, transitions, trajectories, turning points, and timing) and celebrating his role as a generative and joyful mentor. He fostered open intellectual dialog, promoted and celebrated career development, and took pleasure in life inside and outside work, helping early career scientists to develop innovative and impactful research programs. Schulenberg's commitment to positive relationships and celebrating success is an enduring model for future generations of developmental scientists and mentors.
Phomopsis Head Rot caused by Diaporthe helianthi: A New Disease on Sunflower in Argentina
Authors: Colombo D. N. , Figueruelo A. , Paniego N. B. , Comerio R. M. , Corró Molas A.
Published: October 2024

During a survey conducted in the 2021, 2022 and 2023 seasons, sunflower heads showing symptoms of dry rot were collected from 80 fields in the semi‐arid Pampa region of Argentina. A total of 72% of the fields examined in 2021, 71% in 2022 and 63% in 2023 showed the presence of the disease. The highest incidence was recorded as 70% in 2021. Phomopsis head rot began as dry, brown spots on the back of the head, progressing to necrosis and twisting of adjacent leaves. Infected head tissue samples were surface sterilised, cultured on potato dextrose agar (PDA) and incubated at 25°C for 14 days. Diaporthe helianthi was identified based on cultural and morphological characteristics as well as molecular data. A phylogenetic analysis was performed. Internal transcribed spacer (ITS), translation elongation factor 1‐α (ef1‐α) and β‐tubulin sequences were deposited in GenBank, showing the identity with the ex‐type D. helianthi strain CBS 592.81. Pathogenicity experiments confirmed the presence of similar disease symptoms in inoculated sunflower heads, and D. helianthi was consistently reisolated from these organs. Our Koch's postulates testing results on heads constitute the first confirmed report that D. helianthi is the cause of Phomopsis head rot on sunflower in Argentina.
Crossing the Pacific: Genomics Reveals the Presence of Japanese Sardine (Sardinops melanosticta) in the California Current Large Marine Ecosystem
Authors: Longo Gary C. , Minich Jeremiah J. , Allsing Nicholas , James Kelsey , Adams‐Herrmann Ella S. , Larson Wes , Hartwick Nolan , Duong Tiffany , Muhling Barbara , Michael Todd P. , Craig Matthew T.
Published: October 2024

Recent increases in frequency and intensity of warm water anomalies and marine heatwaves have led to shifts in species ranges and assemblages. Genomic tools can be instrumental in detecting such shifts. In the early stages of a project assessing population genetic structure in Pacific Sardine (Sardinops sagax), we detected the presence of Japanese Sardine (Sardinops melanosticta) along the west coast of North America for the first time. We assembled a high quality, chromosome‐scale reference genome of the Pacific Sardine and generated low coverage, whole genome sequence (lcWGS) data for 345 sardine collected in the California Current Large Marine Ecosystem (CCLME) in 2021 and 2022. Fifty individuals sampled in 2022 were identified as Japanese Sardine based on strong differentiation observed in lcWGS SNP and full mitogenome data. Although we detected a single case of mitochondrial introgression, we did not observe evidence for recent hybridization events. These findings change our understanding of Sardinops spp. distribution and dispersal in the Pacific and highlight the importance of long‐term monitoring programs.
The US Strategic Shifts Necessary For Stability in the Middle East
Authors: Mousavian Seyed Hossein
Published: October 2024

The combination of the October 7 attacks and Israel's retaliation in the Gaza Strip has brought the Middle East closer than ever to all‐out war. While analysts focus on the long‐running enmity between Tel Aviv and Tehran, this article contends that the region can move toward stability only with changes in US policy, especially toward Iran. Ending 40 years of hostile relations would not only help reduce the likelihood of a prolonged Israel‐Iran war but also create the conditions necessary to resolve crises in Lebanon, Syria, Yemen, and Iraq. The key is to revive the nuclear negotiations and move to a deal that can tamp down rivalries that threaten West Asian security. The author, who as an Iranian official participated in early rounds of nuclear talks in the early 2000s, analyzes the US‐Iran rivalry, recommends how to move toward a nuclear‐free region, and makes recommendations for shifts in American strategy.
Utilization of stable isotopes in teeth to investigate pygmy sperm whales (Kogia breviceps) in the southeastern United States
Authors: Hackel Nicole R. , McFee Wayne E.
Published: October 2024

The pygmy sperm whale (Kogia breviceps) is currently the second‐most stranded cetacean in the southeastern United States (SEUS), but information concerning their population structure is severely limited. This study used stable isotope analysis to investigate the isotopic niches and population structure of K. breviceps among three regions in the SEUS determined by the distance of the continental shelf break and a fourth region in the Gulf of Mexico. Teeth from stranded individuals were subsampled via dental drill at four separate areas on each tooth, representing four different age classes: calf, juvenile, subadult, and adult. Stable isotope ratios of carbon and nitrogen were measured in the organic component of 42 teeth, and oxygen isotope ratios were measured in the inorganic (hydroxyapatite) component of 19 teeth. No differences were found in δ13C, δ15N, or δ18O values between regions. However, differences between age classes were significant for adults and subadults for δ13C and adults and juveniles for δ15N. Differences between males and females were also significant for δ15N. Results from this study provide the first carbon and nitrogen isotope values from different age classes of pygmy sperm whales as well as the first reported oxygen isotope values for this species.
The Mechanical Properties of Orthodontic Aligners of Clear Aligner After Intraoral Use in Different Time Periods
Authors: Siotou Kalliopi , Chountalas Theofanis , Katsavrias Athanasios , Siotos Charalampos , Mpalias Konstantinos , Semitekolos Dionysios , Charitidis Constantinos , Tsolakis Apostolos I.
Published: October 2024

Objective

Although the technique of orthodontic aligners has risen in popularity, their mechanical properties have not been thoroughly investigated. The aim of this study was to evaluate the mechanical properties of the orthodontic aligners Clear Aligner after intraoral use for 7, 10 and 14 days, and to compare them with as‐received aligners (0 days). It was also sought to examine the properties of the unprocessed raw material (polyethylene glycol terephthalate) used to manufacture these aligners.

Materials/Methods

Thirty‐two aligners by four patients were evaluated and studied at 0, 7, 10, 14 days of use. Each aligner was divided into three segments (two posterior and one anterior), which resulted in 96 samples. Also, 16 samples of unprocessed material were studied. For all samples, elastic modulus, ultimate tensile stress (UTS) and yield stress were calculated by conducting tensile testing. Additionally, material hardness was tested. The two‐tailed Mann–Whitney test was performed, having set the level of significance at p = 0.05.

Results

Analysis of the measurements indicated a statistically significant decrease in elastic modulus between days 0 and 14 of use, of UTS between days 0 and 7, 7 and 10, and of yield stress between days 0 and 7. For hardness, in every period, posterior segments demonstrated significantly higher values than anterior segments. All properties of the unprocessed material were statistically significantly higher than the processed samples.

Conclusions

The unprocessed material presented significant differences in every property tested in comparison to the processed aligners. The processed material showed further deterioration over time during use. The present study provides evidence that thermoforming and ageing affect the mechanical properties of the aligners.
The Australian Identity: Through the Othering of China
Authors: Huh Jung June
Published: October 2024

This article deconstructs the Australian national identity through the “othering” of China amidst the coronavirus pandemic. During this time, Australia–China relations reached one of their lowest points in recent history. It examines the diplomatic fallout and the media frames used to portray China in the image of mistrust, fear, threat, and a place of disease and sickness. Through this process of “othering,” the Australian media reassigned and redefined its national identity and what it meant to be an Australian in the global order. The article engages with public discourse, highlighting the media's influence in narrating, shaping, and reinforcing the values of the national identity. It argues that these negative perceptions of China, place China in the seat of the “other” and serve to juxtapose and strengthen the Australian identity that is democratic, liberal, free, and just.
The Role of Carnosic Acid in the UV‐B Stress Resistance Signalling Pathway in Arabidopsis thaliana
Authors: Han Danlu , Lin Chufang , Xia Simin , Zheng Xiaoting , Zhu Chengluo , Shen Yue , Chen Yue , Peng Changlian , Wang Caijuan , He Jinming , Lai Jianbin , Yang Chengwei
Published: October 2024

Carnosic acid (CA) is recognized as an antioxidant that confers protection to plants against various forms of oxidative stress, including UV‐B stress. However, limited research has been conducted to elucidate the molecular mechanisms underlying its defence against UV‐B stress. In this study, we demonstrated that CA exhibits more efficacy compared to other antioxidants in UV‐B resistance. Moreover, CA was found to enhance the accumulation of secondary metabolites in Arabidopsis leaves. Through the analysis of differentially expressed genes in response to UV‐B stress with or without CA treatment, we uncovered that the exogenous application of CA effectively activates the flavonoid biosynthesis pathway in Arabidopsis to improve resistance of Arabidopsis to UV‐B stress.
Rare nonsynonymous germline and mosaic de novo variants in Japanese patients with schizophrenia
Authors: Watanabe Yuichiro , Nishioka Masaki , Morikawa Ryo , Takano‐Isozaki Satoko , Igeta Hirofumi , Mori Kanako , Kato Tadafumi , Someya Toshiyuki
Published: October 2024

Aim

Whole‐exome sequencing (WES) studies have revealed that germline de novo variants (gDNVs) contribute to the genetic etiology of schizophrenia. However, the contribution of mosaic DNVs (mDNVs) to the risk of schizophrenia remains to be elucidated. In the present study, we systematically investigated the gDNVs and mDMVs that contribute to the genetic etiology of schizophrenia in a Japanese population.

Methods

We performed deep WES (depth: 460×) of 73 affected offspring and WES (depth: 116×) of 134 parents from 67 families with schizophrenia. Prioritized rare nonsynonymous gDNV and mDNV candidates were validated using Sanger sequencing and ultra‐deep targeted amplicon sequencing (depth: 71,375×), respectively. Subsequently, we performed a Gene Ontology analysis of the gDNVs and mDNVs to obtain biological insights. Lastly, we selected DNVs in known risk genes for psychiatric and neurodevelopmental disorders.

Results

We identified 62 gDNVs and 98 mDNVs. The Gene Ontology analysis of mDNVs implicated actin filament and actin cytoskeleton as candidate biological pathways. There were eight DNVs in known risk genes: splice region gDNVs in AKAP11 and CUL1; a frameshift gDNV in SHANK1; a missense gDNV in SRCAP; missense mDNVs in CTNNB1, GRIN2A, and TSC2; and a nonsense mDNV in ZFHX4.

Conclusion

Our results suggest the potential contributions of rare nonsynonymous gDNVs and mDNVs to the genetic etiology of schizophrenia. This is the first report of the mDNVs in schizophrenia trios, demonstrating their potential relevance to schizophrenia pathology.
SNP‐based QTL mapping and identification of panicle structure‐related genes in rice
Authors: Park Jae‐Ryoung , Seo Jeonghwan , Lee Chang‐Min , Jeong O‐Young , Jin Mina , Park Songhee , Park Hyun‐Su
Published: October 2024

Rice is a staple crop providing a significant portion of the global food supply. It is then crucial to develop strategies for breeding high‐yield cultivars to meet global food security challenges, including the UN's zero‐hunger goal. In this study, QTL mapping was employed to pinpoint key genomic regions linked to traits influencing rice yield, with a focus on panicle structure—a critical determinant of grain number. Over two consecutive years, QTLs were identified using 88 JJ625LG/Namchan Recombinant Inbred Lines (JNRILs), revealing several candidate genes. Notably, Gn1a, a known regulator of grain number, was mapped within qNS1 and qNSSr1‐1, while the sd1 gene, linked to plant height, was detected across multiple QTLs. Furthermore, a novel gene, OsNSMq3 (Os03g0843800), encoding a methyltransferase, was identified in various QTLs, with haplotype and sequence homology analysis suggesting its role in enhancing yield by influencing panicle structure development. The increase in primary and secondary branches, driven by these genes, leads to a higher number of spikelets per panicle, thereby boosting yield. These findings underscore the potential of candidate genes from stable QTLs as valuable tools in molecular breeding to develop high‐yield rice cultivars, addressing global hunger and aiding food supply in refugee crises.
Policy design and policy feedback in welfare retrenchment: A survey experiment in China
Authors: He Alex Jingwei , Zhu Ling , Qian Jiwei
Published: October 2024

A growing body of public policy literature examines how welfare retrenchment reform produces attitudinal and behavioral feedback effects. This study adds to the literature on welfare reforms by exploring how different policy designs, combined with individual proximity to reform, produce heterogeneous feedback effects. Bridging the theories of policy feedback and policy design, we theorize how different policy designs shape individuals' self‐interest or sociotropic considerations when they form opinions on welfare reform. The feedback effects of these different policy designs are channeled by individual proximity to the reform, resulting in heterogeneous responses to proposed policy change. Seizing an opportune time window when the Chinese government undertook a public consultation program in 2020 regarding the proposed reform reallocating financial resources in individuals' medical savings accounts, we conducted a survey experiment to examine if two different policy designs led to varying feedback effects. We find that the moderate de facto retrenchment reform indeed triggered public opposition. Unlike previous research that emphasizes partisanship as a major source of heterogeneous feedback effects, our study reveals different sources of heterogeneity—public opposition to the proposed reform varies by the specific policy designs and individuals' past experiences with the existing health insurance policy.
Political will as a source of policy innovation
Authors: Shen Shiran Victoria
Published: October 2024

In an era of disruptive global challenges, from climate crises to pandemics, understanding the drivers of drastic policy innovation is paramount. This study defines drastic policy innovation as a significant shift in governmental priorities through policies untried by most jurisdictions in a country. While policy entrepreneurs are often credited with initiating change, this study argues that political will is essential for enacting and implementing such innovative policies. Political will is defined as the degree of commitment among key decision makers to enact and implement specific policies. It is characterized by three key components: authority (the power to enact and enforce policy), capacity (the resources to implement it effectively), and legitimacy (the perceived rightfulness of actions by stakeholders). Through the case of low‐carbon city experimentation in China, this study examines how political will drives the adoption and implementation of these policies. The findings reveal that a high level of political will is significantly linked to more drastically innovative policies being enacted and implemented and that when political will is institutionalized, implementation continues despite leadership turnover. These insights likely apply to other policy contexts and countries, regardless of regime type, albeit with some caveats.
Uncovering data gaps in biodiversity research within Brazilian Atlantic Forest restoration
Authors: Romanelli João P. , Kroc Ed , Lopes Assad Maria L. , Santos João P. B. , Boschi Raquel S. , Rodrigues Ricardo R.
Published: October 2024

Bringing together and synthesizing data from several primary studies and scales represents a powerful method for identifying patterns and gaps within forest restoration science. In this study, we employ a pioneer quantitative database‐driven review combined with spatial analysis to delineate research trends across biodiversity studies within the Brazilian Atlantic Forest (BAF). We gathered a total of 90 primary studies that met our inclusion criteria, collectively providing 822 observations (comparisons between restoration sites and reference forests) spanning restoration areas with ages ranging from 1 to 90 years old. Vascular plants and invertebrates dominated in terms of data availability, whereas soil microorganisms were the subject of limited inquiry. There is an evident disparity in the number of evidences for different forest types across regions, with mixed forest being underrepresented in relation to seasonal forest and dense forest (rainforest). On the contrary, we observed an even distribution of biodiversity outcomes across the age categories we defined for reference forests (i.e. secondary forest, secondary advanced, and old‐growth forest). Geospatial analysis revealed a concentration of research efforts within the southeastern region of the BAF. However, a significant research deficit remains for the northeast and south regions, crucial for comprehending biodiversity responses to restoration in environmental extremes. By integrating both qualitative and quantitative approaches, this framework review provides a roadmap for deepening our understanding of biodiversity responses to restoration in the BAF. Ultimately, it serves as a bridge between quantitative findings and nuanced contextual insights, guiding future research and similar studies across diverse ecosystems worldwide.
Daily glycome and transcriptome profiling reveals polysaccharide structures and correlated glycosyltransferases critical for cotton fiber growth
Authors: Swaminathan Sivakumar , Grover Corrinne E. , Mugisha Alither S. , Sichterman Lauren E. , Lee Youngwoo , Yang Pengcheng , Mallery Eileen L. , Jareczek Josef J. , Leach Alexis G. , Xie Jun , Wendel Jonathan F. , Szymanski Daniel B. , Zabotina Olga A.
Published: October 2024

Cotton fiber is the most valuable naturally available material for the textile industry and the fiber length and strength are key determinants of its quality. Dynamic changes in the pectin, xyloglucan, xylan, and cellulose polysaccharide epitope content during fiber growth contribute to complex remodeling of fiber cell wall (CW) and quality. Detailed knowledge about polysaccharide compositional and structural alteration in the fiber during fiber elongation and strengthening is important to understand the molecular dynamics of fiber development and improve its quality. Here, large‐scale glycome profiling coupled with fiber phenotype and transcriptome profiling was conducted on fiber collected daily covering the most critical window of fiber development. The profiling studies with high temporal resolution allowed us to identify specific polysaccharide epitopes associated with distinct fiber phenotypes that might contribute to fiber quality. This study revealed the critical role of highly branched RG‐I pectin epitopes such as β‐1,4‐linked‐galactans, β‐1,6‐linked‐galactans, and arabinogalactans, in addition to earlier reported homogalacturonans and xyloglucans in the formation of cotton fiber middle lamella and contributing to fiber plasticity and elongation. We also propose the essential role of heteroxylans (Xyl‐MeGlcA and Xyl‐3Ar), as a guiding factor for secondary CW cellulose microfibril arrangement, thus contributing to fiber strength. Correlation analysis of profiles of polysaccharide epitopes from glycome data and expression profiles of glycosyltransferase‐encoding genes from transcriptome data identified several key putative glycosyltransferases that are potentially involved in synthesizing the critical polysaccharide epitopes. The findings of this study provide a foundation to identify molecular factors that dictate important fiber traits.
Numerical Investigations of a Single Loop Pulsating Heat Pipe for Cryogenic Applications
Authors: Singh Abhinav , Ghosh Indranil
Published: October 2024

The thermohydraulics of a single-loop pulsating heat pipe (PHP) for cryogenic applications have been simulated. The 120 mm long PHP tube is made of a 1.5 mm diameter inner tube of thickness 0.83 mm. The computation fluid dynamics (CFD) analysis performed with the ansysfluent software is a 2D numerical study using pure nitrogen as the working fluid in binary phases. The boundary condition on the evaporator is of constant heat flux, while the same on the condenser is of constant temperature. The phase behavior of the liquid and vapor and their interactions are accounted for through the volume of fluid (VOF) method and the Lee model. The numerical model is validated using the existing experimental data, with an agreement of less than 8% between them. The thermo-hydraulic variations of temperature, pressure, and velocity have been simulated for different heat loads and fractional liquid contents (fill ratios). The temperature and pressure oscillations set in the PHP-fluid increase with the heat added to the evaporator while the fluid velocity remains independent. The heat load and the fill ratio dictate the effective thermal conductivity—attaining nearly 3400 W/mK for a fill ratio of 70% in the chosen PHP geometry. An alteration has been made in the Jacob number to predict the dominance of sensible heat over latent heat in a PHP, postulated by other researchers. The constant fill ratio assumption is not truly valid as it indicates a small yet finite variation with the change in the heat load.
Multimodal Shunt Damping of Monolithic Bladed Drums Using Multiple Digital Vibration Absorbers
Authors: Dietrich Jennifer , Raze Ghislain , Charles Xavier , Kerschen Gaëtan
Published: October 2024

Based on a digital realization of piezoelectric shunt circuits, this work presents a proof-of-concept damping approach tailored to address the complex dynamics of monolithic bladed drums (BluMs) and attenuate their vibrations. This approach comprises the simultaneous use of multiple digital vibration absorbers (DVAs) together with a mean shunt strategy, taking advantage of the fact that multiple absorbers act simultaneously on the structure and that the blade modes of BluMs appear closely spaced. In order to target multiple groups of modes, this strategy is incorporated in a multistaged shunt circuit. The damping concept is numerically and experimentally demonstrated on a BluM with multiple piezoelectric patches, proving its ability to achieve excellent damping performance on multiple groups of modes. This performance is shown to be relatively insensitive to the spatial distribution of the shunted patches. Based on a robustness study, it was also found that the shunts are robust to changes in the host structure which could, e.g., be due to mistuning. Owing their digital nature, DVAs are easily adjustable making them highly attractive in practical applications.
Black hole spectroscopy with ground-based atom interferometer and space-based laser interferometer gravitational wave detectors
Authors: Torres-Orjuela Alejandro
Published: October 2024

Gravitational wave (GW) detection allows us to test general relativity in entirely new regimes. A prominent role takes the detection of quasi-normal modes (QNMs), which are emitted after the merger of a binary black hole (BBH) when the highly distorted remnant emits GWs to become a regular Kerr black hole (BH). The BH uniqueness theorems of Kerr black hole solutions in general relativity imply that the frequencies and damping times of QNMs are determined solely by the mass and spin of the remnant BH. Therefore, detecting QNMs offers a unique way to probe the nature of the remnant BH and to test general relativity. We study the detection of a merging BBH in the intermediate-mass range, where the inspiral–merger phase is detected by space-based laser interferometer detectors TianQin and LISA, while the ringdown is detected by the ground-based atom interferometer (AI) observatory AION. The analysis of the ringdown is done using the regular broadband mode of AI detectors as well as the resonant mode optimizing it to the frequencies of the QNMs predicted from the inspiral–merger phase. We find that the regular broadband mode allows constraining the parameters of the BBH with relative errors of the order 10−1 and below from the ringdown. Moreover, for a variety of systems considered, the frequencies and the damping times of the QNMs can be determined with relative errors below 0.1 and 0.2, respectively. We further find that using the resonant mode can improve the parameter estimation for the BBH from the ringdown by a factor of up to three. Utilizing the resonant mode significantly limits the detection of the frequency of the QNMs but improves the detection error of the damping times by around two orders of magnitude.
Why the action?
Authors: Zengel Keith
Published: October 2024

In this note, I present two variations of the principle of stationary action in order to provide alternative ways for students to think about the action that they may find more intuitive than the traditional approach. These methods involve Lagrange multiplier techniques and are, therefore, best suited for students who are encountering the stationary action principle for a second or third time, perhaps in an advanced undergraduate mathematical methods course or a graduate classical mechanics course.
Associations Between Sedentary Behavior and Motor Competence in 3- to 4-Year-Olds: A Systematic Review
Authors: Kwofie Nana A. , Janssen Xanne , Reilly John J.
Published: October 2024

Background: Several studies have reported low adherence to World Health Organization sedentary behavior (SB) guidelines in the early years. The purpose of this review is to examine the associations between time spent in different types of SB (screen time and habitual SB) and motor competence (MC; fundamental motor skills, fine and gross motor skills, locomotor skills, and object control and balance) in 3- to 4-year-olds. Methods: Five databases were searched on the 27th of July 2021, with an updated search conducted on the 30th of September 2023: Web of Science (core collection), PubMed Central, EMBASE (Ovid), SPORT Discus, and ERIC. Studies were included in the review if they reported on an association between time spent in SB at ages 3–4 years and MC. The methodological quality for each of the included studies was assessed using Joanna Briggs Institute critical appraisal tools. Vote counting was used to determine the direction of associations. Results: Of 5,276 total studies found in the search, 16 studies (12 cross-sectional, four longitudinal) from 11 different countries met the inclusion criteria. Seven studies examined the association between screen time and MC, six examined associations between time spent in SB and MC, and three examined the association of both screen time and time spent in SB with MC. The direction of associations was predominantly negative for both screen time and time spent in habitual SB with different components of MC. Quality of evidence ranged from three to seven out of nine for cross-sectional studies and six to nine out of 12 for longitudinal studies. Conclusions: There may be negative associations between time spent sedentary and MC in 3- to 4-year-olds. However, future studies with stronger study designs are required to confirm these associations. Findings from this review should be considered when designing strategies and interventions to promote adherence to SB guidelines.
Assessing antimicrobial resistance in pasture-based dairy farms: a 15-month surveillance study in New Zealand
Authors: Collis Rose M. , Biggs Patrick J. , Burgess Sara A. , Midwinter Anne C. , Liu Jinxin , Brightwell Gale , Cookson Adrian L.
Published: October 2024

Antimicrobial resistance is a global public and animal health concern. Antimicrobial resistance genes (ARGs) have been detected in dairy farm environments globally; however, few longitudinal studies have utilized shotgun metagenomics for ARG surveillance in pasture-based systems. This 15-month study aimed to undertake a baseline survey using shotgun metagenomics to assess the relative abundance and diversity of ARGs in two pasture-based dairy farm environments in New Zealand with different management practices. There was no statistically significant difference in overall ARG relative abundance between the two dairy farms (
P
= 0.321) during the study period. Compared with overseas data, the relative abundance of ARG copies per 16S rRNA gene in feces (0.08–0.17), effluent (0.03–0.37), soil (0.20–0.63), and bulk tank milk (0.0–0.12) samples was low. Models comparing the presence or absence of resistance classes found in >10% of all feces, effluent, and soil samples demonstrated no statistically significant associations (
P
> 0.05) with “season,” and only multi-metal (
P
= 0.020) and tetracycline (
P
= 0.0003) resistance were significant at the “farm” level. Effluent samples harbored the most diverse ARGs, some with a recognized public health risk, whereas soil samples had the highest ARG relative abundance but without recognized health risks. This highlights the importance of considering the genomic context and risk of ARGs in metagenomic data sets. This study suggests that antimicrobial resistance on pasture-based dairy farms is low and provides essential baseline ARG surveillance data for such farming systems.

IMPORTANCE

Antimicrobial resistance is a global threat to human and animal health. Despite the detection of antimicrobial resistance genes (ARGs) in dairy farm environments globally, longitudinal surveillance in pasture-based systems remains limited. This study assessed the relative abundance and diversity of ARGs in two New Zealand dairy farms with different management practices and provided important baseline ARG surveillance data on pasture-based dairy farms. The overall ARG relative abundance on these two farms was low, which provides further evidence for consumers of the safety of New Zealand’s export products. Effluent samples harbored the most diverse range of ARGs, some of which were classified with a recognized risk to public health, whereas soil samples had the highest ARG relative abundance; however, the soil ARGs were not classified with a recognized public health risk. This emphasizes the need to consider genomic context and risk as well as ARG relative abundance in resistome studies.
A vaccine candidate based on baculovirus displaying chikungunya virus E1-E2 envelope confers protection against challenge in mice
Authors: Caillava Ana J. , Alfonso Victoria , Tejerina Cibello Malena , Demaria María Agostina , Coria Lorena M. , Cassataro Juliana , Taboga Oscar A. , Alvarez Diego E.
Published: October 2024

Chikungunya fever is a re-emerging mosquito-borne disease caused by the chikungunya virus (CHIKV) and produces acute arthritis that can progress to chronic disease with arthralgia. The first approved live-attenuated chikungunya vaccine has only recently become available for use in humans in the USA, but the access in endemic regions remains unmet. Here, we exploited the baculovirus display technology to develop a vectored vaccine candidate that exposes the CHIKV membrane proteins E1 and E2 on the baculovirus surface. Using recombinant baculovirus as vector vaccines has both productive and regulatory advantages: they are safe for handling and easy to produce in high titers and are non-pathogenic and non-replicative in mammals but have strong adjuvant properties by inducing humoral and cellular immune responses. CHIKV E1 and E2 envelope proteins with their own signal and transmembrane sequences were expressed on the surface of budded baculovirus virions. Immunization of C57BL/6 mice with non-adjuvanted recombinant baculovirus induced IgG antibodies against E2 with a predominant IgG2c subtype, neutralizing antibodies and a specific IFN-γ CD8
+
T-cell response. Immunization with a second dose significantly boosted the antibody response, and mice immunized with two doses of the vaccine candidate were completely protected against challenge with CHIKV showing no detectable viremia or signs of disease. Altogether, baculovirus display of CHIKV envelope proteins served as an efficient vaccine platform against CHIKV.

IMPORTANCE

The global spread of chikungunya virus (CHIKV) has disproportionately impacted the Americas that experienced a fourfold increase in 2023 in cases and deaths compared with the same period in 2022. The disease is characterized by acute fever and debilitating joint pain that can become chronic. Despite the socioeconomic burden related to the high morbidity rates of CHIKV infection, a vaccine for CHIKV is currently approved only in the USA. Vaccines are the most effective preventive measure against viral diseases, and advances in the development of different vaccine platforms such as nucleic acids and viral vectors have prompted the rapid deployment of vaccines to contain the COVID-19 pandemic. Here, we report the use of baculovirus display as a strategy for the design of a novel vaccine that provides sterilizing immunity in a mouse model of chikungunya disease. Our results encourage further research regarding the potential of baculovirus as platforms for human vaccine design.
First insights into the prevalence, genetic characteristics, and pathogenicity of
Bacillus cereus
from generations worldwide
Authors: Tong Cuihong , Xiao Danyu , Li Qi , Gou Jing , Wang Shuang , Zeng Zhenling , Xiong Wenguang
Published: October 2024

Bacillus cereus
, a global threat, is one of the major causes of toxin-induced foodborne diseases. However, a comprehensive assessment of the prevalence and characteristics of
B. cereus
worldwide is still lacking. Here, we applied whole-genome sequence analysis to 191
B. cereus
collected in Africa, America, Asia, Europe, and Oceania from the 1900s to 2022, finding that CC142 dominated the global
B. cereus
clonal complex. The results provided direct evidence that
B. cereus
could spread through the food chain and intercontinentally.
B. cereus
from different generations worldwide showed coherence in the antibiotic-resistant gene and virulence and biofilm gene profiles, although with high genomic heterogeneity. The
BCI-BCII-vanZF-fosB
profiles and virulence and biofilm genes were detected at high rates, and we emphasized that
B. cereus
would pose a serious challenge to global public health and clinical treatment.

IMPORTANCE

This study first emphasized the prevalence, genetic characteristics, and pathogenicity of
Bacillus cereus
worldwide from the 1900s to 2022 using whole-genome sequence analysis. The CC142 dominated the global
Bacillus cereus
clonal complex. Moreover, we revealed a close evolutionary relationship between the isolates from different sources.
B. cereus
isolates from different generations worldwide showed coherence in potential pathogenicity, although with high genomic heterogeneity. The
BCI-BCII-vanZF-fosB
profiles and virulence and biofilm genes were detected at high rates, and we emphasized that
B. cereus
would pose a serious challenge to global public health and clinical treatment.
Multi-omics analysis reveals the core microbiome and biomarker for nutrition degradation in alfalfa silage fermentation
Authors: Wang Yuan , Sun Yunlei , Huang KeXin , Gao Yu , Lin Yufan , Yuan Baojie , Wang Xin , Xu Gang , Nussio Luiz Gustavo , Yang Fuyu , Ni Kuikui
Published: October 2024

Alfalfa (
Medicago sativa
L.) is one of the most extensively cultivated forage crops globally, and its nutritional quality critically influences the productivity of dairy cows. Silage fermentation is recognized as a crucial technique for the preservation of fresh forage, ensuring the retention of its vital nutrients. However, the detailed microbial components and their functions in silage fermentation are not fully understood. This study integrated large-scale microbial culturing with high-throughput sequencing to thoroughly examine the microbial community structure in alfalfa silage and explored the potential pathways of nutritional degradation via metagenomic analysis. The findings revealed an enriched microbial diversity in silage, indicated by the identification of amplicon sequence variants. Significantly, the large-scale culturing approach recovered a considerable number of unique microbes undetectable by high-throughput sequencing. Predominant genera, such as
Lactiplantibacillus
,
Leuconostoc
,
Lentilactobacillus
,
Weissella
, and
Liquorilactobacillus
, were identified based on their abundance and prevalence. Additionally, genes associated with Enterobacteriaceae were discovered, which might be involved in pathways leading to the production of ammonia-N and butyric acid. Overall, this study offers a comprehensive insight into the microbial ecology of silage fermentation and provides valuable information for leveraging microbial consortia to enhance fermentation quality.

IMPORTANCE

Silage fermentation is a microbial-driven anaerobic process that efficiently converts various substrates into nutrients readily absorbable and metabolizable by ruminant animals. This study, integrating culturomics and metagenomics, has successfully identified core microorganisms involved in silage fermentation, including those at low abundance. This discovery is crucial for the targeted cultivation of specific microorganisms to optimize fermentation processes. Furthermore, our research has uncovered signature microorganisms that play pivotal roles in nutrient metabolism, significantly advancing our understanding of the intricate relationships between microbial communities and nutrient degradation during silage fermentation.
Evaluation of the CARBA PAcE test, a colorimetric imipenem hydrolysis test for rapid detection of carbapenemase activity
Authors: Rakovitsky Nadya , Lurie-Weinberger Mor N. , Temkin Elizabeth , Hameir Amichay , Efrati-Epchtien Reut , Wulffhart Liat , Keren Paz Alona , Schwartz David , Carmeli Yehuda
Published: October 2024

There is an urgent need for accurate and fast diagnostic tests to identify carbapenemase-producing bacteria. Here, we evaluated a colorimetric imipenem hydrolysis test, called the CARBA PAcE test, to detect carbapenemase-producing Gram-negative bacteria (GNB). We tested a collection of 270 GNB isolates with a characterized carbapenemase content. Our testing set included 205 carbapenemase-producing, carbapenemase-resistant
Enterobacterales
(
CP CRE
) with 40
Klebsiella pneumoniae
carbapenemase (KPC), 49 New Delhi metallo beta lactamase (NDM), 49 OXA-48-like, 15 Verona integron-mediated metallo-β-lactamase (VIM), three IMP, 43 IMI, six isolates producing more than one carbapenemase, and 65 non-carbapenemase-producing
Enterobacterales
(20 ESBL producers, 35 non-carbapenemase-producing, carbapenem-resistant [non-CP CRE], and 10 carbapenem-susceptible
Enterobacterales
[non-CP, non-CSE, third-generation cephalosporin and carbapenem susceptible]). We compared the performances of the CARBA PAcE test, the qualitative colorimetric β-CARBA test, and the modified CarbaNP test to a gold standard of carbapenemase gene detection by PCR. Specificities of all tests were high: 95.4% (62/65) for CARBA PAcE test, 98.5% (64/65) for β-CARBA test, and 100% (65/65) for the modified CarbaNP test. Sensitivity varied by carbapenemase: all three tests had a sensitivity of 100% for NDM, VIM, and IMP and 97.5% for KPC. Sensitivity to detect IMI was 0% for the CARBA PAcE and β-CARBA tests and 11.6% for the modified CarbaNP test. Sensitivity to detect OXA-48-like was 89.7% for the CARBA PAcE test, 87.7% for the β-CARBA test, and 14.2% for the modified CarbaNP test. Reading the results of the CARBA PAcE assay was difficult. The CARBA PAcE assay is highly sensitive for detecting NDM, VIM, IMP, and KPC, but slightly less sensitive for OXA-48-like. It does not detect IMI. It is highly specific, and its overall diagnostic accuracy is similar to that of β-CARBA. Its operational advantages are rapid turnaround time, ease of use, and long shelf life, but reading of results is subjective.

IMPORTANCE

We evaluated the ability of the CARBA PAcE test to detect carbapenemases in 274 Gram-negative isolates with a known carbapenemase content. Specificity was high for all carbapenemases tested (96.9%). Sensitivity was high for KPC, NDM, VIM, and IMP (97.5-100%); but lower for OXA-48-like (89.7%). Activity of IMI could not be detected. Taken together, our results indicate that CARBA PAcE is a useful alternative in regions where NDM and KPC are predominant. The limitations of the test are difficulty in reading results and incompatibility with mSuperCARBA.
High rate of macrolide resistance and closely genetically related
Mycobacterium abscessus
complex strains identified among both cystic fibrosis and non-cystic fibrosis patients within two countries
Authors: Dohál Matúš , Dvořáková Věra , Hromádková Michaela , Pinková Martina , Amlerová Jana , Schwarz Marek , Spitaleri Andrea , di Marco Federico , Hnilicová Jarmila , Gondáš Eduard , Rasmussen Michael E. , Porvazník Igor , Solovič Ivan , Cirillo Daniela M. , Mokrý Juraj
Published: October 2024

Mycobacterium abscessus
is an emerging opportunistic pathogen affecting patients with chronic lung diseases, primarily cystic fibrosis (CF), or those under immunosuppression. Hence, investigations into the epidemiology and transmission of
M. abscessus
and accurate antibiotic susceptibility data are essential for the effective treatment of infections caused by this pathogen. This retrospective nationwide study included all clinical
M. abscessus
isolates (
n
= 59) from 29 patients diagnosed in the Czech Republic and Slovakia between 2018 and 2023. Whole genome sequencing (WGS) was performed to identify clusters and classify isolates into predominant circulating clones (DCC). Subspecies identification of unique isolates showed subspecies
abscessus
as the most prevalent (69.0%). The results of drug-susceptibility testing showed that 65.5% of all isolates were resistant to at least three antibiotics tested. CF patients under 24 years of age were the most at-risk group for
M. abscessus
infection. WGS identified seven clusters (including two cross-border) comprising CF and non-CF patients with a total clustering rate of 48.3%. One cluster involved patients infected with subspecies
massiliense
strains differing by 0 single nucleotide polymorphisms hospitalized in the same center. Furthermore, we identified representatives of all major DCCs. This study revealed predominant
Mycobacterium abscessus
complex clones circulating in the Czech Republic and Slovakia. The results show the high discriminatory power of WGS in the molecular epidemiology of
M. abscessus
and provide supporting evidence of direct or indirect cross-transmission of subspecies
massiliense
among both CF and non-CF patients.

IMPORTANCE

This study highlights the importance of understanding
Mycobacterium abscessus
transmission because it poses a growing threat to vulnerable populations, especially young cystic fibrosis patients. Investigating how it spreads and which antibiotics work best is crucial for effective treatment. This research used whole genome sequencing to track
M. abscessus
and found evidence of potential transmission between patients, including across borders. The findings suggest that dominant strains are circulating and some patients may be infected through direct or indirect contact. This knowledge can inform infection control and treatment strategies.