bluuebunny/crossref_metadata_2025 huggingface dataset:
An explicit solution to harvesting behaviors in a predator–prey system
Authors: Bataille Guillaume
Published: October 2024

This paper derives closed‐form solutions for a strategic, simultaneous harvesting in a predator–prey system. Using a parametric constraint, it establishes the existence and uniqueness of a linear feedback‐Nash equilibrium involving two specialized fleets and allows for continuous time results for a class of payoffs that have constant elasticity of the marginal utility. These results contribute to the scarce literature on analytically tractable predator–prey models with endogenous harvesting. A discussion based on industry size effects is provided to highlight the role played by biological versus strategic interactions in the multispecies context.

Recommendations for Resource Managers

This model presents a thorough examination of the economic inefficiencies inherent in the exploitation dynamics of two interdependent species, elucidating the complex interplay between ecological interactions and economic outcomes.

The size of the fishing industries constitutes a significant variable that must be integrated into the formulation of pertinent policy recommendations.

This constitutes an advancement towards a more time‐consistent approach to Ecosystem‐Based Fishery Management (EBFM).
Ecological‐economic modeling of nutrient enrichment in multispecies fisheries
Authors: Nguyen Thanh Viet
Published: October 2024

In fisheries economics, multispecies or ecosystem models typically focus on interactions among fish species, often overlooking the flow of nutrients. However, biologists widely acknowledge that nutrients–Âİsuch as nitrogen, phosphorus, potassium, and calcium–Âİare vital for organisms and play crucial roles in ecosystem dynamics. This paper delves into a bioeconomic predator‐prey model incorporating nutrient enrichment through Holling Type II and Michaelis–Menten functional forms. Initially, we examine the system's dynamics before formulating an optimal time‐dependent harvest policy using the Pontryagin maximum principle. Our findings reveal that heightened nutrient enrichment can lead to the breakdown of a positive stable equilibrium, resulting in the extinction of both prey and predator. The stability of the ecosystem may also be influenced by the interplay of nutrient enrichment and predator harvest.
Prediction Models for Post‐Stroke Hospital Readmission: A Systematic Review
Authors: Mao Yijun , Liu Qiang , Fan Hui , Li Erqing , He Wenjing , Ouyang Xueqian , Wang Xiaojuan , Qiu Li , Dong Huanni
Published: October 2024

Objective

This study aims to evaluate the predictive performance and methodological quality of post‐stroke readmission prediction models, identify key predictors associated with readmission, and provide guidance for selecting appropriate risk assessment tools.

Methods

A comprehensive literature search was conducted from inception to February 1, 2024. Two independent researchers screened the literature and extracted relevant data using the CHARMS checklist.

Results

Eleven studies and 16 prediction models were included, with sample sizes ranging from 108 to 803,124 cases and outcome event incidences between 5.2% and 50.0%. The four most frequently included predictors in the models were length of stay, hypertension, age, and functional disability. Twelve models reported an area under the curve (AUC) ranging from 0.520 to 0.940, and five models provided calibration metrics. Only one model included both internal and external validation, while six models had internal validation. Eleven studies were found to have a high risk of bias (ROB), predominantly in the area of data analysis.

Conclusion

This systematic review included 16 readmission prediction models for stroke, which generally exhibited good predictive performance and can effectively identify high‐risk patients likely to be readmitted. However, the generalizability of these models remains uncertain due to methodological limitations. Rather than developing new readmission prediction models for stroke, the focus should shift toward external validation and the iterative adaptation of existing models. These models should be tailored to local settings, extended with new predictors if necessary, and presented in an interactive graphical user interface.

Trial Registration

PROSPERO registration number CRD42023466801
Gene markers generating polygenic resistance in melon–Fusarium wilt–FOM1.2 interaction pathosystem
Authors: Sadeghpour N. , Asadi‐Gharneh H. A. , Nasr‐Esfahani M. , Rahimiardkapan B. , Nasr‐Esfahani A. , Nasr‐Esfahani A. , Monazah M.
Published: October 2024

Developing melon genotypes with resistance to Fusarium oxysporum f. sp. Melonis‐(FOM) race1.2 is a major goal in any breeding program. In this study, we identified the role of 11 gene markers that contribute to polygenic resistance during the FOM1.2–melon interaction.

qRT‐PCR analysis elucidated upregulation of candidate marker genes AMT, DXPR, Fom‐2, GLUC, GalS, GRF3, MLO, PRK, RuBlsCo, TLP and WRKY in resistant ‘Shante‐F1’ and ‘Khatouni’, and susceptible ‘Shante‐T' and ‘Shahabadi’ at 7, 14 and 21 days post‐inoculation (dpi). We also studied changes in defence‐related enzyme activity: chitinase (CHI), β‐1,3‐glucanase (GLU) and peroxidase (POX) in melon roots.

AMT, GLUC and DXPR transcripts were upregulatied in leaf and root tissues of the resistant ‘Shante‐F1’ and ‘Shahabadi’. Transcript levels for GalS and GRF3 increased 6.77‐ and 6.83‐fold in roots of ‘Shante‐F1’ at 7 dpi, whereas in PRK, TLP and WRKY theye increased by 7.84‐, 5.15‐ and 12.26‐fold at 14 dpi, respectively. However, transcript levels increased by 5.18‐fold for Fom‐2 and 8.46‐fold for MLO at 21 dpi. Also, RBC transcript level peaked at 14 dpi with 4.9‐fold increase in leaves of resistant genotypes, whereas AMT increased 2.94‐fold at 21 dpi, and GLUC and DXPR increased 7.11‐ and 2.91‐fold at 14 dpi in ‘Shante‐F', respectively. Defence‐related‐enzyme activity was also upregulated three‐fold in resistant varieties.

The dynamic shifts in the melon transcriptome induced by FOM1.2 emphasize that resistance mechanisms are predominantly regulated through signalling pathways involving CHI, GLU, and POX defence response. Surprisingly, the AMT gene, basically resistant to downy mildew, Pseudoperonospora cubensis; GLUC, MLO and PRK resistant to powdery mildew (Sphaerotheca fusca); TLP and WRKY resistant to Phytophthora blight (Phytophthora capsici); and GRF3 and RBC resistant to root knot nematodes (Meloidogyne spp.) were upregulated in resistant genotypes, indicating a dual role of these genes in resistance to more than one disease at a time.
Montane willow scrub restoration in Scotland: reviewing 30 years of progress to reestablish the altitudinal treeline
Authors: Watts Sarah H.
Published: October 2024

Many mountain woodlands across the globe have undergone anthropogenic degradation with negative implications for the ecological and socioeconomic systems dependent on them. Montane willows are arctic‐alpine species of high nature conservation concern within the altitudinal treeline. Scotland has been pioneering the restoration of montane willow scrub for three decades following widespread loss linked particularly to overgrazing by sheep and deer since the eighteenth century. In the 1990s, the total area of montane willows throughout the country was less than 10 ha, with most remaining populations highly fragmented, in rapid decline, and restricted to inaccessible cliffs. Subsequently, montane willow scrub restoration has been part of an overall 2659 ha area managed for the recovery of mountain woodlands in Scotland. By May 2023, 396,868 montane willows were planted in projects encompassing large‐scale habitat creation, relict population reinforcement by genetic rescue, fencing, and landscape‐scale management for low‐density deer populations. This review summarizes restoration methods and outcomes with case study examples to promote conservation evidence and research on plant growth and survival, planting sites, associated biodiversity, molecular ecology, genomics, and long‐term population sustainability. With the potential for montane scrub restoration to be widely expanded, improved connectivity to revive a treeline mosaic shaped by regeneration will tackle biodiversity loss and help mitigate climate change impacts on a national scale. However, caution must be applied to creating definitions of distinct habitats for restoration that are based on non‐natural or ecologically degraded systems. These experiences are particularly relevant to montane and circumpolar regions with strongly modified landscape histories.
Estimation Stand Volume, Basal Area and Quadratic Mean Diameter Using Landsat 8 OLI and Sentinel‐2 Satellite Image With Different Machine Learning Techniques
Authors: Aksoy Hasan
Published: October 2024

The data required for sustainable forest planning is provided by traditional forest inventories, which are labor, time, and cost‐intensive. Providing this data quickly, reliably, and accurately is crucial for planners and researchers. The objective of this study was to predict stand basal area (BA), stand volume (V), and quadratic mean diameter (dq) by leveraging vegetation indices (VIs) and reflectance (R) derived from Landsat 8 OLI and Sentinel 2 satellite images, along with topographic (T) data obtained from ALOS‐PALSAR satellite imagery. Forest inventory data for a total of 250 sample plots were used for modeling in the study. Stand parameters were estimated using support vector machines (SVM), multiple linear regression (MLR), decision tree (DT), and random forest (RF) algorithms. In modeling V, BA, and dq, both individual and combinations of R, VIs, and T values obtained from satellite imagery were used as independent variables. Using the generated datasets, each of the stand parameters was modeled separately with MLR, SVM, RF, and DT algorithms, and the success of the models was compared to determine the modeling technique and dataset with the highest success for the relevant parameter. The results showed that for each stand parameter, the highest model success was achieved in the combined dataset, which was created by combining all datasets. However, in terms of modeling techniques, the highest success for each stand parameter was achieved with different modeling techniques. The highest success for V is obtained in the model using the SVM method (R2 = 0.78; RMSE = 0.28 m3/ha), the RF method yielded the highest model performance for BA (R2 = 0.70; RMSE = 2.53 m2/ha), and finally, the highest success for dq was obtained in the DT method (R2 = 0.74; RMSE = 0.02 cm). In general, the datasets obtained from Sentinel 2 images showed higher model success than the datasets obtained from Landsat 8 OLI images.
Derived deformation theory of crepant curves
Authors: Brown Gavin , Wemyss Michael
Published: October 2024

This paper determines the full, derived deformation theory of certain smooth rational curves in Calabi–Yau 3‐folds, by determining all higher ‐products in its controlling DG‐algebra. This geometric setup includes very general cases where does not contract, cases where the curve neighbourhood is not rational, all known simple smooth 3‐fold flops, and all known divisorial contractions to curves. As a corollary, it is shown that the non‐commutative deformation theory of is described via a superpotential algebra derived from what we call free necklace polynomials, which are elements in the free algebra obtained via a closed formula from combinatorial gluing data. The description of these polynomials, together with the above results, establishes a suitably interpreted string theory prediction due to Ferrari (Adv. Theor. Math. Phys. 7 (2003) 619–665), Aspinwall–Katz (Comm. Math. Phys.. 264 (2006) 227–253) and Curto–Morrison (J. Algebraic Geom. 22 (2013) 599–627). Perhaps most significantly, the main results give both the language and evidence to finally formulate new contractibility conjectures for rational curves in CY 3‐folds, which lift Artin's (Amer. J. Math. 84 (1962) 485–496) celebrated results from surfaces.
MOLECULAR GENETIC CHARACTERISTICS OF MYCOBACTERIUM TUBERCULOSIS ISOLATES CIRCULATING IN ASTANA
Authors: Auganova D. , Atavliyeva S. , Amirgazin A. , Akisheva A. , Abeldenov S. , Tsepke A. , Tarlykov P.
Published: October 2024

According to the World Health Organization, Kazakhstan takes a leading position in the number of cases of multidrug-resistant tuberculosis. This work is aimed at studying clinical isolates of Mycobacterium tuberculosis circulating in Astana in 2021–2022. Among 198 M. tuberculosis isolates collected, 175 (88.38%) belonged to the L2/Beijing family, and the remaining 23 samples (11.62%) belonged to the L4 family. During the research used genotyping aimed at determining the genetic family of M. tuberculosis, as well as whole-genome sequencing of selected 24 L2/Beijing isolates with their subsequent bioinformatics analysis. According to the analysis results, 62.5% of isolates were assigned to the Central Asia Outbreak genotype. The remaining genotypes were represented by Central Asia (20.8%), B0/W148 (12.5%) and Clade A (4.2%). Besides that, phenotypic and genotypic characterization of the resistance of selected isolates to anti-tuberculosis drugs was carried out. One of the possible reasons for the spread of resistant forms of tuberculosis in the country is the predominance of the Central Asia Outbreak genetic cluster associated with MDR-TB.
STRAIN SELECTION AND CULTIVATION OF FOOT-AND-MOUTH DISEASE VIRUSES FOR THE DEVELOPMENT OF A TRIVALENT INACTIVATED VACCINE
Authors: Burashev Y.D. , Orynbayev М.B. , Abeuov K.B. , Sultankulova К.T. , Tulendibayev А.B. , Оmarova Z.D. , Argimbayeva Т.U. , Yermekbai Т.Т. , Aubakir N.А.
Published: October 2024

Foot-and-mouth disease is a well-known transboundary animal disease and has been recognised as a priority disease by the Steering Committee of the Global Framework for the Progressive Control of Transboundary Animal Diseases in Europe.
The territory of the Republic of Kazakhstan is generally free of foot-and-mouth disease, however, sporadic cases of foot-and-mouth disease occur in various regions of the country as a result of importation from unfavorable countries. Epizootic safety in the Republic of Kazakhstan is maintained by vaccinating animals in the border areas of the southern and eastern regions. Inactivated vaccines against serotypes A, O, Asia produced by the All-Russian Research Institute of Animal Health (Russia) are used for vaccination.
Continuous seromonitoring is carried out to maintain the level of post-vaccination antibodies at a high level, ensuring the immunity of animals to foot-and-mouth disease. However, despite all the measures taken, sporadic outbreaks of foot-and-mouth disease cause damage to livestock farming in the Republic of Kazakhstan.
The effectiveness of preventive measures using vaccination depends on the strain used in the vaccine. The closer the strain used in the vaccine is genetically to the viruses circulating in that area, the more effective the preventive measures will be and the research conducted to create the most immunogenic domestic anti-foot-and-mouth disease vaccines have scientific and practical significance.
This article presents the results of the selection of foot-and-mouth disease virus strains previously circulating in the territory of the Republic of Kazakhstan and studies their cultural and biological properties. Studies of the above-mentioned strains on adaptation to a transplantable cell culture line were conducted, the stability of cultural properties was studied over 10 generations and the stability was confirmed by the PCR method. Also, based on the studies, it was found that the maximum accumulation of the virus in cell culture occurs at a multiplicity of infection of 0.01-0.1 TCID50/cell. The reproductive activity of the studied isolates was within 6.5-7.25 lg TCID50/cm3 when cultivated for 16 hours.
Investigating the Effect of Ammonia Addition on the Performance of a Heavy-Duty Natural Gas Spark Ignition Engine Operated at Stoichiometric Conditions
Authors: Yang Ruomiao , Yin Zibin , Yan Yuchao , Ou Juan , Xie Tianfang , Liu Zhentao , Liu Jinlong
Published: October 2024

Due to the pressing issue of global warming, there has been a significant focus on zero- and low-carbon fuels globally. Among hydrocarbon fuels, methane is widely used in spark ignition engines due to its abundance and relatively low-carbon footprint. However, to further reduce carbon emissions, interest is growing in the use of ammonia, a zero-carbon fuel, as a partial replacement for methane. Consequently, it is crucial to investigate the impact of ammonia addition on the performance of natural gas spark ignition engines. A key challenge in studying ammonia–methane engines is that the introduction of ammonia alters the formation mechanisms of nitrogen-based pollutants, resulting in the coupling of fuel-borne and airborne nitrogen pollutants. As a result, research on the nitrogen-based emissions of ammonia–methane engines has been limited. This study addresses this issue by differentiating between atmospheric nitrogen and fuel nitrogen elements, effectively decoupling fuel-borne and airborne nitrogen pollutants. This approach provides valuable insights into the effects of ammonia addition on the nitrogen-based pollutant characteristics of natural gas engines. The results indicate that ammonia addition introduces N2O, a species absent in pure methane engines. The N2O primarily originates from cold wall regions and the partial oxidation of ammonia released from engine crevices during the late oxidation process. Although NO remains the dominant nitrogen-based pollutant and the amount of N2O is small, the significant greenhouse gas potential of N2O warrants further attention. Furthermore, while ammonia addition increases the NO concentration in the burning zone, it slightly reduces the NO concentration at chemical equilibrium under stoichiometric conditions. As a result, engines operating with an ammonia energy substitution ratio of 0.4 exhibit lower nitrogen oxide (NOx) emissions compared to those fueled solely by methane. These findings underscore the need for further research into the combustion and emission characteristics of ammonia–methane spark ignition engines.
A Prediction Method of Oil Recovery for Hot Water Chemical Flooding in Heavy Oil Reservoirs: Semi-Analytical Stream Tube Model
Authors: Du Qingjun , Shen Jie , Shi Lina , Yu Jianmei , Hou Jian , Xue Yu , Wei Bei , Liu Yongge
Published: October 2024

Chemical agents (polymer and surfactant) assisted hot water flooding is an effective means of enhancing oil recovery in heterogeneous and heavy oil reservoirs. The rapid prediction of oil recovery through hot water chemical flooding is very important. The stream tube model is a fast analytical method for predicting water flooding recovery, but it is not suitable for hot water chemical flooding. In this paper, a permeability distribution model for multi-stream tubes is established based on permeability variation coefficient using normal distribution function for reservoir heterogeneity, using Gompertz growth function model to characterize the changes in stream tube temperature, polymer viscosity, and surfactant concentration with injection volume, using Brooks–Corey model to describe the influence of interfacial tension and temperature on the relative permeability curve. Finally, an analytical stream tube model for hot water chemical flooding of heavy oil reservoirs was established. The time-discrete method is used to solve the model, and then, the graphs of the relationship between oil recovery and water cut are obtained. Compared with numerical simulation methods, the prediction error of oil recovery is less than 2%, and the calculation time is reduced by 89%. This model has been successfully applied to X oilfield. Based on historical fitting, it is predicted that hot water chemical flooding can enhance oil recovery by 6.3% compared to water flooding. This paper provides a fast calculation method for predicting and evaluating the effectiveness of hot water chemical flooding in heavy oil reservoirs.
Barefoot Ski Ranch: Navigating Crisis Waters—A Case Study in Brand Management Amidst Tragedy
Authors: McDermand Robert , Reese Jason
Published: October 2024

The Barefoot Ski Ranch Surf Resort case study offers a valuable lesson in brand management during a crisis situation within the inland surf industry. Aimed at undergraduate or graduate students in sports management, sports law, or sports business programs, this case combines a hypothetical depiction of an authentic situation that underscores the repercussions following the tragic death of surfer Fabrizio Stabile from an amoeba infection acquired at the resort. It delves into the subsequent lawsuit by the Stabile family, which accused the resort of inadequate filtration systems, evidence cover-up, and obstructing the discovery process. These allegations compounded the resort’s existing challenges, including damage to its brand reputation and the looming threat of heightened industry regulation. This case underscores the critical need for effective brand management during a crisis, and the imperative for surf facilities to prioritize public safety, and uphold high care standards in water facility operations. It also emphasizes the far-reaching impact of crises on the industry and the necessity for facilities to be prepared to address unforeseen challenges in a responsible and transparent manner. Ultimately, it raises important questions about the responsibility of such parks to ensure guest safety and the potential consequences for those that fail to do so.
Supporting People With Musculoskeletal Conditions From Underserved Communities in the United Kingdom to Engage With Physical Activity: A Realist Synthesis and Q-Methodology Study
Authors: Berry Alice , Brady Terence , Bradley Natasha , Harris Nicky , Flurey Caroline , Niyi-Odumosu Faatihah , Dures Emma , Walsh Nicola
Published: October 2024

Background: In the United Kingdom, 20 million individuals suffer from a musculoskeletal condition, for which physical activity (PA) is a core treatment. Minority ethnic communities experience a disproportionate impact, experiencing higher levels of pain and engaging in less PA. Research has identified various factors that affect their participation in PA, including lack of access to support, limited knowledge of resources, language barriers, fear of racial harassment while exercising, and insufficient communication/information from healthcare professionals. Methods: This project adopted a realist perspective, aiming to understand “what works, in which circumstances, and for whom?” The project had 4 steps: (1) defining review scope with stakeholders; (2) searching and extracting literature, creation of initial program theories; (3) refining/validating initial program theories with stakeholders; and (4) adopting Q-methodology to highlight priority areas. Results: 17 papers were included. Three program theories were identified: (1) Lack of initial access to health service support; (2) Nature of musculoskeletal self-management support—the importance of the therapeutic relationship and value of shared conversations; and (3) Accessible long-term support for PA engagement. The Q-sort exercise highlighted priority areas: (1) complex booking procedures and inadequate translation services, (2) time constraints impact effective patient-centered care, (3) dismissive attitudes/mismatched expectations impact shared decision making, (4) rebuilding trust to strengthen therapeutic relationships, (5) cultural relevance in developing therapeutic relationships, and (6) clinician recommended PA opportunities increase knowledge of PA. Conclusions: Our findings shed light on inequities across the UK’s musculoskeletal pathways, specifically in relation to PA engagement. This points toward priority areas for future research and interventions.
Physical Determinants of Sprint and Long Jump Performance in Male Youth Track-and-Field Athletes With Differing Maturity Statuses
Authors: Baker James , Read Paul , Graham-Smith Philip , Monaco Mauricio , Varamenti Evdokia , Cardinale Marco , Jones Thomas W.
Published: October 2024

Purpose: This study examined the physical determinants of 60-m sprint and long jump (LJ) performance and differences between maturity groups in physical characteristics in young male track-and-field athletes. Methods: Competition results, countermovement jump, isometric leg press, 10-5 repeated jump test, and 50-m sprint were collected over 3 seasons for 54 male athletes (age 13 [1] y; stature 160.0 [8.9] cm; body mass, 48.0 [9.8] kg; percentage predicted adult height 92.2% [5.5%]) grouped by maturity status: approaching- (n = 16), circa- (n = 19), and post-peak height velocity (PHV) (n = 19). Results: There were significant between-group differences in 60 m, LJ, and all physical testing variables (P < .001, g = 0.88–5.44) when comparing the approaching- and circa-PHV groups with the post-PHV group. Significant differences were identified between the approaching- and circa-PHV groups in 40-m (P = .033, g = 0.89), 50-m (P = .024, g = 1.64), and 60-m (P < .001, g = 0.89) sprint times. Countermovement jump and 50-m sprint variables were consistently important for projection of 60 m and LJ performance across the valid multivariate models. Conclusions: Large differences in performance across maturity groups highlight the importance of understanding athletes’ maturity status to accurately interpret performance. Several physical performance variables were important for projecting competition 60 m and LJ performance.
Sentinel Surveillance reveals phylogenetic diversity and detection of linear plasmids harboring
vanA
and
optrA
among enterococci collected in the United States
Authors: Kent Alyssa G. , Spicer Lori M. , Campbell Davina , Breaker Erin , McAllister Gillian A. , Ewing Thomas O. , Longo Cynthia , Balbuena Rocio , Burroughs Mark , Burgin Alex , Padilla Jasmine , Johnson J. Kristie , Halpin Alison Laufer , McKay Susannah L. , Rasheed J. Kamile , Elkins Christopher A. , Karlsson Maria , Lutgring Joseph D. , Gargis Amy S.
Published: October 2024

Enterococcus faecalis
and
Enterococcus faecium
are frequent causes of healthcare-associated infections. Antimicrobial-resistant enterococci pose a serious public health threat, particularly vancomycin-resistant enterococci (VRE), for which treatment options are limited. The Centers for Disease Control and Prevention’s Division of Healthcare Quality Promotion Sentinel Surveillance system conducted surveillance from 2018 to 2019 to evaluate antimicrobial susceptibility profiles and molecular epidemiology of 205
E. faecalis
and 180
E. faecium
clinical isolates collected from nine geographically diverse sites in the United States. Whole genome sequencing revealed diverse genetic lineages, with no single sequence type accounting for more than 15% of
E. faecalis
or
E. faecium
. Phylogenetic analysis distinguished
E. faecium
from 19
E. lactis
(previously known as
E. faecium
clade B). Resistance to vancomycin was 78.3% among
E. faecium
, 7.8% among
E. faecalis
, and did not occur among
E. lactis
isolates. Resistance to daptomycin and linezolid was rare:
E. faecium
(5.6%, 0.6%, respectively),
E. faecalis
(2%, 2%), and
E. lactis
(5.3%, 0%). All VRE harbored the
vanA
gene. Three of the seven isolates that were not susceptible to linezolid harbored
optrA
, one chromosomally located and two on linear plasmids that shared a conserved backbone with other multidrug-resistant conjugative linear plasmids. One of these isolates contained
optrA
and
vanA
co-localized on the linear plasmid. By screening all enterococci, 20% of
E. faecium
were predicted to harbor linear plasmids, whereas none were predicted among
E. faecalis
or
E. lactis
. Continued surveillance is needed to assess the future emergence and spread of antimicrobial resistance by linear plasmids and other mechanisms.

IMPORTANCE

This work confirms prior reports of
E. faecium
showing higher levels of resistance to more antibiotics than
E. faecalis
and identifies that diverse sequence types are contributing to enterococcal infections in the United States. All VRE harbored the
vanA
gene. We present the first report of the linezolid resistance gene
optrA
on linear plasmids in the United States, one of which co-carried a
vanA
cassette. Additional studies integrating epidemiological, antimicrobial susceptibility, and genomic methods to characterize mechanisms of resistance, including the role of linear plasmids, will be critical to understanding the changing landscape of enterococci in the United States.
The point mutation A1387G in the 16S rRNA gene confers aminoglycoside resistance in
Campylobacter jejuni
and
Campylobacter coli
Authors: Zarske Michael , Werckenthin Christiane , Golz Julia C. , Stingl Kerstin
Published: October 2024

Thermotolerant
Campylobacter
spp. are the most frequent cause of foodborne bacterial diarrhea and high-priority antibiotic-resistant pathogens, according to the World Health Organization (WHO). Monitoring revealed current low prevalence of gentamicin resistance in European
Campylobacter
spp. isolates but substantial presence of gentamicin modifying genes circulating globally. Using a combined approach of natural transformation and whole-genome sequencing, we revealed a novel gentamicin resistance mechanism, namely the point mutation A1387G in the 16S rRNA gene, originally identified in a
C. coli
isolate from turkey caecal content. The transformation rate of the resistance using genomic DNA of the resistant donor to sensitive recipient
C. jejuni
and
C. coli
was ~2.5 log
10
lower compared to the control
rpsL
-A128G point mutation conferring streptomycin resistance. Antimicrobial susceptibility tests showed cross-resistance to apramycin, kanamycin, and tobramycin, with transformants exhibiting more than 4- to 8-fold increased MICs to apramycin and tobramycin and over 64-fold higher MICs to kanamycin compared to wild-type isolates. Although transformants showed 177–1,235 variations relative to the recipient, only the A1387G point mutation in the 16S rRNA was in common. This mutation was causal for resistance, as transformation of a 16S rRNA_A1387G PCR fragment into susceptible isolates also led to resistant transformants. Sanger sequencing of the 16S rRNA genes and Oxford nanopore whole-genome sequencing of transformants identified clones harboring either all three copies with A1387G or a mixed population of wild-type and mutated 16S rRNA gene alleles. Within 15 passages on non-selective medium, transformants with mixed populations of the 16S rRNA gene copies partially reverted to wild type, both geno- and phenotypically. In contrast, transformants harboring the A1387G point mutation in all three 16S rRNA gene copies kept full resistance within at least 45 passages. We speculate that partial acquisition and rapid loss of the point mutation limited its spread among
C
. spp. isolates. In-depth knowledge on resistance mechanisms contributes to optimal diagnosis and preventative measures.
Discovery and synthesis of leaderless bacteriocins from the Actinomycetota
Authors: Hourigan David , Miceli de Farias Felipe , O’Connor Paula M. , Hill Colin , Ross R. Paul
Published: October 2024

Leaderless bacteriocins are a unique class of bacteriocins that possess antimicrobial activity after translation and have few cases of documented resistance. Aureocin A53 and lacticin Q are considered two of the most well-studied leaderless bacteriocins. Here, we used
in silico
genome mining to search for novel aureocin A53-like leaderless bacteriocins in GenBank and MGnify. We identified 757 core peptides across 430 genomes with 75 species found currently without characterized leaderless bacteriocin production. These include putative novel species containing bacteriocin gene clusters (BGCs) from the genera
Streptomyces
(sp. NBC_00237) and
Agrococcus
(sp. SL85). To date, all characterized leaderless bacteriocins have been found within the phylum Bacillota, but this study identified 97 core peptides within the phylum Actinomycetota. Members of this phylum are traditionally associated with the production of antibiotics, such is the case with the genus
Streptomyces
. Actinomycetota is an underexplored phylum in terms of bacteriocin production with no characterized leaderless bacteriocin production to date. The two novel leaderless bacteriocins arcanocin and arachnicin from Actinomycetota members
Arcanobacterium
sp. and
Arachnia
sp., respectively, were chemically synthesized and antimicrobial activity was verified. These peptides were encoded in human gut (PRJNA485056) and oral (PRJEB43277) microbiomes, respectively. This research highlights the biosynthetic potential of Actinomycetota in terms of leaderless bacteriocin production and describes the first antimicrobial peptides encoded in the genera
Arcanobacterium
and
Arachnia
.

IMPORTANCE

Bacteriocins are gathering attention as alternatives to current antibiotics given the increasing incidence of antimicrobial resistance. Leaderless bacteriocins are considered a commercially attractive subclass of bacteriocins due to the ability to synthesize active peptide and low levels of documented resistance. Therefore, in this work, we mined publicly available data to determine how widespread and diverse leaderless bacteriocins are within the domain of bacteria. Actinomycetota, known for its antibiotic producers but lacking described and characterized bacteriocins, proved to be a rich source of leaderless bacteriocins—97 in total. Two such peptides, arcanocin and arachnicin, were chemically synthesized and have antimicrobial activity. These bacteriocins may provide a novel source of novel antimicrobials that could aid in the development of future alternative antimicrobials and highlight that the Actinomycetota are an underexplored resource of bacteriocin peptides.
Genomics and evolutionary analysis of
Chlorella variabilis-
infecting viruses demarcate criteria for defining species of giant viruses
Authors: Carvalho João Victor R. P. , Carlson Roger M. , Ghosh Jayadri , Queiroz Victória F. , de Oliveira Ellen G. , Botelho Bruna B. , Filho Clécio A. C. , Agarkova Irina V. , McClung O. William , Van Etten James L. , Dunigan David D. , Rodrigues Rodrigo A. L.
Published: October 2024

Chloroviruses exhibit a close relationship with their hosts with the phenotypic aspect of their ability to form lytic plaques having primarily guided the taxonomy. However, with the isolation of viruses that are only able to complete their replication cycle in one strain of
Chlorella variabilis
, systematic challenges emerged. In this study, we described the genomic features of 53 new chlorovirus isolates and used them to elucidate part of the evolutionary history and taxonomy of this clade. Our analysis revealed new chloroviruses with the largest genomes to date (>400 kbp) and indicated that four genomic features are statistically different in the viruses that only infect the Syngen 2–3 strain of
C. variabilis
(OSy viruses). We found large regions of dissimilarity in the genomes of viruses PBCV-1 and OSy-NE5 when compared with the other genomes. These regions contained genes related to the interaction with the host cell machinery and viral capsid proteins, which provided insights into the evolution of the replicative and structural modules in these giant viruses. Phylogenetic analysis using hallmark genes of
Nucleocytoviricota
revealed that OSy-viruses evolved from the NC64A-viruses, possibly emerging as a result of the strict relationship with their hosts. Merging phylogenetics and nucleotide identity analyses, we propose strategies to demarcate viral species, resulting in seven new species of chloroviruses. Collectively, our results show how genomic data can be used as lines of evidence to demarcate viral species. Using the chloroviruses as a case study, we expect that similar initiatives will emerge using the basis exhibited here.

IMPORTANCE

Chloroviruses are a group of giant viruses with long dsDNA genomes that infect different species of
Chlorella-
like green algae. They are host-specific, and some isolates can only replicate within a single strain of
Chlorella variabilis
. The genomics of these viruses is still poorly explored, and the characterization of new isolates provides important data on their genetic diversity and evolution. In this work, we describe 53 new chlorovirus genomes, including many isolated from alkaline lakes for the first time. Through comparative genomics and molecular phylogeny, we provide evidence of genomic gigantism in chloroviruses and show that a subset of viruses became highly specific for their hosts at a particular point in evolutionary history. We propose criteria to demarcate species of chloroviruses, paving the way for an update in the taxonomy of other groups of viruses. This study is a new and important piece in the complex puzzle of giant algal viruses.
Insights into human norovirus cultivation in human intestinal enteroids
Authors: Ettayebi Khalil , Kaur Gurpreet , Patil Ketki , Dave Janam , Ayyar B. Vijayalakshmi , Tenge Victoria R. , Neill Frederick H. , Zeng Xi-Lei , Speer Allison L. , Di Rienzi Sara C. , Britton Robert A. , Blutt Sarah E. , Crawford Sue E. , Ramani Sasirekha , Atmar Robert L. , Estes Mary K.
Published: October 2024

Human noroviruses (HuNoVs) are a significant cause of epidemic and sporadic acute gastroenteritis worldwide. The lack of a reproducible culture system hindered the study of HuNoV replication and pathogenesis for almost a half-century. This barrier was overcome with our successful cultivation of multiple HuNoV strains in human intestinal enteroids (HIEs), which has significantly advanced HuNoV research. We optimized culture media conditions and generated genetically modified HIE cultures to enhance HuNoV replication in HIEs. Building upon these achievements, we now present new insights into this culture system, which involve testing different media, unique HIE lines, and additional virus strains. HuNoV infectivity was evaluated and compared in new HIE models, including HIEs generated from different intestinal segments of individual adult organ donors, HIEs from human intestinal organoids produced from directed differentiation of human embryonic stem cells that were then transplanted and matured in mice before making enteroids (H9tHIEs), genetically engineered (J4
FUT2
knock-in [
KI
]
,
J2
STAT1
knockout [
KO
]) HIEs, as well as HIEs derived from a patient with common variable immunodeficiency (CVID) and from infants. Our findings reveal that small intestinal HIEs, but not colonoids, from adults, H9tHIEs, HIEs from a CVID patient, and HIEs from infants support HuNoV replication with segment and strain-specific differences in viral infection. J4
FUT2-KI
HIEs exhibit the highest susceptibility to HuNoV infection, allowing the cultivation of a broader range of genogroup I and II HuNoV strains than previously reported. Overall, these results contribute to a deeper understanding of HuNoVs and highlight the transformative potential of HIE cultures in HuNoV research.

IMPORTANCE

Human noroviruses (HuNoVs) cause global diarrheal illness and chronic infections in immunocompromised patients. This paper reports approaches for cultivating HuNoVs in secretor positive human intestinal enteroids (HIEs). HuNoV infectivity was compared in new HIE models, including ones from (i) different intestinal segments of single donors, (ii) human embryonic stem cell-derived organoids transplanted into mice, (iii) genetically modified lines, and (iv) a patient with common variable immunodeficiency disease. HIEs from small intestine, but not colon, support HuNoV replication with donor, segment, and strain-specific variations. Unexpectedly, HIEs from one donor are resistant to GII.3 infection. The genetically modified J4
FUT2
knock-in (
KI
) HIEs enable cultivation of a broad range of GI and GII genotypes. New insights into strain-specific differences in HuNoV replication in HIEs support this platform for advancing understanding of HuNoV biology and developing potential therapeutics.
Chlamydia trachomatis
Inc Ct226 is vital for FLI1 and LRRF1 recruitment to the chlamydial inclusion
Authors: Sturd Natalie A. , Knight Lindsey A. , Wood Macy G. , Durham Legacy , Ouellette Scot P. , Rucks Elizabeth A.
Published: October 2024

The obligate intracellular pathogen,
Chlamydia trachomatis
, establishes an intracellular niche within a host membrane-derived vacuole called the chlamydial inclusion. From within this inclusion,
C. trachomatis
orchestrates numerous host-pathogen interactions, in part, by utilizing a family of type III secreted effectors, termed inclusion membrane proteins (Incs). Incs are embedded within the inclusion membrane, and some function to recruit host proteins to the inclusion. Two such recruited host proteins are
l
eucine
r
ich
r
epeat
F
lightless-1
i
nteracting
p
rotein 1 (LRRF1/LRRFIP1) and its binding partner Flightless 1 (FLI1/FLII). Previously, LRRF1 has been shown to interact with Inc protein Ct226/CTL0478. This is the first study to examine interactions of FLI1 with candidate Incs or with LRRF1 during infection. We hypothesized that FLI1 recruitment to the inclusion would be dependent on LRRF1 localization. We demonstrated that FLI1 co-immunoprecipitated with Ct226 but only in the presence of LRRF1. Furthermore, FLI1 localized to the inclusion when LRRF1 was depleted via small interfering RNA, suggesting that FLI1 may have an alternative recruitment mechanism. We further developed a series of CRISPRi knockdown and complementation strains in
C. trachomatis
serovar L2 targeting ct226 and co-transcribed candidate Incs, ct225 and ct224. Simultaneous knockdown of ct226, ct225, and ct224 prevented localization of both FLI1 and LRRF1 to the inclusion, and only complementation of ct226 restored their localization. Thus, we demonstrated Ct226 is critical for FLI1 and LRRF1 localization to the inclusion. Our results also indicate an LRRF1-independent localization mechanism for FLI1, which likely influence their mechanism(s) of action during chlamydial infection.

IMPORTANCE

Chlamydia trachomatis
is a leading cause of both bacterial sexually transmitted infections and preventable infectious blindness worldwide. As an obligate intracellular pathogen,
C. trachomatis
has evolved multiple ways of manipulating the host to establish a successful infection. As such, it is important to understand host-chlamydial protein-protein interactions as these reveal strategies that
C. trachomatis
uses to shape its intracellular environment. This study looks in detail at interactions of two host proteins, FLI1 and LRRF1, during chlamydial infection. Importantly, the series of CRISPR inference knockdown and complement strains developed in this study suggest these proteins have both independent and overlapping mechanisms for localization, which ultimately will dictate how these proteins function during chlamydial infection.
Late Paleozoic slab rollback events in the southeastern part of the Central Asian orogenic belt: Implications for Paleo-Asian Ocean subduction and continental crust growth
Authors: Gao Qiang , Yan Mao-Qiang , Huizenga Jan Marten , Lai Lian-Xin , Li Bin , Zeng Hong-Hong , Moritz Robert , Wei Jun-Hao
Published: October 2024

The Central Asian orogenic belt is considered to be the largest Phanerozoic accretive orogenic belt on Earth. The late Paleozoic magmatic rocks in central Inner Mongolia are crucial for understanding continental crust growth and the tectonic evolution of the southeastern part of the Central Asian orogenic belt. We present comprehensive geochemical, isotopic, and geochronological data from three late Paleozoic magmatic units in the Mandula area, west of the Solonker suture zone. Zircon U-Pb dating indicates that these rocks formed during the late Carboniferous (316–304 Ma). The Mandula high-Mg diorites exhibit high MgO (3.9–6.5 wt%), high Mg# (61–69), and depleted Nd-Hf isotopic compositions, generated through interaction between a metasomatized mantle and slab melts with the overlying sediments. The Mandula granodiorites display adakite geochemical characteristics with high Sr/Y mass ratios (29–52), high MgO (1.7–2.2 wt%), and high Mg# (52–54), formed by partial melting of the oceanic slab with the addition of overlying sediment. Mafic microgranular enclaves have consistent ages, Sr-Nd-Hf isotope compositions, and hornblende crystallization temperature-pressure conditions with their host granodiorite, formed from a cognate magma associated with the host granodiorites through cumulate. We propose that two phases of slab rollback took place during the late Paleozoic southward subduction-accretion of the Paleo-Asian Ocean. The first phase corresponded to the transformation of low- to medium-angle slab subduction, while the second phase led to subduction-related extension. Considering the tectonic-magmatic evolution, crustal maturity, and thickness variations in the late Paleozoic southeastern part of the Central Asian orogenic belt, we propose that prolonged subduction and slab rollback promoted continental crust growth. The Central Asian orogenic belt coincides temporally and spatially with the Phanerozoic Pangea cycle, suggesting that continuous subduction and supercontinent amalgamation significantly contributed to continental crust growth.
Prescribing strength training for stroke recovery: a systematic review and meta-analysis of randomised controlled trials
Authors: Noguchi Kenneth S , Moncion Kevin , Wiley Elise , Morgan Ashley , Huynh Eric , Balbim Guilherme Moraes , Elliott Brad , Harris-Blake Carlene , Krysa Brent , Koetsier Barb , Pinili Karolyn , Beauchamp Marla K , Phillips Stuart M , Thabane Lehana , Tang Ada
Published: October 2024

Objective

To examine the effects of strength training on patient-important outcomes of stroke recovery and to quantify the influence of the exercise prescription on treatment effects.

Design

Systematic review and meta-analysis.

Data sources

Eight electronic databases (MEDLINE, EMBASE, EMCARE, AMED, PsycINFO, CINAHL, SPORTDiscus, and Web of Science) and two clinical trial registries (ClinicalTrials.gov and WHO International Clinical Trials Registry Platform) were searched from inception to 19 June 2024.

Eligibility criteria

Randomised controlled trials were eligible if they examined the effects of strength training compared with no exercise or usual care and reported at least one exercise prescription parameter. An advisory group of community members with lived experience of stroke helped inform outcomes most relevant to stroke recovery.

Results

Forty-two randomised trials (N=2204) were included. Overall risk of bias was high across most outcomes. Strength training improved outcomes rated as ‘critical for decision-making’ by the advisory group, including walking capacity (standardised mean difference (SMD)=0.95 (95% CI 0.34–1.56)), balance (SMD=1.13 (0.51–1.75)), functional ability and mobility (SMD=0.61 (0.09–1.14)), and habitual (mean difference (MD)=0.05 m/s (0.02–0.09)) and fast-paced walking speed (MD=0.09 m/s (0.01–0.17)), with very low to moderate certainty of evidence, mainly due to risk of bias and inconsistency. More frequent strength training, traditional strength training programmes and power-focused intensities (ie, emphasis on movement velocity) were positively associated with walking capacity, health-related quality of life and fast-paced walking speed.

Conclusion

Strength training alone or combined with usual care improves stroke recovery outcomes that are important for decision-making. More frequent strength training, power-focused intensities and traditional programme designs may best support stroke recovery.

PROSPERO registration number

CRD42023414077.