bluuebunny/crossref_metadata_2025 huggingface dataset:
Power to the researchers: Calculating power after estimation
Authors: Tian Jiarui , Coupé Tom , Khatua Sayak , Reed W. Robert , Wood Benjamin D. K.
Published: July 2024

This study demonstrates a simple and reliable method for calculating ex post power. We first conduct a series of Monte Carlo experiments to assess its performance. The experiments are designed to produce artificial datasets that resemble actual data from 23 studies funded by the International Initiative for Impact Evaluation (3ie). After determining that the method performs adequately, we then apply it to the 23 studies and compare their ex post power with the ex‐ante power claimed on their funding applications. We find the average ex post power of the 3ie studies is close to 80%. However, there are more estimates of low power than would be expected if all studies had 80% true power. Most of the differences between ex post and ex ante power can be explained by differences between planned and actual total observations, number of clusters, and the degree of intracluster correlation. This demonstrates how ex post power can be used by funders to evaluate previously funded research and identify areas for improved power estimation in future research. We further show how ex post power can aid in the interpretation of both insignificant and significant estimates.
Are Contraceptive Method Preferences Stable? Measuring Change in the Preferred Method among Kenyan Women
Authors: Cardona Carolina , Sarnak Dana , Gemmill Alison , Gichangi Peter , Thiongo Mary , Anglewicz Philip
Published: July 2024

Contraceptive preferences are important for reproductive outcomes, such as contraceptive continuation and pregnancy. Current approaches to measuring reproductive preferences in population surveys are limited to exploring only fertility preferences and implicitly assume that contracepting people are using a method they want. We know that people change their fertility preferences over the life course as a response to life events, but there is no information about changes in contraceptive preferences, given the limited evidence about the measurement and distribution of contraceptive preferences. In this study, we examined the extent of change in women's contraceptive preferences over one year and identified characteristics associated with this change in Kenya using three rounds of nationally representative longitudinal data. Over one year, 18 percent of contraceptive users and 46 percent of contraceptive nonusers reported changes in their preferred contraceptive. Experiencing a pregnancy or birth and changes in marital status were associated with changes in contraceptive preferences for users and nonusers. We found that contraceptive preferences are dynamic, suggesting that family planning programs should ensure people's access to various methods to respond to women's changing circumstances and preferences.
Early Predictors of Recovery From Nonoperatively Treated Achilles Tendon Rupture: 1 Year Follow‐Up Study
Authors: Sukanen Maria , Khair Ra’ad M. , Reito Aleksi , Ponkilainen Ville , Paloneva Juha , Cronin Neil , Hautala Arto J. , Finni Taija
Published: July 2024

Purpose

To investigate early structural and mechanical predictors of plantarflexor muscle strength and the magnitude of Achilles tendon (AT) nonuniform displacement at 6 and 12 months after AT rupture.

Methods

Thirty‐five participants (28 males and 7 females; mean ± SD age 41.7 ± 11.1 years) were assessed for isometric plantarflexion maximal voluntary contraction (MVC) and AT nonuniformity at 6 and 12 months after rupture. Structural and mechanical AT and plantarflexor muscle properties were measured at 2 months. Limb asymmetry index (LSI) was calculated for all variables. Multiple linear regression was used with the 6 and 12 month MVC LSI and 12 month AT nonuniformity LSI as dependent variables and AT and plantarflexor muscle properties at 2 months as independent variables. The level of pre‐ and post‐injury sports participation was inquired using Tegner score at 2 and 12 months (scale 0–10, 10 = best possible score). Subjective perception of recovery was assessed with Achilles tendon total rupture score (ATRS) at 12 months (scale 0–100, 100=best possible score).

Results

Achilles tendon resting angle (ATRA) symmetry at 2 months predicted MVC symmetry at 6 and 12 months after rupture (β = 2.530, 95% CI 1.041–4.018, adjusted R2 = 0.416, p = 0.002; β = 1.659, 95% CI 0.330–2.988, adjusted R2 = 0.418, p = 0.016, respectively). At 12 months, participants had recovered their pre‐injury level of sports participation (Tegner 6 ± 2 points). The median (IQR) ATRS score was 92 (7) points at 12 months.

Conclusion

Greater asymmetry of ATRA in the early recovery phase may be a predictor of plantarflexor muscle strength deficits up to 1 year after rupture.

Trial Registration: This research is a part of “nonoperative treatment of Achilles tendon rupture in Central Finland: a prospective cohort study” that has been registered in ClinicalTrials.gov (NCT03704532)
Graph isomorphism network with weighted multi‐aggregators for building shape classification
Authors: Zhang Ya , Liu Jiping , Wang Yong , Cao Yungang , Xu Shenghua , Luo An
Published: July 2024

Building shape cognition is essential for tasks, such as map generalization, urban modeling, and building semantics and distribution pattern recognition. Traditional geometric and statistical methods rely on human‐defined shape indicators, and spectral‐based graph neural networks (GNNs) require Laplacian eigendecomposition, resulting in high algorithmic complexity. Therefore, we proposed a low‐complexity and simple‐to‐use spatial‐domain GNN for differentiating building shapes. To examine the influence of the building vertices on their shape, we treated each building as a graph and proposed a graph isomorphic network with weighted multi‐aggregators (GIN‐WMA) by analyzing the node connectivity of a building graph. The GIN‐WMA utilizes a novel aggregator that combines the sum and max aggregators, enhancing its recognition and differentiation capabilities. This approach can effectively differentiate nodes that have identical features after aggregation by the sum aggregator. We extracted features considering both local node and global shape features, drawing inspiration from Gestalt cognitive psychology and GNN's “node–graph” differentiation strategy. In addition, we compared the performance of GIN‐WMA with existing methods, studying the effect of various node features and their combinations on classification accuracy. The results demonstrated that GIN‐WMA outperforms other methods in discriminating building shapes, demonstrating superior capabilities in shape classification and enabling end‐to‐end extraction and classification of building shapes.
Formate‐tetrahydrofolate ligase: supplying the cytosolic one‐carbon network in roots with one‐carbon units originating from glycolate
Authors: Saeheng Sompop , Bailes Clayton , Bao Han , Gashu Kelem , Morency Matt , Arlynn Tana , Smertenko Andrei , Walker Berkley James , Roje Sanja
Published: July 2024

The metabolism of tetrahydrofolate (H4PteGlun)‐bound one‐carbon (C1) units (C1 metabolism) is multifaceted and required for plant growth, but it is unclear what of many possible synthesis pathways provide C1 units in specific organelles and tissues. One possible source of C1 units is via formate‐tetrahydrofolate ligase, which catalyzes the reversible ATP‐driven production of 10‐formyltetrahydrofolate (10‐formyl‐H4PteGlun) from formate and tetrahydrofolate (H4PteGlun). Here, we report biochemical and functional characterization of the enzyme from Arabidopsis thaliana (AtFTHFL). We show that the recombinant AtFTHFL has lower Km and kcat values with pentaglutamyl tetrahydrofolate (H4PteGlu5) as compared to monoglutamyl tetrahydrofolate (H4PteGlu1), resulting in virtually identical catalytic efficiencies for the two substrates. Stable transformation of Arabidopsis plants with the EGFP‐tagged AtFTHFL, followed with fluorescence microscopy, demonstrated cytosolic signal. Two independent T‐DNA insertion lines with impaired AtFTHFL function had shorter roots compared to the wild type plants, demonstrating the importance of this enzyme for root growth. Overexpressing AtFTHFL led to the accumulation of H4PteGlun + 5,10‐methylene‐H4PteGlun and serine, accompanied with the depletion of formate and glycolate, in roots of the transgenic Arabidopsis plants. This metabolic adjustment supports the hypothesis that AtFTHFL feeds the cytosolic C1 network in roots with C1 units originating from glycolate, and that these units are then used mainly for biosynthesis of serine, and not as much for the biosynthesis of 5‐methyl‐H4PteGlun, methionine, and S‐adenosylmethionine. This finding has implications for any future attempts to engineer one‐carbon unit‐requiring products through manipulation of the one‐carbon metabolic network in non‐photosynthetic organs.
Molecular and Pathobiology of Canine Mammary Tumour: Defining a Translational Model for Human Breast Cancer
Authors: Oliveira‐Lopes Adália F. , Götze Marcelo M. , Lopes‐Neto Belarmino E. , Guerreiro Denise D. , Bustamante‐Filho Ivan Cunha , Moura Arlindo Alencar
Published: July 2024

Canine mammary tumours (CMT) have histological, clinicopathological and molecular resemblances to human breast cancer (HBC), positioning them as viable models for studying the human disease. CMT initiation and progression occur spontaneously in immune‐competent animals, which challenge the suggested limitations of genetically modified mice, also enabling the evaluation of immunotherapies in canine patients. Dogs have shorter life expectancy compared to humans, and cancer advances more rapidly in this species. This makes it possible to perform studies about the clinical efficacy of new therapeutic modalities in a much shorter time than in human patients. The identification of biomarkers for tumour subtypes, progression and treatment response paves the way for the development of novel therapeutic and diagnostic approaches. This review addresses the similarities between CMT and HBC and the molecular signatures identified in CMT samples that have been explored to date. We proposed a detailed molecular exploration of the CMT stroma using state‐of‐the‐art methods in transcriptomics and proteomics. Using CMT as an analog for HBC not only helps to understand the complexities of the disease, but also to advance comparative oncology to the next level to prove the claim of dogs as a valid translational model.
The Use of Nonlinear Guided-Wave Features for Detection and Assessment of Intermetallic Compounds Within Dissimilar Joints—An Experimental Investigation
Authors: Mansour Mirna , Fakih Mohammad Ali , Mustapha Samir , Malinowski Paweł , Al-Badour Fadi
Published: July 2024

Welding dissimilar materials is widely employed in industrial construction and manufacturing to enhance cost-effectiveness and performance, often utilizing non-fusion methods like solid-state and high-energy beam welding. However, a significant challenge is the formation of intermetallic compounds (IMCs) at the joint interface, which can weaken the bond and increase brittleness, leading to hidden internal cracks. Nonlinear ultrasound detection methods are employed as advanced, nondestructive testing techniques for early damage inspection in various materials. This research investigates the assessment of the thickness of the intermetallic layer within dissimilar joints using nonlinear ultrasound-wave features. Experimental investigation was performed using four friction stir welding (FSW) lap joints, between AA5052-H32 aluminum and ASTM 516-70 steel, with various intermetallic thicknesses. The methodology involved examining the generation of second-order harmonic frequency by exciting Lamb waves (LWs) at specific frequencies. To determine the necessary LWs' excitation frequency, synchronism and non-zero power flux conditions were employed. The collected signals were measured and analyzed in the time and frequency domains to understand the behavior of the nonlinear parameter β′ with the thickness of the intermetallic layer. The results show that β′ changes in a linear manner with the thickness of the intermetallic compound layer (several micrometers in thickness). This provides strong evidence that nonlinear LW features are sensitive to microstructural variations in the FSW joints, which would enable them to effectively evaluate their strength.
An Attention-Based Deep Learning Model for Phase-Resolved Wave Prediction
Authors: Chen Jialun , Gunawan David , Taylor Paul H. , Chen Yunzhuo , Milne Ian A. , Zhao Wenhua
Published: July 2024

Phase-resolved wave prediction capability, even if only over two wave periods in advance, is of value for optimal control of wave energy converters, resulting in a dramatic increase in power generation efficiency. Previous studies on wave-by-wave predictions have shown that an artificial neural network (ANN) model can outperform the traditional linear wave theory-based model in terms of both prediction accuracy and prediction horizon when using synthetic wave data. However, the prediction performance of ANN models is significantly reduced by the varying wave conditions and buoy positions that occur in the field. To overcome these limitations, a novel wave prediction method is developed based on the neural network with an attention mechanism. This study validates the new model using wave data measured at sea. The model utilizes past time histories of three Sofar Spotter wave buoys at upwave locations to predict the vertical motion of a Datawell Waverider-4 at a downwave location. The results show that the attention-based neural network model is capable of capturing the slow variation in the displacement of the buoys, which reduces the prediction error compared to a standard ANN and long short-term memory model.
Pathways Toward Improving the Energy Efficiency of Residential Air-Conditioning Systems in Saudi Arabia
Authors: Alotaibi Abdulaziz M. , Makhdoom Taha K. , Alquaity Awad B. S.
Published: July 2024

In Saudi Arabia, the residential electricity consumption approaches 50%, primarily driven by air conditioners (AC). This study explores the potential energy savings and carbon dioxide (CO2) emission reductions up to 2030 through three scenarios: business as usual (BAU), continuous improvement scenario (CIS), and accelerated improvement scenario (AIS). BAU scenario assumes that the current energy efficiency ratio (EER) of 11.8 BTU/Wh is maintained until 2030. CIS considers a 5% EER improvement in new AC stock every two or five years, while AIS assumes a 10% improvement in the EER at the same intervals. Additionally, energy savings and emission reductions possible from varying adoption levels of a new refrigerant (R32) are estimated for three scenarios. Finally, the CO2 emission reduction under each scenario is computed for two extreme cases of grid emission factor. BAU scenario predicts energy savings of up to 17.7 TWh in 2030 compared to 2020 energy consumption figures. AIS with two-year intervals results in additional energy savings of 10.1 TWh in 2030 and cumulative energy savings of 37.1 TWh over a decade compared to the BAU scenario. Even CIS with five-year intervals yields additional energy savings of 1.69 TWh in 2030 and 5.1 TWh cumulatively compared to the BAU scenario. In comparison, the introduction of the new refrigerant results in cumulative energy savings of 10.2 TWh in the best-case scenario. These findings emphasize the importance of enhancing the EER of residential AC systems as a priority in energy efficiency policy.
Oil-Soluble Sulfur-Containing Organic Molybdenum as Lubricant Additives: A Review
Authors: Chen Lei , Li Xiaolei , Ji Zhengjia , Zhang Chenhui , Li Wenbing , Li Jv
Published: July 2024

In situ formation of MoS2 from oil-soluble sulfur-containing organic molybdenum (SOM) additives in lubricating oils is an alternative route of adding MoS2 into oils directly, which is difficult to disperse homogeneously. In this advanced technology, the structures of SOM and the formation of MoS2 during friction determine the efficiencies of SOM additives on the tribological properties of oils. Given the fact that SOM additives have been used intensively in both laboratory researches and industrial applications, this review discusses their molecular structures, tribological behaviors, compatibility with the other additives, and some bottlenecks in practical applications. Moreover, some routes for overcoming the bottlenecks are suggested. This review also concludes the basic lubrication mechanisms of SOM additives and provides some suggestions for utilizing SOM in advanced lubrication systems. Finally, the future development of SOM as oil additives is proposed and summarized.
Elastic Foundation Solution for the End-Notched Flexure Mode II Sandwich Configuration
Authors: Nguyen Minh Hung , Kardomateas George A.
Published: July 2024

This article presents a closed-form solution for the energy release rate of face/core debonds in the mode II end-notched flexure (ENF) sandwich configuration. The finite-length sandwich specimen is considered to have a “debonded” region and a “joined” region. In the later, the interface between the top face and the substrate (core and bottom face) is modeled by an elastic foundation, which is a uniform distribution of shear and normal springs. Based on the Timoshenko beam theory, the solution for a general asymmetric sandwich construction is derived. The energy release rate expression is derived via the J-integral. Another closed-form expression for the energy release rate is derived from the energy released by a differential spring as the debond propagates. In this closed-form solution, there is no fitting and everything, including the foundation constants, are given in a closed form. Results are produced for a range of face/core stiffness ratios and debond length/core thickness ratios and are compared with the corresponding ones from a finite element solution. A very good agreement is observed except for small debond lengths versus specimen thickness.
Extension of ion-neutral reactive collision model DNT+ to polar molecules based on average dipole orientation theory
Authors: Denpoh Kazuki , Kato Taiki , Matsukuma Masaaki
Published: July 2024

The ion-neutral reactive collision model DNT+, which generates comprehensive ion-neutral collision cross section (CS) data sets for atoms and nonpolar molecules, has been extended to polar molecules. The extension is based on the average dipole orientation (ADO) theory, which adds the dipole moment to Langevin–Hassé CS. Furthermore, the ADO CS for short-range reactive collisions is covered with a rigid core to incorporate long-range elastic and charge-exchange collisions. The modified version of DNT+, i.e., DNT+DM, is applied to gas-phase H2O+–H2O and low-energy CF3+–CO collisions for its validation. The cross sections (CSs) for those collisions using DNT+DM show good agreement with literature data, proving that DNT+DM is valid to some extent. Help with ion swarm analyses and measurements is needed to make the predicted CSs more accurate.
Chronic Adaptions in Quadriceps Fascicle Mechanics Are Related to Altered Knee Biomechanics After Anterior Cruciate Ligament Reconstruction
Authors: White McKenzie S. , Mancini Lucia M. , Stoneback Luke , Palmieri-Smith Riann M. , Lepley Lindsey K.
Published: July 2024

Following anterior cruciate ligament reconstruction (ACLR), patients exhibit abnormal walking mechanics and quadriceps dysfunction. Quadriceps dysfunction has been largely attributed to muscle atrophy and weakness. While important, these factors do not capture intrinsic properties of muscle that govern its ability to generate force and withstand load. While fascicle abnormalities after ACLR have been documented in early stages of recovery (<12 mo), long-term effects of ACLR on fascicle mechanics remain unexplored. We evaluated quadriceps fascicle mechanics during walking 3 years post-ACLR and examined the relationship with knee mechanics. Participants included 24 individuals with ACLR and 24 Controls. Linear mixed models compared the ACLR, Contralateral, and Controls limbs for (1) quadriceps strength, (2) fascicle architecture and mechanics, and (3) knee mechanics. No difference in strength or overall fascicle length excursions was found between limbs. The ACLR limb exhibited longer fascicles at heel strike and peak knee extension moment (P < .001–.004), and smaller fascicle angles at heel strike, peak knee extension moment, and overall suppressed fascicle angle excursions (P < .001–.049) relative to the Contralateral and/or Control limb. This indicates an abnormality in fascicle architecture and mechanics following ACLR and suggests abnormalities in contractile function that cannot be explained by muscle weakness and may contribute to long-term gait irregularities.
Measurement Position Influences Sex Comparisons of Distal Femoral Cartilage Thickness With Ultrasound Imaging
Authors: Battersby Harry S. , Evans Ryan J. , Eghobamien Iwi J. , Pamukoff Derek N.
Published: July 2024

The purpose was to examine (1) the effect of measurement position and sex on femoral cartilage outcomes, and (2) the association between gait biomechanics and cartilage outcomes. Fifty individuals participated (25 males and 25 females; age = 20.62 [1.80] y). Ultrasound measured femoral cartilage thickness and echo-intensity at 90°, 115°, and 140° of knee flexion. Gait outcomes included the external knee adduction and knee flexion moments. Cartilage outcomes were compared using 2 (sex) × 3 (position) repeated-measures analysis of variance. Gait and cartilage associations were assessed using stepwise regression. Medial cartilage was thicker when measured at 90° compared with 115° (P = .02) and 140° (P < .01), and 115° compared with 140°, (P < .01) in males but not in females. Cartilage was thicker at 90° compared with 140° across both sexes within all regions (P < .01). Males had thicker cartilage than females in all positions (P < .01). Echo-intensity was lower at 90° than 115° (P < .01) and 140° (P = .01) in the central and lower at 90° than at 115° (P < .01) and 140° (P = .03) in lateral regions. No association was found between gait and cartilage outcomes. Ultrasound imaging position effects cartilage features more in males compared with females. Imaging position and sex influence cartilage outcomes and should be considered in study designs and clinical evaluation.
Non-thermodynamic factors affect competition between thermophilic chemolithoautotrophs from deep-sea hydrothermal vents
Authors: Kubik Briana C. , Holden James F.
Published: July 2024

Various environmental factors, including H
2
availability, metabolic tradeoffs, optimal growth temperature, stochasticity, and hydrology, were examined to determine if they affect microbial competition between three autotrophic thermophiles. The thiosulfate reducer
Desulfurobacterium thermolithotrophum
(
T
opt
72°C) was grown in mono- and coculture separately with the methanogens
Methanocaldococcus jannaschii
(
T
opt
82°C) at 72°C and
Methanothermococcus thermolithotrophicu
s (
T
opt
65°C) at 65°C at high and low H
2
concentrations. Both methanogens showed a metabolic tradeoff shifting from high growth rate–low cell yield at high H
2
concentrations to low growth rate–high cell yield at low H
2
concentrations and when grown in coculture with the thiosulfate reducer. In 1:1 initial ratios,
D. thermolithotrophum
outcompeted both methanogens at high and low H
2
, no H
2
S was detected on low H
2
, and it grew with only CO
2
as the electron acceptor indicating a similar metabolic tradeoff with low H
2
. When the initial methanogen-to-thiosulfate reducer ratio varied from 1:1 to 10
4
:1 with high H
2
,
D. thermolithotrophum
always outcompeted
M. jannaschii
at 72°C. However,
M. thermolithotrophicus
outcompeted
D. thermolithotrophum
at 65°C when the ratio was 10
3
:1. A reactive transport model that mixed pure hydrothermal fluid with cold seawater showed that hyperthermophilic methanogens dominated in systems where the residence time of the mixed fluid above 72°C was sufficiently high. With shorter residence times, thermophilic thiosulfate reducers dominated. If residence times increased with decreasing fluid temperature along the flow path, then thermophilic methanogens could dominate. Thermophilic methanogen dominance spread to previously thiosulfate-reducer-dominated conditions if the initial ratio of thermophilic methanogen-to-thiosulfate reducer increased.

IMPORTANCE

The deep subsurface is the largest reservoir of microbial biomass on Earth and serves as an analog for life on the early Earth and extraterrestrial environments. Methanogenesis and sulfur reduction are among the more common chemolithoautotrophic metabolisms found in hot anoxic hydrothermal vent environments. Competition between H2-oxidizing sulfur reducers and methanogens is primarily driven by the thermodynamic favorability of redox reactions with the former outcompeting methanogens. This study demonstrated that competition between the hydrothermal vent chemolithoautotrophs
Methanocaldococcus jannaschii
,
Methanothermococcus thermolithotrophicus
, and
Desulfurobacterium thermolithotrophum
is also influenced by other overlapping factors such as staggered optimal growth temperatures, stochasticity, and hydrology. By modeling all aspects of microbial competition coupled with field data, a better understanding is gained on how methanogens can outcompete thiosulfate reducers in hot anoxic environments and how the deep subsurface contributes to biogeochemical cycling.
Citrobacter
spp. and
Enterobacter
spp. as reservoirs of carbapenemase
bla
NDM
and
bla
KPC
resistance genes in hospital wastewater
Authors: Duran-Bedolla Josefina , Téllez-Sosa Juan , Bocanegra-Ibarias Paola , Schilmann Astrid , Bravo-Romero Sugey , Reyna-Flores Fernando , Villa-Reyes Tania , Barrios-Camacho Humberto
Published: July 2024

Antibiotic resistance has emerged as a global threat to public health, generating a growing interest in investigating the presence of antibiotic-resistant bacteria in environments influenced by anthropogenic activities. Wastewater treatment plants in hospital serve as significant reservoirs of antimicrobial-resistant bacteria, where a favorable environment is established, promoting the proliferation and transfer of resistance genes among different bacterial species. In our study, we isolated a total of 243 strains from 5 hospital wastewater sites in Mexico, belonging to 21 distinct Gram-negative bacterial species. The presence of β-lactamase was detected in 46.9% (114/243) of the isolates, which belonging to the
Enterobacteriaceae
family. We identified a total of 169 β-lactamase genes;
bla
TEM
in 33.1%,
bla
CTX-M
in 25.4%,
bla
KPC
in 25.4%,
bla
NDM
8.8%,
bla
SHV
in 5.3%, and
bla
OXA-48
in 1.1% distributed in 12 different bacteria species. Among the 114 of the isolates, 50.8% were found to harbor at least one carbapenemase and were discharged into the environment. The carbapenemase
bla
KPC
was found in six
Citrobacter
spp. and
E. coli
, while
bla
NDM
was detected in two distinct
Enterobacter
spp. and
E. coli
. Notably,
bla
NDM-1
was identified in a 110 Kb IncFII conjugative plasmid in
E. cloacae
,
E. xiangfangensis,
and
E. coli
within the same hospital wastewater. In conclusion, hospital wastewater showed the presence of
Enterobacteriaceae
carrying a high frequency of carbapenemase
bla
KPC
and
bla
NDM
. We propose that hospital wastewater serves as reservoirs for resistance mechanism within bacterial communities and creates an optimal environment for the exchange of this resistance mechanism among different bacterial strains.

IMPORTANCE

The significance of this study lies in its findings regarding the prevalence and diversity of antibiotic-resistant bacteria and genes identified in hospital wastewater in Mexico. The research underscores the urgent need for enhanced surveillance and prevention strategies to tackle the escalating challenge of antibiotic resistance, particularly evident through the elevated frequencies of carbapenemase genes such as
bla
KPC
and
bla
NDM
within the
Enterobacteriaceae
family. Moreover, the identification of these resistance genes on conjugative plasmids highlights the potential for widespread transmission via horizontal gene transfer. Understanding the mechanisms of antibiotic resistance in hospital wastewater is crucial for developing targeted interventions aimed at reducing transmission, thereby safeguarding public health and preserving the efficacy of antimicrobial therapies.
Highly sensitive wastewater surveillance of SARS-CoV-2 variants by targeted next-generation amplicon sequencing provides early warning of incursion in Victoria, Australia
Authors: Merrett James E. , Nolan Monica , Hartman Leon , John Nijoy , Flynn Brianna , Baker Louise , Schang Christelle , McCarthy David , Lister David , Cheng Ngai Ning , Crosbie Nick , Poon Rachael , Jex Aaron
Published: July 2024

The future of the COVID pandemic and its public health and societal impact will be determined by the profile and spread of emerging variants and the timely identification and response to them. Wastewater surveillance of SARS-CoV-2 has been widely adopted in many countries across the globe and has played an important role in tracking infection levels and providing useful epidemiological information that cannot be adequately captured by clinical testing alone. However, novel variants can emerge rapidly, spread globally, and markedly alter the trajectory of the pandemic, as exemplified by the Delta and Omicron variants. Most mutations linked to the emergence of new SARS-CoV-2 variants are found within variable regions of the SARS-CoV-2 Spike protein. We have developed a duplex hemi-nested PCR method that, coupled with short amplicon sequencing, allows simultaneous typing of two of the most highly variable and informative regions of the Spike gene: the N-terminal domain and the receptor binding motif. Using this method in an operationalized public health program, we identified the first known incursion of Omicron BA.1 into Victoria, Australia and demonstrated how sensitive amplicon sequencing methods can be combined with wastewater surveillance as a relatively low-cost solution for early warning of variant incursion and spread.

IMPORTANCE

This study offers a rapid, cost-effective, and sensitive approach for monitoring SARS-CoV-2 variants in wastewater. The method’s flexibility permits timely modifications, enabling the integration of emerging variants and adaptations to evolving SARS-CoV-2 genetics. Of particular significance for low- and middle-income regions with limited surveillance capabilities, this technique can potentially be utilized to study a range of pathogens or viruses that possess diverse genetic sequences, similar to influenza.
AhR ligands from
LGG
metabolites promote piglet intestinal ILC3 activation and IL-22 secretion to inhibit PEDV infection
Authors: Wang Junhong , Zhao Yibo , Cui Tong , Bao Hongyu , Gao Ming , Cheng Mingyang , Sun Yu , Lu Yiyuan , Guan Jiayao , Zhang Di , Jiang Yanlong , Huang Haibin , Shi Chunwei , Wang Jianzhong , Wang Nan , Hu Jingtao , Yang Wentao , Qian Hongxi , Jiang Qingrong , Yang Guilian , Zeng Yan , Wang Chunfeng , Cao Xin
Published: July 2024

In maintaining organismal homeostasis, gut immunity plays a crucial role. The coordination between the microbiota and the immune system through bidirectional interactions regulates the impact of microorganisms on the host. Our research focused on understanding the relationships between substantial changes in jejunal intestinal flora and metabolites and intestinal immunity during porcine epidemic diarrhea virus (PEDV) infection in piglets. We discovered that
Lactobacillus rhamnosus GG
(
LGG
) could effectively prevent PEDV infection in piglets. Further investigation revealed that
LGG
metabolites interact with type 3 innate lymphoid cells (ILC3s) in the jejunum of piglets through the aryl hydrocarbon receptor (AhR). This interaction promotes the activation of ILC3s and the production of interleukin-22 (IL-22). Subsequently, IL-22 facilitates the proliferation of IPEC-J2 cells and activates the STAT3 signaling pathway, thereby preventing PEDV infection. Moreover, the AhR receptor influences various cell types within organoids, including intestinal stem cells (ISCs), Paneth cells, and enterocytes, to promote their growth and development, suggesting that AhR has a broad impact on intestinal health. In conclusion, our study demonstrated the ability of
LGG
to modulate intestinal immunity and effectively prevent PEDV infection in piglets. These findings highlight the potential application of
LGG
as a preventive measure against viral infections in livestock.

IMPORTANCE

We observed high expression of the AhR receptor on pig and human ILC3s, although its expression was negligible in mouse ILC3s. ILC3s are closely related to the gut microbiota, particularly the secretion of IL-22 stimulated by microbial signals, which plays a crucial regulatory role in intestinal immunity. In our study, we found that metabolites produced by beneficial gut bacteria interact with ILC3s through AhR, thereby maintaining intestinal immune homeostasis in pigs. Moreover,
LGG
feeding can enhance the activation of ILC3s and promote IL-22 secretion in the intestines of piglets, ultimately preventing PEDV infection.
Delayed treatment of cynomolgus macaques with a FVM04/CA45 monoclonal antibody cocktail provides complete protection against lethal Sudan virus infection
Authors: Chan Mable , Warner Bryce M. , Audet Jonathan , Barker Douglas , Tailor Nikesh , Vendramelli Robert , Truong Thang , Tierney Kevin , Boese Amrit S. , Qiu Honguy , Holtsberg Frederick W. , Aman Javad , Kodihalli Shantha , Kobasa Darwyn
Published: July 2024

Sudan ebolavirus (SUDV) is a member of the genus
Ebolavirus
(Family
Filoviridae
) and has caused sporadic outbreaks of Ebola disease (EBOD), or more specifically Sudan virus disease (SVD), with high mortality rates in Africa. Current vaccines and therapies that have been developed for filoviruses are almost all specific for Ebola virus (EBOV; of the species
Zaire ebolavirus
), and there is a current lack of therapeutics specific for SUDV. The recent SUDV outbreak in Uganda, which was distributed across multiple districts, including Kampala, a densely populated urban center, highlights the critical need for the development of novel SUDV-specific or pan-Ebola virus therapeutics. Previous work has characterized two monoclonal antibodies, FVM04 and CA45, which have neutralization capabilities against both EBOV and SUDV and have shown protective efficacy in animal challenge studies. Here, we expand upon this work, showing that treatment with a monoclonal antibody cocktail consisting of FVM04 and CA45 provides full protection against lethal SUDV infection in cynomolgus macaques. Studies that evaluate outcomes at late time points after infection, once clinical signs of illness are apparent, are vital for assessing the therapeutic efficacy of antibody therapeutics. We have shown that when treatment is initiated as late as 5 days after infection, with a second dose given on day 8, that treated groups showed few clinical signs or morbidity, with complete survival. This work provides further evidence that FVM04 and CA45 have strong therapeutic potential against SUDV and their development as a pan-Ebola virus therapeutic should be pursued.

IMPORTANCE

There are currently no approved vaccines or therapeutics for Sudan virus, a filovirus which is highly related to Ebola virus and causes similar disease and outbreaks. In this study, a cocktail of two potent monoclonal antibodies that effectively neutralize Sudan virus was tested in a nonhuman primate model of Sudan virus disease. Treatment was highly effective, even when initiated as late as 5 days after infection, when clinical signs of infection were already evident. All treated animals showed complete recovery from infection, with little evidence of disease, while all animals that received a control treatment succumbed to infection within 8 days. The study further demonstrated the strong therapeutic potential of the antibody treatment and supported further development for use in Sudan virus outbreaks.
Comparative genomics and stable isotope analysis reveal the saprotrophic-pathogenic lifestyle of a neotropical fungus
Authors: Ribeiro Tomé Luiz Marcelo , Quintanilha-Peixoto Gabriel , Costa-Rezende Diogo Henrique , Salvador-Montoya Carlos A. , Cardoso Domingos , S. Araújo Daniel , Freitas Jorge Marcelo , Bielefeld Nardoto Gabriela , Alves-Silva Genivaldo , Drechsler-Santos Elisandro Ricardo , Góes-Neto Aristóteles
Published: July 2024

In terrestrial forested ecosystems, fungi may interact with trees in at least three distinct ways: (i) associated with roots as symbionts; (ii) as pathogens in roots, trunks, leaves, flowers, and fruits; or (iii) decomposing dead tree tissues on soil or even on dead tissues in living trees. Distinguishing the latter two nutrition modes is rather difficult in Hymenochaetaceae (Basidiomycota) species. Herein, we have used an integrative approach of comparative genomics, stable isotopes, host tree association, and bioclimatic data to investigate the lifestyle ecology of the scarcely known neotropical genus
Phellinotus
, focusing on the unique species
Phellinotus piptadeniae
. This species is strongly associated with living
Piptadenia gonoacantha
(Fabaceae) trees in the Atlantic Forest domain on a relatively high precipitation gradient. Phylogenomics resolved
P. piptadeniae
in a clade that also includes both plant pathogens and typical wood saprotrophs. Furthermore, both genome-predicted Carbohydrate-Active Enzymes (CAZy) and stable isotopes (δ
13
C and δ
15
N) revealed a rather flexible lifestyle for the species. Altogether, our findings suggest that
P. piptadeniae
has been undergoing a pathotrophic specialization in a particular tree species while maintaining all the metabolic repertoire of a wood saprothroph.

IMPORTANCE

This is the first genomic description for
Phellinotus piptadeniae
. This basidiomycete is found across a broad range of climates and ecosystems in South America, including regions threatened by extensive agriculture. This fungus is also relevant considering its pathotrophic-saprotrophic association with
Piptadenia goanocantha
, which we began to understand with these new results that locate this species among biotrophic and necrotrophic fungi.
Complete genome sequence of
Lactococcus garvieae
isolated from a greater amberjack (
Seriola dumerili
) farmed in Japan in 2022
Authors: Salif Maiga , Ogawa Riku , Mikami Aguri , Daibata Masanori , Imajoh Masayuki
Published: July 2024

The complete genome sequence of
Lactococcus garvieae
KN22525, isolated in May 2022 from a diseased greater amberjack (
Seriola dumerili
) with a gross indication of body surface redness in Nomi Bay, Japan, was determined. Multilocus sequencing typing revealed that KN22525’s genotype was sequence type ST95.
Draft genome sequences for a
Staphylococcus aureus
and a
Staphylococcus haemolyticus
isolate from nasal swab samples from healthy females
Authors: Jablonska Sandra , Brown Hannah , Appleberry Helen , Putonti Catherine , Kula Alex
Published: July 2024

Staphylococcus aureus
and
Staphylococcus haemolyticus
are common members of the human microbiota, but they are also opportunistic pathogens. To identify antibiotic resistance in healthy individuals, we present the genome sequences of
S. aureus
139 N-1 and
S. haemolyticus
173 N-3, both isolated from nasal swab samples from asymptomatic female participants.
Genome sequences of four bacterial strains isolated from organofluorine enrichment cultures
Authors: Goff Jennifer L. , Hahn Chris , Ingrassia Rebecca A. , Tiyapun Chanistha , Waldschmidt Gray G. , Smith Emma R. , Marini Miranda N. , Shevchenko Olga , Maresca Julia A.
Published: July 2024

Because fluorinated organic compounds are broadly used and highly persistent, microbes isolated from wastewater may be able to degrade these contaminants. Here, we report the genome sequences of
Flavobacterium
sp. str. WV_118_3,
Nocardioides
sp. str. WV_118_6,
Ochrobactrum anthropi
str. WV_118_8, and
Sphingomonas
sp. str. VL_57B, isolated from wastewater.
Evolution and strain diversity advance exploration of
Candida albicans
biology
Authors: Anderson Matthew Z. , Dietz Siobhan M.
Published: July 2024

Fungi were some of the earliest organismal systems used to explore mutational processes and its phenotypic consequences on members of a species. Yeasts that cause significant human disease were quickly incorporated into these investigations to define the genetic and phenotypic drivers of virulence. Among
Candida
species,
Candida albicans
has emerged as a model for studying genomic processes of evolution because of its clinical relevance, relatively small genome, and ability to tolerate complex chromosomal changes. Here, we describe major recent findings that used evolution of strains from defined genetic backgrounds to delineate mutational and adaptative processes and include how nascent exploration into naturally occurring variation is contributing to these conceptual frameworks. Ultimately, efforts to discern adaptive mechanisms used by
C. albicans
will continue to divulge new biology and can better inform treatment regimens for the increasing prevalence of fungal disease.
A newly identified IncY plasmid from multi-drug-resistant
Escherichia coli
isolated from dairy cattle feces in Poland
Authors: Zalewska Magdalena , Błażejewska Aleksandra , Gawor Jan , Adamska Dorota , Goryca Krzysztof , Szeląg Michał , Kalinowski Patryk , Popowska Magdalena
Published: July 2024

Comprehensive whole-genome sequencing was performed on two multi-drug-resistant
Escherichia coli
strains isolated from cattle manure from a typical dairy farm in Poland in 2020. The identified strains are resistant to beta-lactams, aminoglycosides, tetracyclines, trimethoprim/sulfamethoxazole, and fluoroquinolones. The complete sequences of the harbored plasmids revealed antibiotic-resistance genes located within many mobile genetic elements (e.g., insertional sequences or transposons) and genes facilitating conjugal transfer or promoting horizontal gene transfer. These plasmids are hitherto undescribed. Similar plasmids have been identified, but not in Poland. The identified plasmids carried resistance genes, including the tetracycline resistance gene
tet(A
), aph family aminoglycoside resistance genes
aph(3
″)
-lb
and
aph (6)-ld
, beta-lactam resistance genes
bla
TEM-1
and

bla
CTX-M-15

, sulfonamide resistance gene
sul2
, fluoroquinolone resistance gene
qnrS1
, and the trimethoprim resistance gene
dfrA14
. The characterized resistance plasmids were categorized into the IncY incompatibility group, indicating a high possibility for dissemination among the
Enterobacteriaceae
. While similar plasmids (99% identity) have been found in environmental and clinical samples, none have been identified in farm animals. These findings are significant within the One Health framework, as they underline the potential for antimicrobial-resistant
E. coli
from livestock and food sources to be transmitted to humans and
vice versa
. It highlights the need for careful monitoring and strategies to limit the spread of antibiotic resistance in the One Health approach.

IMPORTANCE

This study reveals the identification of new strains of antibiotic-resistant
Escherichia coli
in cattle manure from a dairy farm in Poland, offering critical insights into the spread of drug resistance. Through whole-genome sequencing, researchers discovered novel plasmids within these bacteria, which carry genes resistant to multiple antibiotics. These findings are particularly alarming, as these plasmids can transfer between different bacterial species, potentially escalating the spread of antibiotic resistance. This research underscores the vital connection between the health of humans, animals, and the environment, emphasizing the concept of One Health. It points to the critical need for global vigilance and strategies to curb the proliferation of antibiotic resistance. By showcasing the presence of these strains and their advanced resistance mechanisms, the study calls for enhanced surveillance and preventive actions in both agricultural practices and healthcare settings to address the imminent challenge of antibiotic-resistant bacteria.
Algebraic Closures in Divisible Rigid Groups
Authors: Romanovskii N. S.
Published: July 2024

We prove that in a divisible $ m $-rigid group
the algebraic closure of each set
generating a subgroup of solvability length $ m $
coincides with the elementary closure of this set.
Impact of elevated fine particulate matter (PM
2.5
) during landscape fire events on cardiorespiratory hospital admissions in Perth, Western Australia
Authors: Shirangi Adeleh , Lin Ting , Yun Grace , Williamson Grant J , Franklin Peter , Jian Le , Reid Christopher M , Xiao Jianguo
Published: July 2024

Background

Australia has experienced extreme fire weather in recent years. Information on the impact of fine particulate matter (PM

2.5

) from landscape fires (LFs) on cardiorespiratory hospital admissions is limited.

Methods

We conducted a population-based time series study to assess associations between modelled daily elevated PM

2.5

at a 1.5×1.5 km resolution using a modified empirical PM

2.5

exposure model during LFs and hospital admissions for all-cause and cause-specific respiratory and cardiovascular diseases for the study period (2015–2017) in Perth, Western Australia. Multivariate Poisson regressions were used to estimate cumulative risk ratios (RR) with lag effects of 0–3 days, adjusted for sociodemographic factors, weather and time.

Results

All-cause hospital admissions and overall cardiovascular admissions increased significantly across each elevated PM

2.5

concentration on most lag days, with the strongest associations of 3% and 7%, respectively, at the high level of ≥12.60 µg/m
3
on lag 1 day. For asthma hospitalisation, there was an excess relative risk of up to 16% (RR 1.16, 95% CI 1.00 to 1.35) with same-day exposure for all people, up to 93% on a lag of 1 day in children and up to 52% on a lag of 3 days in low sociodemographic groups. We also observed an increase of up to 12% (RR 1.12, 95% CI 1.02 to 1.24) for arrhythmias on the same exposure day and with over 154% extra risks for angina and 12% for heart failure in disadvantaged groups.

Conclusions

Exposure to elevated PM

2.5

concentrations during
LFs
was associated with increased risks of all-cause hospital admissions, total cardiovascular conditions, asthma and arrhythmias.