bluuebunny/crossref_metadata_2025 huggingface dataset:
Early Candida colonisation impact on patients and healthcare professionals in an intensive care unit
Authors: Dalben Yago R. , Pimentel Jhully , Maifrede Simone B. , Carvalho Jamile A. , Bessa‐Neto Francisco O. , Gomes Jean Fabrício S. , Leite Gustavo R. , Rodrigues Anderson M. , Cayô Rodrigo , Grão‐Velloso Tânia Regina , Gonçalves Sarah S.
Published: August 2024

Objectives

Candida spp. is an opportunistic pathogen that causes superficial and invasive infections with nosocomial outbreaks without strict hygiene protocols. Herein, we assessed oral colonisation by Candida spp. in 209 Intensive Care Unit (ICU) patients between July 2021 and April 2022, conducting clinical, epidemiological, and microbiological characterisation of those developing oral or invasive candidiasis.

Methods

Initial oral swabs were collected within 24 h of admission in the ICU, followed by collections on Days 2, 4, 6 and 8. Swabs from denture‐wearing patients, abiotic surfaces, healthcare professionals' hands, and retroauricular regions were also obtained. Recovered yeasts and filamentous fungi were identified using MALDI‐TOF MS and morphological characteristics, respectively. Genetic similarity of Candida spp. isolates was evaluated using Amplified fragment length polymorphism (AFLP), and the antifungal susceptibility profile was determined by broth microdilution.

Results

In the study, 64.11% of patients were orally colonised by Candida spp. Of these, 80.59% were colonised within the first 24 h. Oral colonisation also occurred on subsequent days: 50%/Day 2, 26.92%/Day 4, and 11.53%/Days 6 and 8. Of the patients, 8.61% had oral candidiasis, mainly pseudomembranous. Among orally colonised patients, 2.23% developed invasive candidiasis. Besides, 89.47% of healthcare professionals evaluated were colonised. MALDI‐TOF MS identified different yeast species, and C. albicans (45.34%), C. tropicalis (15.7%), and C. parapsilosis sensu stricto (9.88%) were the most prevalent. AFLP analysis indicated a high genetic correlation (≥97%) between C. parapsilosis sensu stricto isolates from patients and professionals. Three resistant C. albicans isolates were also found.

Conclusion

This study reported a diversity of yeast and filamentous fungi species in ICU patients and highlighted early Candida spp. colonisation risks for invasive candidiasis, as well as the potential horizontal transmission in the nosocomial setting, emphasising the need for effective infection control measures.
Community‐based diet and obesity‐related policy, system, and environmental interventions for obesity prevention during the first 1000 days: A scoping review
Authors: Kracht Chelsea L. , Neshteruk Cody D. , Moding Kameron J. , Rolke Laura J. , Wagner Brooke E. , Kielb Elizabeth , Ferrante Mackenzie J. , Robinson Cayla , Keinsley Jason , Colella Jordan , Speirs Katherine E. , Luecking Courtney T.
Published: August 2024

Community‐based policy, systems, and environmental interventions have the potential to reduce modifiable risk factors for obesity early in life. The purpose of this scoping review was to characterize the breadth, generalizability, and methodological quality of community‐based diet and obesity‐related policy, system, and environmental interventions during the first 1000 days of life, from pregnancy to 24 months of age. Eight databases were searched, and 83 studies (122 references) were included. Data were extracted for breadth (intervention characteristics), generalizability (reach, effectiveness, adoption, implementation, and maintenance), and study quality (Downs and Black Checklist). Systems and environmental approaches were common (> 80%), relative to policy approaches (39%). The majority (60–69%) occurred in the prenatal period and early infancy (0–3 months), assessed breastfeeding or child growth/obesity (53% for both), and included people with lower income (80%) or racial and/or ethnic minority groups (63%). Many interventions reported positive outcomes (i.e., in the expected direction) for child diet, breastfeeding, and feeding practices (> 62%). Few reported intervention maintenance or spanned the full 1000 days. Most studies were classified as good (32%) or fair (56%) methodological quality. The interventions mainly addressed pregnancy and early infancy. Rigorous and representative investigation is needed to improve intervention reach, sustainability, and application in toddlerhood.
Identification and Fine Mapping of a Mutant pv‐nts Gene Responsible for Dwarf and Thin Stem of Snap Bean (Phaseolus vulgaris L.)
Authors: Sun Zhuang , Feng Guojun , Yang Xiaoxu , Liu Dajun , Liang Zicong , Qin Yao , Wang Ziyan , Yan Zhishan , Liu Chang
Published: August 2024

Plant height is one of the most important traits in the breeding of snap bean, which determines the planting density and the resistance to failure, which in turn affects its yield and quality. Therefore, studying the molecular mechanism of plant height in snap bean is an important measure to realize the improvement of snap bean. We obtained a dwarf, thin‐stemmed mutant nts (normal to slim) from a dwarf variety of snap bean A18 via 60CO‐γ‐ray treatment. We conducted phenotypic observations, endogenous hormone content measurements and genetic analyses of the dwarfing thin‐stemmed mutant nts and explored gene localization and candidate gene screening for the mutant trait in snap bean. Compared with wild‐type A18, nts mutant exhibited various abnormal phenotypes such as dwarfing, reduced branching, thinner top stem, reduced plant width, reduced number of leaf area and thousand grain weight and increased content of hormones such as indole‐3‐acetic acid (IAA) in the top stem. Genetic analysis indicated that the mutant trait was controlled by a single recessive nuclear gene, and the mutant gene was named pv‐nts. pv‐nts was localized to a 361.1‐kb segment on chromosome 8 as revealed by bovine serum albumin (BSA) hybrid pool sequencing and simple sequence repeat (SSR) molecular markers. Phvul.008G106300 (encoding LAX2 protein) was identified as a candidate gene corresponding to pv‐nts via gene function annotation. Phvul.008G106300 was significantly upregulated in nts mutant compared with wild‐type A18, which was consistent with the results of endogenous IAA levels. Sequence analysis showed that the Phvul.008G106300 gene in nts had a base mutation that altered the protein structure, thus causing the dwarfed, thin‐stemmed phenotype of cauliflower. Taken together, these results contribute to a better understanding of the genetic basis of dwarfing traits in snap bean.
Segmental congenital vascular anomaly with atrophy, ulceration, and scarring (SeCVAUS): Case series and review of literature
Authors: Ivars Marta , Frieden Ilona J. , Provini Lauren , Wassef Michel , Weibel Lisa , Theiler Martin , Lanoel Agustina , Martinez‐Glez Victor , Rodriguez‐Laguna Lara , van der Vleuten Carine , Guibaud Laurent , Puttgen Katherine , Azaña‐Defez Jose Manuel , Chamlin Sarah , Drolet Beth , Torres Natalia , Wyrzykowsky Dariusz , Colmenero Isabel , Lopez‐Gutierrez Juan Carlos
Published: August 2024

Background

Next‐generation sequencing has greatly increased our understanding of vascular birthmarks. Many port‐wine birthmarks are due to somatic mutations in GNAQ/GNA11 exon 183, but other genomic causes have been identified. Most congenital hemangiomas are due to somatic mutations in GNAQ/GNA11 at exon 209. Although genomically distinct, clinical overlap of congenital hemangiomas and port‐wine birthmarks has occasionally been described.

Objective

We report a case series of a unique segmentally distributed vascular anomaly with overlapping characteristics of port‐wine birthmarks and congenital hemangiomas with other distinctive features including ulceration, atrophy, and scarring.

Methods

This was a multicenter study with retrospective identification of patients via a detailed review of medical records. We also reviewed previously published cases.

Results

The clinical, histological, radiological, and genomic characteristics of 19 new and 13 previously reported cases characterized by segmental distribution, sharply demarcated borders, with variable thickening are presented. All cases had central atrophy with or without episodic ulceration. Those with genomic studies (13 out of 32) had somatic activating missense mutations in GNA11 or GNAQ codon 209.

Conclusions

We describe the features and propose a descriptive name segmental congenital vascular anomaly with atrophy, ulceration, and scarring (SeCVAUS) for this condition.
Negative immune regulation contributes to disease tolerance in Drosophila melanogaster
Authors: Prakash Arun , Monteith Katy M. , Vale Pedro F.
Published: August 2024

Disease tolerance is an infection phenotype where hosts show relatively high health despite harbouring elevated pathogen loads. Variation in the ability to reduce immunopathology may explain why some hosts can tolerate higher pathogen burdens with reduced pathology. Negative immune regulation would therefore appear to be a clear candidate for a mechanism underlying disease tolerance. Here, we examined how the negative regulation of the immune deficiency (IMD) pathway affects disease tolerance in Drosophila melanogaster when infected with four doses of the gram‐negative bacterial pathogen Pseudomonas entomophila. We find that while flies unable to regulate the IMD response exhibited higher expression of antimicrobial peptides and lower bacterial loads as expected, this was not accompanied by a proportional reduction in mortality. Instead, ubiquitous UAS‐RNAi knockdown of negative regulators of IMD (pirk and caudal) substantially increased the per‐pathogen‐mortality in both males and females across all tested infectious doses. Our results therefore highlight that in addition to regulating an efficient pathogen clearance response, negative regulators of IMD also contribute to disease tolerance.
The importance of change communication and state motivation when adapting to changes
Authors: Stasielowicz Lukasz
Published: August 2024

Employees often work in dynamic environments requiring adaptive performance (e.g., emergencies, clients from other cultures). To optimize change management, employee training, and personnel selection in organizations, researchers have focused on trait‐like predictors of adaption to change, such as personality traits or cognitive ability. The study (N = 300) shifts the focus to more proximal performance predictors – change communication and task‐related state motivation. Adaptive performance was modeled using latent growth models. Providing two change‐related hints, one at the beginning of the task and another directly after the change, mitigated performance impairment observed directly after the change. Moreover, this advantage largely persisted throughout the later stages of the task. In contrast, a single hint at the beginning of the task did not substantially facilitate adaption. Finally, task‐related state motivation was linked to better performance on the subsequent measurement occasion. Organizations might minimize change‐induced losses by deploying adequate change communication and maintaining employee motivation.
Characterising large‐type Artin groups
Authors: Martin Alexandre , Vaskou Nicolas
Published: August 2024

We show that the class of large‐type Artin groups is invariant under isomorphism, in stark contrast with the corresponding situation for Coxeter groups. We obtain this result by providing a purely algebraic characterisation of large‐type Artin groups (i.e. independent of the presentation graph). As a corollary, we completely describe the Artin groups isomorphic to a given large‐type Artin group, and characterise those large‐type Artin groups that are rigid.
Plasticity of the heart in response to changes in physical activity
Authors: Hedge Eric T. , Brazile Tiffany L. , Hughson Richard L. , Levine Benjamin D.
Published: August 2024

The human heart is very adaptable, with chamber size, wall thickness and ventricular stiffness all modified by periods of inactivity or exercise training. Herein, we summarize the cardiac adaptations induced by changes in physical activity, ranging from bed rest and spaceflight to endurance exercise training, while also highlighting how the ageing process (a long‐term model of inactivity) affects cardiac plasticity. Severe inactivity during bed rest or spaceflight leads to cardiac atrophy and ventriculo‐vascular stiffening. Conversely, endurance training induces eccentric hypertrophy and enhances ventricular compliance, and can be used as an effective countermeasure to prevent adverse cardiac changes during prolonged periods of bed rest or spaceflight. With sedentary ageing, the heart undergoes concentric remodelling and irreversibly stiffens at advanced age. Specifically, older adults who initiate endurance training later in life are unable to improve ventricular compliance and diastolic function, suggesting reduced cardiac plasticity with advanced age; however, lifelong exercise training prevents age‐associated cardiac remodelling and maintains cardiac compliance of older adults at a level similar to those of younger healthy individuals. Nevertheless, there are still many knowledge gaps related to cardiac remodelling and changes in cardiac function induced by bed rest, exercise training and spaceflight, as well as how these different stimuli may interact with advancing age. Future studies should focus on understanding what factors (sex, age, heritability, etc.) may influence the heart's responsiveness to training or deconditioning, as well as understanding the long‐term cardiac consequences of spaceflight beyond low‐Earth orbit with the added stimulus of galactic cosmic radiation.

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Numerical Analysis on Thermal Behavior of Composite Wall Combined Autoclaved Aerated Concrete With Thermal Insulting Material in Summer Day
Authors: Yu Cairui , Shen Dongmei , Tu Jinsong , Chen Gulei , Chai Luxiu
Published: August 2024

Thermal insulation material (TIM) is commonly employed to enhance the thermal behavior of the lightweight walls. To further obtain the energy-saving effect of the walls, the composite wall (ATIM) combined autoclaved aerated concrete (AAC) block with TIM was present in this study. A testing rig with an ATIM wall was constructed and tested in summer design days, while the numerical modeling was developed and validated using the experimental data. Furthermore, reference walls of the brick and AAC with the same dimension as the ATIM wall were established to evaluate its thermal behavior. The thermal behavior and economic evaluation of the ATIM wall were then investigated by varying the thickness and position of the TIM using the numerical method. And the research results indicated that: (1) the average inner surface temperature of the ATIM wall is approximately 1.1 °C lower than that of the AAC wall, 1.3 °C lower than that of brick wall, the thickness of TIM is positively correlated with decreasing wall surface temperature, while TIM positions have minimal impact on reducing surface temperature; (2) heat gain reduction ratio for ATIM wall (δ = 20 mm) is approximately 52.7%, which is 8.1% higher than that of AAC wall, and variation in TIM position can decrease the heat gain, with inside or outside placement being more effective than positioning it in the middle part; (3) CO2 emission saving (CO2ES) and electricity cost saving (ECS) for room C (ATIM wall) is approximately 7.05 kg/100 m3/day and 5.23 RMB/100 m3/day, respectively, outperforming room A (brick wall) and room B (AAC wall) in terms of energy efficiency and economic benefits.
Convergence Acceleration of Favre-Averaged Non-Linear Harmonic Method
Authors: Wang Feng , Weber Kurt , Radford David , di Mare Luca , Meyer Marcus
Published: August 2024

This paper develops a numerical procedure to accelerate the convergence of the Favre-averaged non-linear harmonic (FNLH) method. The scheme provides a unified mathematical framework for solving the sparse linear systems formed by the mean flow and the time-linearized harmonic flows of FNLH in an explicit or implicit fashion. The approach explores the similarity of the sparse linear systems of FNLH and leads to a memory-efficient procedure, so that its memory consumption does not depend on the number of harmonics to compute. The proposed method has been implemented in the industrial computational fluid dynamics solver Hydra. Three test cases are used to conduct a comparative study of explicit and implicit schemes in terms of convergence, computational efficiency, and memory consumption. Comparisons show that the implicit scheme yields better convergence than the explicit scheme and is also roughly 7–10 times more computationally efficient than the explicit scheme with four levels of multigrid. Furthermore, the implicit scheme consumes only approximately 50% of the memory required by the explicit scheme with four levels of multigrid. Compared with the full-annulus unsteady Reynolds-averaged Navier–Stokes simulations, the implicit scheme produces comparable results to URANS with computational time and memory consumption that are two orders of magnitude smaller.
Accurate Energy Consumption Prediction for Cleaner Fused Deposition Modeling (FDM)
Authors: Ferraro Vincenzo , Sciancalepore Corrado , Lutey Adrian Hugh Alexander
Published: August 2024

Additive Manufacturing (AM) has revolutionized rapid prototyping and mechanical production in a range of different fields, including e-mobility and aerospace, as well as personalized medical devices. In an era dominated by increasing environmental awareness, requirements to reduce CO2 emissions and climate change associated with manufacturing energy consumption are paramount, further to the development of clean energy systems. With the aim of achieving cleaner production, accurate prediction of energy consumption during additive manufacturing processes is the first step in obtaining tangible reductions in manufacturing-related emissions. Energy optimization not only promotes environmental sustainability, but also gives an additional competitive advantage to additive manufacturing processes in today’s market, bringing considerable benefits to these technologies. The present work provides an in-depth study into energy consumption during additive manufacturing, applying a novel and highly accurate methodology for evaluating electrical energy usage during Fused Deposition Modeling (FDM) as a test case for applying this approach to a wider range of additive manufacturing technologies such as Laser Powder Bed Fusion (LPBF), Selective Laser Sintering (SLS), Stereolithography (SLA) and others. FDM is renowned for its popularity in multiple sectors due to its versatility in achieving customized results at low cost with relative ease and safety. To date, the vast majority of scientific literature relating to additive manufacturing has focused on the mechanical properties of printed objects, topology optimization, support structures and energy consumption. Investigations into the energy consumption during additive manufacturing have mainly focused on the measurement and estimation of total energy consumption over the entire printing process based on general considerations and, in some cases, machine learning algorithms. The present study distinguishes itself from previous works by providing precise and detailed analysis of each individual step in the printing process. Experimental evaluation of each machine action was performed, allowing translation of the machine instructions (G-code) employed for printing an object into distinct energy contributions for each action during the process. This approach makes it possible to estimate the total energy consumption very accurately as the sum of all energy contributions, allowing an additional energy optimization parameter to be introduced. Such a detailed analysis allows the main drivers of energy consumption during FDM to be identified, leading to relatively simple solutions to dramatically reduce energy consumption during the process. The presented approach was developed as a test bed for detailed evaluation of energy consumption during additive manufacturing, with potential for application over a wide range of different technologies with similar approaches.
Disassembly Analysis to Promote Rare Earth Permanent Magnet Recovery From End-of-Life Electric Vehicle Motors
Authors: Maani Thomas , Deng Sidi , Sutherland John W.
Published: August 2024

Driven by growing decarbonization initiatives, looming energy security risks, and heightened environmental awareness, there is escalating attention devoted to clean energy technologies such as electric vehicles (EVs), and wind turbines. Data from the U.S. Environmental Protection Agency (EPA) in 2022 revealed that the transportation sector alone contributed a staggering 29% of the total greenhouse gas emissions in the United States. Consequently, EVs have emerged as a promising solution to achieve sustainable transportation. The global adoption of EVs has seen exponential growth, with sales projected to surpass 14 million in 2023. EVs heavily rely on rare earth permanent magnets (REPMs), specifically Neodymium-Iron-Boron (NdFeB) magnets. These magnets are integral components within the traction motors that drive EVs and are reliant on rare earth elements (REEs), notably Neodymium (Nd) and Dysprosium (Dy). Both Nd and Dy are critical elements vulnerable to supply chain risks, particularly in light of the projected surge in EV demand. Furthermore, the growing number of EVs will lead to a corresponding increase in vehicles reaching their end-of-life (EoL). To mitigate the supply chain vulnerabilities associated with REEs and effectively manage the impending waste generated by EoL EV components, circular economy strategies have been proposed. Consequently, efforts are underway to develop technologies and processes aimed at the circularization of EoL EV components like traction motors, through approaches such as reusing, remanufacturing, and recycling. The disassembly of EoL motors containing REPMs is an essential but challenging step in these operations. The difficulty arises from the unknown sizes and volumes of components and significant variations in transmission and motor designs across different vehicle types. The high costs associated with the disassembly process have made it a prominent research concern, particularly in the remanufacturing industry. In this study, we propose integrating disassembly techniques into value recovery plans for traction motors to reduce landfill waste and encourage the reuse and recycling of REPMs. The primary objective of this paper is to quantitatively assess the level of difficulty (using time as a metric) involved in the manual disassembly of EoL transmissions, focusing on the traction motor. The results of this disassembly evaluation will be used to provide recommendations for design and process improvements. Furthermore, the paper will explore the feasibility of automating specific disassembly procedures, drawing from the insights gained from the manual disassembly assessment. Monte Carlo simulations of the system will be employed to analyze disassembly times in various scenarios characterized by uncertainty, and opportunities to streamline the disassembly process will be investigated.
Quantifying High Density Polyethylene Flows in the United States Using Material Flow Analysis
Authors: Chatterjee Abheek , Mathur Nehika , Figola Daniel , Triebe Matthew J. , Hapuwatte Buddhika , Hartwell Ashley , Morris K. C.
Published: August 2024

A Circular Economy (CE) aims to reduce natural resource consumption, waste generation, and related detrimental environmental, social, and economic impacts by retaining valuable materials in the economy as long as possible. This research focuses on the implementation of CE for High-density polyethylene (HDPE) plastics. Recycled HDPE retains desirable properties such as high durability, flexibility, and corrosion resistance leading to a high demand for recycled HDPE by piping and other building and construction industries. Unfortunately, most HDPE comprising products are mismanaged at their end-of-use (EoU) resulting in significant HDPE stocks being incinerated, landfilled, or disposed of in water bodies. This mismanagement of EoU HDPE products contributes to the plastics waste crisis, leads to deleterious environmental and human health impacts, and further reinforces an unsustainable linear economy model. Therefore, improved plastic waste collection mechanisms are needed to keep the different plastic polymer waste streams segregated and to enable the implementation of efficient recovery processes, particularly for recyclable plastics such as HDPE. A challenge in developing end-of-use infrastructure for HDPE recovery is the knowledge gap related to the systematic accounting of HDPE flows.

Material Flow Analysis (MFA) provides the means to track the stocks and flows of a resource within a defined system. This paper investigates HDPE flows in the United States (US) economy and presents two static MFA models for the years 2015 and 2019. The HDPE recycling rates were found to be at 7.4% and 10.1% in the US in 2015 and 2019, respectively. Based on the available data, EoU packaging and container goods are identified as the primary source for recycled HDPE. Our analysis also revealed discrepancies in historical data about HDPE flow across different industry sectors and life-cycle stages. To overcome limitations associated with data unavailability, HDPE flows for the MFA models were computed based on assumptions discussed in the paper. The availability of more granular data, which includes HDPE flows through industry sectors and sub-sectors, would lead to a more thorough MFA. By providing the static MFA models of HDPE flows and stocks in 2015 and 2019 in the US economy, and identifying specific data collection needs, this investigation takes the first step towards a comprehensive characterization of HDPE flows in the US. Quantifying and characterizing HDPE flows is an important component of anticipating the availability of secondary HDPE feedstocks, scaling up recovery infrastructure adequately, and contributing to our overall understanding of the current and future secondary HDPE market dynamics.
Virtual Navigation-Guided Remote Control System for Pulmonary Puncture Localization Assistance
Authors: Wang Zhen , Hu Yingda , Xu Tian , Du Shilun , Lei Yong
Published: August 2024

Minimally invasive puncture surgery is widely used for tissue sampling, ablation, and drug delivery, but its success relies heavily on the surgeon’s experience. To address this, we present a remote surgical robot system utilizing virtual navigation for precise puncture procedures during lung surgeries. First, we developed a master-slave control system based on low CT artifacts and wearable positioning-assisted robot, providing safe and reliable guidance for lung puncture surgery. Second, a virtual navigation system, integrated with the needle-tissue interaction model, was developed to provide surgeons with visual guidance and tissue deformation compensation for assisting in puncture trajectory planning. Third, a registration method was introduced for swift calibration between the virtual and physical worlds. Ex vivo porcine lung puncture experiments were conducted to validate the accuracy and feasibility of the system. The results of 70 porcine lung punctures experiments demonstrated an average system positioning accuracy of 2.3 mm with a deviation of 1.4 mm, meeting clinical requirements. The experimental results demonstrate feasibility of the system in lung puncture surgery.
Nonlinear dynamics of inverse tapered granular chains for mechanical amplification in voice frequency range
Authors: Machado Luis Paulo Silveira , Kowal Cody , Bayma Rafael Suzuki , Sen Surajit
Published: August 2024

Here, the dynamics of inverse tapered granular chains, which are alignments of beads with progressively increasing radii, are investigated. These chains are subjected to harmonic excitation by a moving wall and probed at the tapered end. Intermediate taperings using Ni-Ti (metal) and Teflon (plastic) granules are considered. The proposed chain is based on the frequency responses. The incident signal is set between 1 Hz and 3 kHz. The system transmits or filters incident signals at low or high driving frequencies, respectively. For intermediate frequencies, similar to the human voice and most musical instruments, the driving frequency is amplified, presenting a median gain of 24 dB (an increase in energy by a factor of 250) over long durations. A transition map, showing regions of transmission, amplification, and filtration as a function of driving amplitude and frequency, is provided. This system could serve as a starting point for studies on natural voice amplifiers, which are important for addressing hearing loss and vocal disorders, as well as other applications requiring mechanical signal amplification. The findings suggest that a proper granular arrangement could enable the amplification of low or extremely low driving frequencies.
A series of vectors for inducible gene expression in multidrug-resistant
Acinetobacter baumannii
Authors: Intorcia Valerie , Sava Rosa L. , Schroeder Grace P. , Gebhardt Michael J.
Published: August 2024

The continued emergence of antibiotic resistance among bacterial pathogens remains a significant challenge. Indeed, the enhanced antibiotic resistance profiles of contemporary pathogens often restrict the number of suitable molecular tools that are available. We have constructed a series of plasmids that confer resistance to two infrequently used antibiotics with variants of each plasmid backbone incorporating several regulatory control systems. The regulatory systems include both commonly used systems based on the
lac-
and arabinose-controlled promoters found in
Escherichia coli
, as well as less frequently used systems that respond to tetracycline/anhydrotetracycline and toluic acid. As a test case, we demonstrate the utility of these plasmids for regulated and tunable gene expression in a multidrug-resistant (MDR) isolate of
Acinetobacter baumannii
, strain AB5075-UW. The plasmids include derivatives of a freely replicating, broad-host-range plasmid allowing for inducible gene expression as well as a set of vectors for introducing genetic material at the highly conserved Tn7-attachment site. We also modified a set of CRISPR-interference plasmids for use in MDR organisms, thus allowing researchers to more readily interrogate essential genes in currently circulating clinical isolates. These tools will enhance molecular genetic analyses of bacterial pathogens in situations where existing plasmids cannot be used due to their antibiotic resistance determinants or lack of suitable regulatory control systems.

IMPORTANCE

Clinical isolates of bacterial pathogens often harbor resistance to multiple antibiotics, with
Acinetobacter baumannii
being a prime example. The drug-resistance phenotypes associated with these pathogens represent a significant hurdle to researchers who wish to study modern isolates due to the limited availability of plasmid tools. Here, we present a series of freely replicating and Tn7-insertion vectors that rely on selectable markers to less frequently encountered antibiotics, apramycin, and hygromycin. We demonstrate the utility of these plasmid tools through a variety of experiments looking at a multidrug-resistant strain of
A. baumannii
, strain AB5075. Strain AB5075 is an established model strain for present-day
A. baumannii
, due in part to its genetic tractability and because it is a representative isolate of the globally disseminated multidrug-resistant clade of
A. baumannii
, global clone 1. In addition to the drug-selection markers facilitating use in strains resistant to more commonly used antibiotics, the vectors allow for controllable expression driven by several regulatory systems, including isopropyl β-D-1-thiogalactopyranoside (IPTG), arabinose, anhydrotetracycline, and toluic acid.
A retrospective observational study of mNGS test utilization to examine the role of diagnostic stewardship at two academic medical centers
Authors: Shean Ryan C. , Garrett Elizabeth , Malleis James , Lieberman Joshua A. , Bradley Benjamin T.
Published: August 2024

Given the cost and unclear clinical impact of metagenomic next-generation sequencing (mNGS), laboratory stewardship may improve utilization. This retrospective observational study examines mNGS results from two academic medical centers employing different stewardship approaches. Eighty mNGS orders [54 cerebrospinal fluid (CSF) and 26 plasma] were identified from 2019 to 2021 at the University of Washington (UW), which requires director-level approval for mNGS orders, and the University of Utah (Utah), which does not restrict ordering. The impact of mNGS results and the relationship to traditional microbiology orders were evaluated. Nineteen percent (10/54) of CSF and 65% (17/26) of plasma studies detected at least one organism. Compared to CSF results, plasma results more frequently identified clinically significant organisms (31% vs 7%) and pathogens not detected by traditional methods (12% vs 0%). Antibiotic management was more frequently impacted by plasma versus CSF results (31% vs 4%). These outcome measures were not statistically different between study sites. The number and cumulative cost of traditional microbiology tests at UW were greater than Utah for CSF mNGS testing (UW: 46 tests, $6,237; Utah: 26 tests, $2,812;
P
< 0.05) but similar for plasma mNGS (UW: 31 tests, $3,975; Utah: 21 tests, $2,715;
P
= 0.14). mNGS testing accounted for 30%–50% of the total microbiology costs. Improving the diagnostic performance of mNGS by stewardship remains challenging due to low positivity rates and difficulties assessing clinical impact. From a fiscal perspective, stewardship efforts should focus on reducing testing in low-yield populations given the high costs of mNGS relative to overall microbiology testing expenditures.

IMPORTANCE

Metagenomic next-generation sequencing (mNGS) stewardship practices remain poorly standardized. This study aims to provide actionable insights for institutions that seek to reduce the unnecessary usage of mNGS. Importantly, we highlight that clinical impact remains challenging to measure without standardized guidelines, and we provide an actual cost estimate of microbiology expenditures on individuals undergoing mNGS.
Interpolation of microbiome composition in longitudinal data sets
Authors: Peleg Omri , Borenstein Elhanan
Published: August 2024

The human gut microbiome significantly impacts health, prompting a rise in longitudinal studies that capture microbiome samples at multiple time points. Such studies allow researchers to characterize microbiome changes over time, but importantly, also present major analytical challenges due to incomplete or irregular sampling. To address this challenge, longitudinal microbiome studies often employ various interpolation methods, aiming to infer missing microbiome data. However, to date, a comprehensive assessment of such microbiome interpolation techniques, as well as best practice guidelines for interpolating microbiome data, is still lacking. This work aims to fill this gap, rigorously implementing and systematically evaluating a large array of interpolation methods, spanning several different categories, for longitudinal microbiome interpolation. To assess each method and its ability to accurately infer microbiome composition at missing time points, we used three longitudinal microbiome data sets that follow individuals over a long period of time and a leave-one-out approach. Overall, our analysis demonstrated that the K-nearest neighbors algorithm consistently outperforms other methods in interpolation accuracy, yet, accuracy varied widely across data sets, individuals, and time. Factors such as microbiome stability, sample size, and the time gap between interpolated and adjacent samples significantly influenced accuracy, allowing us to develop a model for predicting the expected interpolation accuracy at a missing time point. Our findings, combined, suggest that accurate interpolation in longitudinal microbiome data is feasible, especially in dense cohorts. Furthermore, using our predictive model, future studies can interpolate data only in time points where the expected interpolation accuracy is high.

IMPORTANCE

Since missing samples are common in longitudinal microbiome dataset due to inconsistent collection practices, it is important to evaluate and benchmark different interpolation methods for predicting microbiome composition in such samples and facilitate downstream analysis. Our study rigorously evaluated several such methods and identified the K-nearest neighbors approach as particularly effective for this task. The study also notes significant variability in interpolation accuracy among individuals, influenced by factors such as age, sample size, and sampling frequency. Furthermore, we developed a predictive model for estimating interpolation accuracy at a specific time point, enhancing the reliability of such analyses in future studies. Combined, our study, thus, provides critical insights and tools that enhance the accuracy and reliability of data interpolation methods in the growing field of longitudinal microbiome research.
Acetylation of SAMHD1 at lysine 580 is crucial for blocking HIV-1 infection
Authors: Bulnes-Ramos Angel , Schott Kerstin , Rabinowitz Jesse , Luchsinger Charlotte , Bertelli Cinzia , Miyagi Eri , Yu Corey H. , Persaud Mirjana , Shepard Caitlin , König Renate , Kim Baek , Ivanov Dmitri N. , Strebel Klaus , Diaz-Griffero Felipe
Published: August 2024

In humans, sterile alpha motif (SAM) domain- and histidine–aspartic acid (HD) domain-containing protein 1 (SAMHD1) is a dNTPase enzyme that prevents HIV-1 infection in non-cycling cells, such as differentiated THP-1 cells and human primary macrophages. Although phosphorylation of threonine 592 (T592) in SAMHD1 is recognized as the primary regulator of the ability to prevent HIV-1 infection, the contributions of SAMHD1 acetylation to this ability remain unknown. Mass spectrometry analysis of SAMHD1 proteins derived from cycling and non-cycling THP-1 cells, primary cycling B cells, and primary macrophages revealed that SAMHD1 is preferentially acetylated at lysine residues 354, 494, and 580 (K354, K494, and K580). In non-cycling cells, SAMHD1 is preferentially acetylated at K580, suggesting that this post-translational modification may contribute to the ability of SAMHD1 to block HIV-1 infection. Consistent with this finding, we found that mutations in K580 disrupted the ability of SAMHD1 to block HIV-1 infection without affecting the ability of SAMHD1 to deplete cellular dNTP levels. Gene editing of SAMHD1 in macrophage-like cells revealed that an intact K580 is required for HIV-1 restriction. This finding suggests that K580 acetylation in SAMHD1 is essential for blocking HIV-1 infection. More importantly, we found that a larger proportion of SAMHD1 featuring K580 acetylation could be detected in human primary macrophages when compared to human primary monocytes. In agreement, we found that SAMHD1 is acetylated during the monocyte-to-macrophage differentiation process. This finding agrees with the idea that the blockade of HIV-1 infection in macrophages requires SAMHD1 acetylation.

IMPORTANCE

The natural inhibitor of HIV-1, sterile alpha motif (SAM) domain- and histidine–aspartic acid (HD) domain-containing protein 1 (SAMHD1), plays a pivotal role in preventing HIV-1 infection of macrophages and dendritic cells, which are vital components of the immune system. This study unveils that SAMHD1 undergoes post-translational modifications, specifically acetylation at lysines 354, 494, and 580. Our research underscores the significance of these modifications, demonstrating that acetylation at residue K580 is indispensable for SAMHD1's efficacy in blocking HIV-1 infection. Notably, K580 is found in a critical regulatory domain of SAMHD1, highlighting acetylation as a novel layer of SAMHD1 regulation for HIV-1 restriction in humans. A comprehensive understanding of the regulation mechanisms governing this anti-HIV-1 protein is crucial for leveraging nature's defense mechanisms against HIV-1 and could pave the way for innovative therapeutic strategies.
Protein disulfide isomerase PDI8 is indispensable for parasite growth and associated with secretory protein processing in
Toxoplasma gondii
Authors: Wang Chaoyue , Sun Pei , Jia Yonggen , Tang Xinming , Liu Xianyong , Suo Xun , Peng Hongjuan
Published: August 2024

Protein disulfide isomerase, containing thioredoxin (Trx) domains, serves as a vital enzyme responsible for oxidative protein folding (the formation, reduction, and isomerization of disulfide bonds in newly synthesized proteins) in the endoplasmic reticulum (ER). However, the role of ER-localized PDI proteins in parasite growth and their interaction with secretory proteins remain poorly understood. In this study, we identified two ER-localized PDI proteins, TgPDI8 and TgPDI6, in
Toxoplasma gondii
. Conditional knockdown of TgPDI8 resulted in a significant reduction in intracellular proliferation and invasion abilities, leading to a complete block in plaque formation on human foreskin fibroblast monolayers, whereas parasites lacking TgPDI6 did not exhibit any apparent fitness defects. The complementation of TgPDI8 with mutant variants highlighted the critical role of the CXXC active site cysteines within its Trx domains for its enzymatic activity. By utilizing TurboID-based proximity labeling, we uncovered a close association between PDI proteins and canonical secretory proteins. Furthermore, parasites lacking TgPDI8 showed a significant reduction in the expression of secretory proteins, especially those from micronemes and dense granules. In summary, our study elucidates the roles of TgPDI8 and sets the stage for future drug discovery studies.

IMPORTANCE

Apicomplexans, a phylum of intracellular parasites, encompass various zoonotic pathogens, including
Plasmodium
,
Cryptosporidium
,
Toxoplasma
, and
Babesia
, causing a significant economic burden on human populations. These parasites exhibit hypersensitivity to disruptions in endoplasmic reticulum (ER) redox homeostasis, necessitating the presence of ER-localized thioredoxin (Trx) superfamily proteins, particularly protein disulfide isomerase (PDI), for proper oxidative folding. However, the functional characteristics of ER-localized PDI proteins in
Toxoplasma gondii
remain largely unexplored. In this study, we identified two ER-localized proteins, namely, TgPDI8 and TgPDI6, and demonstrated the indispensable role of TgPDI8 in parasite survival. Through a comprehensive multi-omics analysis, we elucidated the crucial role of TgPDI8 in the processing of secretory proteins in
T. gondii
. Additionally, we introduced a novel ER-anchored TurboID method to label and identify canonical secretory proteins in
T. gondii
. This research opens up new avenues for understanding oxidative folding and the secretory pathway in apicomplexan parasites, laying the groundwork for future advancements in antiparasitic drug development.
Complete genome of a rare
Salmonella enterica
subsp.
enterica
serovar Hessarek from human stool
Authors: Selway Caitlin A. , May Jacob P. , Goonetilleke Shenoi M. A. , Hocking Helen , Turra Mark , Leong Lex E. X.
Published: August 2024

We present a complete genome of
Salmonella enterica
subsp.
enterica
serovar Hessarek isolated from a human stool from an outbreak linked to egg consumption in South Australia. Orientation of the
rrn
operon and characteristics of the
Salmonella
virulence plasmid indicates that this serovar is virulent toward humans and birds.
Nanopore sequencing of IPNV vp2 gene in Peruvian Andean trout (
Oncorhynchus mykiss
) cultures
Authors: Tapia Stephanie , Orellana Joseph , Duran Yerson , Rodriguez Jose , Angulo Derly , Dominguez-Mendoza Luz , Grabiel Sandra , Silva Jose , Caballero Romina , Zapata Katherine , Gómez Muriel , Tataje-Lavanda Luis , Velazco Rodolfo
Published: August 2024

Nanopore sequencing of the infectious pancreatic necrosis virus (IPNV) vp2 gene from Andean trout cultures in Peru reveals genogroups 1 and 5. This insight aids in understanding strain diversity and pathogenicity, vital for effective disease surveillance, and control measures in aquaculture.
Transcriptomic analyses of a
Salmonella enterica-Escherichia coli
pair following exposure to tetracycline during
in vitro
conjugation experiments
Authors: Algarni Suad , Gudeta Dereje D. , Sopovski Danielle , Han Jing , Feye Kristina M. , Foley Steven L.
Published: August 2024

Antimicrobial exposure can potentially lead to increased antimicrobial resistance plasmid transfer. Sequencing data were collected from the RNA of pairs of
Salmonella enterica
and
Escherichia coli
exposed or not exposed to tetracycline over time to determine differences in transcription-associated tetracycline exposure during
in vitro
conjugation experiments.
Genome sequences of 36
Streptococcus pneumoniae
strains optimized for the multiplexed opsonophagocytosis killing assay
Authors: Graffice Emma , Meewes Chloe , Ganaie Feroze A. , Nahm Moon H. , Calix Juan J.
Published: August 2024

A multiplexed opsonophagocytosis assay (MOPA) was developed as a cost-effective, high-throughput biological assay to evaluate the efficacy of pneumococcal vaccines by
in vitro
measurement of opsonophagocytic activity of anti-capsular antibodies. Here, we report draft genomes of the 36 strains of
Streptococcus pneumoniae
developed for use in the reference pneumococcal MOPA.
Draft genome sequence of
Acinetobacter haemolyticus
strain MUWRP1017 isolated from the pus of a female inpatient at Bwera General Hospital in Uganda
Authors: Wokorach Godfrey , Erima Bernard , Alafi Stephen , Kabatesi Hope O. , Muhindo Julius T. , Najjuka Florence , Kiyengo James , Kibuuka Hannah , Musinguzi Ambrose K. , Wabwire-Mangen Fred , Byarugaba Denis K.
Published: August 2024

The bacterium
Acinetobacter haemolyticus
, with a genome size of 3.4 Mb, was isolated from a pus swab of a wound on the left lower limb above the ankle joint of a female patient. This strain carries the antimicrobial resistance genes cephalosporinase
blaADC-25
, oxallinase
blaOXA-264
,
floR
, and
sul2
and other resistance and virulence genes.