bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reduced-Order Modeling in Rotordynamics and Its Robustness to Random Matrix Perturbation
Authors: Ritto Thiago G. , Lacerda Guilherme N. , Cavallini, Jr Aldemir A. , Timbó Raphael , Pereira Leonardo V. 
Published: March 2024

Abstract
The aim of this paper is to apply and compare four reduced-order modeling strategies to compute the unbalanced vibration response of a rotating machine and evaluate its robustness to random matrix perturbation. The full finite element model of the rotor is built using a rotordynamic open source software (ROSS), and is reduced through different methods, namely: (1) modal reduction, (2) Krylov subspace, (3) Guyan reduction, and (4) system equivalent reduction–expansion process (SEREP). To evaluate the robustness of the obtained results, this paper proposes to perturb the stiffness matrix obtained using the reduced-order models applying the random matrix theory. A simple rotor (three discs) and a more complex gas turbine model (21 discs) are analyzed. Results show that Guyan is not the most appropriate reduction technique for the systems analyzed, but the other three strategies yield good results. In addition, the same random perturbation in the reduced-order stiffness matrices produces a similar level of uncertainty on the stochastic unbalanced responses.
Prediction of Thermionic Energy Conversion Performance and Parametric Effects Using Genetic Algorithms to Fit Physics-Inspired Model Equations to Prototype Test Data
Authors: Juette Elizabeth D. , Carey Van P. , Fleurial Jean-Pierre 
Published: March 2024

Abstract
Thermionic converters have potential as an energy conversion technology for high-temperature space and terrestrial applications using concentrated solar, nuclear reaction, and combustion processes as the heat source. Recent studies have generated experimental performance data for narrow-gap thermionic energy conversion devices. This investigation explores the use of genetic algorithms to fit existing data with physics-inspired model equations. The resulting model equations can be used for performance prediction for system design optimization or to explore parametric effects on performance. The model equations incorporate Richardson’s law for current density, including both the saturated and Boltzmann regimes, with appropriate relations for power delivered to the external load. The transition regime is characterized using two separate models, each accounting for nonuniformity in emission surfaces and irregularities in the manufacturing process. The trained models enable performance prediction of small-gap thermionic energy conversion devices. In this study, data were fitted for two different prototype designs. The prototype test data and postulated values for the work functions and a transition regime parameter are substituted into physics-inspired model equations, yielding performance models with three adjustable constants. Optimized values of these constants are determined using a genetic algorithm to best fit the experimentally determined performance data for prototype thermionic conversion devices tested in earlier studies. This approach is demonstrated to fit the performance data to within 9%. This methodology also allows the user to back-infer the effective work function values, which were found in this study to be consistent with independent measurement.
Two-way pharmacodynamic modeling of drug combinations and its application to pairs of repurposed Ebola and SARS-CoV-2 agents
Authors: Xu Shuang , Esmaeili Shadisadat , Cardozo-Ojeda E. Fabian , Goyal Ashish , White Judith M. , Polyak Stephen J. , Schiffer Joshua T. 
Published: March 2024

ABSTRACT

Existing pharmacodynamic (PD) mathematical models for drug combinations discriminate antagonistic, additive, multiplicative, and synergistic effects, but fail to consider how concentration-dependent drug interaction effects may vary across an entire dose-response matrix. We developed a two-way pharmacodynamic (TWPD) model to capture the PD of two-drug combinations. TWPD captures interactions between upstream and downstream drugs that act on different stages of viral replication, by quantifying upstream drug efficacy and concentration-dependent effects on downstream drug pharmacodynamic parameters. We applied TWPD to previously published
in vitro
drug matrixes for repurposed potential anti-Ebola and anti-SARS-CoV-2 drug pairs. Depending on the drug pairing, the model recapitulated combined efficacies as or more accurately than existing models and can be used to infer efficacy at untested drug concentrations. TWPD fits the data slightly better in one direction for all drug pairs, meaning that we can tentatively infer the upstream drug. Based on its high accuracy, TWPD could be used in concert with PK models to estimate the therapeutic effects of drug pairs
in vivo
.
The prokaryotic and eukaryotic microbiome of Pacific oyster spat is shaped by ocean warming but not acidification
Authors: Zhong Kevin Xu , Chan Amy M. , Collicutt Brenna , Daspe Maxim , Finke Jan F. , Foss Megan , Green Timothy J. , Harley Christopher D. G. , Hesketh Amelia V. , Miller Kristina M. , Otto Sarah P. , Rolheiser Kate , Saunders Rob , Sutherland Ben J. G. , Suttle Curtis A. 
Published: March 2024

ABSTRACT

Pacific oysters (
Magallana gigas,
a.k.a.
Crassostrea gigas
), the most widely farmed oysters, are under threat from climate change and emerging pathogens. In part, their resilience may be affected by their microbiome, which, in turn, may be influenced by ocean warming and acidification. To understand these impacts, we exposed early-development Pacific oyster spat to different temperatures (18°C and 24°C) and
p
CO
2
levels (800, 1,600, and 2,800 µatm) in a fully crossed design for 3 weeks. Under all conditions, the microbiome changed over time, with a large decrease in the relative abundance of potentially pathogenic ciliates (
Uronema marinum
) in all treatments with time. The microbiome composition differed significantly with temperature, but not acidification, indicating that Pacific oyster spat microbiomes can be altered by ocean warming but is resilient to ocean acidification in our experiments. Microbial taxa differed in relative abundance with temperature, implying different adaptive strategies and ecological specializations among microorganisms. Additionally, a small proportion (~0.2% of the total taxa) of the relatively abundant microbial taxa were core constituents (>50% occurrence among samples) across different temperatures,
p
CO
2
levels, or time. Some taxa, including A4b bacteria and members of the family
Saprospiraceae
in the phyla
Chloroflexi
(syn.
Chloroflexota
) and
Bacteroidetes
(syn.
Bacteroidota
), respectively, as well as protists in the genera
Labyrinthula
and
Aplanochytrium
in the class
Labyrinthulomycetes
, and
Pseudoperkinsus tapetis
in the class
Ichthyosporea
were core constituents across temperatures,
p
CO
2
levels, and time, suggesting that they play an important, albeit unknown, role in maintaining the structural and functional stability of the Pacific oyster spat microbiome in response to ocean warming and acidification. These findings highlight the flexibility of the spat microbiome to environmental changes.

IMPORTANCE

Pacific oysters are the most economically important and widely farmed species of oyster, and their production depends on healthy oyster spat. In turn, spat health and productivity are affected by the associated microbiota; yet, studies have not scrutinized the effects of temperature and
p
CO
2
on the prokaryotic and eukaryotic microbiomes of spat. Here, we show that both the prokaryotic and, for the first time, eukaryotic microbiome of Pacific oyster spat are surprisingly resilient to changes in acidification, but sensitive to ocean warming. The findings have potential implications for oyster survival amid climate change and underscore the need to understand temperature and
p
CO
2
effects on the microbiome and the cascading effects on oyster health and productivity.
Assessment of the performance of the plasma separation card for HIV-1 viral load monitoring in South Africa
Authors: Chimoyi Lucy , Hans Lucia , Oladimeji Matthew , Kindra Gurpreet , Diallo Karidia , Ayalew Kassahun , Setswe Geoffrey K. , Carmona Sergio 
Published: March 2024

ABSTRACT

Scaling up of newer innovations that address the limitations of the dried blood spot and the logistics of plasma monitoring is needed. We employed a multi-site, cross-sectional assessment of the plasma separation card (PSC) on blood specimens collected from all consenting adults, assenting young and pediatric patients living with HIV from 10 primary healthcare clinics in South Africa. Venous blood for EDTA-plasma samples was collected and analyzed according to the standard of care assay, while collected capillary blood for the PSC samples was analyzed using the Roche COBAS AmpliPrep/Cobas TaqMan (CAP/CTM) HIV-1 Test at the National Reference laboratories. McNemar tests assessed the differences in concordance between the centrifuged plasma and dried plasma spots. The usability of PSC by blood spotting, PSC preparation, and pre-analytical work was assessed by collecting seven-point Likert-scale data from healthcare and laboratory workers. We enrolled 538 patients, mostly adults [
n
= 515, 95.7% (95% CI: 93.7%–97.1%)] and females [
n
= 322, 64.2% (95% CI: 60.0%–68.1%)]. Overall, 536 paired samples were collected using both PSC- and EDTA-plasma diagnostics, and 502 paired PSC- and EDTA-plasma samples assessed. Concordance between the paired samples was obtained for 446 samples. Analysis of these 446 paired samples at 1,000 copies per milliliter threshold yielded an overall sensitivity of 87.5% [95% CI: 73.2%–95.8%] and specificity of 99.3% [95% CI: 97.9%–99.8%]. Laboratory staff reported technical difficulties in most tasks. The usability of the PSC by healthcare workers was favorable. For policymakers to consider PSC scale-up for viral load monitoring, technical challenges around using PSC at the clinic and laboratory level need to be addressed.

IMPORTANCE
Findings from this manuscript emphasize the reliability of the plasma separation card (PSC), a novel diagnostic method that can be implemented in healthcare facilities in resource-constrained settings. The agreement of the PSC with the standard of care EDTA plasma for viral load monitoring is high. Since the findings showed that these tests were highly specific, we recommend a scale-up of PSC in South Africa for diagnosis of treatment failure.
Complex
N
-glycans are important for interspecies transmission of H7 influenza A viruses
Authors: Spruit Cindy M. , Palme Diana I. , Li Tiehai , Ríos Carrasco María , Gabarroca García Alba , Sweet Igor R. , Kuryshko Maryna , Maliepaard Joshua C. L. , Reiding Karli R. , Scheibner David , Boons Geert-Jan , Abdelwhab Elsayed M. , de Vries Robert P. 
Published: March 2024

ABSTRACT

Influenza A viruses (IAVs) can overcome species barriers by adaptation of the receptor-binding site of the hemagglutinin (HA). To initiate infection, HAs bind to glycan receptors with terminal sialic acids, which are either
N
-acetylneuraminic acid (NeuAc) or
N
-glycolylneuraminic acid (NeuGc); the latter is mainly found in horses and pigs but not in birds and humans. We investigated the influence of previously identified equine NeuGc-adapting mutations (S128T, I130V, A135E, T189A, and K193R) in avian H7 IAVs
in vitro
and
in vivo
. We observed that these mutations negatively affected viral replication in chicken cells but not in duck cells and positively affected replication in horse cells.
In vivo
, the mutations reduced virus virulence and mortality in chickens. Ducks excreted high viral loads longer than chickens, although they appeared clinically healthy. To elucidate why these viruses infected chickens and ducks despite the absence of NeuGc, we re-evaluated the receptor binding of H7 HAs using glycan microarray and flow cytometry studies. This re-evaluation demonstrated that mutated avian H7 HAs also bound to α2,3-linked NeuAc and sialyl-LewisX, which have an additional fucose moiety in their terminal epitope, explaining why infection of ducks and chickens was possible. Interestingly, the α2,3-linked NeuAc and sialyl-LewisX epitopes were only bound when presented on tri-antennary
N
-glycans, emphasizing the importance of investigating the fine receptor specificities of IAVs. In conclusion, the binding of NeuGc-adapted H7 IAV to tri-antennary
N
-glycans enables viral replication and shedding by chickens and ducks, potentially facilitating interspecies transmission of equine-adapted H7 IAVs.

IMPORTANCE

Influenza A viruses (IAVs) cause millions of deaths and illnesses in birds and mammals each year. The viral surface protein hemagglutinin initiates infection by binding to host cell terminal sialic acids. Hemagglutinin adaptations affect the binding affinity to these sialic acids and the potential host species targeted. While avian and human IAVs tend to bind to
N
-acetylneuraminic acid (sialic acid), equine H7 viruses prefer binding to
N
-glycolylneuraminic acid (NeuGc). To better understand the function of NeuGc-specific adaptations in hemagglutinin and to elucidate interspecies transmission potential NeuGc-adapted viruses, we evaluated the effects of NeuGc-specific mutations in avian H7 viruses in chickens and ducks, important economic hosts and reservoir birds, respectively. We also examined the impact on viral replication and found a binding affinity to tri-antennary
N
-glycans containing different terminal epitopes. These findings are significant as they contribute to the understanding of the role of receptor binding in avian influenza infection.
Wall teichoic acid substitution with glucose governs phage susceptibility of
Staphylococcus epidermidis
Authors: Beck Christian , Krusche Janes , Notaro Anna , Walter Axel , Kränkel Lara , Vollert Anneli , Stemmler Regine , Wittmann Johannes , Schaller Martin , Slavetinsky Christoph , Mayer Christoph , De Castro Cristina , Peschel Andreas 
Published: March 2024

ABSTRACT

The species- and clone-specific susceptibility of
Staphylococcus
cells for bacteriophages is governed by the structures and glycosylation patterns of wall teichoic acid (WTA) glycopolymers. The glycosylation-dependent phage-WTA interactions in the opportunistic pathogen
Staphylococcus epidermidis
and in other coagulase-negative staphylococci (CoNS) have remained unknown. We report a new
S. epidermidis
WTA glycosyltransferase TagE whose deletion confers resistance to siphoviruses such as ΦE72 but enables binding of otherwise unbound podoviruses.
S. epidermidis
glycerolphosphate WTA was found to be modified with glucose in a
tagE
-dependent manner. TagE is encoded together with the enzymes PgcA and GtaB providing uridine diphosphate-activated glucose. ΦE72 transduced several other CoNS species encoding TagE homologs, suggesting that WTA glycosylation via TagE is a frequent trait among CoNS that permits interspecies horizontal gene transfer. Our study unravels a crucial mechanism of phage-
Staphylococcus
interaction and horizontal gene transfer, and it will help in the design of anti-staphylococcal phage therapies.

IMPORTANCE

Phages are highly specific for certain bacterial hosts, and some can transduce DNA even across species boundaries. How phages recognize cognate host cells remains incompletely understood. Phages infecting members of the genus
Staphylococcus
bind to wall teichoic acid (WTA) glycopolymers with highly variable structures and glycosylation patterns. How WTA is glycosylated in the opportunistic pathogen
Staphylococcus epidermidis
and in other coagulase-negative staphylococci (CoNS) species has remained unknown. We describe that
S. epidermidis
glycosylates its WTA backbone with glucose, and we identify a cluster of three genes responsible for glucose activation and transfer to WTA. Their inactivation strongly alters phage susceptibility patterns, yielding resistance to siphoviruses but susceptibility to podoviruses. Many different CoNS species with related glycosylation genes can exchange DNA via siphovirus ΦE72, suggesting that glucose-modified WTA is crucial for interspecies horizontal gene transfer. Our finding will help to develop antibacterial phage therapies and unravel routes of genetic exchange.
Emergence of multidrug-resistant
Pandoraea sputorum
in Japan
Authors: Koizumi Juri , Nasu Yutaka , Hirai Yuji , Nakaminami Hidemasa 
Published: March 2024

ABSTRACT

Pandoraea
is a pathogenic bacterium naturally resistant to various antimicrobials, including colistin. Here, we report the whole-genome sequence of
Pandoraea sputorum
, which exhibits high-level multidrug resistance, isolated from a hospitalized patient in Japan.
Bioactive exometabolites drive maintenance competition in simple bacterial communities
Authors: Chodkowski John L. , Shade Ashley 
Published: March 2024

ABSTRACT

During prolonged resource limitation, bacterial cells can persist in metabolically active states of non-growth. These maintenance periods, such as those experienced in stationary phase, can include upregulation of secondary metabolism and release of exometabolites into the local environment. As resource limitation is common in many environmental microbial habitats, we hypothesized that neighboring bacterial populations employ exometabolites to compete or cooperate during maintenance and that these exometabolite-facilitated interactions can drive community outcomes. Here, we evaluated the consequences of exometabolite interactions over the stationary phase among three environmental strains:
Burkholderia thailandensis
E264,
Chromobacterium subtsugae ATCC 31532
, and
Pseudomonas syringae
pv.
tomato
DC3000. We assembled them into synthetic communities that only permitted chemical interactions. We compared the responses (transcripts) and outputs (exometabolites) of each member with and without neighbors. We found that transcriptional dynamics were changed with different neighbors and that some of these changes were coordinated between members. The dominant competitor
B. thailandensis
consistently upregulated biosynthetic gene clusters to produce bioactive exometabolites for both exploitative and interference competition. These results demonstrate that competition strategies during maintenance can contribute to community-level outcomes. It also suggests that the traditional concept of defining competitiveness by growth outcomes may be narrow and that maintenance competition could be an additional or alternative measure.

IMPORTANCE
Free-living microbial populations often persist and engage in environments that offer few or inconsistently available resources. Thus, it is important to investigate microbial interactions in this common and ecologically relevant condition of non-growth. This work investigates the consequences of resource limitation for community metabolic output and for population interactions in simple synthetic bacterial communities. Despite non-growth, we observed active, exometabolite-mediated competition among the bacterial populations. Many of these interactions and produced exometabolites were dependent on the community composition but we also observed that one dominant competitor consistently produced interfering exometabolites regardless. These results are important for predicting and understanding microbial interactions in resource-limited environments.
Decoding the chemical language of
Suillus
fungi: genome mining and untargeted metabolomics uncover terpene chemical diversity
Authors: Mudbhari Sameer , Lofgren Lotus , Appidi Manasa R. , Vilgalys Rytas , Hettich Robert L. , Abraham Paul E. 
Published: March 2024

ABSTRACT

Ectomycorrhizal fungi establish mutually beneficial relationships with trees, trading nutrients for carbon.
Suillus
are ectomycorrhizal fungi that are critical to the health of boreal and temperate forest ecosystems. Comparative genomics has identified a high number of non-ribosomal peptide synthetase and terpene biosynthetic gene clusters (BGC) potentially involved in fungal competition and communication. However, the functionality of these BGCs is not known. This study employed co-culture techniques to activate BGC expression and then used metabolomics to investigate the diversity of metabolic products produced by three
Suillus
species (
Suillus hirtellus
EM16,
Suillus decipiens
EM49, and
Suillus cothurnatus
VC1858), core members of the pine microbiome. After 28 days of growth on solid media, liquid chromatography–tandem mass spectrometry identified a diverse range of extracellular metabolites (exometabolites) along the interaction zone between
Suillus
co-cultures. Prenol lipids were among the most abundant chemical classes. Out of the 62 unique terpene BGCs predicted by genome mining, 41 putative prenol lipids (includes 37 putative terpenes) were identified across the three
Suillus
species using metabolomics. Notably, some terpenes were significantly more abundant in co-culture conditions. For example, we identified a metabolite matching to isomers isopimaric acid, sandaracopimaric acid, and abietic acid, which can be found in pine resin and play important roles in host defense mechanisms and
Suillus
spore germination. This research highlights the importance of combining genomics and metabolomics to advance our understanding of the chemical diversity underpinning fungal signaling and communication.

IMPORTANCE

Using a combination of genomics and metabolomics, this study’s findings offer new insights into the chemical diversity of
Suillus
fungi, which serve a critical role in forest ecosystems.
Loeys-Dietz syndrome and Goldenhar syndrome unveiled together
Authors: Verma Henuka , Verma Prashant Kumar , Rajvanshi Nikhil , Bhat Nowneet Kumar 
Published: March 2024

Haemifacial microsomia is an asymmetrical congenital tissue malformation developed from the first and second branchial arches with or without multi-system involvement. Alternatively recognised as Goldenhar syndrome or oculoauriculovertebral spectrum (OAVS), it is an aetiologically heterogeneous group of disorders showing dominant trends in inheritable form.We present a case of a boy in early childhood with concomitant craniofacial features of craniofacial microsomia with Loeys-Dietz syndrome. He had a unilateral hypoplastic face, asymmetrical ear malformations and multiple preauricular tags with epibulbar dermoid (features suggestive of Goldenhar syndrome). On detailed clinical evaluation, he met Beighton’s criteria and was diagnosed with arterial tortuosity. Further molecular testing confirmed the diagnosis of Loeys-Dietz syndrome type II.Loeys-Dietz syndrome is characterised by aortic root enlargement or type A dissection with or without other vascular malformations and facial midline defects. Molecular testing is required to establish the diagnosis because of overlapping features with other connective tissue disorders.