bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical trial protocol for continuous glucose monitoring in critical care at Hospital Clinic of Barcelona (CGM‐UCI23)
Authors: Pañero‐Moreno Marc , Guix‐Comellas Eva Maria , Villamor‐Ordozgoiti Alberto
Published: October 2024

Background

Hyperglycaemia is common in intensive care units (ICUs), with a prevalence of up to 86.2%, increasing mortality. Technology has evolved towards continuous glucose monitoring (CGM), and its use in ICUs began especially during the coronavirus pandemic (COVID‐19). Various studies have evaluated the reliability of CGM, indicating that it is safe for use in critically ill patients.

Aims

The aim of this study was to compare the use of CGM with point‐of‐care glucose (POC‐G) testing in ICU. Specific objectives include evaluating the glycaemic control, the frequency of POC‐G measurements, the incidence of hyperglycaemia, hypoglycaemia and morbidity and mortality at 90 days.

Study Design

An experimental, controlled and randomized clinical trial with a single‐blind design will be conducted at Hospital Clinic of Barcelona (HCB). A sample size of 376 participants will be recruited and randomly assigned to two groups: an experimental group, where glycaemic management will be based on CGM; and a control group, where glucose will be managed through POC‐G testing, with a blinded CGM.

Results

The primary variable considered will be time in range (TIR), with secondary outcomes including, time above range (TAR), time below range (TBR), number of POC‐G measurements, incidence of hyperglycaemia and hypoglycaemia, and mortality. Hypothesis testing will use the Kolmogorov–Smirnov test to assess data normality, with appropriate statistical tests applied, considering a p‐value <.05.

Relevance to Clinical Practice

The results obtained will help us understand the impact of CGM on critically ill patients. CGM could potentially reduce the workload of nurses and improve the efficiency of decision‐making by the ICU team, enabling early identification and treatment of glucose complications, thereby enhancing safety. Patient safety, a reduction in patient fingerstick and a decreased care burden are the criteria that add value to this research.
Factors Associated With Health‐Promoting Behaviors Among South Korean Adults: A Cross‐Sectional Study
Authors: Kim Yoonjung , Chae Heemin , Kwak Yeun Hee , Kim Ji‐su
Published: October 2024

Objective

To examine the association between positive psychological capital, social support, illness attitudes toward COVID‐19, and health‐promoting behaviors in Korean adults.

Design

An online cross‐sectional study.

Sample

The participants were 820 South Korean adults aged 19–64, recruited through quota sampling. The sample was census‐matched in terms of age and gender based on the Korean Population Census.

Measurements

The participants completed measures assessing psychological capital, social support, illness attitude toward COVID‐19, and health‐promoting behaviors. The t‐test, one‐way analysis of variance, Pearson's correlation, and multiple stepwise regression analysis were used to analyze the data.

Results

Participants who were religious, perceived themselves as physically healthy, had negative illness attitudes, had high positive psychological capital, and received high social support were more likely to engage in health‐promoting behaviors. These variables explained 44.5% of the participants’ health‐promoting behaviors.

Conclusions

This study is the first to examine illness attitudes toward COVID‐19 and health‐promoting behaviors among South Korean adults during the COVID‐19 pandemic. The results can pave the way for effective public health intervention strategies that consider religiosity, physical health status, illness attitude, and social support, to promote healthy living during future public health crises.
The phobic brain: Morphometric features correctly classify individuals with small animal phobia
Authors: Scarano Alessandro , Fumero Ascensión , Baggio Teresa , Rivero Francisco , Marrero Rosario J. , Olivares Teresa , Peñate Wenceslao , Álvarez‐Pérez Yolanda , Bethencourt Juan Manuel , Grecucci Alessandro
Published: October 2024

Specific phobia represents an anxiety disorder category characterized by intense fear generated by specific stimuli. Among specific phobias, small animal phobia (SAP) denotes a particular condition that has been poorly investigated in the neuroscientific literature. Moreover, the few previous studies on this topic have mostly employed univariate analyses, with limited and unbalanced samples, leading to inconsistent results. To overcome these limitations, and to characterize the neural underpinnings of SAP, this study aims to develop a classification model of individuals with SAP based on gray matter features, by using a machine learning method known as the binary support vector machine. Moreover, the contribution of specific structural macro‐networks, such as the default mode, the salience, the executive, and the affective networks, in separating phobic subjects from controls was assessed. Thirty‐two subjects with SAP and 90 matched healthy controls were tested to this aim. At a whole‐brain level, we found a significant predictive model including brain structures related to emotional regulation, cognitive control, and sensory integration, such as the cerebellum, the temporal pole, the frontal cortex, temporal lobes, the amygdala and the thalamus. Instead, when considering macro‐networks analysis, we found the Default, the Affective, and partially the Central Executive and the Sensorimotor networks, to significantly outperform the other networks in classifying SAP individuals. In conclusion, this study expands knowledge about the neural basis of SAP, proposing new research directions and potential diagnostic strategies.
Diagnosis and management of hypersensitivity pneumonitis in adults: A position statement from the Thoracic Society of Australia and New Zealand
Authors: Barnes Hayley , Corte Tamera J. , Keir Gregory , Khor Yet H. , Limaye Sandhya , Wrobel Jeremy P. , Veitch Elizabeth , Harrington John , Dowman Leona , Beckert Lutz , Milne David , De Losa Rebekah , Cooper Wendy A. , Bell Peter T. , Balakrishnan Pradeep , Troy Lauren K.
Published: October 2024

Hypersensitivity pneumonitis (HP) is an immune‐mediated interstitial lung disease (ILD) relating to specific occupational, environmental or medication exposures. Disease behaviour is influenced by the nature of exposure and the host response, with varying degrees of lung inflammation and fibrosis seen within individuals. The differentiation of HP from other ILDs is important due to distinct causes, pathophysiology, prognosis and management implications. This Thoracic Society of Australia and New Zealand (TSANZ) position statement aims to provide an up‐to‐date summary of the evidence for clinicians relating to the diagnosis and management of HP in adults, in the Australian and New Zealand context. This document highlights recent relevant findings and gaps in the literature for which further research is required.

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The economics of gender norms
Authors: Lundberg Shelly
Published: October 2024

An important dimension of social norms in any society are rules that describe and regulate the expected behavior, appearance, and demeanor of men and women. In this paper, I offer a short survey of how gender norms have been introduced and used in economics, what we know about how they are formed and transmitted and how they persist or change, and then consider how we might incorporate norms into economists’ perennial concerns about policy.
Establishment and Application of a Multiplex PCR NGS Method for the Genotyping of HLA‐Class I and HPA
Authors: He Yanmin , Wang Fang , Wu Zhipan , Zhang Wei , Zhu Faming
Published: October 2024

Selecting compatible HLA‐Class I and/or HPA platelets based on genotyping could alleviate immune platelet transfusion refractoriness (PTR). A fast and reliable method of HLA‐Class I and HPA genotyping is necessary to construct a platelet donor bank with known HLA‐Class I and HPA genotypes. Ten pairs of specific primers for HLA‐A, HLA‐B, HLA‐C, HPA‐1 through HPA‐6w, HPA‐15 and HPA‐21w were designed. The appropriate fragments were optimised for amplification in a single multiplex reaction. After a cleanup step using paramagnetic beads, the amplicon library was prepared and sequenced. To validate the accuracy of the developed method, commercial NGS kits for the genotyping of HLA‐A, HLA‐B and HLA‐C and the TaqMan real‐time PCR method in‐house for the genotyping of HPA‐1 through HPA‐6w, HPA‐15 and HPA‐21w were used to detect all the specimens in parallel. A total of 386 specimens were detected and the results of genotyping HLA‐A, HLA‐B, HLA‐C and HPA‐1 through HPA‐6w, HPA‐15 and HPA‐21w were obtained simultaneously, which is 100% consistent between the two methods. Four new HLA alleles, HLA‐A*11:451, HLA‐A*30:01:26, HLA‐B*39:201 and HLA‐B*40:538, were also reconfirmed. Two novel SNVs, c.2671C > T and c.2681T > G, in the coding region of ITGA2B were detected, all of which are heterozygous in individuals. A novel NGS method based on multiplex PCR was established to detect HLA‐Class I and HPA simultaneously, which is high‐throughput, rapid and accurate and could be applied to build a platelet donor bank.
The Novel HLA‐B*15:693 Allele Identified by Next‐Generation Sequencing
Authors: Davies Olivia S. E. , Konzett Nicola , Prantl Livia , Siller Anita , Vales Anja
Published: October 2024

The novel allele HLA‐B*15:693 has 5 nucleotide differences compared with HLA‐B*15:18:07.
Characterisation of the Novel HLA‐A*02:406 Allele by Sequencing‐Based Typing in a Chinese Individual
Authors: Li Jian‐Ping , Wei Ying‐Dong , Li Xiao‐Feng
Published: October 2024

HLA‐A*02:406 differs from HLA‐A*02:01:01:01 by one nucleotide substitution in codon 116 in exon 3.
Chained Spatial Beam Adomian Decomposition Model: A Novel Model of Flexible Slender Beams for Large Spatial Deflections
Authors: Chen Yuhan , Chen Guimin
Published: October 2024

The main element of compliant mechanisms and continuum robots is flexible slender beams. However, the modeling of beams can be complicated due to the geometric nonlinearity becoming significant at large elastic deflections. This paper presents an explicit nonlinear model called the spatial beam Adomian decomposition model (SBADM) for intermediate spatial deflections of a slender beam with uniform, bisymmetric sections subjected to general end-loading. Specifically, the elongation, bending, torsion, and shear deformations of the beams are modeled based on Timoshenko’s assumptions and Cosserat rod theory. Then, the quaternion transformation and Adomian decomposition are used to solve the nonlinear governing differential equations for the beam by truncating the higher-order terms, yielding an explicit expression for spatially deflected beams within intermediate deflection ranges. Simulations demonstrate the accuracy and time-wise efficiency of the SBADM, as well as its advantages over the state-of-the-art. In addition, this paper also introduces a discretization-based scheme called the chained SBADM (CSBADM) for large spatial deflections of flexible beams. Real-world experiments with two different configurations have also been performed to validate the effectiveness of the CSBADM. The results indicate that the CSBADM can accurately calculate the load–displacement relations for large deformed beams.
Design and Kinematic Analysis of a Novel Series-Parallel Hybrid Finger for Robotic Hands
Authors: Zaw Thiha , Mahalingam Dasharadhan , Baiata Nicholas , Patankar Aditya , Chakraborty Nilanjan
Published: October 2024

In this paper, we present a novel three-degree-of-freedom (3-DoF) series-parallel hybrid mechanism for a robotic finger that is capable of abduction/adduction and flexion/extension. The series-parallel fingers proposed in the literature have either less than 3-DoF or the fingertip motion which cannot be controlled, since they are difficult to analyze kinematically. We present the complete position kinematics and differential kinematics of our proposed finger mechanism and show through simulation examples that the fingertip can be kinematically controlled to follow a given path. Both position control and velocity control capabilities are demonstrated.
Optimization of Tip Seal Grooves for Aerodynamic and Durability Improvements of Small-Core Turbines
Authors: Wiese Connor J. , Berdanier Reid A. , Thole Karen A.
Published: October 2024

While the clearance gap between the turbine rotor tip and the outer case in a gas turbine engine is necessary for the operation of the machine, the gap is kept as small as possible due to the detrimental effect of the flow over the turbine tip. With the increased investments in ultra-high-bypass ratio gas turbines, blade tip clearances are increasing in relative size to the turbine rotor, as engines move toward smaller core sizes. In this work, a constrained topology optimization of a rotor tip seal with discrete axisymmetric grooves was explored computationally using Reynolds-averaged Navier–Stokes simulations. The differential-evolution-based optimization was applied at two tip clearances representing a nominal and small-core scaled geometry. Furthermore, optimizations were performed at each tip clearance for blade designs with flat and squealer tips. The multi-objective optimization was designed to simultaneously maximize rotor efficiency and minimize rotor tip heat load. Several tip seal designs were identified for each tip geometry and tip gap that both increased aerodynamic efficiency and reduced the total heat load into the rotor tip. However, some optimal tip seal designs were composed of grooves that were demonstrated to be detrimental in prior work. Furthermore, grooves were more effective at increasing aerodynamic efficiency when applied to flat tipped geometries—increasing the estimated rotor efficiency by up to 0.9 points over the ungrooved seal baseline with flat tipped blades, as opposed to 0.25 points of improvement over the ungrooved case with squealer-tipped blades. Finally, for both tip configurations, optimal seal geometries that were obtained from the small-core scaled clearance gap optimizations generally maintained near optimal performance when evaluated at the design tip clearance, while those geometries developed at the design clearance experienced greater sensitivity to clearance gap changes.
Heat Transfer Enhancement in Pulsating Flows: A Bayesian Approach to Experimental Correlations
Authors: Ignuta-Ciuncanu Matei C. , Noon Chris , Martinez-Botas Ricardo F.
Published: October 2024

This research focuses on improving the modeling of heat transfer effects in pulsating exhaust flows. We address the challenges of understanding oscillating flow by employing the Metropolis–Hastings Markov Chain Monte Carlo sampling method for parameter estimation, accounting for measurement uncertainties. The knowledge can be applied to waste heat from reciprocating devices, pulsating turbocharger performance, and flow fields with significant cyclic variations. We demonstrate the feasibility of characterizing heat transfer capacity in pulsating flows using Bayesian inference and polynomial regression for experimental data correlation. This methodology is furthermore applied to identify heat transfer patterns in cold gas flow through a heated pipe across a range of mass flowrates and pulsating frequencies. To achieve this, the thermal performance variations across the length of the pipe through temperature and pressure changes are quantified. The model developed exhibits robust performance and high data efficiency (R2∈[0.83,0.89]) and notable extrapolation capacity in predicting mean heat transfer behavior based on boundary measurements. The results address the lack of experimental insights into pulsating flows encountered in heavy-duty transport applications and can be extended for heat recovery in systems such as exhaust manifolds and organic Rankine cycle gas turbines.
Loss Breakdown in Axial Turbines: A New Method for Vortex Loss and Wake Detection From 3D RANS Simulations
Authors: Raina Greta , Bousquet Yannick , Luquet David , Lippinois Eric , Binder Nicolas
Published: October 2024

To enhance turbine efficiency, it is essential to mitigate the loss generated by irreversible phenomena taking place in turbine flows, including boundary layers, shock waves, vortices, and trailing edge wakes. A fast and accurate detection of losses is therefore crucial from the earliest stages of turbine design, in which reduced order models based on oversimplified correlations are employed. Achieving this objective requires a deep comprehension of the physics behind each loss-generating mechanism, a goal attainable through the examination of the 3D flow. While existing criteria allow the identification of various phenomena, accurately quantifying losses generated by vortices remains a challenge: these losses frequently extend beyond the vortical structure. The aim of this paper is to provide a straightforward and effective approach to localize and assess vortex-related losses. This method is grounded in Zlatinov’s decomposition of the entropy generation rate equation into a streamwise and a secondary flow component. A criterion based on the vortex kinematics is used to evaluate the strength of the vortex, thereby enabling the determination of its spatial influence and its contribution to the overall losses. To validate the method, a post-processing code is developed which allows to perform loss breakdown. This tool makes use of existing identification criteria and some new techniques introduced within this work, especially for wake detection. 3D Reynolds-averaged Navier–Stokes simulations are carried out on several configurations, ranging from simple curved ducts to more realistic nozzle guide vanes, to gradually test and validate the computational tool. Results confirm that the highest rates of entropy generation occur outside of the vortical structure, and show good ability to identify both the vortex shape and its area of influence in terms of losses. A drastic improvement in the prediction of vortex losses is especially observed in the case of turbine blades with tip or hub leakage vortices.
Experimental Investigation of Biofouled Ship Control Surface Performance
Authors: Laun Alexander
Published: October 2024

Marine biofouling threatens ship safety by causing unexpected control surface performance. To explore these adverse biofouling effects, this paper presents the results of wind tunnel testing using a model-scale, low aspect ratio NACA 0018 control surface. Simulated calcareous biofouling was introduced as coarse-grit sandpaper, and, uniquely, roughness locations and sandpaper grits were varied to better understand any resulting degradation in hydrodynamic performance. Direct experimentation at high (turbulent) chord Reynolds number values suggests that leading-edge (LE) roughness with 36-grit sandpaper results in worst-case performance, with the control surface's average lift-to-drag ratio reduced by 63%. Additional findings are presented, and recommendations for future experimental work are also provided.
Rapid Prototyping of Multiscale Flexible Printed Circuit Boards With NeXus, a Robotic Additive Manufacturing System
Authors: Sills Daniel T. , Sherehiy Andriy , Zhang Ruoshi , Jackson Douglas , Reynolds Henry , Ratanayake Dilan , Caid Cassidy , Popa Dan O.
Published: October 2024

This paper demonstrates the NeXus system, a multiscale robotic additive manufacturing platform developed at the Louisville Automation and Robotics Research Institute, as a rapid prototyping tool through additively manufacturing a multilayer flexible printed circuit board (FPC) with a printed strain sensor and soldered surface mounted devices (SMD). Manufacturing of the demonstrator requires the application and curing of multiple materials with specialized properties, tools for automated assembly, and software advances to streamline the process enabling the use of industry-standardized programs to command the NeXus system. Additive manufacturing processes supported by the NeXus include aerosol jet printing (AJP) for fine feature silver conducting lines, direct write ink-jet printing for insulating materials, and intense pulsed light (IPL) for curing materials between depositions. The NeXus system transports and manipulates parts using a six-degree-of-freedom (DOF) high-precision positioner. Solder paste deposition and pick-and-place (PnP) procedures are performed by a 4DOF Selective Compliance Articulated Robot Arm (SCARA). Conversion methods between traditional printed circuit board (PCB) design software and production-ready command scripts were developed to translate basic drawings into command scripts. Multilayer structures with AJP 50-μm wide lines, an insulating bridge with a thickness of around 100 μm, and SMDs soldered to silver AJP pads were integrated within the demonstrator. An operational amplifier and other SMDs reduce the complexity of the accompanying control circuit and amplify the sensor's response by 1830 times. The successful fabrication of the demonstrator FPC highlights the rapid prototyping ability of the NeXus system.
Assessment of Conical Solar Stills Empowered by N-Replicated Partially Shaded PVT-CPC Collectors: Unveiling Exergo-Enviro-Economic Dynamics, Productivity, and Cogeneration Efficiency
Authors: Kumar Nandan , Tiwari Sumit , Singh Desh Bandhu , Saxena Abhishek , Harender Sinhmar
Published: October 2024

The economic and environmental dimensions play a pivotal role in evaluating solar still systems. The aim of this study is to evaluate the performance, efficiency, and viability of conical solar still integrated with multiple identical photovoltaic thermal compound parabolic collector (PVT-CPC) through comprehensive analyses of cogeneration efficiency, exergo-economic and enviro-economic factors, and productivity metrics. The results of this study were obtained through matlab programming, enabling accurate and detailed computations. The model has been validated at N = 0 and N = 1, showing strong correlation results: 0.96 and 0.97 for water temperature, 0.99 for yield in both cases, and 0.99 and 0.98 for glass temperature. The system has achieved a total carbon emissions mitigation of 108.29 tCO2 based on energy and 12.44 tCO2 based on exergy while recording an annual yield of 2199.61 kg. The annual cogeneration efficiency, exergo-economic parameter, enviro-economic parameter, and annual productivity are 38.96%, 31.98 kWh/$, $1570.20, and 244.68%, respectively. Furthermore, the obtained results have been compared with prior research and concluded that the exergo-economic and enviro-economic parameters for the proposed system are increased by 93.54% than the solar still with water-cooled condensing surface and 94.71% than solar still containing partially coated condensing cover with thermoelectric cooling.
Influence of Cryogenic Treatment and Tempering Temperature on Microstructural Evolution and Dry Sliding Wear Behavior of AISI D3 Cold-Work Tool Steel
Authors: Boztepe Alican , Gecu Ridvan
Published: October 2024

AISI D3 cold-work steel was shallow and deep cryogenically treated and double-tempered at 150, 250, and 350 °C temperatures. Cryogenic processes transformed the retained austenite into martensite, while double tempering produced Fe-, Cr-, and W-rich carbides. The wear losses of cryogenically treated specimens decreased by up to 60% compared to conventionally heat-treated samples. Worn surfaces mainly experienced abrasive and adhesive wear mechanisms. Due to the formation of homogeneously dispersed fine carbides at 250 °C, oxidative wear occurred at the matrix phase, resulting in the lowest wear rate. The samples tempered at 150 °C suffered from the severe abrasive action of hard carbide particles, while the samples treated at 350 °C failed because of carbide coarsening.
Scanning electron microscopy imaging of multilayer-doped GaN: Effects of surface band bending, surface roughness, and contamination layers on doping contrast
Authors: Wang Siyuan , Zhang Kai , Zhai Le , Huang Li
Published: October 2024

Dopant profiling by a scanning electron microscope possesses great potential in the semiconductor industry due to its rapid, contactless, non-destructive, low cost, high spatial resolution, and high accuracy characteristics. Here, the influence of plasma and wet chemical treatments on doping contrast was investigated for a multilayered p-n GaN specimen, which is one of the most promising third-generation wide bandgap semiconductors. Angle-resolved x-ray photoelectron spectroscopy and atomic force microscope were employed to characterize the degree of surface band bending, surface roughness, gallium oxides, and hydrocarbons on the surface of GaN. N2 and air plasmas were unable to remove the surface contamination layers, although the degree of surface band bending was suppressed. In contrast, wet chemical methods offer superior capability in removing contamination layers; however, the surface roughness was increased to varying degrees. Notably, NH4F solution is capable of improving the doping contrast. The underlying mechanism was elucidated from the perspective of surface band bending, surface roughness, and contamination. The findings reported here will provide a feasible solution for effective characterization of semiconductor materials and devices.
Motivational Predictors of Schoolchildren’s Moods in a Recess Intervention
Authors: Méndez-Giménez Antonio , García-Rodríguez Iván
Published: October 2024

Recess provides an opportunity to promote physical activity among schoolchildren. There is limited research on the effects of specific recess interventions, such as moveable equipment, physical structures, or painting playground, on motivational and affective-emotional variables. The study investigated the impact of a recess intervention based on children’s play using their own self-made materials. The researchers examined how this intervention affected basic psychological needs (including novelty), motivational regulations, self-determination index (SDI), and mood states, such as fear, happiness, sadness, and anger in 219 schoolchildren from third to sixth grade. The multivariate analysis of variance and univariate analyses found a decrease in identified, introjected, and external regulations, amotivation, and fear and an increase in SDI by grade. Boys scored higher on autonomy, competence, external regulation, and anger while girls scored higher on happiness. SDI and novelty were predictors of happiness in boys while relatedness was the main predictor for girls. Relatedness negatively predicted anger in boys. SDI negatively predicted fear and sadness in both genders. These findings suggest that recess interventions should consider motivational and emotional differences by grade and gender to promote physical activity and well-being in schoolchildren.
The Relationship Between Cold-Water-Immersion Activities, Mental Health, Self-Efficacy, Resilience, and Mental Toughness
Authors: Mullooly Annmarie , Colbert Dylan
Published: October 2024

While a breadth of literature has asserted the potential physiological benefits of cold-water-immersion (CWI) activities (such as sea swimming, ice baths, and cold showers), analyses on their possible psychological effects is more limited. The current analysis (N = 164) aimed to explore the relationship between CWI and a number of psychological variables pertaining to mental health and psychological fortitude by comparing those who engage in CWI via various modalities (n = 120) and at various levels of frequency to those who do not (n = 44). When controlling for levels of daily stress, engagement in cold-water activities was found to be associated with lower levels of depression, anxiety, and stress, as well as higher levels of resilience, self-efficacy, and mental toughness. Furthermore, analyses suggested a “dosage effect” as more frequent CWI was associated with significantly more positive levels of mental toughness and self-efficacy.
Application of Raman spectroscopy and machine learning for
Candida auris
identification and characterization
Authors: Xue Junjing , Yue Huizhen , Lu Weilai , Li Yanying , Huang Guanghua , Fu Yu Vincent
Published: October 2024

Candida auris,
an emerging fungal pathogen characterized by multidrug resistance and high-mortality nosocomial infections, poses a serious global health threat. However, the precise and rapid identification and characterization of
C. auris
remain a challenge. Here, we employed Raman spectroscopy combined with machine learning to identify
C. auris
isolates and its closely related species as well as to predict antifungal resistance and key virulence factors at the single-cell level. The average accuracy of identification among all
Candida
species was 93.33%, with an accuracy of 98% for the clinically simulated samples. The drug susceptibility of
C. auris
to fluconazole and amphotericin B was 99% and 94%, respectively. Furthermore, the phenotypic prediction of
C. auris
yielded an accuracy of 100% for aggregating cells and 97% for filamentous cells. This proof-of-concept methodology not only precisely identifies
C. auris
at the clade-specific level but also rapidly predicts the antifungal resistance and biological characteristics, promising a valuable medical diagnostic tool to combat this multidrug-resistant pathogen in the future.

IMPORTANCE

Currently, combating
Candida auris
infections and transmission is challenging due to the lack of efficient identification and characterization methods for this species. To address these challenges, our study presents a novel approach that utilizes Raman spectroscopy and artificial intelligence to achieve precise identification and characterization of
C. auris
at the singe-cell level. It can accurately identify a single cell from the four
C. auris
clades. Additionally, we developed machine learning models designed to detect antifungal resistance in
C. auris
cells and differentiate between two distinct phenotypes based on the single-cell Raman spectrum. We also constructed prediction models for detecting aggregating and filamentous cells in
C. auris
, both of which are closely linked to its virulence. These results underscore the merits of Raman spectroscopy in the identification and characterization of
C. auris
, promising improved outcomes in the battle against
C. auris
infections and transmission.
Conserved residues of the immunosuppressive domain of MLV are essential for regulating the fusion-critical SU-TM disulfide bond
Authors: Hogan Victoria A. , Harmon Julia , Cid-Rosas Miguel , Hall Laura R. , Johnson Welkin E.
Published: October 2024

The Env protein of murine leukemia virus (MLV) is the prototype of a large clade of retroviral fusogens, collectively known as gamma-type Envs. Gamma-type Envs are found in retroviruses and endogenous retroviruses (ERVs) representing a broad range of vertebrate hosts. All gamma-type Envs contain a highly conserved stretch of 26-residues in the transmembrane subunit (TM) comprising two motifs, a putative immunosuppressive domain (ISD) and a CX
6
CC motif. Extraordinary conservation of the ISD and its invariant association with the CX
6
CC suggests a fundamental contribution to Env function. To investigate ISD function, we characterized several mutants with single amino acid substitutions at conserved positions in the MLV ISD. A majority abolished infectivity, although we did not observe a corresponding loss in intrinsic ability to mediate membrane fusion. Ratios of the surface subunit (SU) to capsid protein (CA) in virions were diminished for a majority of the ISD mutants, while TM:CA ratios were similar to wild type. Specific loss of SU reflected premature isomerization of the labile disulfide bond that links SU and TM prior to fusion. Indeed, all non-infectious mutants displayed significantly lower disulfide stability than wild-type Env. These results reveal a role for ISD positions 2, 3, 4, 7, and 10 in regulating a late step in entry after fusion peptide insertion but prior to creation of the fusion pore. This implies that the ISD is part of a larger domain, comprising the ISD and CX
6
CC motifs, that is critical for the formation and regulation of the metastable, intersubunit disulfide bond.

IMPORTANCE

The gamma-type Env is a prevalent viral fusogen, found within retroviruses and endogenous retroviruses across vertebrate species and in filoviruses such as Ebolavirus. The fusion mechanism of gamma-type Envs is unique from other Class I fusogens such as those of influenza A virus and HIV-1. Gamma-type Envs contain a hallmark feature known as the immunosuppressive domain (ISD) that has been the subject of some controversy in the literature surrounding its putative immunosuppressive effects. Despite the distinctive conservation of the ISD, little has been done to investigate the role of this region for the function of this widespread fusogen. Our work demonstrates the importance of the ISD for the function of gamma-type Envs in infection, particularly in regulating the intermediate steps of membrane fusion. Understanding the fusion mechanism of gamma-type Envs has broad implications for understanding the entry of extant viruses and aspects of host biology connected to co-opted endogenous gamma-type Envs.
Structures of Epstein-Barr virus and Kaposi’s sarcoma-associated herpesvirus virions reveal species-specific tegument and envelope features
Authors: Zhen James , Chen Jia , Huang Haigen , Liao Shiqing , Liu Shiheng , Yuan Yan , Sun Ren , Longnecker Richard , Wu Ting-Ting , Zhou Z. Hong
Published: October 2024

Epstein-Barr virus (EBV) and Kaposi’s sarcoma-associated herpesvirus (KSHV) are classified into the gammaherpesvirus subfamily of
Herpesviridae
, which stands out from its alpha- and betaherpesvirus relatives due to the tumorigenicity of its members. Although structures of human alpha- and betaherpesviruses by cryogenic electron tomography (cryoET) have been reported, reconstructions of intact human gammaherpesvirus virions remain elusive. Here, we structurally characterize extracellular virions of EBV and KSHV by deep learning-enhanced cryoET, resolving both previously known monomorphic capsid structures and previously unknown pleomorphic features beyond the capsid. Through subtomogram averaging and subsequent tomogram-guided sub-particle reconstruction, we determined the orientation of KSHV nucleocapsids from mature virions with respect to the portal to provide spatial context for the tegument within the virion. Both EBV and KSHV have an eccentric capsid position and polarized distribution of tegument. Tegument species span from the capsid to the envelope and may serve as scaffolds for tegumentation and envelopment. The envelopes of EBV and KSHV are less densely populated with glycoproteins than those of herpes simplex virus 1 (HSV-1) and human cytomegalovirus (HCMV), representative members of alpha- and betaherpesviruses, respectively. Also, we observed fusion protein gB trimers exist within triplet arrangements in addition to standalone complexes, which is relevant to understanding dynamic processes such as fusion pore formation. Taken together, this study reveals nuanced yet important differences in the tegument and envelope architectures among human herpesviruses and provides insights into their varied cell tropism and infection.

IMPORTANCE

Discovered in 1964, Epstein-Barr virus (EBV) is the first identified human oncogenic virus and the founding member of the gammaherpesvirus subfamily. In 1994, another cancer-causing virus was discovered in lesions of AIDS patients and later named Kaposi’s sarcoma-associated herpesvirus (KSHV), the second human gammaherpesvirus. Despite the historical importance of EBV and KSHV, technical difficulties with isolating large quantities of these viruses and the pleiomorphic nature of their envelope and tegument layers have limited structural characterization of their virions. In this study, we employed the latest technologies in cryogenic electron microscopy (cryoEM) and tomography (cryoET) supplemented with an artificial intelligence-powered data processing software package to reconstruct 3D structures of the EBV and KSHV virions. We uncovered unique properties of the envelope glycoproteins and tegument layers of both EBV and KSHV. Comparison of these features with their non-tumorigenic counterparts provides insights into their relevance during infection.
Acquisition of a multibasic cleavage site does not increase MERS-CoV entry into Calu-3 human lung cells
Authors: Hoffmann Markus , Kleine-Weber Hannah , Graichen Luise , Nehlmeier Inga , Kempf Amy , Moldenhauer Anna-Sophie , Braun Elisabeth , Assiri Abdullah M. , Kirchhoff Frank , Sauter Daniel , Alkharsah Khaled R. , Pöhlmann Stefan
Published: October 2024

Human-to-human transmission of the highly pathogenic Middle East respiratory syndrome coronavirus (MERS-CoV) is currently inefficient. However, there is concern that the virus might mutate and thereby increase its transmissibility and thus pandemic potential. The pandemic SARS-CoV-2 depends on a highly cleavable furin motif at the S1/S2 site of the viral spike (S) protein for efficient lung cell entry, transmission, and pathogenicity. Here, by employing pseudotyped particles, we investigated whether augmented cleavage at the S1/S2 site also increases MERS-CoV entry into Calu-3 human lung cells. We report that polymorphism T746K at the S1/S2 cleavage site or optimization of the furin motif increases S protein cleavage but not lung cell entry. These findings suggest that, unlike what has been reported for SARS-CoV-2, a highly cleavable S1/S2 site might not augment MERS-CoV infectivity for human lung cells.

IMPORTANCE

The highly cleavable furin motif in the spike protein is required for robust lung cell entry, transmission, and pathogenicity of SARS-CoV-2. In contrast, it is unknown whether optimization of the furin motif in the spike protein of the pre-pandemic MERS-CoV increases lung cell entry and allows for robust human–human transmission. The present study indicates that this might not be the case. Thus, neither a naturally occurring polymorphism that increased MERS-CoV spike protein cleavage nor artificial optimization of the cleavage site allowed for increased spike-protein-driven entry into Calu-3 human lung cells.
A near-complete genome of the uncultured
Staphylococcus aureus
phage COMBAT-CF_PAR1 isolated from the lungs of an infant with cystic fibrosis
Authors: Agudelo-Romero Patricia , Caparros-Martin Jose A. , Sharma Abhinav , Saladié Montserrat , Sly Peter D. , Stick Stephen M. , O´Gara Fergal ,   COMBAT study group
Published: October 2024

In cystic fibrosis, bacteria–bacteriophage interaction in the lower airways is poorly understood. We present the near-complete genome of the uncultured Siphovirus-like bacteriophage,
Staphylococcus aureus
phage COMBAT-CF_PAR1, isolated from the lower airways. The genome spans 41,510 bp with 33.45% guanine–cytosine content and contains 65 open reading frames.
Metagenomic sequencing of CRISPRs as a new marker to aid in personal identification with low-biomass samples
Authors: Toyomane Kochi , Kimura Yuri , Fukagawa Takashi , Yamagishi Takayuki , Watanabe Ken , Akutsu Tomoko , Asahi Ai , Kubota Satoshi , Sekiguchi Kazumasa
Published: October 2024

The high specificity of the human skin microbiome is expected to provide a new marker for personal identification. Metagenomic sequencing of clustered regularly interspaced short palindromic repeats (CRISPRs), which we call metaCRISPR typing, was shown to achieve personal identification accurately. However, the intra-individual variability observed in previous studies, which may be due to poor DNA yields from skin samples, has resulted in non-reproducible results. Furthermore, whether metaCRISPR typing can assist in the forensic human DNA analysis of low-biomass samples, from which the information obtained is insufficient, is unknown. In the present study, we sequenced serially diluted control streptococcal CRISPRs cloned into plasmids to determine the minimum copy number required to obtain reproducible results from metaCRISPR typing. We found that at least 10
2
copies of CRISPRs are necessary to obtain reproducible results. We then analyzed the skin swab samples using both metaCRISPR typing and human DNA typing. When the DNA extracted from the skin swabs was diluted, no information was obtained from six out of eight samples by human DNA typing. On the other hand, beta diversity indices of spacer sequences compared with reference samples were below 0.8 for three out of six samples, for which no information was obtained from human DNA analysis, indicating that the spacers observed in these samples were similar to those in the references. These results indicate that metaCRISPR typing may contribute to the identification of individuals from whom the samples were obtained, even in cases where human DNA yields are insufficient to perform human DNA analysis.

IMPORTANCE

Previous studies have developed new personal identification methods utilizing personal differences in the skin microbiome. However, intra-individual diversity of skin microbiome may preclude the application of microbiome-based personal identification. Moreover, no study has compared microbiome-based personal identification and practical human DNA analysis. Here, we revealed that the results of metaCRISPR typing, a previously developed microbiome-based personal identification method, are stable if the copy number of the marker gene is sufficient. We then analyzed the skin swab samples using both metaCRISPR typing and human DNA analysis. Our results indicate that metaCRISPR typing may provide additional information for personal identification using low-biomass samples that cannot be used for conventional human DNA analysis.
False-positive results for seasonal coronavirus infections on using the FilmArray Pneumonia Panel
Authors: Park Kuenyoul , Park Bosung , Won Eun Jeong , Sung Heungsup , Kim Mi-Na
Published: October 2024

The FilmArray Pneumonia Panel (FilmArrayPN; bioMérieux) was tagged for potential false-positive seasonal coronavirus results, possibly caused by non-specific amplification or cross-reactivity with human genomic DNA. This study was conducted to determine the real-world false-positive rate of seasonal coronavirus infections using FilmArrayPN at a tertiary care hospital. We retrospectively reviewed FilmArrayPN results to detect lower respiratory tract pathogens from July 2023 to April 2024. Allplex Respiratory Panel (AllplexRP; Seegene) and/or FilmArray Respiratory Panel (FilmArrayRP) results for the same patient were considered as reference results. In the last month of the study period, all positive samples in FilmArrayPN were confirmed by AllplexRP and pan-coronavirus targeted PCR (pan-CoV PCR). A total of 2,120 specimens, including 1,847 expectorated sputum and 273 bronchial aspirate (BA) samples, were tested by FilmArrayPN. Of these, 161 (8.7%) sputum and 7 (2.6%) BA specimens from 152 patients were positive for coronavirus targets in FilmArrayPN. Of the 122 cases also tested by AllplexRP and/or FilmArrayRP, 106 specimens (86.9%) were coronavirus-negative, except for 9 OC43-positive, 6 229E-positive, and 1 NL63-positive. Notably, 83.1% of the 106 cases that tested negative in the other tests had melting temperatures above 83℃. A total of 61 specimens that tested positive for coronavirus in FilmArrayPN but negative in AllplexRP were confirmed to be negative in pan-CoV PCR. The coronavirus positivity of 7.8% in the FilmArrayPN resulted in 5% of samples being potentially misreported as false-positives. This report thus highlights the need for continuous monitoring of melting temperatures to avoid potential false-positives.

IMPORTANCE

The FilmArray Pneumonia Panel (FilmArrayPN; bioMérieux) was tagged for potential false-positive seasonal coronavirus results, possibly caused by non-specific amplification or cross-reactivity with human genomic DNA. FilmArrayPN results were retrospectively reviewed from July 2023 to May 2024. Of 2,120 tested specimens, 168 specimens from 152 patients were positive for coronavirus targets in FilmArrayPN. Of the 122 cases also tested by Allplex Respiratory Panel and/or FilmArray Respiratory Panel, 106 specimens (86.9%) were coronavirus-negative. Notably, 83.1% of the 106 cases that tested negative in the other tests had melting temperatures above 83℃. A total of 61 specimens that tested positive for coronavirus in FilmArrayPN but negative in Allplex were confirmed to be negative in pan-coronavirus targeted PCR. The coronavirus positivity of 7.8% in the FilmArrayPN resulted in 5% of samples being potentially misreported as false-positives. This report highlights the need for continuous monitoring of melting temperatures to avoid potential false-positives.
Unveiling environmental transmission risks: comparative analysis of azole resistance in
Aspergillus fumigatus
clinical and environmental isolates from Yunnan, China
Authors: Gong Jianchuan , Huang Jiarui , Liu Yongju , Zhang Ying , Gao Yuhong
Published: October 2024

Azole resistance in
Aspergillus fumigatus
poses a significant clinical challenge globally. Our previous epidemiological analysis revealed a remarkably high frequency (~80%) of azole-resistant
A. fumigatus
in Yunnan’s greenhouse environments, prompting increased local and regional research for targeted control strategies. In this study, we analyzed 94 clinical
A. fumigatus
isolates from Yunnan, comparing their susceptibility profiles and genotypic characteristics with environmental strains previously isolated. While the overall frequency of azole resistance in clinical isolates was lower than that in environmental samples, a significant prevalence of cross-resistance, with varying resistance patterns based on minimum inhibitory concentration (MIC) levels was observed, which exceeded rates in other regions of China. Specific mutation combinations in the
cyp51A
gene were linked to elevated MIC values in clinical and/or environmental samples, while some resistant strains with wild-type
cyp51A
remain unexplained, indicating a need for further investigation into their resistance mechanisms. The differences in unique genetic elements and the distinct genetic differentiation observed between clinical and environmental isolates can be attributed to Yunnan’s unique geomorphology and potential genotype importation from other provinces and abroad. Extensive allele exchanges and sharing contributed to the selection of azole-resistant clinical isolates, suggesting a common environmental origin, and the transmission routes of local drug-resistant strains cannot be excluded. These findings emphasize the imperative for regional and targeted surveillance to monitor resistance trends and guide effective antifungal therapy, and management strategies to mitigate invasive aspergillosis risk in this region.

IMPORTANCE

Azole resistance in
Aspergillus fumigatus
is a major global health concern, with particularly high rates (~80%) observed in Yunnan’s greenhouse environments. This study compares azole resistance in 94 clinical isolates from Yunnan with environmental strains, revealing lower clinical resistance but significant cross-resistance and distinct resistance patterns. Specific mutations in the
cyp51A
gene were associated with elevated minimum inhibitory concentration values, though some resistant strains had wild-type
cyp51A
, highlighting the need for further research. The unique genetic profiles and potential external genotype influences in Yunnan emphasize the need for targeted regional surveillance. Effective monitoring and control strategies are essential to manage and mitigate the risk of invasive aspergillosis.