Accurate virus identification with interpretable Raman signatures by machine learning.

Rapid identification of newly emerging or circulating viruses is an important first step toward managing the public health response to potential outbreaks. A portable virus capture device, coupled with label-free Raman spectroscopy, holds the promise of fast detection by rapidly obtaining the Raman signature of a virus followed by a machine learning (ML) approach applied to recognize the virus based on its Raman spectrum, which is used as a fingerprint. We present such an ML approach for analyzing Raman spectra of human and avian viruses. A convolutional neural network (CNN) classifier specifically designed for spectral data achieves very high accuracy for a variety of virus type or subtype identification tasks. In particular, it achieves 99% accuracy for classifying influenza virus type A versus type B, 96% accuracy for classifying four subtypes of influenza A, 95% accuracy for differentiating enveloped and nonenveloped viruses, and 99% accuracy for differentiating avian coronavirus (infectious bronchitis virus [IBV]) from other avian viruses. Furthermore, interpretation of neural net responses in the trained CNN model using a full-gradient algorithm highlights Raman spectral ranges that are most important to virus identification. By correlating ML-selected salient Raman ranges with the signature ranges of known biomolecules and chemical functional groups­for example, amide, amino acid, and carboxylic acid­we verify that our ML model effectively recognizes the Raman signatures of proteins, lipids, and other vital functional groups present in different viruses and uses a weighted combination of these signatures to identify viruses.

Designing artificial two-dimensional landscapes via atomic-layer substitution.

Technology advancements in history have often been propelled by material innovations. In recent years, two-dimensional (2D) materials have attracted substantial interest as an ideal platform to construct atomic-level material architectures. In this work, we design a reaction pathway steered in a very different energy landscape, in contrast to typical thermal chemical vapor deposition method in high temperature, to enable room-temperature atomic-layer substitution (RT-ALS). First-principle calculations elucidate how the RT-ALS process is overall exothermic in energy and only has a small reaction barrier, facilitating the reaction to occur at room temperature. As a result, a variety of Janus monolayer transition metal dichalcogenides with vertical dipole could be universally realized. In particular, the RT-ALS strategy can be combined with lithography and flip-transfer to enable programmable in-plane multiheterostructures with different out-of-plane crystal symmetry and electric polarization. Various characterizations have confirmed the fidelity of the precise single atomic layer conversion. Our approach for designing an artificial 2D landscape at selective locations of a single layer of atoms can lead to unique electronic, photonic, and mechanical properties previously not found in nature. This opens a new paradigm for future material design, enabling structures and properties for unexplored territories.

Engineered 2D materials for optical bioimaging and path toward therapy and tissue engineering.

Two-dimensional (2D) layered materials as a new class of nanomaterial are characterized by a list of exotic properties. These layered materials are investigated widely in several biomedical applications. A comprehensive understanding of the state-of-the-art developments of 2D materials designed for multiple nanoplatforms will aid researchers in various fields to broaden the scope of biomedical applications. Here, we review the advances in 2D material-based biomedical applications. First, we introduce the classification and properties of 2D materials. Next, we summarize surface and structural engineering methods of 2D materials where we discuss surface functionalization, defect, and strain engineering, and creating heterostructures based on layered materials for biomedical applications. After that, we discuss different biomedical applications. Then, we briefly introduced the emerging role of machine learning (ML) as a technological advancement to boost biomedical platforms. Finally, the current challenges, opportunities, and prospects on 2D materials in biomedical applications are discussed.

Characterizing a Novel Staphylococcal Cassette Chromosome mec with a Composite Structure from a Clinical Strain of Staphylococcus hominis, C34847.

Staphylococcal cassette chromosome mec (SCCmec) has predominantly been described in methicillin-resistant Staphylococcus aureus. However, studies have indicated that coagulase-negative staphylococci (CoNS) carry a larger diversity of SCC elements. We characterized a composite SCCmec element carrying an uncharacterized ccr1 and type A mec gene combination, in conjunction with a secondary element bearing ccr4, from a clinical strain of Staphylococcus hominis. The element's complex structure points to a high degree of recombination occurring in SCCmec in CoNS.

Enhancement of van der Waals Interlayer Coupling through Polar Janus MoSSe.

Interlayer coupling plays essential roles in the quantum transport, polaritonic, and electrochemical properties of stacked van der Waals (vdW) materials. In this work, we report the unconventional interlayer coupling in vdW heterostructures (HSs) by utilizing an emerging 2D material, Janus transition metal dichalcogenides (TMDs). In contrast to conventional TMDs, monolayer Janus TMDs have two different chalcogen layers sandwiching the transition metal and thus exhibit broken mirror symmetry and an intrinsic vertical dipole moment. Such a broken symmetry is found to strongly enhance the vdW interlayer coupling by as much as 13.2% when forming MoSSe/MoS2 HS as compared to the pristine MoS2 counterparts. Our noncontact ultralow-frequency Raman probe, linear chain model, and density functional theory calculations confirm the enhancement and reveal the origins as charge redistribution in Janus MoSSe and reduced interlayer distance. Our results uncover the potential of tuning interlayer coupling strength through Janus heterostacking.

Topological Singularity Induced Chiral Kohn Anomaly in a Weyl Semimetal.

The electron-phonon interaction (EPI) is instrumental in a wide variety of phenomena in solid-state physics, such as electrical resistivity in metals, carrier mobility, optical transition, and polaron effects in semiconductors, lifetime of hot carriers, transition temperature in BCS superconductors, and even spin relaxation in diamond nitrogen-vacancy centers for quantum information processing. However, due to the weak EPI strength, most phenomena have focused on electronic properties rather than on phonon properties. One prominent exception is the Kohn anomaly, where phonon softening can emerge when the phonon wave vector nests the Fermi surface of metals. Here we report a new class of Kohn anomaly in a topological Weyl semimetal (WSM), predicted by field-theoretical calculations, and experimentally observed through inelastic x-ray and neutron scattering on WSM tantalum phosphide. Compared to the conventional Kohn anomaly, the Fermi surface in a WSM exhibits multiple topological singularities of Weyl nodes, leading to a distinct nesting condition with chiral selection, a power-law divergence, and non-negligible dynamical effects. Our work brings the concept of the Kohn anomaly into WSMs and sheds light on elucidating the EPI mechanism in emergent topological materials.

Methicillin-Resistant Staphylococcus aureus: Molecular Characterization, Evolution, and Epidemiology.

Staphylococcus aureus, a major human pathogen, has a collection of virulence factors and the ability to acquire resistance to most antibiotics. This ability is further augmented by constant emergence of new clones, making S. aureus a "superbug." Clinical use of methicillin has led to the appearance of methicillin-resistant S. aureus (MRSA). The past few decades have witnessed the existence of new MRSA clones. Unlike traditional MRSA residing in hospitals, the new clones can invade community settings and infect people without predisposing risk factors. This evolution continues with the buildup of the MRSA reservoir in companion and food animals. This review focuses on imparting a better understanding of MRSA evolution and its molecular characterization and epidemiology. We first describe the origin of MRSA, with emphasis on the diverse nature of staphylococcal cassette chromosome mec (SCCmec). mecA and its new homologues (mecB, mecC, and mecD), SCCmec types (13 SCCmec types have been discovered to date), and their classification criteria are discussed. The review then describes various typing methods applied to study the molecular epidemiology and evolutionary nature of MRSA. Starting with the historical methods and continuing to the advanced whole-genome approaches, typing of collections of MRSA has shed light on the origin, spread, and evolutionary pathways of MRSA clones.

Novel Multiplex PCR Assay for Detection of Chlorhexidine-Quaternary Ammonium, Mupirocin, and Methicillin Resistance Genes, with Simultaneous Discrimination of Staphylococcus aureus from Coagulase-Negative Staphylococci.

Methicillin-resistant Staphylococcus aureus (MRSA) is a clinically significant pathogen that is resistant to a wide variety of antibiotics and responsible for a large number of nosocomial infections worldwide. The Agency for Healthcare Research and Quality and the Centers for Disease Control and Prevention recently recommended the adoption of universal mupirocin-chlorhexidine decolonization of all admitted intensive care unit patients rather than MRSA screening with targeted treatments, which raises a serious concern about the selection of resistance to mupirocin and chlorhexidine in strains of staphylococci. Thus, a simple, rapid, and reliable approach is paramount in monitoring the prevalence of resistance to these agents. We developed a simple multiplex PCR assay capable of screening Staphylococcus isolates for the presence of antiseptic resistance genes for chlorhexidine and quaternary ammonium compounds, as well as mupirocin and methicillin resistance genes, while simultaneously discriminating S. aureus from coagulase-negative staphylococci (CoNS). The assay incorporates 7 PCR targets, including the Staphylococcus 16S rRNA gene (specifically detecting Staphylococcus spp.), nuc (distinguishing S. aureus from CoNS), mecA (distinguishing MRSA from methicillin-susceptible S. aureus), mupA and mupB (identifying high-level mupirocin resistance), and qac and smr (identifying chlorhexidine and quaternary ammonium resistance). Our assay demonstrated 100% sensitivity, specificity, and accuracy in a total of 23 variant antiseptic- and/or antibiotic-resistant control strains. Further validation of our assay using 378 randomly selected and previously well-characterized local clinical isolates confirmed its feasibility and practicality. This may prove to be a useful tool for multidrug-resistant Staphylococcus monitoring in clinical laboratories, particularly in the wake of increased chlorhexidine and mupirocin treatments.

Neutrophil crawling in capillaries; a novel immune response to Staphylococcus aureus.

Methicillin-resistant Staphylococcus aureus (MRSA), particularly the USA300 strain, is a highly virulent pathogen responsible for an increasing number of skin and soft tissue infections globally. Furthermore, MRSA-induced soft tissue infections can rapidly progress into life-threatening conditions, such as sepsis and necrotizing fasciitis. The importance of neutrophils in these devastating soft tissue infections remains ambiguous, partly because of our incomplete understanding of their behaviour. Spinning disk confocal microscopy was used to visualize the behaviour of GR1-labelled neutrophils in subcutaneous tissue in response to GFP-expressing MRSA attached to a foreign particle (agarose bead). We observed significant directional neutrophil recruitment towards the S. aureus agarose bead but not a control agarose bead. A significant increase in neutrophil crawling within the capillaries surrounding the infectious nidus was noted, with impaired capillary perfusion in these vessels and increased parenchymal cell death. No neutrophils were able to emigrate from capillaries. The crawling within these capillaries was mediated by the ß(2) and α(4) integrins and blocking these integrins 2 hours post infection eliminated neutrophil crawling, improved capillary perfusion, reduced cell death and reduced lesion size. Blocking prior to infection increased pathology. Neutrophil crawling within capillaries during MRSA soft tissue infections, while potentially contributing to walling off or preventing early dissemination of the pathogen, resulted in impaired perfusion and increased tissue injury with time.

Community-associated methicillin-resistant Staphylococcus aureus necrotizing pneumonia without evidence of antecedent viral upper respiratory infection.

BACKGROUND: USA300 community-associated (CA) methicillin-resistant Staphylococcus aureus (MRSA) strains causing necrotizing pneumonia have been reported in association with antecedent viral upper respiratory tract infections (URI). METHODS: A case series of necrotizing pneumonia presenting as a primary or coprimary infection, secondary to CA-MRSA without evidence of antecedent viral URI, is presented. Cases were identified through the infectious diseases consultation service records. Clinical and radiographic data were collected by chart review and electronic records. MRSA strains were isolated from sputum, bronchoalveolar lavage, pleural fluid or blood cultures and confirmed using standard laboratory procedures. MRSA strains were characterized by susceptibility testing, pulsed-field gel electrophoresis, spa typing, agr typing and multilocus sequence typing. Testing for respiratory viruses was performed by appropriate serological testing of banked sera, or nucleic acid testing of nasopharyngeal or bronchoalveloar lavage specimens. RESULTS: Ten patients who presented or copresented with CA necrotizing pneumonia secondary to CA-MRSA from April 2004 to October 2011 were identified. The median length of stay was 22.5 days. Mortality was 20.0%. Classical risk factors for CA-MRSA were identified in seven of 10 (70.0%) cases. Chest tube placement occurred in seven of 10 patients with empyema. None of the patients had historical evidence of antecedent URI. In eight of 10 patients, serological or nucleic acid testing testing revealed no evidence of acute viral coinfection. Eight strains were CMRSA-10 (USA300). The remaining two strains were a USA300 genetically related strain and a USA1100 strain. CONCLUSION: Pneumonia secondary to CA-MRSA can occur in the absence of an antecedent URI. Infections due to CA-MRSA are associated with significant morbidity and mortality. Clinicians need to have an awareness of this clinical entity, particularly in patients who are in risk groups that predispose to exposure to this bacterium.

HISTORIQUE: Des souches USA300 de Staphylococcus aureus résistant à la méthicilline (SARM) d'origine non nosocomiale (ONN) responsables d'une pneumonie nécrosante ont été signalées après des infections des voies respiratoires supérieures. MÉTHODOLOGIE: Les chercheurs présentent une série de cas de pneumonie nécrosante se manifestant sous forme d'infection ou de co-infection primaire découlant du SARM-ONN, sans manifestation d'IVRS virale antérieure. Ils ont dépisté les cas en dépouillant les dossiers des services de consultation en infectiologie. Ils ont colligé les données cliniques et radiographiques en analysant les dossiers papier et électroniques. Les souches de SARM avaient été isolées dans les expectorations, le lavage broncho-alvéolaire, le liquide pleural ou les hémo-cultures et confirmées au moyen d'analyses de laboratoire standards. Les souches de SARM étaient caractérisées par les tests de susceptibilité, l'électrophorèse sur gel en champ pulsé, le typage du gène spa ou du gène agr ou le typage génomique multilocus. Les tests de dépistage des virus respiratoires ont été faits au moyen du test sérologique pertinent du sérum en réserve ou du test d'amplification des acides nucléiques des échantillons de lavage nasopharyngé ou broncho-alvéolaire. RÉSULTATS: Entre avril 2004 et octobre 2011, les chercheurs ont dépisté dix patients qui présentaient, seule ou conjointement, une pneumonie nécrosante d'ONN secondaire à une infection par le SARM-ONN. Ils ont été hospitalisés pendant une période médiane de 22,5 jours. Le taux de mortalité s'élevait à 20,0 %. Les chercheurs ont constaté des facteurs de risque classiques de SARM-ONN dans sept des dix cas (70,0 %). Sept des dix patients faisant de l'empyème avaient eu un drain thoracique. Aucun des patients n'avait d'antécédents démontrés d'IVRS. Chez huit des dix patients, le test sérologique et le test d'amplification des acides nucléiques n'ont révélé aucune manifestation de co-infection virale aiguë. Huit souches étaient des SARMC-10 (USA300). Les deux autres étaient une souche liée génétiquement au USA300 et une souche USA1100. CONCLUSION: La pneumonie secondaire au SARM-ONN peut se manifester en l'absence d'IVRS antérieure. Les infections causées par le SARM-ONN s'associent à une morbidité et une mortalité importantes. Les cliniciens doivent connaître cette entité clinique, notamment chez les patients qui font partie de groupes vulnérables qui les prédisposent à être exposés à cette bactérie.

The Role of Prophage ϕSa3 in the Adaption of Staphylococcus aureus ST398 Sublineages from Human to Animal Hosts.

Staphylococcus aureus sequence type (ST) 398 is a lineage affecting both humans and livestock worldwide. However, the mechanisms underlying its clonal evolution are still not clearly elucidated. We applied whole-genome sequencing (WGS) typing to 45 S. aureus strains from China and Canada between 2005 and 2014, in order to gain insight into their evolutionary pathway. Based on WGS phylogenetic analysis, 42 isolates were assigned to the human-associated clade (I/II-GOI) and 3 isolates to livestock-associated clade (IIa). Phylogeny of ϕSa3 sequences revealed five phage groups (Groups 1-5), with Group 1 carrying ϕSa3-Group 1 (ϕSa3-G1), Group 2 carrying ϕSa3-G2, Group 3 carrying ϕSa3-G3, Group 4 carrying ϕSa3-G4 and Group 5 lacking ϕSa3. ϕSa3-G1 was only found in strains that accounted for the most ancestral human clade I, while ϕSa3-G2, ϕSa3-G3 and ϕSa3-G4 were found restricted to sublineages within clade II-GOI. Some isolates of clade II-GOI were also found to be ϕSa3-negative or resistant to methicillin which are unusual characteristics for human-adapted isolates. This study demonstrated a strong association between phylogenetic grouping and phage type, suggesting an important role of ϕSa3 prophage in the evolution of human-adapted ST398 subclones. In addition, our results suggest that this subclone slowly began to adapt to animal hosts by losing ϕSa3 and acquiring methicillin resistance, which was observed in some strains of human-associated clade II-GOI, an intermediate human to livestock transmission clade.

Oxygen generating biomaterials at the forefront of regenerative medicine: advances in bone regeneration.

Globally, an annual count of more than two million bone transplants is conducted, with conventional treatments, including metallic implants and bone grafts, exhibiting certain limitations. In recent years, there have been significant advancements in the field of bone regeneration. Oxygen tension regulates cellular behavior, which in turn affects tissue regeneration through metabolic programming. Biomaterials with oxygen release capabilities enhance therapeutic effectiveness and reduce tissue damage from hypoxia. However, precise control over oxygen release is a significant technical challenge, despite its potential to support cellular viability and differentiation. The matrices often used to repair large-size bone defects do not supply enough oxygen to the stem cells being used in the regeneration process. Hypoxia-induced necrosis primarily occurs in the central regions of large matrices due to inadequate provision of oxygen and nutrients by the surrounding vasculature of the host tissues. Oxygen generating biomaterials (OGBs) are becoming increasingly significant in enhancing our capacity to facilitate the bone regeneration, thereby addressing the challenges posed by hypoxia or inadequate vascularization. Herein, we discussed the key role of oxygen in bone regeneration, various oxygen source materials and their mechanism of oxygen release, the fabrication techniques employed for oxygen-releasing matrices, and novel emerging approaches for oxygen delivery that hold promise for their potential application in the field of bone regeneration.

Tuning the Fermi Level of Graphene by Two-Dimensional Metals for Raman Detection of Molecules.

Graphene-enhanced Raman scattering (GERS) offers great opportunities to achieve optical sensing with a high uniformity and superior molecular selectivity. The GERS mechanism relies on charge transfer between molecules and graphene, which is difficult to manipulate by varying the band alignment between graphene and the molecules. In this work, we synthesized a few atomic layers of metal termed two-dimensional (2D) metal to precisely and deterministically modify the graphene Fermi level. Using copper phthalocyanine (CuPc) as a representative molecule, we demonstrated that tuning the Fermi level can significantly improve the signal enhancement and molecular selectivity of GERS. Specifically, aligning the Fermi level of graphene closer to the highest occupied molecular orbital (HOMO) of CuPc results in a more pronounced Raman enhancement. Density functional theory (DFT) calculations of the charge density distribution reproduce the enhanced charge transfer between CuPc molecules and graphene with a modulated Fermi level. Extending our investigation to other molecules such as rhodamine 6G, rhodamine B, crystal violet, and F16CuPc, we showed that 2D metals enabled Fermi level tuning, thus improving GERS detection for molecules and contributing to an enhanced molecular selectivity. This underscores the potential of utilizing 2D metals for the precise control and optimization of GERS applications, which will benefit the development of highly sensitive, specific, and reliable sensors.

Nonlinear Optical Responses of Janus MoSSe/MoS2 Heterobilayers Optimized by Stacking Order and Strain.

Nonlinear optical responses in second harmonic generation (SHG) of van der Waals heterobilayers, Janus MoSSe/MoS2, are theoretically optimized as a function of strain and stacking order by adopting an exchange-correlation hybrid functional and a real-time approach in first-principles calculation. We find that the calculated nonlinear susceptibility, χ(2), in AA stacking (550 pm/V) becomes three times as large as AB stacking (170 pm/V) due to the broken inversion symmetry in the AA stacking. The present theoretical prediction is compared with the observed SHG spectra of Janus MoSSe/MoS2 heterobilayers, in which the peak SHG intensity of AA stacking becomes four times as large as AB stacking. Furthermore, a relatively large, two-dimensional strain (4%) that breaks the C3v point group symmetry of the MoSSe/MoS2, enhances calculated χ(2) values for both AA (900 pm/V) and AB (300 pm/V) stackings 1.6 times as large as that without strain.

Baseline prevalence of antimicrobial resistance in patients who develop a surgical site infection in hip and knee replacements: A brief report.

Prior to clean surgeries, decolonization with topical antimicrobials may lead to an increase in antimicrobial resistance. To provide a baseline prevalence of resistance to topical antimicrobials, in Alberta, specimens were collected from surgical site infections following hip and knee replacements. Among 81 samples with complex surgical site infections, in 43 specimens Staphylococcus species were isolated. Only coagulase-negative staphylococci isolates carried resistance genes with 10 carrying the gene qac and 6 carrying the MupA gene.

Step engineering for nucleation and domain orientation control in WSe2 epitaxy on c-plane sapphire.

Epitaxial growth of two-dimensional transition metal dichalcogenides on sapphire has emerged as a promising route to wafer-scale single-crystal films. Steps on the sapphire act as sites for transition metal dichalcogenide nucleation and can impart a preferred domain orientation, resulting in a substantial reduction in mirror twins. Here we demonstrate control of both the nucleation site and unidirectional growth direction of WSe2 on c-plane sapphire by metal-organic chemical vapour deposition. The unidirectional orientation is found to be intimately tied to growth conditions via changes in the sapphire surface chemistry that control the step edge location of WSe2 nucleation, imparting either a 0° or 60° orientation relative to the underlying sapphire lattice. The results provide insight into the role of surface chemistry on transition metal dichalcogenide nucleation and domain alignment and demonstrate the ability to engineer domain orientation over wafer-scale substrates.

Recent Advances in 2D Material Theory, Synthesis, Properties, and Applications.

Two-dimensional (2D) material research is rapidly evolving to broaden the spectrum of emergent 2D systems. Here, we review recent advances in the theory, synthesis, characterization, device, and quantum physics of 2D materials and their heterostructures. First, we shed insight into modeling of defects and intercalants, focusing on their formation pathways and strategic functionalities. We also review machine learning for synthesis and sensing applications of 2D materials. In addition, we highlight important development in the synthesis, processing, and characterization of various 2D materials (e.g., MXnenes, magnetic compounds, epitaxial layers, low-symmetry crystals, etc.) and discuss oxidation and strain gradient engineering in 2D materials. Next, we discuss the optical and phonon properties of 2D materials controlled by material inhomogeneity and give examples of multidimensional imaging and biosensing equipped with machine learning analysis based on 2D platforms. We then provide updates on mix-dimensional heterostructures using 2D building blocks for next-generation logic/memory devices and the quantum anomalous Hall devices of high-quality magnetic topological insulators, followed by advances in small twist-angle homojunctions and their exciting quantum transport. Finally, we provide the perspectives and future work on several topics mentioned in this review.

Assessment of virulence diversity of methicillin-resistant Staphylococcus aureus strains with a Drosophila melanogaster infection model.

BACKGROUND: Staphylococcus aureus strains with distinct genetic backgrounds have shown different virulence in animal models as well as associations with different clinical outcomes, such as causing infection in the hospital or the community. With S. aureus strains carrying diverse genetic backgrounds that have been demonstrated by gene typing and genomic sequences, it is difficult to compare these strains using mammalian models. Invertebrate host models provide a useful alternative approach for studying bacterial pathogenesis in mammals since they have conserved innate immune systems of biological defense. Here, we employed Drosophila melanogaster as a host model for studying the virulence of S. aureus strains. RESULTS: Community-associated methicillin-resistant S. aureus (CA-MRSA) strains USA300, USA400 and CMRSA2 were more virulent than a hospital-associated (HA)-MRSA strain (CMRSA6) and a colonization strain (M92) in the D. melanogaster model. These results correlate with bacterial virulence in the Caenorhabditis elegans host model as well as human clinical data. Moreover, MRSA killing activities in the D. melanogaster model are associated with bacterial replication within the flies. Different MRSA strains induced similar host responses in D. melanogaster, but demonstrated differential expression of common bacterial virulence factors, which may account for the different killing activities in the model. In addition, hemolysin α, an important virulence factor produced by S. aureus in human infections is postulated to play a role in the fly killing. CONCLUSIONS: Our results demonstrate that the D. melanogaster model is potentially useful for studying S. aureus pathogenicity. Different MRSA strains demonstrated diverse virulence in the D. melanogaster model, which may be the result of differing expression of bacterial virulence factors in vivo.