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.

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.

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.

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.

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.

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.

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.

Epidemiology and molecular characterization of Staphylococcus aureus causing bovine mastitis in water buffaloes from the Hazara division of Khyber Pakhtunkhwa, Pakistan.

Buffalo represent a major source of milk in Pakistan. However, production is impacted by the disease bovine mastitis. Mastitis causes significant economic losses, with Staphylococcus aureus (S. aureus) being one of its major causative agents. While much work has been done understanding the epidemiology of bovine mastitis in Pakistan, detailed molecular characterization of the associated S. aureus is unavailable. In the current study both the epidemiological and molecular characterization of S. aureus from bovine mastitis in the Hazara division of Pakistan are examined. S. aureus was isolated from 18.41% of the animals, and left quarters more prone to infection (69.6%) than right quarters (30.4%). Sub-clinical mastitis (75.31%) was more prevalent than clinical mastitis (24.69%), with infections evenly distributed amongst the eight districts. Molecular characterization revealed that only 19.6% of the isolates were methicillin-resistant, and four strains types identified, including ST9-t7867-MSSA, ST9-MSSA, ST101-t2078-MSSA, and ST22-t8934-MRSA-IVa. Antiseptic resistance genes were not detected in the isolates, and low levels of antibiotic resistance were also noted, however the methicillin-resistant strains had higher overall antibiotic resistance. This study represents the most complete molecular typing data for S. aureus causing bovine mastitis in the Hazara district of Pakistan, and the country as a whole.

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.

Rapid Biomarker Screening of Alzheimer's Disease by Interpretable Machine Learning and Graphene-Assisted Raman Spectroscopy.

The study of Alzheimer's disease (AD), the most common cause of dementia, faces challenges in terms of understanding the cause, monitoring the pathogenesis, and developing early diagnoses and effective treatments. Rapid and accurate identification of AD biomarkers in the brain is critical to providing key insights into AD and facilitating the development of early diagnosis methods. In this work, we developed a platform that enables a rapid screening of AD biomarkers by employing graphene-assisted Raman spectroscopy and machine learning interpretation in AD transgenic animal brains. Specifically, we collected Raman spectra on slices of mouse brains with and without AD and used machine learning to classify AD and non-AD spectra. By contacting monolayer graphene with the brain slices, the accuracy was increased from 77% to 98% in machine learning classification. Further, using a linear support vector machine (SVM), we identified a spectral feature importance map that reveals the importance of each Raman wavenumber in classifying AD and non-AD spectra. Based on this spectral feature importance map, we identified AD biomarkers including Aß and tau proteins and other potential biomarkers, such as triolein, phosphatidylcholine, and actin, which have been confirmed by other biochemical studies. Our Raman-machine learning integrated method with interpretability will facilitate the study of AD and can be extended to other tissues and biofluids and for various other diseases.

Understanding the Excitation Wavelength Dependence and Thermal Stability of the SARS-CoV-2 Receptor-Binding Domain Using Surface-Enhanced Raman Scattering and Machine Learning.

COVID-19 has cost millions of lives worldwide. The constant mutation of SARS-CoV-2 calls for thorough research to facilitate the development of variant surveillance. In this work, we studied the fundamental properties related to the optical identification of the receptor-binding domain (RBD) of SARS-CoV-2 spike protein, a key component of viral infection. The Raman modes of the SARS-CoV-2 RBD were captured by surface-enhanced Raman spectroscopy (SERS) using gold nanoparticles (AuNPs). The observed Raman enhancement strongly depends on the excitation wavelength as a result of the aggregation of AuNPs. The characteristic Raman spectra of RBDs from SARS-CoV-2 and MERS-CoV were analyzed by principal component analysis that reveals the role of secondary structures in the SERS process, which is corroborated with the thermal stability under laser heating. We can easily distinguish the Raman spectra of two RBDs using machine learning algorithms with accuracy, precision, recall, and F1 scores all over 95%. Our work provides an in-depth understanding of the SARS-CoV-2 RBD and paves the way toward rapid analysis and discrimination of complex proteins of infectious viruses and other biomolecules.

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.

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.

Spectroscopic Signatures of Interlayer Coupling in Janus MoSSe/MoS2 Heterostructures.

The interlayer coupling in van der Waals heterostructures governs a variety of optical and electronic properties. The intrinsic dipole moment of Janus transition metal dichalcogenides (TMDs) offers a simple and versatile approach to tune the interlayer interactions. In this work, we demonstrate how the van der Waals interlayer coupling and charge transfer of Janus MoSSe/MoS2 heterobilayers can be tuned by the twist angle and interface composition. Specifically, the Janus heterostructures with a sulfur/sulfur (S/S) interface display stronger interlayer coupling than the heterostructures with a selenium/sulfur (Se/S) interface as shown by the low-frequency Raman modes. The differences in interlayer interactions are explained by the interlayer distance computed by density-functional theory (DFT). More intriguingly, the built-in electric field contributed by the charge density redistribution and interlayer coupling also play important roles in the interfacial charge transfer. Namely, the S/S and Se/S interfaces exhibit different levels of photoluminescence (PL) quenching of MoS2 A exciton, suggesting enhanced and reduced charge transfer at the S/S and Se/S interface, respectively. Our work demonstrates how the asymmetry of Janus TMDs can be used to tailor the interfacial interactions in van der Waals heterostructures.

Staphylococcus aureus ST59: Concurrent but Separate Evolution of North American and East Asian Lineages.

Despite initially being described in North America, Staphylococcus aureus (SA) sequence type ST59 is the most commonly isolated sequence type in Eastern Asia. The origins and evolution of this strain type remains unclear and therefore we gathered a collection of ST59 isolates from Canada and mainland China for a detailed genetic analysis of the lineage. Bayesian inference phylogenomic analysis of our isolates, along with previously published ST59 sequences indicated that the lineage could be divided into 6 distinct subgroups (WGS-1 thorough 6), each having distinct molecular characteristics. Analysis also demonstrated the concurrent but separate evolution of North American and East Asian lineages, as well as the extensive diversification of the East Asian lineage. The presence of a mobile element structure (MES) was found to be the major difference between these two continental lineages, absent in all North American isolates, and present in all East Asian ones. Other mobile genetic elements, such as the Immune Evasion Complex (IEC), Panton Valentine Leukocidin (PVL), and Staphylococcal Cassette Chromosome mec (SCCmec), showed significant variability within each sub-group and likely represents local selective pressures rather than major characteristics defining the groups. Our analysis also demonstrated the existence of a more ancient ST59 sub-lineage from North America, which was MES negative and contained some of the earliest reported ST59 isolates. Combined with the existence of a MES negative isolate from Taiwan, predicted to have appeared prior to diversification of the East Asian lineages, these results hint at the possibility of a North American origin for the lineage, which gained hold in Eastern Asia following acquisition of MES, and subsequently diversified.

A Murine Skin Infection Model Capable of Differentiating the Dermatopathology of Community-Associated MRSA Strain USA300 from Other MRSA Strains.

USA300 is a predominant and highly virulent community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) strain that is a leading cause of skin and soft tissue infections. We established a murine intradermal infection model capable of demonstrating dermatopathological differences between USA300 and other MRSA strains. In this model, USA300 induced dermonecrosis, uniformly presenting as extensive open lesions with a histologically documented profound inflammatory cell infiltrate extending below the subcutis. In contrast, USA400 and a colonizing control strain M92 caused only localized non-ulcerated skin infections associated with a mild focal inflammatory infiltrate. It was also determined that the dermonecrosis induced by USA300 was associated with significantly increased neutrophil recruitment, inhibition of an antibacterial response, and increased production of cytokines/chemokines associated with disease severity. These results suggest that induction of severe skin lesions by USA300 is related to over-activation of neutrophils, inhibition of host antibacterial responses, and selective alteration of host cytokine/chemokine profiles.

Chirality-Dependent Second Harmonic Generation of MoS2 Nanoscroll with Enhanced Efficiency.

Materials with high second harmonic generation (SHG) efficiency and reduced dimensions are favorable for integrated photonics and nonlinear optical applications. Here, we fabricate MoS2 nanoscrolls with different chiralities and study their SHG performances. As a 1D material, MoS2 nanoscroll shows reduced symmetry and strong chirality dependency in the polarization-resolved SHG characterizations. This SHG performance can be well explained by the superposition theory of second harmonic field of the nanoscroll walls. MoS2 nanoscrolls with certain chiralities and diameters in our experiment can have SHG intensity up to 95 times stronger than that of monolayer MoS2, and the full potential can still be further exploited. The same chirality-dependent SHG can be expected for nanoscrolls or nanotubes composed of other noncentrosymmetric 2D materials, such as WS2, WSe2, and hBN. The characterization and analysis results presented here can also be exploited as a nondestructive technique to determine the chiralities of these nanoscrolls and nanotubes.

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.