WGS of a cluster of MDR Shigella sonnei utilizing Oxford Nanopore R10.4.1 long-read sequencing.

OBJECTIVES: To utilize long-read nanopore sequencing (R10.4.1 flowcells) for WGS of a cluster of MDR Shigella sonnei, specifically characterizing genetic predictors of antimicrobial resistance (AMR). METHODS: WGS was performed on S. sonnei isolates identified from stool and blood between September 2021 and October 2022. Bacterial DNA from clinical isolates was extracted on the MagNA Pure 24 and sequenced on the GridION utilizing R10.4.1 flowcells. Phenotypic antimicrobial susceptibility testing was interpreted based on CLSI breakpoints. Sequencing data were processed with BugSeq, and AMR was assessed with BugSplit and ResFinder. RESULTS: Fifty-six isolates were sequenced, including 53 related to the cluster of cases. All cluster isolates were identified as S. sonnei by sequencing, with global genotype 3.6.1.1.2 (CipR.MSM5), MLST 152 and PopPUNK cluster 3. Core genome MLST (cgMLST, examining 2513 loci) and reference-based MLST (refMLST, examining 4091 loci) both confirmed the clonality of the isolates. Cluster isolates were resistant to ampicillin (blaTEM-1), trimethoprim/sulfamethoxazole (dfA1, dfrA17; sul1, sul2), azithromycin (ermB, mphA) and ciprofloxacin (gyrA S83L, gyrA D87G, parC S80I). No genomic predictors of resistance to carbapenems were identified. CONCLUSIONS: WGS with R10.4.1 enabled rapid sequencing and identification of an MDR S. sonnei community cluster. Genetic predictors of AMR were concordant with phenotypic antimicrobial susceptibility testing.

Knowledge graph embedding for profiling the interaction between transcription factors and their target genes.

Interactions between transcription factor and target gene form the main part of gene regulation network in human, which are still complicating factors in biological research. Specifically, for nearly half of those interactions recorded in established database, their interaction types are yet to be confirmed. Although several computational methods exist to predict gene interactions and their type, there is still no method available to predict them solely based on topology information. To this end, we proposed here a graph-based prediction model called KGE-TGI and trained in a multi-task learning manner on a knowledge graph that we specially constructed for this problem. The KGE-TGI model relies on topology information rather than being driven by gene expression data. In this paper, we formulate the task of predicting interaction types of transcript factor and target genes as a multi-label classification problem for link types on a heterogeneous graph, coupled with solving another link prediction problem that is inherently related. We constructed a ground truth dataset as benchmark and evaluated the proposed method on it. As a result of the 5-fold cross experiments, the proposed method achieved average AUC values of 0.9654 and 0.9339 in the tasks of link prediction and link type classification, respectively. In addition, the results of a series of comparison experiments also prove that the introduction of knowledge information significantly benefits to the prediction and that our methodology achieve state-of-the-art performance in this problem.

Validation of Machine Learning-Aided and Power Line Communication-Based Cable Monitoring Using Measurement Data.

The implementation of power line communications (PLC) in smart electricity grids provides us with exciting opportunities for real-time cable monitoring. In particular, effective fault classification and estimation methods employing machine learning (ML) models have been proposed in the recent past. Often, the research works presenting PLC for ML-aided cable diagnostics are based on the study of synthetically generated channel data. In this work, we validate ML-aided diagnostics by integrating measured channels. Specifically, we consider the concatenation of clustering as a data pre-processing procedure and principal component analysis (PCA)-based dimension reduction for cable anomaly detection. Clustering and PCA are trained with measurement data when the PLC network is working under healthy conditions. A possible cable anomaly is then identified from the analysis of the PCA reconstruction error for a test sample. For the numerical evaluation of our scheme, we apply an experimental setup in which we introduce degradations to power cables. Our results show that the proposed anomaly detector is able to identify a cable degradation with high detection accuracy and low false alarm rate.

People With Human Immunodeficiency Virus Receiving Suppressive Antiretroviral Therapy Show Typical Antibody Durability After Dual Coronavirus Disease 2019 Vaccination and Strong Third Dose Responses.

BACKGROUND: Longer-term humoral responses to 2-dose coronavirus disease 2019 (COVID-19) vaccines remain incompletely characterized in people living with human immunodeficiency virus (HIV) (PLWH), as do initial responses to a third dose. METHODS: We measured antibodies against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein receptor-binding domain, angiotensin-converting enzyme 2 (ACE2) displacement, and viral neutralization against wild-type and Omicron strains up to 6 months after 2-dose vaccination, and 1 month after the third dose, in 99 PLWH receiving suppressive antiretroviral therapy and 152 controls. RESULTS: Although humoral responses naturally decline after 2-dose vaccination, we found no evidence of lower antibody concentrations or faster rates of antibody decline in PLWH compared with controls after accounting for sociodemographic, health, and vaccine-related factors. We also found no evidence of poorer viral neutralization in PLWH after 2 doses, nor evidence that a low nadir CD4+ T-cell count compromised responses. Post-third-dose humoral responses substantially exceeded post-second-dose levels, though Omicron-specific responses were consistently weaker than responses against wild-type virus. Nevertheless, post-third-dose responses in PLWH were comparable to or higher than controls. An mRNA-1273 third dose was the strongest consistent correlate of higher post-third-dose responses. CONCLUSION: PLWH receiving suppressive antiretroviral therapy mount strong antibody responses after 2- and 3-dose COVID-19 vaccination. Results underscore the immune benefits of third doses in light of Omicron.

Reduced Magnitude and Durability of Humoral Immune Responses to COVID-19 mRNA Vaccines Among Older Adults.

BACKGROUND: The magnitude and durability of immune responses to coronavirus disease 2019 (COVID-19) mRNA vaccines remain incompletely characterized in the elderly. METHODS: Anti-spike receptor-binding domain (RBD) antibodies, angiotensin-converting enzyme 2 (ACE2) competition, and virus neutralizing activities were assessed in plasma from 151 health care workers and older adults (range, 24-98 years of age) 1 month following the first vaccine dose, and 1 and 3 months following the second dose. RESULTS: Older adults exhibited significantly weaker responses than younger health care workers for all humoral measures evaluated and at all time points tested, except for ACE2 competition activity after 1 vaccine dose. Moreover, older age remained independently associated with weaker responses even after correction for sociodemographic factors, chronic health condition burden, and vaccine-related variables. By 3 months after the second dose, all humoral responses had declined significantly in all participants, and remained significantly lower among older adults, who also displayed reduced binding antibodies and ACE2 competition activity towards the Delta variant. CONCLUSIONS: Humoral responses to COVID-19 mRNA vaccines are significantly weaker in older adults, and antibody-mediated activities in plasma decline universally over time. Older adults may thus remain at elevated risk of infection despite vaccination.

Older Adults Mount Less Durable Humoral Responses to Two Doses of COVID-19 mRNA Vaccine but Strong Initial Responses to a Third Dose.

BACKGROUND: Third coronavirus disease 2019 (COVID-19) vaccine doses are broadly recommended, but immunogenicity data remain limited, particularly in older adults. METHODS: We measured circulating antibodies against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein receptor-binding domain, ACE2 displacement, and virus neutralization against ancestral and omicron (BA.1) strains from prevaccine up to 1 month following the third dose, in 151 adults aged 24-98 years who received COVID-19 mRNA vaccines. RESULTS: Following 2 vaccine doses, humoral immunity was weaker, less functional, and less durable in older adults, where a higher number of chronic health conditions was a key correlate of weaker responses and poorer durability. One month after the third dose, antibody concentrations and function exceeded post-second-dose levels, and responses in older adults were comparable in magnitude to those in younger adults at this time. Humoral responses against omicron were universally weaker than against the ancestral strain after both the second and third doses. Nevertheless, after 3 doses, anti-omicron responses in older adults reached equivalence to those in younger adults. One month after 3 vaccine doses, the number of chronic health conditions, but not age, was the strongest consistent correlate of weaker humoral responses. CONCLUSIONS: Results underscore the immune benefits of third COVID-19 vaccine doses, particularly in older adults.

Power Line Communication and Sensing Using Time Series Forecasting.

Smart electrical grids rely on data communication to support their operation and on sensing for diagnostics and maintenance. Usually, the roles of communication and sensing equipment are different, i.e., communication equipment does not participate in sensing tasks and vice versa. Power line communication (PLC) offers a cost-effective solution for joint communication and sensing for smart grids. This is because the high-frequency PLC signals used for data communication also reveal detailed information regarding the health of the power lines that they travel through. Traditional PLC-based power line or cable diagnostic solutions are dependent on prior knowledge of the cable type, network topology, and/or characteristics of the anomalies. In this paper, we develop a power line sensing technique that can detect various types of cable anomalies without any prior domain knowledge. To this end, we design a solution that first uses time-series forecasting to predict the PLC channel state information at any given point in time based on its historical data. Under the approximation that the prediction error follows a Gaussian distribution, we then perform chi-squared statistical test to build an anomaly detector which identifies the occurrence of a cable fault. We demonstrate the effectiveness and universality of our sensing solution via evaluations conducted using both synthetic and real-world data extracted from low- and medium-voltage distribution networks.

Current Perspectives on Nucleus Pulposus Fibrosis in Disc Degeneration and Repair.

A growing body of evidence in humans and animal models indicates an association between intervertebral disc degeneration (IDD) and increased fibrotic elements in the nucleus pulposus (NP). These include enhanced matrix turnover along with the abnormal deposition of collagens and other fibrous matrices, the emergence of fibrosis effector cells, such as macrophages and active fibroblasts, and the upregulation of the fibroinflammatory factors TGF-ß1 and IL-1/-13. Studies have suggested a role for NP cells in fibroblastic differentiation through the TGF-ßR1-Smad2/3 pathway, inflammatory activation and mechanosensing machineries. Moreover, NP fibrosis is linked to abnormal MMP activity, consistent with the role of matrix proteases in regulating tissue fibrosis. MMP-2 and MMP-12 are the two main profibrogenic markers of myofibroblastic NP cells. This review revisits studies in the literature relevant to NP fibrosis in an attempt to stratify its biochemical features and the molecular identity of fibroblastic cells in the context of IDD. Given the role of fibrosis in tissue healing and diseases, the perspective may provide new insights into the pathomechanism of IDD and its management.

Rapid Detection of SARS-CoV-2 Variants of Concern, Including B.1.1.28/P.1, British Columbia, Canada.

To screen all severe acute respiratory syndrome coronavirus 2-positive samples in Vancouver, British Columbia, Canada, and determine whether they represented variants of concern, we implemented a real-time reverse transcription PCR-based algorithm. We rapidly identified 77 samples with variants: 57 with B.1.1.7, 7 with B.1.351, and an epidemiologic cluster of 13 with B.1.1.28/P.1.

Repeat virological and serological profiles in hospitalized patients initially tested by nasopharyngeal RT-PCR for SARS-CoV-2.

Real-time polymerase chain reaction (PCR) for SARS-CoV-2 is the mainstay of COVID-19 diagnosis, yet there are conflicting reports on its diagnostic performance. Wide ranges of false-negative PCR tests have been reported depending on clinical presentation, the timing of testing, specimens tested, testing method, and reference standard used. We aimed to estimate the frequency of discordance between initial nasopharyngeal (NP) PCR and repeat NP sampling PCR and serology in acutely ill patients admitted to the hospital. Panel diagnosis of COVID-19 infection is further utilized in discordance analysis. Included in the study were 160 patients initially tested by NP PCR with repeat NP sampling PCR and/or serology performed. The percent agreement between initial and repeat PCR was 96.7%, while the percent agreement between initial PCR and serology was 98.9%. There were 5 (3.1%) cases with discordance on repeat testing. After discordance analysis, 2 (1.4%) true cases tested negative on initial PCR. Using available diagnostic methods, discordance on repeat NP sampling PCR and/or serology is a rare occurrence.

Practical challenges to the clinical implementation of saliva for SARS-CoV-2 detection.

Due to global shortages of flocked nasopharyngeal swabs and appropriate viral transport media during the COVID-19 pandemic, alternate diagnostic specimens for SARS-CoV-2 detection are sought. The accuracy and feasibility of saliva samples collected and transported without specialized collection devices or media were evaluated. Saliva demonstrated good concordance with paired nasopharyngeal swabs for SARS-CoV-2 detection in 67/74 cases (90.5%), though barriers to saliva collection were observed in long-term care residents and outbreak settings. SARS-CoV-2 RNA was stable in human saliva at room temperature for up to 48 h after initial specimen collection, informing appropriate transport time and conditions.

Suboptimal Biological Sampling as a Probable Cause of False-Negative COVID-19 Diagnostic Test Results.

False-negative severe acute respiratory syndrome coronavirus 2 test results can negatively impact the clinical and public health response to coronavirus disease 2019 (COVID-19). We used droplet digital polymerase chain reaction (ddPCR) to demonstrate that human DNA levels, a stable molecular marker of sampling quality, were significantly lower in samples from 40 confirmed or suspected COVID-19 cases that yielded negative diagnostic test results (ie, suspected false-negative test results) compared with a representative pool of 87 specimens submitted for COVID-19 testing. Our results support suboptimal biological sampling as a contributor to false-negative COVID-19 test results and underscore the importance of proper training and technique in the collection of nasopharyngeal specimens.

Editorial Expression of Concern: Comparative effectiveness of ß-lactam versus vancomycin empiric therapy in patients with methicillin-susceptible Staphylococcus aureus (MSSA) bacteremia.

An amendment to this paper has been published and can be accessed via the original article.

Type of Pelvic Disease as a Risk Factor for Surgical Site Infectionin Women Undergoing Hysterectomy.

STUDY OBJECTIVE: To quantify the relationship between type of benign pelvic disease and risk of surgical site infection (SSI) after hysterectomy. DESIGN: Retrospective cohort study (Canadian Task Force classification II-2). SETTING: Hospitals participating in the American College of Surgeons National Surgical Quality Improvement Program (NSQIP). PATIENTS: Women who underwent hysterectomy from 2006-2015 and recorded in NSQIP database. INTERVENTION: None. MEASUREMENTS AND MAIN RESULTS: SSI risk was compared for type of benign pelvic disease, patient characteristics (i.e., age, race, and selected comorbidities) and process of care variables (i.e., admission status, type of hysterectomy, and operative time). SSI occurred in 2.48% of the 125,337 women who underwent hysterectomy. SSI was most frequent in patients with endometriosis and least frequent in those with genital prolapse (3.13% vs 1.39%; p <.0001). Following adjustment for potential confounders, the odds of SSI were higher in women undergoing hysterectomy for endometriosis (adjusted odds ratio [aOR], 1.79; 95% confidence interval [CI], 1.43- 2.25), uterine myomas (aOR, 1.28; 95% CI, 1.05-1.55), menstrual disorders (aOR, 1.46; 95% CI, 1.20-1.78), and pelvic pain (aOR, 1.75; 95% CI, 1.34-2.27) compared with women undergoing hysterectomy for genital prolapse. Other patient factors associated with SSI included age, body mass index, smoking, diabetes mellitus, chronic obstructive pulmonary disease, hypertension, and American Society of Anesthesiologists classification. Among process-of-care factors, inpatient status, route of hysterectomy, total vs subtotal hysterectomy, and operative time were also associated with SSI. CONCLUSION: In addition to various patient and process-of-care factors known to be associated with SSI, type of underlying pelvic disease is an independent risk factor for SSI in women undergoing hysterectomy for benign indications.

Clinical trials of intervertebral disc regeneration: current status and future developments.

Intervertebral disc (IVD) degeneration (IDD) is considered as one of the major causes for low back pain (LBP). However, conventional surgical approaches for treating LBP do not aim to counter the degeneration. Biological interventions have been investigated with an attempt to regenerate the IVD by restoring its matrices and cell activities. This review summarizes the current clinical trials that explore the efficacy of covering cell-, growth factor-, and small molecule-based approaches. While investigations of growth factor- and small molecule-based therapies are still preliminary, intradiscal delivery of mesenchymal stromal cells has been more widely adopted and shown positive results in addressing the pain and the associated physical disability, albeit to a lower extent than observed in previous animal studies. Strategies that potentiate the endogenous disc progenitors may offer a valid alternative to the exogenous cell transplantation. Identification of the novel biologics to arrest IDD phenotype may potentiate disc repair in future. Large-scale, high-quality long-term trials should be conducted to clarify the safety and efficacy of these therapies.

Expression and Activity of TRPA1 and TRPV1 in the Intervertebral Disc: Association with Inflammation and Matrix Remodeling.

Transient receptor potential (TRP) channels have emerged as potential sensors and transducers of inflammatory pain. The aims of this study were to investigate (1) the expression of TRP channels in intervertebral disc (IVD) cells in normal and inflammatory conditions and (2) the function of Transient receptor potential ankyrin 1 (TRPA1) and Transient receptor potential vanilloid 1 (TRPV1) in IVD inflammation and matrix homeostasis. RT-qPCR was used to analyze human fetal, healthy, and degenerated IVD tissues for the gene expression of TRPA1 and TRPV1. The primary IVD cell cultures were stimulated with either interleukin-1 beta (IL-1ß) or tumor necrosis factor alpha (TNF-α) alone or in combination with TRPA1/V1 agonist allyl isothiocyanate (AITC, 3 and 10 µM), followed by analysis of calcium flux and the expression of inflammation mediators (RT-qPCR/ELISA) and matrix constituents (RT-qPCR). The matrix structure and composition in caudal motion segments from TRPA1 and TRPV1 wild-type (WT) and knock-out (KO) mice was visualized by FAST staining. Gene expression of other TRP channels (A1, C1, C3, C6, V1, V2, V4, V6, M2, M7, M8) was also tested in cytokine-treated cells. TRPA1 was expressed in fetal IVD cells, 20% of degenerated IVDs, but not in healthy mature IVDs. TRPA1 expression was not detectable in untreated cells and it increased upon cytokine treatment, while TRPV1 was expressed and concomitantly reduced. In inflamed IVD cells, 10 µM AITC activated calcium flux, induced gene expression of IL-8, and reduced disintegrin and metalloproteinase with thrombospondin motifs 5 (ADAMTS5) and collagen 1A1, possibly via upregulated TRPA1. TRPA1 KO in mice was associated with signs of degeneration in the nucleus pulposus and the vertebral growth plate, whereas TRPV1 KO did not show profound changes. Cytokine treatment also affected the gene expression of TRPV2 (increase), TRPV4 (increase), and TRPC6 (decrease). TRPA1 might be expressed in developing IVD, downregulated during its maturation, and upregulated again in degenerative disc disease, participating in matrix homeostasis. However, follow-up studies with larger sample sizes are needed to fully elucidate the role of TRPA1 and other TRP channels in degenerative disc disease.

Cognitive information measurements: A new perspective.

From a traditional point of view, the value of information does not change during transmission. The Shannon information theory considers information transmission as a statistical phenomenon for measuring the communication channel capacity. However, in modern communication systems, information is spontaneously embedded with a cognitive link during the transmission process, which requires a new measurement that can incorporate continuously changing information values. In this paper, we introduce the concept of cognitive information value and a method of measuring such information. We first describe the characteristics of cognitive information followed by an introduction of the concept of cognitive information in measuring information popularity. The new measurement is based on the mailbox principle in the information value chain. This is achieved by encapsulating the information as a mailbox for transmission where the cognition is continuously implemented during the transmission process. Finally, we set up a cognitive communication system based on a combination of the traditional communication system and cognitive computing. Experimental results attest to the impact of incorporating cognitive value in the performance of 5G networks.

Antimicrobial Resistance Gene Acquisition and Depletion Following Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection.

Fecal microbiota transplantation (FMT) may be a novel approach to eliminate multidrug-resistant bacteria from the gut and to prevent future infections. Using whole metagenome sequencing data from 8 FMT donor-recipient pairs, we identified 37 and 95 antimicrobial resistance genes that were acquired by or removed from FMT recipients, respectively.

Clinical heterogeneity of patients with stool samples testing PCR+/Tox- from a two-step Clostridium difficile diagnostic algorithm.

The clinical significance of indeterminate (PCR+/Tox-) results for patients tested with a two-step algorithm for Clostridium difficile infection (CDI) is uncertain. We aimed to evaluate the clinical presentation and 8-week outcomes of patients with indeterminate test results. Patients with stool samples testing positive by PCR and negative by toxin A/B immunoassay between February 1, 2017, and April 30, 2018, were assessed by antimicrobial stewardship program (ASP) clinicians and classified as colonized or infected. Retrospective chart review was performed to obtain outcomes occurring within 8 weeks of testing, including recurrent C. difficile diarrhea, subsequent treatment for CDI, follow-up C. difficile testing, all-cause mortality, and CDI-related complications. In total, 110 PCR+/Tox- patients were evaluated. ASP classified 54% of patients as infected and 46% as colonized. Patients assessed and classified as colonized did not have increased adverse outcomes by 8 weeks compared to those assessed as infected, despite not receiving treatment for CDI. We conclude that PCR+/Tox- patients are heterogeneous with respect to clinical presentation. Negative toxin A/B immunoassay in a two-step algorithm should not be interpreted in isolation to distinguish colonization from infection as many PCR+/Tox- results may be clinically significant for CDI.