SssP1, a Fimbria-like component of Streptococcus suis, binds to the vimentin of host cells and contributes to bacterial meningitis.

Streptococcus suis (S. suis) is one of the important pathogens that cause bacterial meningitis in pigs and humans. Evading host immune defences and penetrating the blood-brain barrier (BBB) are the preconditions for S. suis to cause meningitis, while the underlying mechanisms during these pathogenic processes are not fully understood. By detecting the red blood and white blood cells counts, IL-8 expression, and the pathological injury of brain in a mouse infection model, a serine-rich repeat (SRR) glycoprotein, designated as SssP1, was identified as a critical facilitator in the process of causing meningitis in this study. SssP1 was exported to assemble a fimbria-like component, thus contributed to the bacterial adhesion to and invasion into human brain microvascular endothelial cells (HBMECs), and activates the host inflammatory response during meningitis but is not involved in the actin cytoskeleton rearrangement and the disruption of tight junctions. Furthermore, the deletion of sssP1 significantly attenuates the ability of S. suis to traverse the BBB in vivo and in vitro. A pull-down analysis identified vimentin as the potential receptors of SssP1 during meningitis and following Far-Western blot results confirmed this ligand-receptor binding mediated by the NR2 (the second nonrepeat region) region of SssP1. The co-localisation of vimentin and S. suis observed by laser scanning confocal microscopy with multiplex fluorescence indicated that vimentin significantly enhances the interaction between SssP1 and BBB. Further study identified that the NR216-781 and NR1711-2214 fragments of SssP1 play critical roles to bind to the BBB depending on the sialylation of vimentin, and this binding is significantly attenuated when the antiserum of NR216-781 or NR1711-2214 blocked the bacterial cells, or the vimentin antibody blocked the BBB. Similar binding attenuations are observed when the bacterial cells were preincubated with the vimentin, or the BBB was preincubated with the recombinant protein NR216-781, NR1711-2214 or sialidase. In conclusion, these results reveal a novel receptor-ligand interaction that enhances adhesion to and penetration of the BBB to cause bacterial meningitis in the S. suis infection and highlight the importance of vimentin in host-pathogen interactions.

Outcomes Following Implementation of an Electronic Model for Perioperative Hematologic Consultation.

INTRODUCTION: Electronic consultations (e-consults) for periprocedural hematologic questions were introduced at the VA Connecticut Healthcare System in 2011. We sought to explore the relationship between the availability of e-consults, referral patterns, and surgical outcomes. METHODS: A single-center retrospective study of all perioperative hematologic consultations from 2006 to 2018 was conducted. Patient characteristics, indications, and outcomes were analyzed. Primary outcome measures were time from consult to surgery and operative morbidity via Clavien-Dindo classification. Secondary outcomes included consult volume and procedural outcomes of interest. RESULTS: Of 357 consultations, 62% were conducted via e-consults. 68.3% had associated procedural data and constituted the study cohort. Annual consult volume increased from 7 in 2006 to 41 in 2018, a 5.8-fold increase. E-consults comprised 20% of consults in 2011 but had risen to 92.3% in 2018. Time to resolution of e-consults after 2011 improved compared to pre-face-to-face (FTF-pre, P = 0.001) and FTF-post (P = 0.002). Time from consult to surgery remained unchanged. 8.4% had major complications (Clavien-Dindo >2) with readmission or reoperation occurring in 4.0% and 3.7%, respectively. Intraoperative and postoperative transfusions were required in 15.2% and 13.1% of cases, respectively. Hematologic complications (i.e., deep vein thrombosis/pulmonary embolism) occurred in 3.5%. Comparison between FTF and e-consults revealed no significant differences in these outcomes (P > 0.05, all). CONCLUSIONS: E-consults for perioperative hematologic issues were rapidly adopted and addressed more quickly than FTF consultation while time to surgery was unchanged despite increased consult volume. Adoption of the e-consult model was not associated with changes in the assessed operative outcomes.

The Impact of Extended Treatment With Artemether-lumefantrine on Antimalarial Exposure and Reinfection Risks in Ugandan Children With Uncomplicated Malaria: A Randomized Controlled Trial.

BACKGROUND: Artemether-lumefantrine (AL) is the most widely used artemisinin-based combination therapy in Sub-Saharan Africa and is threatened by the emergence of artemisinin resistance. Dosing is suboptimal in young children. We hypothesized that extending AL duration will improve exposure and reduce reinfection risks. METHODS: We conducted a prospective, randomized, open-label pharmacokinetic/pharmacodynamic study of extended duration AL in children with malaria in high-transmission rural Uganda. Children received 3-day (standard 6-dose) or 5-day (10-dose) AL with sampling for artemether, dihydroartemisinin, and lumefantrine over 42-day clinical follow-up. Primary outcomes were (1) comparative pharmacokinetic parameters between regimens and (2) recurrent parasitemia analyzed as intention-to-treat. RESULTS: A total of 177 children aged 16 months to 16 years were randomized, contributing 227 total episodes. Terminal median lumefantrine concentrations were significantly increased in the 5-day versus 3-day regimen on days 7, 14, and 21 (P < .001). A predefined day 7 lumefantrine threshold of 280 ng/mL was strongly predictive of recurrence risk at 28 and 42 days (P < .001). Kaplan-Meier estimated 28-day (51% vs 40%) and 42-day risk (75% vs 68%) did not significantly differ between 3- and 5-day regimens. No significant toxicity was seen with the extended regimen. CONCLUSIONS: Extending the duration of AL was safe and significantly enhanced overall drug exposure in young children but did not lead to significant reductions in recurrent parasitemia risk in our high-transmission setting. However, day 7 levels were strongly predictive of recurrent parasitemia risk, and those in the lowest weight-band were at higher risk of underdosing with the standard 3-day regimen. CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov number NCT03453840.

Identification of Subunits for Novel Universal Vaccines against Three Predominant Serogroups and the Emerging O145 among Avian Pathogenic Escherichia coli by Pan-RV Pipeline.

Avian pathogenic Escherichia coli, a causative agent of avian colibacillosis, has been causing serious economic losses in the poultry industry. The increase in multidrug-resistant isolates and the complexity of the serotypes of this pathogen, especially the recently reported emergence of a newly predominant serogroup of O145, make the control of this disease difficult. To address this challenge, a high-throughput screening approach, called Pan-RV (Reverse vaccinology based on pangenome analysis), is proposed to search for universal protective antigens against the three traditional serogroups and the newly emerged O145. Using this approach, a total of 61 proteins regarded as probable antigens against the four important serogroups were screened from the core genome of 127 Avian pathogenic Escherichia coli (APEC) genomes, and six were verified by Western blots using antisera. Overall, our research will provide a foundation for the development of an APEC subunit vaccine against avian colibacillosis. Given the exponential growth of whole-genome sequencing (WGS) data, our Pan-RV pipeline will make screening of bacterial vaccine candidates inexpensive, rapid, and efficient. IMPORTANCE With the emergence of drug resistance and the newly predominant serogroup O145, the control of Avian pathogenic Escherichia coli is facing a serious challenge; an efficient immunological method is urgently needed. Here, for the first time, we propose a high-throughput screening approach to search for universal protective antigens against the three traditional serogroups and the newly emerged O145. Importantly, using this approach, a total of 61 proteins regarded as probable antigens against the four important serogroups were screened, and three were shown to be immunoreactive with all antisera (covering the four serogroups), thereby providing a foundation for the development of APEC subunit vaccines against avian colibacillosis. Further, our Pan-RV pipeline will provide immunological control strategies for pathogens with complex and variable genetic backgrounds such as Escherichia coli and will make screening of bacterial vaccine candidates more inexpensive, rapid, and efficient.

Changes in opioid prescribing in veterans with headache during the COVID-19 pandemic: A regression discontinuity in time analysis.

OBJECTIVE: To determine changes in opioid prescribing among veterans with headaches during the coronavirus disease of 2019 (COVID-19) pandemic by comparing the stay-at-home phase (March 15 to May 30, 2020) and the reopening phase (May 31 to December 31, 2020). BACKGROUND: Opioid prescribing for chronic pain has declined substantially since 2016; however, changes in opioid prescribing during the COVID-19 pandemic among veterans with headaches remain unknown. METHODS: This retrospective cohort study utilized regression discontinuity in time and difference-in-differences design to analyze veterans aged ≥18 years with a previous diagnosis of headache disorders and an outpatient visit to the Veterans Health Administration (VHA) during the study period. We measured the weekly number of opioid prescriptions, the number of days supplied, the daily dose in morphine milligram equivalents (MMEs), and the number of prescriptions with ≥50 morphine equivalent daily doses (MEDD). RESULTS: A total of 81,376 veterans were analyzed with 589,950 opioid prescriptions. The mean (SD) age was 51.6 (13.5) years, 57,242 (70.3%) were male, and 53,464 (65.7%) were White. During the pre-pandemic period, 323.6 opioid prescriptions (interquartile range 292.1-325.8) were dispensed weekly, with an median (IQR) of 24.1 (24.0-24.4) days supplied and 31.8 (31.2-32.5) MMEs. Transition to stay-at-home was associated with a 7.7% decrease in the number of prescriptions (incidence rate ratio [IRR] 1.077, 95% confidence interval [CI] 0.866-0.984) and a 9.8% increase in days supplied (IRR 1.098, 95% CI 1.078-1.119). Similar trends were observed during the reopening period. Subgroup analysis among veterans on long-term opioid therapy also revealed 1.7% and 1.4% increases in days supplied during the stay-at-home (IRR 1.017, 95% CI 1.009-1.025) and reopening phase (IRR 1.014, 95% CI 1.007-1.021); however, changes in the total number of prescriptions, MME/day, or the number of prescriptions >50 MEDD were insignificant. CONCLUSION: Prescription opioid access was maintained for veterans within VHA during the pandemic. The de-escalation of opioid prescribing observed prior to the pandemic was not seen in our study.

Reverse transcription recombinase-aided amplification assay for avian influenza virus.

Avian influenza virus (AIV) infection can lead to severe economic losses in the poultry industry and causes a serious risk for humans. A rapid and simple test for suspected viral infection cases is crucial. In this study, a reverse transcription recombinase-aided amplification assay (RT-RAA) for the rapid detection of all AIV subtypes was developed. The reaction temperature of the assays is at 39 °C and the detection process can be completed in less than 20 min. The specificity results of the assay showed that this method had no cross-reaction with other main respiratory viruses that affect birds, including Newcastle disease virus (NDV) and infectious bronchitis virus (IBV). The analytical sensitivity at a 95% confidence interval was 102 RNA copies per reaction. In comparison with a published assay for reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR), the κ value of the RT-RAA assay in 384 avian clinical samples was 0.942 (p < 0.001). The sensitivity and specificity of the RT-RAA assay for avian clinical sample detection was determined as 97.59% (95% CI 93.55-99.23%) and 96.79% (95% CI 93.22-98.59%), respectively. The RT-RAA assay for AIV in this study provided an effective and practicable tool for AIV molecular detection.

Molecular epidemiology analysis of fowl adenovirus detected from apparently healthy birds in eastern China.

BACKGROUND: Fowl adenovirus is of major concern to the poultry industry worldwidely. In order to monitor the prevalent status of Fowl adenovirus in China, a total of 1920 clinical samples from apparently healthy birds in the 25 sites of poultry flocks, Slaughterhouse and living bird markets from 8 provinces in eastern China were collected and detected by PCR, sequencing, and phylogenetic analysis. RESULTS: The epidemiological survey showed that Fowl adenoviruses were detected in living bird markets, and circulating in a variety of fowl species, including chickens, ducks, goose and pigeons. Among the 1920 clinical samples, 166 samples (8.65%) were positive in the fowl adenovirus PCR detection. In this study, totally all the 12 serotypes (serotypes of 1, 2, 3, 4, 5, 6, 7, 8A, 8B, 9, 10 and 11) fowl adenoviruses were detected, the most prevalent serotype was serotype 1. Phylogenetic analysis indicated that 166 FAdVs of 12 serotypes were divided into 5 fowl adenovirus species (Fowl aviadenovirus A, B, C, D, E). CONCLUSIONS: In the epidemiological survey, 8.65% of the clinical samples from apparently healthy birds were positive in the fowl adenovirus PCR detection. Totally all the 12 serotypes fowl adenoviruses were detected in a variety of fowl species, which provided abundant resources for the research of fowl adenoviruses in China. The newly prevalent FAdV serotypes provides valuable information for the development of an effective control strategy for FAdV infections in fowls.

A Composite End Point of Graft Status and eGFR at 1 Year to Improve the Scientific Registry of Transplant Recipients' Five-Tier Rating System.

BACKGROUND: Performance of kidney transplant programs in the United States is monitored and publicly reported by the Scientific Registry of Transplant Recipients (SRTR). With relatively few allograft failure events per program and increasing homogeneity in program performance, quantifying meaningful differences in program competency based only on 1-year survival rates is challenging. METHODS: We explored whether the traditional end point of allograft failure at 1 year can be improved by incorporating a measure of allograft function (i.e., eGFR) into a composite end point. We divided SRTR data from 2008 through 2018 into a training and validation set and recreated SRTR tiers, using the traditional and composite end points. The conditional 5-year deceased donor allograft survival and 5-year eGFR were then assessed using each approach. RESULTS: Compared with the traditional end point, the composite end point of graft failure or eGFR <30 ml/min per 1.73 m2 at 1-year post-transplant performed better in stratifying transplant programs based on long-term deceased donor graft survival. For tiers 1 through 5 respectively, the 5-year conditional graft survival was 72.9%, 74.8%, 75.4%, 77.0%, and 79.7% using the traditional end point and 71.1%, 74.4%, 76.9%, 77.0%, and 78.4% with the composite end point. Additionally, with the five-tier system derived from the composite end point, programs in tier 3, tier 4, and tier 5 had significantly higher mean eGFRs at 5 years compared with programs in tier 1. There were no significant eGFR differences among tiers derived from the traditional end point alone. CONCLUSIONS: This proof-of-concept study suggests that a composite end point incorporating allograft function may improve the post-transplant component of the five-tier system by better differentiating between transplant programs with respect to long-term graft outcomes.

Characterization of G-type Clostridium perfringens bacteriophages and their disinfection effect on chicken meat.

OBJECTIVE: Clostridium perfringens is one of most important bacterial pathogens in the poultry industry and mainly causes necrotizing enteritis (NE). This pathogen and its toxins can cause foodborne diseases in humans through the food chain. In China, with the rise of antibiotic resistance and the banning of antibiotic growth promoters (AGPs) in poultry farming, food contamination and NE are becoming more prevalent. Bacteriophages are a viable technique to control C. perfringens as an alternative to antibiotics. We isolated Clostridium phage from the environment, providing a new method for the prevention of NE and C. perfringens contamination in meat. METHODS: In this study, we selected C. perfringens strains from various regions and animal sources in China for phage isolation. The biological characteristics of Clostridium phage were studied in terms of host range, MOI, one-step curve, temperature and pH stability. We sequenced and annotated the genome of the Clostridium phage and performed phylogenetic and pangenomic analyses. Finally, we studied its antibacterial activity against bacterial culture and its disinfection effect against C. perfringens in meat. RESULTS: A Clostridium phage, named ZWPH-P21 (P21), was isolated from chicken farm sewage in Jiangsu, China. P21 has been shown to specifically lyse C. perfringens type G. Further analysis of basic biological characteristics showed that P21 was stable under the conditions of pH 4-11 and temperature 4-60 °C, and the optimal multiple severity of infection (MOI) was 0.1. In addition, P21 could form a "halo" on agar plates, suggesting that the phage may encode depolymerase. Genome sequence analysis showed that P21 was the most closely related to Clostridium phage CPAS-15 belonging to the Myoviridae family, with a recognition rate of 97.24% and a query coverage rate of 98%. No virulence factors or drug resistance genes were found in P21. P21 showed promising antibacterial activity in vitro and in chicken disinfection experiments. In conclusion, P21 has the potential to be used for preventing and controlling C. perfringens in chicken food production.

Spectral Characteristics and Functional Responses of Phospholipid Bilayers in the Terahertz Band.

Understanding the vibrational information encoded within the terahertz (THz) spectrum of biomolecules is critical for guiding the exploration of its functional responses to specific THz radiation wavelengths. This study investigated several important phospholipid components of biological membranes-distearoyl phosphatidylethanolamine (DSPE), dipalmitoyl phosphatidylcholine (DPPC), sphingosine phosphorylcholine (SPH), and lecithin bilayer-using THz time-domain spectroscopy. We observed similar spectral patterns for DPPC, SPH, and the lecithin bilayer, all of which contain the choline group as the hydrophilic head. Notably, the spectrum of DSPE, which has an ethanolamine head group, was different. Interestingly, density functional theory calculations confirmed that the absorption peak common to DSPE and DPPC at approximately 3.0 THz originated from a collective vibration of their similar hydrophobic tails. Accordingly, the cell membrane fluidity of RAW264.7 macrophages with irradiation at 3.1 THz was significantly enhanced, leading to improved phagocytosis. Our results highlight the importance of the spectral characteristics of the phospholipid bilayers when studying their functional responses in the THz band and suggest that irradiation at 3.1 THz is a potential non-invasive strategy to increase the fluidity of phospholipid bilayers for biomedical applications such as immune activation or drug administration.

Trajectory of blood pressure after initiating anti-calcitonin gene-related peptide treatment of migraine: a target trial emulation from the veterans health administration.

BACKGROUND: Calcitonin gene-related peptide (CGRP) is involved in migraine pathophysiology and blood pressure regulation. Although clinical trials have established the cardio-cerebrovascular safety profile of anti-CGRP treatment, limited high-quality real-world evidence exists on its long-term effects on blood pressure (BP). To address this gap, we examined the safety of anti-CGRP treatment on BP in patients with migraine headache in the Veterans Health Administration (VHA). METHODS: We emulated a target trial of patients who initiated anti-CGRP treatment or topiramate for migraine prevention between May 17th, 2018 and February 28th, 2023. We calculated stabilized inverse probability weights to balance between groups and then used weighted linear mixed-effect models to estimate the systolic and diastolic BP changes over the study period. For patients without hypertension at baseline, we estimated the cumulative incidence of hypertension using Kaplan-Meier curve. We also used weight mixed-effect Poisson model to estimate the number of antihypertension medications for patients with hypertension at baseline. RESULTS: This analysis included 69,589 patients and 554,437 blood pressure readings. of these, 18,880 patients received anti-CGRP treatment, and they were more likely to be women, have a chronic migraine diagnosis and higher healthcare utilization than those received topiramate. Among patients without hypertension at baseline, we found no significant differences in systolic BP changes over the four-year follow-up between anti-CGRP (slope [standard error, SE] = 0.48[0.06]) and topiramate treated patients (slope[SE] = 0.39[0.04]). The incidence of hypertension was similar for anti-CGRP and topiramate group (4.4 vs 4.3 per 100 person-years). Among patients with hypertension at baseline who initiated anti-CGRP treatment, we found a small but persistent effect on exacerbating hypertension during the first four years of treatment, as evidenced by a significant annual 3.7% increase in the number of antihypertensive medications prescribed (RR = 1.037, 95%CI 1.025-1.048). CONCLUSIONS: Our findings suggest that anti-CGRP treatment is safe regarding blood pressure in patients without hypertension. However, for those with baseline hypertension, anti-CGRP treatment resulted in a small but persistent increase in the number of antihypertensives, indicating an exacerbation of hypertension. Future studies are needed to evaluate the cardio-cerebrovascular safety of anti-CGRP treatment beyond the first four years.

Provider Satisfaction With Infectious Diseases Telemedicine Consults for Hospitalized Patients During the Coronavirus Disease 2019 (COVID-19) Pandemic.

During the coronavirus disease 2019 (COVID-19) pandemic, our institution transitioned infectious diseases (ID) consultations on hospitalized patients to telemedicine. We evaluated satisfaction with telemedicine among referring providers and ID consultants. Respondents were satisfied with telemedicine consults for hospitalized patients, although there were significant differences in perceptions of quality and timeliness between consultants and referring providers.

Correction: Genetics, Receptor Binding Property, and Transmissibility in Mammals of Naturally Isolated H9N2 Avian Influenza Viruses.

[This corrects the article DOI: 10.1371/journal.ppat.1004508.].

Reverse transcription recombinase-aided amplification assay for H5 subtype avian influenza virus.

BACKGROUND: The H5 subtype avian influenza virus (AIV) has caused huge economic losses to the poultry industry and is a threat to human health. A rapid and simple test is needed to confirm infection in suspected cases during disease outbreaks. METHODS: In this study, we developed a reverse transcription recombinase-aided amplification (RT-RAA) assay for the detection of H5 subtype AIV. Assays were performed at a single temperature (39 °C), and the results were obtained within 20 min. RESULTS: The assay showed no cross-detection with Newcastle disease virus or infectious bronchitis virus. The analytical sensitivity was 103 RNA copies/µL at a 95% confidence interval according to probit regression analysis, with 100% specificity. Compared with published reverse transcription quantitative real-time polymerase chain reaction assays, the κ value of the RT-RAA assay in 420 avian clinical samples was 0.983 (p < 0.001). The sensitivity for avian clinical sample detection was 97.26% (95% CI, 89.56-99.52%), and the specificity was 100% (95% CI, 98.64-100%). CONCLUSIONS: These results indicated that our RT-RAA assay may be a valuable tool for detecting H5 subtype AIV.

Telehealth perceptions and utilization for the delivery of headache care before and during the COVID-19 pandemic: A mixed-methods study.

OBJECTIVE: The objective of this study was to evaluate the utilization of telehealth for headache services within the Veterans Health Administration's facilities housing a Headache Centers of Excellence and multiple stakeholder's perspectives to inform future telehealth delivery. BACKGROUND: Telehealth delivery of headache treatment may enhance patient access to headache care, yet little is known about the utilization or patient and provider perceptions of telehealth for veterans with headache. METHODS: This mixed-methods study analyzed multiple data sources: (1) administrative data, which included 58,798 patients with medically diagnosed headache disorders, documented in at least one outpatient visit, from August 2019 through September 2020 from the 12 Veterans Health Administration's facilities with a Headache Center of Excellence and (2) qualitative semistructured interviews with 20 patients and 43 providers 6 months before the coronavirus disease 2019 (COVID-19) pandemic, and 10 patients and 20 providers 6 months during the beginning of the pandemic. RESULTS: During the pandemic, in-person visits declined from 12,794 to 6099 (52.0%), whereas video (incidence rate ratio [IRR] = 2.05, 95% confidence interval [CI] = 1.66, 2.52), and telephone visits (IRR = 15.2, 95% CI = 10.7, 21.6) significantly increased. Utilization differed based on patient age, race/ethnicity, and rurality. Patients and providers perceived value in using telehealth, yet had limited experience with this modality pre-pandemic. Providers preferred in-person appointments for initial encounters and telehealth for follow-up visits. Providers and patients identified benefits and challenges of telehealth delivery, often relying on multiple delivery methods for telehealth to enhance patient engagement. CONCLUSIONS: The uptake of telehealth delivery of headache-related care rapidly expanded in response to the pandemic. Patients and providers were amenable to utilizing telehealth, yet also experienced technological barriers. To encourage equitable access to telehealth and direct resources to those in need, it is crucial to understand patient preferences regarding in-person versus telehealth visits and identify patient groups who face barriers to access.

Compositional and functional alterations of gut microbiota in patients with stroke.

BACKGROUND AND AIMS: There is accumulating evidence that gut microbiota plays a key role in cardiovascular diseases. Gut bacteria can transform dietary choline, l-carnitine, and trimethylamine N-oxide (TMAO) into trimethylamine, which can be oxidized into TMAO again in the liver. However, the alterations of the gut microbiota in large artery atherosclerotic (LAA) stroke and cardioembolic (CE) stroke have been less studied. METHODS AND RESULTS: We performed a case-control study in patients with LAA and CE types of strokes. We profiled the gut microbiome using Illumina sequencing of the 16S ribosomal RNA gene (V4-V5 regions), and TMAO was determined via liquid chromatography-tandem mass spectrometry. Our results showed that the TMAO levels in the plasma of patients with LAA and CE strokes were significantly higher than those in controls (LAA stroke, 2931 ± 456.4 ng/mL; CE stroke, 4220 ± 577.6 ng/mL; healthy control, 1663 ± 117.8 ng/mL; adjusted p < 0.05). The TMAO level in the plasma of patients with LAA stroke was positively correlated with the carotid plaque area (rho = 0.333, 95% CI = 0.08-0.55, p = 0.0093). Notably, the composition and the function of gut microbiota in the LAA stroke group were significantly different from those in the control group (FDR-adjusted p-value < 0.05). There was no significant association between gut microbiota and CE stroke in our study. CONCLUSION: This study provides evidence for significant compositional and functional alterations of the gut microbiome in patients with LAA stroke. Gut microbiota might serve as a potential biomarker for patients with LAA stroke.

Complex Permittivity Characterization of Liquid Samples Based on a Split Ring Resonator (SRR).

A complex permittivity characterization method for liquid samples has been proposed. The measurement is carried out based on a self-designed microwave sensor with a split ring resonator (SRR), the unload resonant frequency of which is 5.05 GHz. The liquid samples in capillary are placed in the resonant zone of the fabricated senor for high sensitivity measurement. The frequency shift of 58.7 MHz is achieved when the capillary is filled with ethanol, corresponding a sensitivity of 97.46 MHz/µL. The complex permittivity of methanol, ethanol, isopropanol (IPA) and deionized water at the resonant frequency are measured and calibrated by the first order Debye model. Then, the complex permittivity of different concentrations of aqueous solutions of these materials are measured by using the calibrated sensor system. The results show that the proposed sensor has high sensitivity and accuracy in measuring the complex permittivity of liquid samples with volumes as small as 0.13 µL. It provides a useful reference for the complex permittivity characterization of small amount of liquid chemical samples. In addition, the characterization of an important biological sample (inositol) is carried out by using the proposed sensor.

Deep neural networks for human microRNA precursor detection.

BACKGROUND: MicroRNAs (miRNAs) play important roles in a variety of biological processes by regulating gene expression at the post-transcriptional level. So, the discovery of new miRNAs has become a popular task in biological research. Since the experimental identification of miRNAs is time-consuming, many computational tools have been developed to identify miRNA precursor (pre-miRNA). Most of these computation methods are based on traditional machine learning methods and their performance depends heavily on the selected features which are usually determined by domain experts. To develop easily implemented methods with better performance, we investigated different deep learning architectures for the pre-miRNAs identification. RESULTS: In this work, we applied convolution neural networks (CNN) and recurrent neural networks (RNN) to predict human pre-miRNAs. We combined the sequences with the predicted secondary structures of pre-miRNAs as input features of our models, avoiding the feature extraction and selection process by hand. The models were easily trained on the training dataset with low generalization error, and therefore had satisfactory performance on the test dataset. The prediction results on the same benchmark dataset showed that our models outperformed or were highly comparable to other state-of-the-art methods in this area. Furthermore, our CNN model trained on human dataset had high prediction accuracy on data from other species. CONCLUSIONS: Deep neural networks (DNN) could be utilized for the human pre-miRNAs detection with high performance. Complex features of RNA sequences could be automatically extracted by CNN and RNN, which were used for the pre-miRNAs prediction. Through proper regularization, our deep learning models, although trained on comparatively small dataset, had strong generalization ability.

The Effect of KcsA Channel on Lipid Bilayer Electroporation Induced by Picosecond Pulse Trains.

Membrane proteins are the major component of plasma membranes, and they play crucial roles in all organisms. To understand the influence of the presence of KcsA channel on cell membrane electroporation induced by picosecond pulse trains (psPT), in this paper, the electroporation of KcsA membrane protein system and bare lipid bilayer system (POPC) with the applied psPT are simulated using molecular dynamics (MD) method. First, we find that the average pore formation time of the KcsA system is longer than the bare system with the applied psPT. In the KcsA system, water protrusions appear more slowly. Then, the system size effects of psPT in the MD simulations are investigated. When the system size decreases, the average pore formation time of small KcsA membrane protein system is shorter than the bare system with the applied psPT. It is found that the psPT makes the protein fluctuation of small system increase greatly; meanwhile the instability of protein disturbs the water and then affects the water protrusion appearance time. Furthermore, it shows that the protein fluctuation of constant electric field is smaller than that of psPT and no field, and protein fluctuation increases with the psPT repetition frequency increasing.

Differences in pathogenicity and virulence-associated gene expression among Pasteurella multocida strains with high and low virulence in a lung tissue model.

Pasteurella multocida capsular type A can cause a pulmonary infection, leading to serious pecuniary losses in cattle. The heterogeneity of infection outcome of P. multocida strains showing different virulence may be related to divergent expression of virulence genes. In this study, we compared the transcriptional response of virulence-associated genes in high (PMPAN001) and low (PMPAN007) virulence P. multocida capsular type A strains in lung tissues and in vitro. These clinical isolates differ in their organ bacterial loads, mRNA abundance of the same virulence genes between lung and culture medium, and extent of lung damage. Among the eight virulence-associated genes (fimA, tbpA, exbD, fur, oma87, pmHAS, nanH, and tonB), seven genes showed higher expression in lung compared with in vitro at 16 h (P ≤ 0.05) in PMPAN001, but not in PMPAN007. FimA, exbD, fur, oma87, pmHAS, and tonB gene transcripts showed significantly higher expression in PMPAN001 than in PMPAN007 in the lung tissues at 16 h post-infection (P ≤ 0.05). Specially, the virulence gene, nanH, in both strains was associated with poor expression in vitro and lung tissue (mean relative mRNA abundance values < 0.6). Strain PMPAN001 had a higher proliferation rate in vivo than strain PMPAN007. The bacterial loads of PMPAN001 in the organs increased from 12 h post-infection, with maximum bacteria count ranging from 1 million to 20 million/mg. In addition, lungs treated with PMPAN001 produced serious and extensive lesions marked with inflammation at 20 h. Overall, our results reveal that the highly expressed virulence-associated genes, fimA, exbD, fur, oma87, pmHAS, and tonB can be used as markers for assessing the virulence of P. multocida capsular type A strains.