Identical Type Research Articles

Estimation of Inter-System Biases between BDS-3/GPS/Galileo and Its Application in RTK Positioning

For the development of a global navigation satellite system (GNSS), the third generation of BeiDou Navigation Satellite System (BDS-3) achieved full constellation for worldwide service on 23 June 2020. The new signals, B1C and B2a of BDS-3, further enhance the compatibility and interoperability between different GNSSs. In this study, we first assessed the quality of all the signals in BDS-3/GPS/Galileo. Then, to achieve the interoperability among BDS-3/GPS/Galileo, the inter-system bias (ISB), which appears if an inter-system difference exists between two GNSSs, was estimated at overlapping frequencies. Finally, we used the estimated ISBs in real-time kinematic (RTK) positioning. The results show the higher quality of the overlapping frequency B2a/L5/E5a than B1C/L1/E1 in terms of pseudo range multipath. The ISBs are stable both in the short term for one day and in the long term for over a year, which fit a zero-mean normal distribution well when the identical type of receiver is applied. Thus, it is reasonable to ignore the ISBs in the inter-system differences. With the estimated ISBs, the inter-system double-difference RTK can be achieved, which is called a tightly combined model (TCM) RTK. Compared with the traditional intra-system double-difference RTK, which is called a loosely combined model (LCM) RTK, the TCM RTK can achieve a higher success rate (SR) in terms of ambiguity resolution and higher positioning accuracy. In addition, the higher the cutoff elevation angle set, the greater the promotion can be obtained in SR. Even with a cutoff elevation angle of 50°, the SR of TCM is over 80%. Thus, it is important to apply TCM RTK when the observation conditions are limited, such as in dense jungles or the urban canyons.

Digital Quantification of Chemical Oligonucleotide Synthesis Errors

Chemically synthesized oligonucleotides are vital to most nucleic acids-based technologies and several applications are sensitive to oligonucleotide sequence errors. However, it is challenging to identify and quantify the types and amount of errors in synthetic oligonucleotides. We applied a digital sequencing approach using unique molecular identifiers to quantify errors in chemically synthesized oligonucleotides from multiple manufacturers with different synthesis strategies, purity grades, batches, and sequence context. We detected both deletions and substitutions in chemical oligonucleotide synthesis, but deletions were 7 times more common. We found that 97.2% of all analyzed oligonucleotide molecules were intact across all manufacturers and purity grades, although the number of oligonucleotide molecules with deletions ranged between 0.2% and 11.7% for different types. Different batches of otherwise identical oligonucleotide types also varied significantly, and batch effect can impact oligonucleotide quality more than purification. We observed a bias of increased deletion rates in chemically synthesized oligonucleotides toward the 5'-end for 1 out of 2 sequence configurations. We also demonstrated that the performance of sequencing assays depends on oligonucleotide quality. Our data demonstrate that manufacturer, synthesis strategy, purity, batch, and sequence context all contribute to errors in chemically synthesized oligonucleotides and need to be considered when choosing and evaluating oligonucleotides. High-performance oligonucleotides are essential in numerous molecular applications, including clinical diagnostics.

Genomic Characterization of Multidrug-Resistant Salmonella Serovars Derby and Rissen From the Pig Value Chain in Vietnam.

Nontyphoidal Salmonella (NTS) is the most reported cause of bacterial foodborne zoonoses in Vietnam, and contaminated pork is one of the main sources of human infection. In recent years, the prevalence of NTS carrying multiple antimicrobial resistance genes (ARGs) have been increased. The genomic characterization along the pig value chain and the identification of ARGs and plasmids have the potential to improve food safety by understanding the dissemination of ARGs from the farm to the table. We report an analysis of 13 S. Derby and 10 S. Rissen isolates, collected in 2013 at different stages in Vietnamese slaughterhouses and markets. VITEK 2 Compact System was used to characterize the phenotypical antimicrobial resistance of the isolates. In addition, whole-genome sequencing (WGS) was used to detect ARGs and plasmids conferring multidrug resistance. Whole genome single nucleotide polymorphism typing was used to determine the genetic diversity of the strains and the spread of ARGs along the pig value chain. Altogether, 86.9% (20/23) of the samples were resistant to at least one antibiotic. Resistance to ampicillin was most frequently detected (73.9%), followed by piperacillin and moxifloxacin (both 69.6%). At least one ARG was found in all strains, and 69.6% (16/23) were multidrug-resistant (MDR). The observed phenotype and genotype of antimicrobial resistance were not always concordant. Plasmid replicons were found in almost all strains [95.6% (22/23)], and the phylogenetic analysis detected nine clusters (S. Derby, n = 5; S. Rissen, n = 4). ARGs and plasmid content were almost identical within clusters. We found six MDR IncHI1s with identical plasmid sequence type in strains of different genetic clusters at the slaughterhouse and the market. In conclusion, high rates of multidrug resistance were observed in Salmonella strains from Vietnam in 2013. Genomic analysis revealed many resistance genes and plasmids, which have the potential to spread along the pig value chain from the slaughterhouse to the market. This study pointed out that bioinformatics analyses of WGS data are essential to detect, trace back, and control the MDR strains along the pig value chain. Further studies are necessary to assess the more recent MDR Salmonella strains spreading in Vietnam.

DeepMNN: Deep Learning-Based Single-Cell RNA Sequencing Data Batch Correction Using Mutual Nearest Neighbors.

It is well recognized that batch effect in single-cell RNA sequencing (scRNA-seq) data remains a big challenge when integrating different datasets. Here, we proposed deepMNN, a novel deep learning-based method to correct batch effect in scRNA-seq data. We first searched mutual nearest neighbor (MNN) pairs across different batches in a principal component analysis (PCA) subspace. Subsequently, a batch correction network was constructed by stacking two residual blocks and further applied for the removal of batch effects. The loss function of deepMNN was defined as the sum of a batch loss and a weighted regularization loss. The batch loss was used to compute the distance between cells in MNN pairs in the PCA subspace, while the regularization loss was to make the output of the network similar to the input. The experiment results showed that deepMNN can successfully remove batch effects across datasets with identical cell types, datasets with non-identical cell types, datasets with multiple batches, and large-scale datasets as well. We compared the performance of deepMNN with state-of-the-art batch correction methods, including the widely used methods of Harmony, Scanorama, and Seurat V4 as well as the recently developed deep learning-based methods of MMD-ResNet and scGen. The results demonstrated that deepMNN achieved a better or comparable performance in terms of both qualitative analysis using uniform manifold approximation and projection (UMAP) plots and quantitative metrics such as batch and cell entropies, ARI F1 score, and ASW F1 score under various scenarios. Additionally, deepMNN allowed for integrating scRNA-seq datasets with multiple batches in one step. Furthermore, deepMNN ran much faster than the other methods for large-scale datasets. These characteristics of deepMNN made it have the potential to be a new choice for large-scale single-cell gene expression data analysis.

Specific Probiotics for the Treatment of Pediatric Acute Gastroenteritis in India: A Systematic Review and Meta-Analysis.

Pediatric acute gastroenteritis (PAGE) is a significant cause of morbidity, mortality and healthcare costs in many countries, but differences in PAGE vary from country-to-country; thus, we limited our analysis to 1 country. Probiotics have been recommended as an adjunct to standard treatment, but the choice of probiotic is unclear. PubMed, Google Scholar, and reviews were searched from inception to May 2020 for randomized controlled trials (RCTs) in India using probiotics for a treatment for PAGE. Meta-analyses using subgroups of identical probiotic types (≥2 RCT/type) were conducted for primary outcomes (duration of diarrhea, cured by day 3, rapidity of response, and length of hospital stay). Twenty-two RCTs were included in the systematic review (N = 4059 participants) including 5 single-strained probiotics and 3 multi-strained mixtures. For the meta-analyses, 17 RCT (20 treatment arms) were included. Saccharomyces boulardii CNCM I-745 had the strongest effect on shortening the duration of diarrhea (standardized mean difference, -1.86 d; 95% confidence interval, -2.8 to -0.9), while both Lactobacillus rhamnosus GG and a mixture of 4 Bacillus clausii strains (O/C, SIN, N/R, T) significantly reduced the duration of diarrhea (-1.7 and -1.4 d, respectively). S. boulardii and L. rhamnosus GG significantly reduced hospital stays (-1.8 and -1.1 d, respectively), while B. clausii had no effect. The frequency of stools/day was significantly reduced by day 4 for S. boulardii and by day 5 for L. rhamnosus GG. In India, 2 types of probiotics (S. boulardii CNCM I-745 and L. rhamnosus GG) significantly shortened both the duration of diarrhea and hospitalization stays in pediatric patients with PAGE. While these 2 probiotic strains were safe and effective for children in India, further research is needed to confirm if other probiotic strains or mixtures may be effective.

Flow features and thermal stress evaluation in turbulent mixing flows

The present paper depicts a numerical study of flow and thermal features in T-junctions with circular cross-section. The numerical simulation is based on the experimental validated wall-resolved Large-Eddy Simulation method. The Reynolds number in the warm main pipe flow covers a range of Rem=27000 to Rem=134000 and the temperature difference of the mixing fluids is up to ΔT=249 K. The location of maximum fluctuations does not change due to a nearly identical flow pattern type in all simulations. This condition allows the investigation of the flow evolution, mixing process and heat transfer for the same thermal flow pattern type. The numerical simulations are coupled with the heat conduction in the structure due to the thermal fluid-structure-interaction. Further, this study offers a deeper insight into the hidden physics of turbulent mixing flows and the transport as well as damping of thermal fluctuations in the near-wall fluid/solid region. Our study considers also thermal stress analysis by Finite-Element Method by utilizing the wall temperature distribution of previously performed numerical simulations. Therefore, fatigue damage is evaluated based on the stress received from the Finite-Element analysis. The results show that the highest Reynolds number case corresponds to the highest flux intensity and turbulence. This affects the flow field and the thermal features in the core flow and the transport of fluctuations close to the wall. The locations with peak fluctuation intensity in the fluid generates also high fluctuating temperature areas in the structure. The finite element analysis demonstrates that the highest temperature difference case leads to the highest alternating stress intensity which has potential for thermal fatigue. The generated maximal alternating stress is coupled with the flow conditions of the mixing fluids. With an increasing Reynolds number of the main and branch pipe flow as well as temperature difference raises also the resulting maximum alternating stress intensity.

Pathogenicity and genomic features of vapN-harboring Rhodococcus equi isolated from human patients

Rhodococcus equi is a saprophytic soil bacterium and intracellular pathogen that causes refractory suppurative pneumonia in foals and has emerged as a pathogenic cause of zoonotic disease. Several studies have reported human infections caused by R. equi harboring a recently described third type of virulence plasmid, the ruminant-associated pVAPN, which carries the vapN virulence determinant. Herein, we analyzed pathogenicity and genomic features of nine vapN-harboring R. equi isolated from human patients with and without HIV/AIDS. Four of these strains showed significant VapN production and proliferation in cultured macrophages. These strains were lethally pathogenic after inoculation with 1.0 × 108 CFU in mice and reproduced a necrotizing granulomatous inflammation in the liver and spleen similar to that observed in humans. Additionally, we determined entire genome sequences of all nine strains. Lengths of sequences were 5.0–5.3 Mbp, and GC contents were 68.7 %–68.8 %. All strains harbored a 120- or 125-kbp linear plasmid carrying vapN (Type I or Type II pVAPN) classified on the basis of differences in the distal sequences on the 3′ side. Interestingly, VapN production differed significantly among strains harboring nearly identical types of pVAPN with variation limited to several SNPs and short base pair indels. The pVAPN sequences possessed by the VapN-producing strains did not retain any common genetic characteristics, and more detailed analyses, including chromosomal genes, are needed to further elucidate the VapN expression mechanism.

Deterministic and Probabilistic Seismic Hazard Analysis of Petroleum Storage of Sabzevar

Failure of appropriate resource structures for petroleum products located close to residential areas has irreparable financial and fatal consequences. Thus, a seismic hazard analysis in estimating strong ground motions seems essential for constructing or improving such structures. For this purpose, firstly, by using the deterministic method and empirical equations of the largest earthquake likely to occur, the result of active faults activity was determined using attenuation equations via an appropriate logic tree, and the maximum horizontal and vertical acceleration component was calculated based on two types of soil. The first type of soil matches types I and II, and the second type matches III and IV, from standard No.2800. Then, to analyze the potential hazard, we define the seismic sources, seismic parameters, rupture parameters, and the attenuation equations with the same logic tree using SeisRisk III software, plus the maximum vertical and horizontal acceleration component, based on the two identical types of soil. Subsequently, the seismic improvement regulation of structures (360 magazine) for the second level hazard was calculated and finally compared with the results of the deterministic analysis. Results indicated that the acceleration component in the deterministic method presents a higher amount than the probable method. As a result, probable methods can be used instead of a deterministic method proving far more economical.

Sex Differences in the Incidence and Outcomes of COPD Patients Hospitalized with Ischemic Stroke in Spain: A Population-Based Observational Study.

PurposeTo compare the incidence, clinical characteristics and outcomes of patients admitted with ischemic stroke (IS) according to the presence of COPD and sex in Spain (2016–2018).Patients and MethodsWe selected all admissions with IS (≥35 years) included in the Spanish National Hospital Discharge Database. We matched each patient suffering COPD with a non-COPD patient with identical age, sex, IS type and year of hospitalization.ResultsIS was coded in 92,524 men and 79,731 women (8.67% with COPD). The incidence of IS was higher in COPD men than in non-COPD men (IRR 1.04; 95% CI 1.03–1.06), although the differences were not significant among women. COPD men had twice higher incidence of IS than COPD women (IRR 2.00; 95% CI 1.93–2.07). After matching, COPD men had a higher in-hospital mortality (IHM) than non-COPD men (11.48% vs 9.80%; p<0.001), and the same happened among women (14.09% vs 11.96%; p=0.002). COPD men received thrombolytic therapy less frequently than non-COPD men. For men and women, the risk of dying in the hospital increased with age, some comorbidities and mechanical ventilation use. After multivariable adjustment, COPD increased the risk of IHM in men (OR 1.16; 95% CI 1.06–1.28) and women (OR 1.12; 95% CI 1.01–1.27). Finally, among COPD patients, being women increased the risk of dying during the hospitalization with IS by 15% (OR 1.15; 95% CI 1.03–1.28).ConclusionIncidence of IS was higher in COPD patients, although the difference was only significant for men. COPD was associated with an increased risk of IHM. Among COPD patients, women had higher IHM.

Выявление признаков «дробления бизнеса» на территориях с особым экономическим статусом Дальнего Востока

The issue of “business fragmentation” has been relevant in Russia for over ten years. Business striving to ensure competitiveness makes it necessary to look for mechanisms to reduce the tax burden, applying special tax regimes or preferential tax conditions for residents of territories with special economic status. In this paper, the authors analyze the theoretical prerequisites for substantiating the signs of “business fragmentation,” and study the scope of application of “business fragmentation” schemes within the framework of preferential tax conditions for territories with special economic status in the Far East. The basic research methods were content analysis, comparative analysis and synthesis. As a result of the content analysis of judicial practice, the criteria for business fragmentation, confirming the formal division of a business, were substantiated. The authors carried out a comparative analysis of resident companies and identified, based on open data, 159 residents of priority social and economic development areas (PSEDAs) and 625 residents of the Free Port of Vladivostok (FPV) with signs of “business fragmentation.” Those amounted to 28.49 % and 29.48 % in the total number of active residents, respectively. Vladivostok is the leader in terms of the number of residents with signs of “business fragmentation,” with 443 residents of the FPV. The most common signs of “business fragmentation” among resident companies in territories with a special economic status of the Far East are substantiated: common persons managing companies, common or identical type of activity, and common address of location. Common types of activity among resident companies with signs of “business fragmentation” within territories with special economic status of the Far East are warehousing and auxiliary transport (15 % of PSEDA; 12.3 % of the FPV); construction of buildings (16.5 % of the FPV); and operations with real estate (14 % of the FPV).

Genome assisted molecular typing and pathotyping of rice blast pathogen, Magnaporthe oryzae, reveals a genetically homogenous population with high virulence diversity

Genome sequence-driven molecular typing tools have the potential to uncover the population biology and genetic diversity of rapidly evolving plant pathogens like Magnaporthe oryzae. Here, we report a new molecular typing technique -a digitally portable tool for population genetic analysis of M. oryzae to decipher the genetic diversity. Our genotyping tool exploiting allelic variations in housekeeping and virulence genes coupled with pathotyping revealed a prevalence of genetically homogenous populations within a single-field and plant niches such as leaf and panicle. The M. oryzae inciting leaf-blast and panicle-blast were confirmed to be genetically identical with no or minor nucleotide polymorphism in 17 genomic loci analyzed. Genetic loci such as Mlc1, Mpg1, Mps1, Slp1, Cal, Ef-Tu, Pfk, and Pgk were highly polymorphic as indicated by the haplotype-diversity, the number of polymorphic sites, and the number of mutations. The genetically homogenous single field population showed high virulence variability or diversity on monogenic rice differentials. The study indicated that the genetic similarity displayed by the isolates collected from a particular geographical location had no consequence on their virulence pattern on rice differentials carrying single/multiple resistance genes. The data on virulence diversity showed by the identical Sequence Types (STs) is indicative of no congruence between polymorphic virulence genes-based pathotyping and conserved housekeeping genes-based genotyping.

First Report of blaNDM-1 Bearing IncX3 Plasmid in Clinically Isolated ST11 Klebsiella pneumoniae from Pakistan.

The New Delhi Metallo-β-lactamase (NDM) is among the most threatening forms of carbapenemases produced by K. pneumoniae, well-known to cause severe worldwide infections. The molecular epidemiology of blaNDM-1-harboring K. pneumoniae is not well elucidated in Pakistan. Herein, we aim to determine the antibiotics-resistance profile, genes type, molecular type, and plasmid analysis of 125 clinically isolated K. pneumoniae strains from urine samples during July 2018 to January 2019 in Pakistan. A total of 34 (27.2%) K. pneumoniae isolates were carbapenemases producers, and 23 (18.4%) harbored the blaNDM-1 gene. The other carbapenemases encoding genes, i.e., blaIMP-1 (7.2%), blaVIM-1 (3.2%), and blaOXA-48 (2.4%) were also detected. The Multi Locus Sequence Typing (MLST) results revealed that all blaNDM-1-harboring isolates were ST11. The other sequence types detected were ST1, ST37, and ST105. The cluster analysis of Xbal Pulsed Field Gel Electrophoresis (PFGE) revealed variation amongst the clusters of the identical sequence type isolates. The blaNDM-1 gene in all of the isolates was located on a 45-kb IncX3 plasmid, successfully transconjugated. For the first time, blaNDM-1-bearing IncX3 plasmids were identified from Pakistan, and this might be a new primary vehicle for disseminating blaNDM-1 in Enterobacteriaceae as it has a high rate of transferability.

Molecular epidemiology of Leptospira spp. among wild mammals and a dog in Amami Oshima Island, Japan.

Leptospirosis is a worldwide zoonosis caused by the pathogenic Leptospira spp. Canine and human leptospirosis sometimes occur on Amami Oshima Island, located in the Nansei Archipelago, southwestern Japan; however, information on the causative Leptospira spp. on this island is quite limited. This study aimed to investigate the molecular and serological characteristics of Leptospira spp. isolated from wild animals and a dog in Amami Oshima Island. We obtained seven Leptospira strains by culturing kidney tissues of wild animals, such as black rats (2), wild boars (3), and rabbit (1) as well as blood from a symptomatic dog. Using flaB sequencing and microscopic agglutination test with antisera for 18 serovars, the isolates were identified as Leptospira borgpetersenii serogroups Javanica (black rat), L. interrogans serogroup Australis (black rat and dog), and L. interrogans serogroup Hebdomadis (wild boar and rabbit). The sequence type (ST) of L. borgpetersenii serogroup Javanica was determined to be ST143 via multilocus sequence typing (MLST) using seven housekeeping genes. For L. interrogans, MLST and multiple-locus variable-tandem repeat analysis (MLVA) revealed identical ST and MLVA types in rat and canine isolates, whereas two STs and MLVA types were identified in wild boar isolates. The STs and MLVA types of rabbit and one of the wild boars were identical. Bacterial culture and flaB-nested polymerase chain reaction demonstrated a high rate of Leptospira infection in wild boars (58.3%, 7/12), whereas Leptospira spp. were detected in 4.8% of black rats (2/42). This study revealed diverse Leptospira genotype and serotype maintenance in wild mammals on Amami Oshima Island. MLST and MLVA indicated that black rats were a source of canine infection. Wild boars carry L. interrogans and are considered an important maintenance host because antibodies against serogroup Hebdomadis were detected in human and canine leptospirosis patients on this island.

Thermal Performance Comparison and Augmentation of Two Identical Box-Type Solar Cookers Operating in Tropical Climatic Conditions

Abstract In the present study, experimental studies have been performed to compare the thermal performance of two geometrically identical box type solar (B-T-S) cookers. To carry out this aim, the thermal performance of BTS cooker in terms of figure of merits, namely, first figure of merit (F1) and second figure of merit (F2) are calculated for both cookers as specified by the Bureau of Indian Standards (BIS). At no-load condition (i.e., stagnation test), it is found that first figure of merit for both cookers that is cooker 1 and cooker 2 is around 0.12. This implies that both the cookers are identical in thermal performance. In addition to this, the effect of lugs height, reflector, number of pots, and load on B-T-S cooker performance have also been investigated. From the results and discussion, it is concluded that the use of lugs reduced the heat transfer rate between cooking pot and absorber plate. Further, it is found that the pot content temperature is enhanced by 25.5% and 23.4% by using mirror and aluminum reflector with cooker, respectively. However, it is observed that the performance parameters of B-T-S cooker in terms of F2 increases linearly with the increase of number of cooking pot (with correlation F2 = 0.0316n + 0.2238, where n is the number of pots) and load (correlation as F2 = 0.0451 m + 0.1844, where m is the mass of water in cooking pot) on the pot.

Diversity and characterization of temperate bacteriophages induced in Pasteurella multocida from different host species

BackgroundBacteriophages play important roles in the evolution of bacteria and in the emergence of new pathogenic strains by mediating the horizontal transfer of virulence genes. Pasteurella multocida is responsible for different disease syndromes in a wide range of domesticated animal species. However, very little is known about the influence of bacteriophages on disease pathogenesis in this species.ResultsTemperate bacteriophage diversity was assessed in 47 P. multocida isolates of avian (9), bovine (8), ovine (10) and porcine (20) origin. Induction of phage particles with mitomycin C identified a diverse range of morphological types representing both Siphoviridae and Myoviridae family-types in 29 isolates. Phage of both morphological types were identified in three isolates indicating that a single bacterial host may harbour multiple prophages. DNA was isolated from bacteriophages recovered from 18 P. multocida isolates and its characterization by restriction endonuclease (RE) analysis identified 10 different RE types. Phage of identical RE types were identified in certain closely-related strains but phage having different RE types were present in other closely-related isolates suggesting possible recent acquisition. The host range of the induced phage particles was explored using plaque assay but only 11 (38%) phage lysates produced signs of infection in a panel of indicator strains comprising all 47 isolates. Notably, the majority (9/11) of phage lysates which caused infection originated from two groups of phylogenetically unrelated ovine and porcine strains that uniquely possessed the toxA gene.ConclusionsPasteurella multocida possesses a wide range of Siphoviridae- and Myoviridae-type bacteriophages which likely play key roles in the evolution and virulence of this pathogen.

Primer biases in the molecular assessment of diet in multiple insectivorous mammals

Our understanding of trophic interactions of small insectivorous mammals has been drastically improved with the advent of DNA metabarcoding. The technique has continued to be optimised over the years, with primer choice repeatedly being a vital factor for dietary inferences. However, the majority of dietary studies examining the effect of primer choice often rely on in silico analyses or comparing between species that occupy an identical niche type. Here, we apply DNA metabarcoding to empirically compare the prey detection capabilities of two widely used primer sets when assessing the diets of a flying (lesser horseshoe bat; Rhinolophus hipposideros) and two ground-dwelling insectivores (greater white-toothed shrew; Crocidura russula and pygmy shrew; Sorex minutus). Although R. hipposideros primarily rely on two prey orders (Lepidoptera and Diptera), the unique taxa detected by each primer shows that a combination of primers may be the best approach to fully describe bat trophic ecology. However, random forest classifier analysis suggests that one highly degenerate primer set detected the majority of both shrews’ diet despite higher levels of host amplification. The wide range of prey consumed by ground-dwelling insectivores can therefore be accurately documented from using a single broad-range primer set, which can decrease cost and labour. The results presented here show that dietary inferences will differ depending on the primer or primer combination used for insectivores occupying different niches (i.e., hunting in the air or ground) and demonstrate the importance of performing empirical pilot studies for novel study systems.

Genomics of an endemic cystic fibrosis Burkholderia multivorans strain reveals low within-patient evolution but high between-patient diversity.

Burkholderia multivorans is a member of the Burkholderia cepacia complex (Bcc), notorious for its pathogenicity in persons with cystic fibrosis. Epidemiological surveillance suggests that patients predominantly acquire B. multivorans from environmental sources, with rare cases of patient-to-patient transmission. Here we report on the genomic analysis of thirteen isolates from an endemic B. multivorans strain infecting four cystic fibrosis patients treated in different pediatric cystic fibrosis centers in Belgium, with no evidence of cross-infection. All isolates share an identical sequence type (ST-742) but whole genome analysis shows that they exhibit peculiar patterns of genomic diversity between patients. By combining short and long reads sequencing technologies, we highlight key differences in terms of small nucleotide polymorphisms indicative of low rates of adaptive evolution within patient, and well-defined, hundred kbps-long segments of high enrichment in mutations between patients. In addition, we observed large structural genomic variations amongst the isolates which revealed different plasmid contents, active roles for transposase IS3 and IS5 in the deactivation of genes, and mobile prophage elements. Our study shows limited within-patient B. multivorans evolution and high between-patient strain diversity, indicating that an environmental microdiverse reservoir must be present for this endemic strain, in which active diversification is taking place. Furthermore, our analysis also reveals a set of 30 parallel adaptations across multiple patients, indicating that the specific genomic background of a given strain may dictate the route of adaptation within the cystic fibrosis lung.

RF design studies on a 325 MHz rebuncher cavity for high intensity linear accelerators producing neutrons

Two identical Coupled Cavity Linac type (CCL) rebuncher cavities to be integrated in the Medium Energy Beam Transport line (MEBT) of a high intensity linac Accelerator have been studied for matching a 40-mA proton beam accelerated by a 3 MeV Radio-Frequency Quadrupole (RFQ) to a 13 MeV Drift Tube Linac (DTL). The rebuncher operates at 325 MHz, and is designed for β = 0.080. The rebuncher aperture radius is 20 mm required by transverse beam dynamics. It is a single gap structure operating in the TM_010 mode for providing longitudinal beam focusing. The unloaded quality Q0 and the required input power to achieve an effective voltage of 150 kV are 27253 and 20.5 kW, respectively. In this work, we present the RF design studies for the high power rebuncher resonator, as well as the considerations of the tuning scheme and the coupler design.

Genomic data reveals the emergence of an IncQ1 small plasmid carrying blaKPC-2 in Escherichia coli of the pandemic sequence type 648

ObjectivesThe global success of carbapenem-resistant pathogens has been attributed to large plasmids carrying blaKPC genes circulating among high-risk clones. In this study, we sequenced the genome of a carbapenem-resistant Escherichia coli strain (Ec351) isolated from a human infection. Phylogenomic analysis based on single nucleotide polymorphisms (SNPs) as well as the comparative resistome and plasmidome of globally disseminated blaKPC-2-positive E. coli strains with identical sequence type (ST) were further investigated. MethodsTotal DNA was sequenced using an Illumina NextSeq 500 platform and was assembled using Unicycler. Genomic data were evaluated through bioinformatics tools available from the Center of Genomic Epidemiology and by in silico analysis. ResultsGenomic analysis revealed the convergence of a wide resistome and virulome in E. coli ST648, showing a high-level phylogenetic relationship with a KPC-2-positive ST648 cluster identified in the USA and association with international clade 2. Additionally, the emergence of an IncQ1 small plasmid (pEc351) carrying blaKPC-2 (on an NTEKPC-IId element), aph(3')-VIa, and plasmid regulatory and replication genes in the pandemic clone ST648 is reported. ConclusionIdentification of a blaKPC-2-positive IncQ1 plasmid in a high-risk E. coli clone represents rapid adaptation and expansion of these small plasmids encoding carbapenemases to novel bacterial hosts with global distribution, which deserves continued monitoring.

Human gastrointestinal epithelia of the esophagus, stomach, and duodenum resolved at single-cell resolution

The upper gastrointestinal tract, consisting of the esophagus, stomach, and duodenum, controls food transport, digestion, nutrient uptake, and hormone production. By single-cell analysis of healthy epithelia of these human organs, we molecularly define their distinct cell types. We identify a quiescent COL17A1high KRT15high stem/progenitor cell population in the most basal cell layer of the esophagus and detect substantial gene expression differences between identical cell types of the human and mouse stomach. Selective expression of BEST4, CFTR, guanylin, and uroguanylin identifies a rare duodenal cell type, referred to as BCHE cell, which likely mediates high-volume fluid secretion because of continual activation of the CFTR channel by guanylin/uroguanylin-mediated autocrine signaling. Serotonin-producing enterochromaffin cells in the antral stomach significantly differ in gene expression from duodenal enterochromaffin cells. We, furthermore, discover that the histamine-producing enterochromaffin-like cells in the oxyntic stomach express the luteinizing hormone, yet another member of the enteroendocrine hormone family.