Search Results (8)

During the COVID-19 pandemic, the monitoring of SARS-CoV-2 RNA in wastewater was used to track the evolution and emergence of variant lineages and gauge infection levels in the community, informing appropriate public health responses without relying solely on clinical testing. As more sublineages were discovered, it increased the difficulty in identifying distinct variants in a mixed population sample, particularly those without a known lineage. Here, we compare the sequencing technology from Illumina and from Oxford Nanopore Technologies, in order to determine their efficacy at detecting variants of differing abundance, using 248 wastewater samples from various Quebec and Ontario cities. Our study used two analytical approaches to identify the main variants in the samples: the presence of signature and marker mutations and the co-occurrence of signature mutations within the same amplicon. We observed that each sequencing method detected certain variants at different frequencies as each method preferentially detects mutations of distinct variants. Illumina sequencing detected more mutations with a predominant lineage that is in low abundance across the population or unknown for that time period, while Nanopore sequencing had a higher detection rate of mutations that are predominantly found in the high abundance B.1.1.7 (Alpha) lineage as well as a higher sequencing rate of co-occurring mutations in the same amplicon. We present a workflow that integrates short-read and long-read sequencing to improve the detection of SARS-CoV-2 variant lineages in mixed population samples, such as wastewater. Full article

Dysregulated transplacental lipid transfer and fetal–placental lipid metabolism affect birthweight, as does maternal hyperglycemia. As the mechanisms are unclear, we aimed to identify the lipids in umbilical cord plasma that were most associated with birthweight. Seventy-five Chinese women with singleton pregnancies recruited into the GUSTO mother–offspring cohort were selected from across the glycemic range based on a mid-gestation 75 g oral glucose tolerance test, excluding pre-existing diabetes. Cord plasma samples collected at term delivery were analyzed using targeted liquid-chromatography tandem mass-spectrometry to determine the concentrations of 404 lipid species across 17 lipid classes. The birthweights were standardized for sex and gestational age by local references, and regression analyses were adjusted for the maternal age, BMI, parity, mode of delivery, insulin treatment, and fasting/2 h glucose, with a false discovery-corrected p < 0.05 considered significant. Ten lysophosphatidylcholines (LPCs) and two lysophosphatidylethanolamines were positively associated with the birthweight percentiles, while twenty-four triacylglycerols were negatively associated with the birthweight percentiles. The topmost associated lipid was LPC 20:2 [21.28 (95%CI 12.70, 29.87) percentile increase in the standardized birthweight with each SD-unit increase in log₁₀-transformed concentration]. Within these same regression models, maternal glycemia did not significantly associate with the birthweight percentiles. Specific fetal circulating lysophospholipids and triacylglycerols associate with birthweight independently of maternal glycemia, but a causal relationship remains to be established. Full article

Free-electron lasers (FEL), with their ultrashort pulses, ultrahigh intensities, and high repetition rates at short wavelength, have provided new approaches to Atomic and Molecular Optical Science. One such approach is following the birth of a photo electron to observe ion dynamics on an ultrafast timescale. Such an approach presents the opportunity to decipher the photon-initiated structural dynamics of an isolated atomic and molecular species. It is a fundamental step towards understanding single- and non-linear multi-photon processes and coherent electron dynamics in atoms and molecules, ultimately leading to coherent control following FEL research breakthroughs in pulse shaping and polarization control. A key aspect for exploring photoinduced quantum phenomena is visualizing the collective motion of electrons and nuclei in a single reaction process, as dynamics in atoms/ions proceed at femtosecond (10${}^{-15}$ s) timescales while electronic dynamics take place in the attosecond timescale (10${}^{-18}$ s). Here, we report on the design of a Dynamic Reaction Microscope (DREAM) endstation located at the second interaction point of the Time-Resolved Molecular and Optical (TMO) instrument at the Linac Coherent Light Source (LCLS) capable of following the photon–matter interactions by detecting ions and electrons in coincidence. The DREAM endstation takes advantage of the pulse properties and high repetition rate of LCLS-II to perform gas-phase soft X-ray experiments in a wide spectrum of scientific domains. With its design ability to detect multi-ions and electrons in coincidence while operating in step with the high repetition rate of LCLS-II, the DREAM endstation takes advantage of the inherent momentum conservation of reaction product ions with participating electrons to reconstruct the original X-ray photon–matter interactions. In this report, we outline in detail the design of the DREAM endstation and its functionality, with scientific opportunities enabled by this state-of-the-art instrument. Full article

Studies JVDB and JVCZ examined alternative ramucirumab dosing regimens as monotherapy or combined with paclitaxel, respectively, in patients with advanced/metastatic gastric/gastroesophageal junction (GEJ) adenocarcinoma. For JVDB, randomized patients (N = 164) received ramucirumab monotherapy at four doses: 8 mg/kg every 2 weeks (Q2W) (registered dose), 12 mg/kg Q2W, 6 mg/kg weekly (QW), or 8 mg/kg on days 1 and 8 (D1D8) every 3 weeks (Q3W). The primary objectives were the safety and pharmacokinetics of ramucirumab monotherapy. For JVCZ, randomized patients (N = 245) received paclitaxel (80 mg/m²-D1D8D15) plus ramucirumab (8 mg/kg- or 12 mg/kg-Q2W). The primary objective was progression-free survival (PFS) of 12 mg/kg-Q2W arm versus placebo from RAINBOW using meta-analysis. Relative to the registered dose, exploratory dosing regimens (EDRs) led to higher ramucirumab serum concentrations in both studies. EDR safety profiles were consistent with previous studies. In JVDB, serious adverse events occurred more frequently in the 8 mg/kg-D1D8-Q3W arm versus the registered dose; 6 mg/kg-QW EDR had a higher incidence of bleeding/hemorrhage. In JVCZ, PFS was improved with the 12 mg/kg plus paclitaxel combination versus placebo in RAINBOW; however, no significant PFS improvement was observed between the 12 mg/kg and 8 mg/kg arms. The lack of a dose/exposure-response relationship in these studies supports the standard dose of ramucirumab 8 mg/kg-Q2W as monotherapy or in combination with paclitaxel as second-line treatment for advanced/metastatic gastric/GEJ adenocarcinoma. Full article

An electronic nose (E-nose) system equipped with a gas sensor array and real-time control panel was developed for a fast diagnosis of whitefly infestation in tomato plants. Profile changes of volatile organic compounds (VOCs) released from tomato plants under different treatments (i.e., whitefly infestation, mechanical damage, and no treatment) were successfully determined by the developed E-nose system. A rapid sensor response with high sensitivity towards whitefly-infested tomato plants was observed in the E-nose system. Results of principal component analysis (PCA) and hierarchical clustering analysis (HCA) indicated that the E-nose system was able to provide accurate distinguishment between whitefly-infested plants and healthy plants, with the first three principal components (PCs) accounting for 87.4% of the classification. To reveal the mechanism of whitefly infestation in tomato plants, VOC profiles of whitefly-infested plants and mechanically damaged plants were investigated by using the E-nose system and GC-MS. VOCs of 2-nonanol, oxime-, methoxy-phenyl, and n-hexadecanoic acid were only detected in whitefly-infested plants, while compounds of dodecane and 4,6-dimethyl were only found in mechanically damaged plant samples. Those unique VOC profiles of different tomato plant groups could be considered as bio-markers for diagnosing different damages. Moreover, the E-nose system was demonstrated to have the capability to differentiate whitefly-infested plants and mechanically damaged plants. The relationship between sensor performance and VOC profiles confirmed that the developed E-nose system could be used as a fast and smart device to detect whitefly infestation in greenhouse cultivation. Full article

In greenhouse energy balance models, the soil thermal parameters are important for evaluating the heat transfer between the greenhouse air and the soil. In this study, the soil thermal diffusivity was estimated from greenhouse soil temperature data using the amplitude, phase-shift, arctangent, logarithmic, and min-max methods. The results showed that the amplitude method and the min-max method performed well in estimating the soil thermal diffusivity. The obtained soil thermal diffusivity was input into a sinusoidal model to determine the greenhouse soil temperature at different soil depths. For greenhouse applications, the daily average soil temperature at different depths was predicted according to the temperature at the surface and the annual mean soil temperature. The model was validated using soil temperature data from summer and winter, when the greenhouse was cooled and heated, respectively. Full article

An electronic nose (E-nose) system equipped with a sensitive sensor array was developed for fast diagnosis of aphid infestation on greenhouse tomato plants at early stages. Volatile organic compounds (VOCs) emitted by tomato plants with and without aphid attacks were detected using both the developed E-nose system and gas chromatography mass spectrometry (GC-MS), respectively. Sensor performance, with fast sensor responses and high sensitivity, were observed using the E-nose system. A principle component analysis (PCA) indicated accurate diagnosis of aphid-stressed plants compared to healthy ones, with the first two PCs accounting for 86.7% of the classification. The changes in VOCs profiles of the healthy and infested tomato plants were quantitatively determined by GC-MS. Results indicated that a group of new VOCs biomarkers (linalool, carveol, and nonane (2,2,4,4,6,8,8-heptamethyl-)) played a role in providing information on the infestation on the tomato plants. More importantly, the variation in the concentration of sesquiterpene VOCs (e.g., caryophyllene) and new terpene alcohol compounds was closely associated with the sensor responses during E-nose testing, which verified the reliability and accuracy of the developed E-nose system. Tomato plants growing in spring had similar VOCs profiles as those of winter plants, except several terpenes released from spring plants that had a slightly higher intensity. Full article

We analyzed maternal plasma cell-free DNA samples from twin pregnancies in a prospective blinded study to validate a single-nucleotide polymorphism (SNP)-based non-invasive prenatal test (NIPT) for zygosity, fetal sex, and aneuploidy. Zygosity was evaluated by looking for either one or two fetal genome complements, fetal sex was evaluated by evaluating Y-chromosome loci, and aneuploidy was assessed through SNP ratios. Zygosity was correctly predicted in 100% of cases (93/93; 95% confidence interval (CI) 96.1%–100%). Individual fetal sex for both twins was also called with 100% accuracy (102/102; 95% weighted CI 95.2%–100%). All cases with copy number truth were also correctly identified. The dizygotic aneuploidy sensitivity was 100% (10/10; 95% CI 69.2%–100%), and overall specificity was 100% (96/96; 95% weighted CI, 94.8%–100%). The mean fetal fraction (FF) of monozygotic twins (n = 43) was 13.0% (standard deviation (SD), 4.5%); for dizygotic twins (n = 79), the mean lower FF was 6.5% (SD, 3.1%) and the mean higher FF was 8.1% (SD, 3.5%). We conclude SNP-based NIPT for zygosity is of value when chorionicity is uncertain or anomalies are identified. Zygosity, fetal sex, and aneuploidy are complementary evaluations that can be carried out on the same specimen as early as 9 weeks’ gestation. Full article