The complete chloroplast genome of common walnut (Juglans regia)

Common walnut (Juglans regia L.) is cultivated in temperate regions worldwide for its wood and nuts. The complete chloroplast genome of J. regia was sequenced using the Illumina MiSeq platform. This is the first complete chloroplast sequence for the Juglandaceae, a family that includes numerous species of economic importance. The chloroplast genome of J. regia was 160 367 bp in length, with 36.11% GC content. It contains a pair of inverted repeats (26 035 bp) which were separated by a large single copy (89 872 bp) and a small single copy region (18 425 bp). A total of 137 genes were annotated, which included 86 protein-coding genes, three pseudogenes (two ycf15 and one infA), 40 tRNA genes and eight rRNA genes. The neighbour-joining phylogenetic analysis with the reported chloroplast genomes showed that common walnut chloroplasts are most closely related to those of the Fagaceae family

Climatic and Soil Factors Shape the Demographical History and Genetic Diversity of a Deciduous Oak (Quercus liaotungensis) in Northern China

Past and current climatic changes have affected the demography, patterns of genetic diversity, and genetic structure of extant species. The study of these processes provides valuable information to forecast evolutionary changes and to identify conservation priorities. Here, we sequenced two functional nuclear genes and four chloroplast DNA regions for 105 samples from 21 populations of Quercus liaotungensis across its distribution range. Coalescent-based Bayesian analysis, approximate Bayesian computation (ABC), and ecological niche modeling (ENM) were integrated to investigate the genetic patterns and demographical history of this species. Association estimates including Mantel tests and multiple linear regressions were used to infer the effects of geographical and ecological factors on temporal genetic variation and diversity of this oak species. Based on multiple loci, Q. liaotungensis populations clustered into two phylogenetic groups; this grouping pattern could be the result of adaptation to habitats with different temperature and precipitation seasonality conditions. Demographical reconstructions and ENMs suggest an expansion decline trend of this species during the Quaternary climatic oscillations. Association analyses based on nuclear data indicated that intraspecific genetic differentiation of Q. liaotungensis was clearly correlated with ecological distance; specifically, the genetic diversity of this species was significantly correlated with temperature seasonality and soil pH, but negatively correlated with precipitation. Our study highlights the impact of Pleistocene climate oscillations on the demographic history of a tree species in Northern China, and suggests that climatic and soil conditions are the major factors shaping the genetic diversity and population structure of Q. liaotungensis

Information theory-based algorithm for in silico prediction of PCR products with whole genomic sequences as templates

BACKGROUND: A new algorithm for assessing similarity between primer and template has been developed based on the hypothesis that annealing of primer to template is an information transfer process. RESULTS: Primer sequence is converted to a vector of the full potential hydrogen numbers (3 for G or C, 2 for A or T), while template sequence is converted to a vector of the actual hydrogen bond numbers formed after primer annealing. The former is considered as source information and the latter destination information. An information coefficient is calculated as a measure for fidelity of this information transfer process and thus a measure of similarity between primer and potential annealing site on template. CONCLUSION: Successful prediction of PCR products from whole genomic sequences with a computer program based on the algorithm demonstrated the potential of this new algorithm in areas like in silico PCR and gene finding

Completion of Eight Gynostemma BL. (Cucurbitaceae) Chloroplast Genomes: Characterization, Comparative Analysis, and Phylogenetic Relationships

Gynostemma BL., belonging to the family Cucurbitaceae, is a genus containing 17 creeping herbaceous species mainly distributed in East Asia. It can be divided into two subgenera based on different fruit morphology. Herein, we report eight complete chloroplast genome sequences of the genus Gynostemma, which were obtained by Illumina paired-end sequencing, assembly, and annotation. The length of the eight complete cp genomes ranged from 157,576 bp (G. pentaphyllum) to 158,273 bp (G. laxiflorum). Each encoded 133 genes, including 87 protein-coding genes, 37 tRNA genes, eight rRNA genes, and one pseudogene. The four types of repeated sequences had been discovered and indicated that the repeated structure for species in the Subgen. Triostellum was greater than that for species in the Subgen. Gynostemma. The percentage of variation of the eight cp genomes in different regions were calculated, which demonstrated that the coding and inverted repeats regions were highly conserved. Phylogenetic analysis based on Bayesian inference and maximum likelihood methods strongly supported the phylogenetic position of the genus Gynostemma as a member of family Cucurbitaceae. The phylogenetic relationships among the eight species were clearly resolved using the complete cp genome sequences in this study. It will also provide potential molecular markers and candidate DNA barcodes for future studies and enrich the valuable complete cp genome resources of Cucurbitaceae

Intraperitoneal ropivacaine and early postoperative pain and postsurgical outcomes after laparoscoipc herniorrhaphy in toddlers: a randomized clinical trial

Background Postoperative pain can cause physiological distress, postoperative complications, and extended lengths of hospitalized stay. In children, management of postoperative pain is still recognized as being inadequate. Objective The aim of this trial was to investigate the effects of intraperitoneal ropivacaine on postoperative pain, and recovery of bowel function and emetic events after laparoscopic herniorrhaphy in toddlers. Methods Seventy-six children aged from 9 months to 3 years were recruited between August 2013 and June 2014 at Tongji Hospital and randomly assigned into two groups. One group received intraperitoneal ropivacaine right before surgery and the control group received intraperitoneal saline. A standard combined general anesthesia procedure was performed under regular monitoring. Postoperative pain was assessed by the FLACC scale. Postoperative analgesic consumption, time to flatus, time to first stool, and postoperative emetic events were also recorded. Results When compared with the control group, children who received intraperitoneal ropivacaine experienced less pain 0–4 h after surgery [P < 0.001, difference in median FLACC (95% CI) for 2 h time point is 2.00 (0.87–3.13), for 4 h time point is 1.00 (0.55–1.45)]. In addition, the number of toddlers who received analgesia 0–24 h after surgery in the ropivacaine group was lower than that in the control group [P < 0.001, difference in proportions (95% CI) is 0.575 (0.3865–0.7638)]. Compared with the control group, time to flatus in ropivacaine group was also much shorter [21.1 h vs 16.7 h, P = 0.04, difference in mean (95% CI) is 4.4 (1.49–7.28)], and the time to first stool after surgery was earlier in the ropivacaine group [30.7 h vs 25.6 h, P = 0.003, difference in mean (95% CI) is 5.1 (1.78–8.45)]. Furthermore, the incidence of emetic events in the ropivacaine group was significantly lower than the control group [32.4% vs 11.1%, P = 0.03, difference in proportions (95% CI) is 0.212 (0.0246–0.4002)]. Conclusion The present results indicate that intraperitoneal ropivacaine reduces early postoperative pain and improves recovery after laparoscopic herniorrhaphy in toddlers. Therefore, IPLA is a good stratagem for postoperative pain management after laparoscopic surgery in toddlers

Infrared Drying as a Quick Preparation Method for Dried Tangerine Peel

To establish the most convenient and effective method to dry tangerine peels, different methods (sun drying, hot-air drying, freeze drying, vacuum drying, and medium- and short-wave infrared drying) were exploited. Our results indicated that medium- and short-wave infrared drying was the best method to preserve nutraceutical components; for example, vitamin C was raised to 6.77 mg/g (D.W.) from 3.39 mg/g (sun drying). Moreover, the drying time can be shortened above 96% compared with sun drying. Importantly, the efficiency of DPPH radical scavenging was enhanced from 26.66% to 55.92%. These findings would provide a reliable and time-saving methodology to produce high-quality dried tangerine peels

Time-division-multiplexed few-mode passive optical network

We demonstrate the first few-mode-fiber based passive optical network, effectively utilizing mode multiplexing to eliminate combining loss for upstream traffic. Error-free performance has been achieved for 20-km low-crosstalk 3-mode transmission in a commercial GPON system carrying live Ethernet traffic. The alternative approach of low modal group delay is also analyzed with simulation results over 10 modes

One-stop stroke management platform reduces workflow times in patients receiving mechanical thrombectomy

Background and purposeClinical outcome in patients who received thrombectomy treatment is time-dependent. The purpose of this study was to evaluate the efficacy of the one-stop stroke management (OSSM) platform in reducing in-hospital workflow times in patients receiving thrombectomy compared with the traditional model.MethodsThe data of patients who received thrombectomy treatment through the OSSM platform and traditional protocol transshipment pathway were retrospectively analyzed and compared. The treatment-related time interval and the clinical outcome of the two groups were also assessed and compared. The primary efficacy endpoint was the time from door to groin puncture (DPT).ResultsThere were 196 patients in the OSSM group and 210 patients in the control group, in which they were treated by the traditional approach. The mean DPT was significantly shorter in the OSSM group than in the control group (76 vs. 122 min; P &lt; 0.001). The percentages of good clinical outcomes at the 90-day time point of the two groups were comparable (P = 0.110). A total of 121 patients in the OSSM group and 124 patients in the control group arrived at the hospital within 360 min from symptom onset. The mean DPT and time from symptom onset to recanalization (ORT) were significantly shorter in the OSSM group than in the control group. Finally, a higher rate of good functional outcomes was achieved in the OSSM group than in the control group (53.71 vs. 40.32%; P = 0.036).ConclusionCompared to the traditional transfer model, the OSSM transfer model significantly reduced the in-hospital delay in patients with acute stroke receiving thrombectomy treatment. This novel model significantly improved the clinical outcomes of patients presenting within the first 6 h after symptom onset