title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1221 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The Rametrix™ PRO Toolbox v1.0 for MATLAB® link: https://peerj.com/articles/8179 last-modified: 2020-01-06 description: BackgroundExisting tools for chemometric analysis of vibrational spectroscopy data have enabled characterization of materials and biologicals by their broad molecular composition. The Rametrix™ LITE Toolbox v1.0 for MATLAB® is one such tool available publicly. It applies discriminant analysis of principal components (DAPC) to spectral data to classify spectra into user-defined groups. However, additional functionality is needed to better evaluate the predictive capabilities of these models when “unknown” samples are introduced. Here, the Rametrix™ PRO Toolbox v1.0 is introduced to provide this capability.MethodsThe Rametrix™ PRO Toolbox v1.0 was constructed for MATLAB® and works with the Rametrix™ LITE Toolbox v1.0. It performs leave-one-out analysis of chemometric DAPC models and reports predictive capabilities in terms of accuracy, sensitivity (true-positives), and specificity (true-negatives). Rametrix™PRO is available publicly through GitHub under license agreement at: https://github.com/SengerLab/RametrixPROToolbox. Rametrix™ PRO was used to validate Rametrix™ LITE models used to detect chronic kidney disease (CKD) in spectra of urine obtained by Raman spectroscopy. The dataset included Raman spectra of urine from 20 healthy individuals and 31 patients undergoing peritoneal dialysis treatment for CKD.ResultsThe number of spectral principal components (PCs) used in building the DAPC model impacted the model accuracy, sensitivity, and specificity in leave-one-out analyses. For the dataset in this study, using 35 PCs in the DAPC model resulted in 100% accuracy, sensitivity, and specificity in classifying an unknown Raman spectrum of urine as belonging to a CKD patient or a healthy volunteer. Models built with fewer or greater number of PCs showed inferior performance, which demonstrated the value of Rametrix™ PRO in evaluating chemometric models constructed with Rametrix™ LITE. creator: Ryan S. Senger creator: John L. Robertson uri: https://doi.org/10.7717/peerj.8179 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Senger and Robertson title: sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data link: https://peerj.com/articles/8214 last-modified: 2020-01-06 description: Structural variants (SVs) are an important class of genetic variation implicated in a wide array of genetic diseases including cancer. Despite the advances in whole genome sequencing, comprehensive and accurate detection of SVs in short-read data still poses some practical and computational challenges. We present sv-callers, a highly portable workflow that enables parallel execution of multiple SV detection tools, as well as provide users with example analyses of detected SV callsets in a Jupyter Notebook. This workflow supports easy deployment of software dependencies, configuration and addition of new analysis tools. Moreover, porting it to different computing systems requires minimal effort. Finally, we demonstrate the utility of the workflow by performing both somatic and germline SV analyses on different high-performance computing systems. creator: Arnold Kuzniar creator: Jason Maassen creator: Stefan Verhoeven creator: Luca Santuari creator: Carl Shneider creator: Wigard P. Kloosterman creator: Jeroen de Ridder uri: https://doi.org/10.7717/peerj.8214 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Kuzniar et al. title: Comparative analysis of codon usage patterns in chloroplast genomes of six Euphorbiaceae species link: https://peerj.com/articles/8251 last-modified: 2020-01-06 description: Euphorbiaceae plants are important as suppliers of biodiesel. In the current study, the codon usage patterns and sources of variance in chloroplast genome sequences of six different Euphorbiaceae plant species have been systematically analyzed. Our results revealed that the chloroplast genomes of six Euphorbiaceae plant species were biased towards A/T bases and A/T-ending codons, followed by detection of 17 identical high-frequency codons including GCT, TGT, GAT, GAA, TTT, GGA, CAT, AAA, TTA, AAT, CCT, CAA, AGA, TCT, ACT, TAT and TAA. It was found that mutation pressure was a minor factor affecting the variation of codon usage, however, natural selection played a significant role. Comparative analysis of codon usage frequencies of six Euphorbiaceae plant species with four model organisms reflected that Arabidopsis thaliana, Populus trichocarpa, and Saccharomyces cerevisiae should be considered as suitable exogenous expression receptor systems for chloroplast genes of six Euphorbiaceae plant species. Furthermore, it is optimal to choose Saccharomyces cerevisiae as the exogenous expression receptor. The outcome of the present study might provide important reference information for further understanding the codon usage patterns of chloroplast genomes in other plant species. creator: Zhanjun Wang creator: Beibei Xu creator: Bao Li creator: Qingqing Zhou creator: Guiyi Wang creator: Xingzhou Jiang creator: Chenchen Wang creator: Zhongdong Xu uri: https://doi.org/10.7717/peerj.8251 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Effects of environmental variables on abundance of ammonia-oxidizing communities in sediments of Luotian River, China link: https://peerj.com/articles/8256 last-modified: 2020-01-06 description: Ammonia-oxidizing communities play important functional roles in the nitrification. However, environmental stresses can significantly affect this process by controlling the abundant communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities. In this study, we examined the abundance variations of ammonia-oxidizing communities using quantitative polymerase chain reaction (qPCR) and terminal-restriction fragment length polymorphism (T-RFLP) in a typical subtropical river, Luotian County, South Dabie Mountains, China. Clone libraries were conducted to evaluate the community structure and abundance of AOA and AOB in sediments. Results showed that Nitrososphaera sp and Nitrosopumilus sp were the most dominant AOA. The abundance of the AOA and AOB amoA gene ranged from 5.28 × 108 gene copies (g-soil−1) to 2.23 × 108 gene copies (g-soil−1) and 5.45 × 108 gene copies (g-soil−1) to 3.30 × 107 gene copies (g-soil−1), respectively. Five environmental variables, namely, ORP, DO, NO${}_{3}^{-}$3−, Temp, and NH${}_{4}^{+}$4+ were played a major function in microbial communities of AOA and AOB in sediments. The T-RFLP profiles of AOA showed that 488 and 116 bp T-RFs were dominated. Overall, the results of this study showed that anthropogenic activities andenvironmental stress in rivers can alter the structure and function of microbes in their variable environment. creator: Amjed Ginawi creator: Lixiao Wang creator: Huading Wang creator: Bingbing Yu creator: Yan Yunjun uri: https://doi.org/10.7717/peerj.8256 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ginawi et al. title: Comparative analysis of primary metabolites and transcriptome changes between ungrafted and pumpkin-grafted watermelon during fruit development link: https://peerj.com/articles/8259 last-modified: 2020-01-06 description: Grafting has been reported as a factor that influences fruit quality. However, a comprehensive study of the metabolic profile related to fruit quality and the underlying molecular mechanism in grafted watermelon has not been carried out. Metabolomics and transcriptome analysis were performed on both pumpkin-grafted watermelon and ungrafted watermelon at different developmental stages. In total, 56 primary metabolites were identified with either high or low abundance between ungrafted and pumpkin-grafted watermelon. The results indicated that ornithine, arginine, lysine (amino acids), glucose, sucrose, glucosamine (sugars), malic acid, fumaric acid and succinic acid (organic acids) were among the dominant metabolites influencing fruit quality. Additionally, comparative RNA sequence analysis on grafted and ungrafted watermelon yielded 729, 174, 128 and 356 differentially expressed genes at 10, 18, 26 and 34 days after pollination (DAP), respectively. Functional annotations of these genes indicated that grafting significantly altered the biological and metabolic processes related to fruit quality. Our comparative metabolomics and transcriptome analysis revealed that FBA2, FK, SuSy, SPS, IAI, AI and sugar transporter gene (SWT3b) might play a central role in the accumulation of glucose and sucrose, whereas higher malic acid content was attributed to high down regulation of ALMT13 and ALMT8 in pumpkin-grafted watermelon. Changes in the ornithine, glutamine, alanine, tyrosine, valine, asparagine, phenylalanine, arginine and tryptophan contents were consistent with the transcript level of their metabolic genes such as NAOD, GS, AGT, TaT, aDH1, OGDH, aDC, 4CL 1, PaL, CaT and two nitrate transporter genes (NRT1) in pumpkin-grafted watermelon. This study provides the basis for understanding the graft-responsive changes in the metabolic profile and regulatory mechanism related to fruit quality. creator: Ali Aslam creator: Shengjie Zhao creator: Muhammad Azam creator: Xuqiang Lu creator: Nan He creator: Bingbing Li creator: Junling Dou creator: Hongju Zhu creator: Wenge Liu uri: https://doi.org/10.7717/peerj.8259 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Aslam et al. title: Diagnosis and treatment of epididymal tuberculosis: a review of 47 cases link: https://peerj.com/articles/8291 last-modified: 2020-01-06 description: ObjectiveTo analyze the clinical manifestations, diagnosis and treatment outcomes in a series of patients with epididymal tuberculosis.MethodsThis study is a retrospective data analysis of 47 cases of histologically-confirmed epididymal tuberculosis in patients treated at our hospital from November 2012 to December 2018.ResultsThe average age of the patients was approximately 42 years. The epididymal lesion location was left-sided in 15 patients (31.9%), right-sided in 22 patients (46.8%) and bilateral in 10 patients (21.3%). The main symptoms were painless swelling of the scrotum in 21 cases (44.7%) and scrotal drop pain in 21 cases (44.7%). Scrotal physical examination revealed epididymal beaded enlargement in 12 patients (25.5%), testicular mass in one patient (2.1%), scrotal tenderness alone in seven patients (14.9%), ill-defined epididymal-testicular border in 21 patients (44.7%) and sinus formation in six patients (12.8%). After 2–4 weeks of anti-tuberculosis chemotherapy, the patients underwent a surgical procedure. We found that 10 (83.3%) of the 12 patients whose main symptom was epididymal beaded enlargement underwent simple epididymal surgery. Of the 21 patients whose main clinical manifestation was ill-defined testis-epididymis demarcation, 16 (72.2%) underwent epididymis-testicular surgery. All patients underwent postoperative chemotherapy for 3–6 months. Postoperative follow-up showed good response to treatment.ConclusionIt is difficult to diagnose early-stage epididymal tuberculosis. Epididymal tuberculosis is likely to have invaded surrounding tissues when signs such as epididymal beaded changes and ill-defined epididymis-testis border are present. Surgical treatment combined with preoperative and postoperative chemotherapy is an effective approach to treating this condition. creator: Jiangwei Man creator: Lei Cao creator: Zhilong Dong creator: Junqiang Tian creator: Zhiping Wang creator: Li Yang uri: https://doi.org/10.7717/peerj.8291 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Man et al. title: The first pterosaur basihyal, shedding light on the evolution and function of pterosaur hyoid apparatuses link: https://peerj.com/articles/8292 last-modified: 2020-01-06 description: The pterosaur is the first known vertebrate clade to achieve powered flight. Its hyoid apparatus shows a simplification similar to that of birds, although samples of the apparatus are rare, limiting the ability to make an accurate determination. In this study we reveal a new pterosaur specimen, including the first definite basihyal. Through the comparison of pterosaur hyoids, a trend has been discovered for the shortened hyoid relative to the length of the skull, indicating a diminished role of lingual retraction during the evolution of the pterosaur. The new material, possibly from a gallodactylid Gladocephaloideus, represents one of the least effective lingual retractions in all pterosaurs. Based on the structure of an elongated ceratobranchial and retroarticular process on mandibles, the function of the Y-shaped istiodactylid tongue bone is similar to those of scavenger crows rather than chameleons, which is consistent with the interpretation of the scavenging behavior of this taxon. More fossil samples are needed for further study on the function of other pterosaur hyoids. creator: Shunxing Jiang creator: Zhiheng Li creator: Xin Cheng creator: Xiaolin Wang uri: https://doi.org/10.7717/peerj.8292 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Jiang et al. title: Changes in long non-coding RNA transcriptomic profiles after ischemia-reperfusion injury in rat spinal cord link: https://peerj.com/articles/8293 last-modified: 2020-01-06 description: With the aim of exploring expression profiles and biological functions of long non-coding RNA (lncRNA) and mRNAs after spinal cord ischemia-reperfusion injury (SCII), differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) in rat spinal cords were identified following SCII through high-throughput RNA sequencing. In total, 1,455 lncRNAs and 6,707 mRNAs were observed to be differentially expressed (—Fold Change— ≥ 2 and P < 0.05) after SCII, including 761 up-regulated and 694 down-regulated lncRNAs, 3,772 up-regulated and 2,935 down-regulated mRNAs. Gene ontology and KEGG pathway analysis showed that the DElncRNAs and DEmRNAs were implicated in many different biological processes and pathways. Further, lncRNA-mRNA co-expression networks were built to explore the potential roles of these DElncRNAs. Our results demonstrate genome-wide lncRNA and mRNA expression patterns in spinal cords after SCII, which may play vital roles in post-SCII pathophysiological processes. These findings are important for future functional research on the lncRNAs involved in SCII and might be critical for providing new insight into identification of potential targets for SCII therapy. creator: Zhibin Zhou creator: Bin Han creator: Hai Jin creator: Aimin Chen creator: Lei Zhu uri: https://doi.org/10.7717/peerj.8293 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhou et al. title: The effect on twinning rate of transferring double vitrified-warmed embryos in women of advanced reproductive age: a retrospective study link: https://peerj.com/articles/8308 last-modified: 2020-01-06 description: Twin pregnancies are associated with greater risk of neonatal morbidity and mortality than a singleton. This study was performed to investigate the twin pregnancy rate when two vitrified-warmed embryos are transferred in women of advanced reproductive age (≥35 years at the time of oocyte retrieval) and to evaluate the implications of findings in selecting candidates for elective single embryo transfer (eSET). A retrospective analysis of data which included 2,038 women aged 35–45 years, who underwent vitrified-warmed double embryo transfer (DET), from January 2013 to December 2016 was undertaken. Pregnancy and twin rates were estimated after stratifying by prognostic profile. The twin pregnancy rate was lower in women with poor prognosis (12/96, 12.5%) as compared with that in women with favorable prognosis (102/374, 27.3%) and average prognosis (78/346, 22.5%) with significant differences (P < 0.05). The twin rate for women with favorable prognosis was 29.2% (70/240) in the cycles of women aged 35–37 years, 26.8% (26/97) in the cycles of women aged 38–40 years and 16.2% (6/37) in the cycles of women >40 years. The twin rate for women with average prognosis was 25.8% (51/198) in the cycles of women aged 35–37 years, 22.0% (22/100) in the cycles of women aged 38–40 years and 10.4% (5/48) in the cycles of women >40 years. The twin rate for women with poor prognosis was 15.3% (9/59) in the cycles of women aged 35–37 years, 10.3% (3/29) in the cycles of women aged 38–40 years and 0% (0/8) in the cycles of women >40 years. From these results, it was concluded that women with a favorable or average prognosis have a high risk of twin pregnancies. The finding can be used to guide future practice: that is, performing eSET in women with favorable or average prognosis and DET in women with poor prognosis. creator: Yamei Xue creator: Kun Li creator: Songying Zhang uri: https://doi.org/10.7717/peerj.8308 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Xue et al. title: Gene co-expression network for analysis of plasma exosomal miRNAs in the elderly as markers of aging and cognitive decline link: https://peerj.com/articles/8318 last-modified: 2020-01-06 description: BackgroundEvidence has shown that microRNA (miRNAs) are involved in molecular pathways responsible for aging and age-related cognitive decline. However, there is a lack of research linked plasma exosome-derived miRNAs changes with cognitive function in older people and aging, which might prove a new insight on the transformation of miRNAs on clinical applications for cognitive decline for older people.MethodsWe applied weighted gene co-expression network analysis to investigated miRNAs within plasma exosomes of older people for a better understanding of the relationship of exosome-derived miRNAs with cognitive decline in elderly adults. We identified network modules of co-expressed miRNAs in the elderly exosomal miRNAs dataset. In each module, we selected vital miRNAs and carried out functional enrichment analyses of their experimentally known target genes and their function.ResultsWe found that plasma exosomal miRNAs hsa-mir-376a-3p, miR-10a-5p, miR-125-5p, miR-15a-5p have critical regulatory roles in the development of aging and cognitive dysfunction in the elderly and may serve as biomarkers and putative novel therapeutic targets for aging and cognitive decline. creator: Zheng Ye creator: Bo Sun creator: Xue Mi creator: Zhongdang Xiao uri: https://doi.org/10.7717/peerj.8318 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ye et al.