title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1767 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Metal to phosphorus stoichiometries for freshwater phytoplankton in three remote lakes link: https://peerj.com/articles/2749 last-modified: 2016-12-20 description: Simultaneous measurements of changes in phytoplankton biomass and the metal and phosphorus (P) content of cells have been captured to attest to metal to P stoichiometries for freshwater phytoplankton. Three Scottish lakes that had received high, medium or low metal contamination from the atmosphere were selected for study. Phytoplankton cells were collected and Inductively Coupled Plasma-Mass Spectrometry was used to measure their lead (Pb), cadmium (Cd), mercury (Hg), copper (Cu), zinc (Zn), nickel (Ni), chromium (Cr), manganese (Mn), cobalt (Co) and P content. Increased phytoplankton growth in the lakes resulted in significant algae growth dilution of the mass-specific Pb, Cd, Hg, Cu, Ni and Cr in the phytoplankton. Changes in the phytoplankton cell count and their Hg, Pb, Cd, Cu, Mn, Co, Ni and Cr concentrations showed the process of algae bloom dilution to be subject to exponential decay, which accelerated in the order of Mn < Cu < Ni < Pb and Cd < Cr and Hg < Co. This indicated a metabolic and detoxification mechanism was involved in the active selection of metals. For the first time simultaneous measurements of metals and P stoichiometry in freshwater phytoplankton are reported. The mean metal to P stoichiometry generated was (C106P1N16)1000Pb0.019Hg0.00004Cu0.013Cd0.005Cr0.2Co0.0008Mn0.2Ni0.012 based on field measurements and the Redfield average C, N and P stoichiometry of (CH2O)106(NH3)16H3PO4. creator: Aine M. Gormley-Gallagher creator: Richard W. Douglas creator: Brian Rippey uri: https://doi.org/10.7717/peerj.2749 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Gormley-Gallagher et al. title: Seqenv: linking sequences to environments through text mining link: https://peerj.com/articles/2690 last-modified: 2016-12-20 description: Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS) studies are presently generating huge volumes of data to address this biogeographical topic. However, these studies are often focused on specific environment types or processes leading to the production of individual, unconnected datasets. The large amounts of legacy sequence data with associated metadata that exist can be harnessed to better place the genetic information found in these surveys into a wider environmental context. Here we introduce a software program, seqenv, to carry out precisely such a task. It automatically performs similarity searches of short sequences against the “nt” nucleotide database provided by NCBI and, out of every hit, extracts–if it is available–the textual metadata field. After collecting all the isolation sources from all the search results, we run a text mining algorithm to identify and parse words that are associated with the Environmental Ontology (EnvO) controlled vocabulary. This, in turn, enables us to determine both in which environments individual sequences or taxa have previously been observed and, by weighted summation of those results, to summarize complete samples. We present two demonstrative applications of seqenv to a survey of ammonia oxidizing archaea as well as to a plankton paleome dataset from the Black Sea. These demonstrate the ability of the tool to reveal novel patterns in HTS and its utility in the fields of environmental source tracking, paleontology, and studies of microbial biogeography. To install seqenv, go to: https://github.com/xapple/seqenv. creator: Lucas Sinclair creator: Umer Z. Ijaz creator: Lars Juhl Jensen creator: Marco J.L. Coolen creator: Cecile Gubry-Rangin creator: Alica Chroňáková creator: Anastasis Oulas creator: Christina Pavloudi creator: Julia Schnetzer creator: Aaron Weimann creator: Ali Ijaz creator: Alexander Eiler creator: Christopher Quince creator: Evangelos Pafilis uri: https://doi.org/10.7717/peerj.2690 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Sinclair et al. title: Identification and characterization of Daldinia eschscholtzii isolated from skin scrapings, nails, and blood link: https://peerj.com/articles/2637 last-modified: 2016-12-20 description: BackgroundDaldinia eschscholtzii is a filamentous wood-inhabiting endophyte commonly found in woody plants. Here, we report the identification and characterization of nine D. eschscholtzii isolates from skin scrapings, nail clippings, and blood.MethodsThe nine isolates were identified based on colony morphology, light microscopy, and internal transcribed spacer (ITS)-based phylogeny. In vitro antifungal susceptibility of the fungal isolates was evaluated by the Etest to determine the minimum inhibitory concentration (MIC).ResultsThe nine isolates examined were confirmed as D. eschscholtzii. They exhibited typical features of Daldinia sp. on Sabouraud Dextrose Agar, with white felty colonies and black-gray coloration on the reverse side. Septate hyphae, branching conidiophore with conidiogenous cells budding from its terminus, and nodulisporium-like conidiophores were observed under the microscope. Phylogenetic analysis revealed that the nine isolates were clustered within the D. eschscholtzii species complex. All the isolates exhibited low MICs against azole agents (voriconazole, posaconazole, itraconazole, and ketoconazole), as well as amphotericin B, with MIC of less than 1 µg/ml.DiscussionEarly and definitive identification of D. eschscholtzii is vital to reducing misuse of antimicrobial agents. Detailed morphological and molecular characterization as well as antifungal profiling of D. eschscholtzii provide the basis for future studies on its biology, pathogenicity, and medicinal potential. creator: Kee Peng Ng creator: Chai Ling Chan creator: Su Mei Yew creator: Siok Koon Yeo creator: Yue Fen Toh creator: Hong Keat Looi creator: Shiang Ling Na creator: Kok Wei Lee creator: Wai-Yan Yee creator: Chee Sian Kuan uri: https://doi.org/10.7717/peerj.2637 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ng et al. title: Preventative and therapeutic effects of a GABA transporter 1 inhibitor administered systemically in a mouse model of paclitaxel-induced neuropathic pain link: https://peerj.com/articles/2798 last-modified: 2016-12-15 description: BackgroundThere is a dearth of drugs to manage a dose-limiting painful peripheral neuropathy induced by paclitaxel in some patients during the treatment of cancer. Gamma-aminobutyric acid transporter-1 (GAT-1) whose expression is increased in the brain and spinal cord during paclitaxel-induced neuropathic pain (PINP) might be a potential therapeutic target for managing PINP. Thus, our aim was to evaluate if systemic administration of a GAT-1 inhibitor ameliorates PINP.MethodsThe reaction latency to thermal stimuli (hot plate test; at 55 °C) and cold stimuli (cold plate test; at 4 °C) of female BALB/c mice was recorded before and after intraperitoneal treatment with paclitaxel, its vehicle, and/or a selective GAT-1 inhibitor NO-711. The effects of NO-711 on motor coordination were evaluated using the rotarod test at a constant speed of 4 rpm or accelerating mode from 4 rpm to 40 rpm over 5 min.ResultsThe coadministration of paclitaxel with NO-711 3 mg/kg prevented the development of paclitaxel-induced thermal hyperalgesia and cold allodynia at day 7 after drug treatment. NO-711 at 3 mg/kg produced antihyperalgesic activity up to 1 h and antiallodynic activity up to 2 h in mice with established paclitaxel-induced thermal hyperalgesia and cold allodynia. No motor deficits were observed with NO-711 at a dose of 3 mg/kg, whereas a higher dose 5 mg/kg caused motor impairment and reduced mean time spent on the rotarod at a constant speed of 4 rpm. However, at a rotarod accelerating mode from 4 rpm to 40 rpm over 5 min, NO-711 3 mg/kg caused motor impairment up to 1 h, but had recovered by 2 h.ConclusionsThese results show that systemic administration of the GAT-1 inhibitor NO-711 has preventative and therapeutic activity against paclitaxel-induced thermal hyperalgesia and cold allodynia. NO-711’s antiallodynic effects, but not antihyperalgesic effects, were independent of its motor impairment/sedation properties. Thus, low doses of GAT-1 inhibitors could be useful for the prevention and treatment of PINP with proper dose titration to reduce motor impairment/sedation side effects. creator: Willias Masocha creator: Subramanian S. Parvathy uri: https://doi.org/10.7717/peerj.2798 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Masocha and Parvathy title: Mortality in tongue cancer patients treated by curative surgery: a retrospective cohort study from CGRD link: https://peerj.com/articles/2794 last-modified: 2016-12-15 description: BackgroundOur study aimed to compare the outcomes of surgical treatment of tongue cancer patients in three different age groups.MethodsFrom 2004 to 2013, we retrospectively analyzed the clinical data of 1,712 patients who were treated in the four institutions constituting the Chang Gung Memorial Hospitals (CGMH). We divided and studied the patients in three age groups: Group 1, younger (<65 years); Group 2, young old (65 to <75); and Group 3, older old patients (≥75 years).ResultsMultivariate analyses determined the unfavorable, independent prognostic factors of overall survival to be male sex, older age, advanced stage, advanced T, N classifications, and surgery plus chemotherapy. No significant differences were found in adjusted hazard ratios (HR) of death in early-stage disease (stage I–II) among Group 1 (HR 1.0), Group 2 (HR 1.43, 95% confidence interval (CI) [0.87–2.34], p = 0.158), and Group 3 (HR 1.22, 95% CI [0.49–3.03], p = 0.664) patients. However, amongst advanced-stage patients (stage (III–IV)), Group 3 (HR 2.53, 95% CI [1.46–4.38], p  = 0.001) showed significantly worse survival than the other two groups after other variables were adjusted for. Fourteen out of 21 older old, advanced-staged patients finally died, and most of the mortalities were non-cancerogenic (9/14, 64.3%), and mostly occurred within one year (12/14, 85%) after cancer diagnosis. These non-cancer cause of death included underlying diseases in combination with infection, pneumonia, poor nutrition status, and trauma.ConclusionsOur study showed that advanced T classification (T3–4), positive nodal metastasis (N1–3) and poorly differentiated tumor predicted poor survival for all patients. Outcome of early-stage patients (stage I–II) among three age groups were not significantly different. However, for advanced-stage patients (stage III–IV), the older old patients (≥75) had significantly worse survival than the other two patient groups. Therefore, for early-stage patients, age should not deny them to receive optimal treatments. However, older old patients (≥75) with advanced cancer should be comprehensively assessed by geriatric tools before surgical treatment and combined with intensive postoperative care to improve outcome, especially the unfavorable non-cancerogenic mortalities within one year after cancer diagnosis. creator: Ming-Shao Tsai creator: Chia-Hsuan Lai creator: Chuan-Pin Lee creator: Yao-Hsu Yang creator: Pau-Chung Chen creator: Chung-Jan Kang creator: Geng-He Chang creator: Yao-Te Tsai creator: Chang-Hsien Lu creator: Chih-Yen Chien creator: Chi-Kuang Young creator: Ku-Hao Fang creator: Chin-Jui Liu creator: Re-Ming A. Yeh creator: Wen-Cheng Chen uri: https://doi.org/10.7717/peerj.2794 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Tsai et al. title: Psychometric properties of the Perceived Stress Scale (PSS): measurement invariance between athletes and non-athletes and construct validity link: https://peerj.com/articles/2790 last-modified: 2016-12-15 description: BackgroundAlthough Perceived Stress Scale (PSS, Cohen, Kamarack & Mermelstein, 1983) has been validated and widely used in many domains, there is still no validation in sports by comparing athletes and non-athletes and examining related psychometric indices.PurposeThe purpose of this study was to examine the measurement invariance of PSS between athletes and non-athletes, and examine construct validity and reliability in the sports contexts. MethodsStudy 1 sampled 359 college student-athletes (males = 233; females = 126) and 242 non-athletes (males = 124; females = 118) and examined factorial structure, measurement invariance and internal consistency. Study 2 sampled 196 student-athletes (males = 139, females = 57, Mage = 19.88 yrs, SD = 1.35) and examined discriminant validity and convergent validity of PSS. Study 3 sampled 37 student-athletes to assess test-retest reliability of PSS.ResultsResults found that 2-factor PSS-10 fitted the model the best and had appropriate reliability. Also, there was a measurement invariance between athletes and non-athletes; and PSS positively correlated with athletic burnout and life stress but negatively correlated with coping efficacy provided evidence of discriminant validity and convergent validity. Further, the test-retest reliability for PSS subscales was significant (r = .66 and r = .50).DiscussionIt is suggested that 2-factor PSS-10 can be a useful tool in assessing perceived stress either in sports or non-sports settings. We suggest future study may use 2-factor PSS-10 in examining the effects of stress on the athletic injury, burnout, and psychiatry disorders. creator: Yi-Hsiang Chiu creator: Frank Jing-Horng Lu creator: Ju-Han Lin creator: Chiao-Lin Nien creator: Ya-Wen Hsu creator: Hong-Yu Liu uri: https://doi.org/10.7717/peerj.2790 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Chiu et al. title: Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes in Amolops chunganensis and Quasipaa boulengeri link: https://peerj.com/articles/2786 last-modified: 2016-12-15 description: Recent improvements in next-generation sequencing (NGS) technologies can facilitate the obtainment of mitochondrial genomes. However, it is not clear whether NGS could be effectively used to reconstruct the mitogenome with high gene rearrangement. These high rearrangements would cause amplification failure, and/or assembly and alignment errors. Here, we choose two frogs with rearranged gene order, Amolops chunganensis and Quasipaa boulengeri, to test whether gene rearrangements affect the mitogenome assembly and alignment by using NGS. The mitogenomes with gene rearrangements are sequenced through Illumina MiSeq genomic sequencing and assembled effectively by Trinity v2.1.0 and SOAPdenovo2. Gene order and contents in the mitogenome of A. chunganensis and Q. boulengeri are typical neobatrachian pattern except for rearrangements at the position of “WANCY” tRNA genes cluster. Further, the mitogenome of Q. boulengeri is characterized with a tandem duplication of trnM. Moreover, we utilize 13 protein-coding genes of A. chunganensis, Q. boulengeri and other neobatrachians to reconstruct the phylogenetic tree for evaluating mitochondrial sequence authenticity of A. chunganensis and Q. boulengeri. In this work, we provide nearly complete mitochondrial genomes of A. chunganensis and Q. boulengeri. creator: Siqi Yuan creator: Yun Xia creator: Yuchi Zheng creator: Xiaomao Zeng uri: https://doi.org/10.7717/peerj.2786 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Yuan et al. title: Discovery of novel inhibitors disrupting HIF-1α/von Hippel–Lindau interaction through shape-based screening and cascade docking link: https://peerj.com/articles/2757 last-modified: 2016-12-15 description: Major research efforts have been devoted to the discovery and development of new chemical entities that could inhibit the protein–protein interaction between HIF-1α and the von Hippel–Lindau protein (pVHL), which serves as the substrate recognition subunit of an E3 ligase and is regarded as a crucial drug target in cancer, chronic anemia, and ischemia. Currently there is only one class of compounds available to interdict the HIF-1α/pVHL interaction, urging the need to discover chemical inhibitors with more diversified structures. We report here a strategy combining shape-based virtual screening and cascade docking to identify new chemical scaffolds for the designing of novel inhibitors. Based on this strategy, nine active hits have been identified and the most active hit, 9 (ZINC13466751), showed comparable activity to pVHL with an IC50 of 2.0 ± 0.14 µM, showing the great potential of utilizing these compounds for further optimization and serving as drug candidates for the inhibition of HIF-1α/von Hippel–Lindau interaction. creator: Xin Xue creator: Ning-Yi Zhao creator: Hai-Tao Yu creator: Yuan Sun creator: Chen Kang creator: Qiong-Bin Huang creator: Hao-Peng Sun creator: Xiao-Long Wang creator: Nian-Guang Li uri: https://doi.org/10.7717/peerj.2757 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Xue et al. title: In vitro gastrointestinal digestion study of a novel bio-tofu with special emphasis on the impact of microbial transglutaminase link: https://peerj.com/articles/2754 last-modified: 2016-12-15 description: We have developed a novel bio-tofu, made from mixed soy and cow milk (MSCM), using Lactobacillus helveticus MB2-1 and Lactobacillus plantarum B1-6 incorporated with microbial transglutaminase (MTGase) as coagulant. MTGase was added to improve the textural properties and suit for cooking. However, the effect of MTGase on the digestion of mixed-protein fermented by lactic acid bacteria was unclear. This study aimed at evaluating the effect of MTGase on protein digestion of bio-tofu under simulated gastrointestinal digestion condition. The results showed that addition of MTGase could affect the particle size distribution, degree of hydrolysis, the content of soluble proteins and free amino acids. Based on the electrophoresis data, MTGase addition enhanced protein polymerization. During gastric and intestinal digestion process, proteins from bio-tofu were degraded into low molecular mass peptides. Our results suggested that incorporation of MTGase could lead to enzymatic modification of proteins of bio-tofu which may help in controlling energy intake and decrease the chance of food allergy. creator: Guangliang Xing creator: Xin Rui creator: Mei Jiang creator: Yu Xiao creator: Ying Guan creator: Dan Wang creator: Mingsheng Dong uri: https://doi.org/10.7717/peerj.2754 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Xing et al. title: In situ earthworm breeding in orchards significantly improves the growth, quality and yield of papaya (Carica papaya L.) link: https://peerj.com/articles/2752 last-modified: 2016-12-15 description: The aim of this study was to compare the effects of four fertilizer applications—control (C), chemical fertilizer (F), compost (O), and in situ earthworm breeding (E)—on the growth, quality and yield of papaya (Carica papaya L.). In this study, 5 g plant−1 urea (CH4N2O, %N = 46.3%) and 100 g plant−1 microelement fertilizer was applied to each treatment. The fertilizer applications of these four treatments are different from each other. The results showed that the E treatment had the highest growth parameters over the whole growth period. At 127 days after transplantation, the order of plant heights from greatest to smallest was E > F > O > C, and the stem diameters were E > F > O > C, with significant differences between all treatments. Soluble-solid, sugar, vitamin C, and protein content significantly increased in the E treatment. In addition, the total acid and the electrical conductivity of the fruit significantly decreased in the E treatment. Fruit firmness clearly increased in the O treatment, and decreased in the F treatment. The fresh individual fruit weights, fruit numbers, and total yields were greatly improved in the F and E treatments, and the total yield of the E treatment was higher than that in the F treatment. In conclusion, the in situ earthworm breeding treatment performed better than conventional compost and chemical fertilizer treatments. Furthermore, in situ earthworm breeding may be a potential organic fertilizer application in orchards because it not only improves the fruit quality and yield but also reduces the amount of organic wastes from agriculture as a result of the activities of earthworms. creator: Huimin Xiang creator: Jia-en Zhang creator: Lei Guo creator: Benliang Zhao uri: https://doi.org/10.7717/peerj.2752 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Xiang et al.