title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1068 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Two new nematode species (Plectida: Leptolaimidae, Rhadinematidae) from Chatham Rise, New Zealand link: https://peerj.com/articles/9923 last-modified: 2020-09-11 description: Two new species of the order Plectida are described from Chatham Rise, New Zealand. Leptolaimus dififtinus sp. nov. is characterised by the short body 319–420 microns long, truncate labial region slightly offset from body contour and bearing conspicuous outer labial papillae, cephalic setae 1.3–1.4 microns long, amphid located 4–9 microns from anterior end, lateral alae originating from middle of buccal cavity length, female without supplements, male with precloacal and postcloacal pairs of subventral setae, nine tubular supplements (alveolar supplements absent), tubular supplements weakly S-shaped with pointed tip, spicules arcuate 24 microns or 1.4 cloacal body diameters long and dorsal gubernacular apophyses. Lavareda iramscotti sp. nov. is characterised by adult body length 3,023–3,121 microns long, eight longitudinal rows of body pores each with short papilla, cephalic setae 4–5 microns long, tail 146–165 microns long, male with spicules 54 microns long, gubernaculum with triangular apophyses, 20 precloacal supplements with bifid distal tips arranged in 9 + 1 + 10 pattern, female with vulva at 55% of body length from anterior and cuticularisation perpendicular to vagina at level of vulva. The present study provides the first record of a Leptolaimus species from the New Zealand region and the first description of a female specimen of the genus Lavareda. creator: Daniel Leduc uri: https://doi.org/10.7717/peerj.9923 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Leduc title: Antimicrobial and micronutrient interventions for the management of infants under 6 months of age identified with severe malnutrition: a literature review link: https://peerj.com/articles/9175 last-modified: 2020-09-10 description: BackgroundInfants under 6 months (U6M) contribute a significant proportion of the burden and mortality of severe malnutrition globally. Evidence of underlying aetiology in this population is sparse, but it is known that the group includes ex-preterm and low birthweight (LBW) infants. They represent a unique population given their dependence on breastmilk or a safe, secure alternative. Nutrition agencies and health providers struggle to make programming decisions on which interventions should be provided to this group based upon the 2013 WHO Guidelines for the ‘Management of Severe Acute Malnutrition in Infants and Young Children’ since there are no published interventional trial data focussed on this population. Interim guidance for this group might be informed by evidence of safety and efficacy in adjacent population groups.MethodologyA narrative literature review was performed of systematic reviews, meta-analyses and randomised controlled trials of antimicrobial and micronutrient interventions (antibiotics, deworming, vitamin A, vitamin D, iron, zinc, folic acid and oral rehydration solution (ORS) for malnutrition) across the population groups of low birthweight/preterm infants, infants under 6 months, infants and children over 6 months with acute malnutrition or through supplementation to breastfeeding mothers. Outcomes of interest were safety and efficacy, in terms of mortality and morbidity.ResultsNinety-four articles were identified for inclusion within this review. None of these studied interventions exclusively in severely malnourished infants U6M. 64% reported on the safety of studied interventions. Significant heterogeneity was identified in definitions of study populations, interventions provided, and outcomes studied. The evidence for efficacy and safety across population groups is reviewed and presented for the interventions listed.ConclusionsThe direct evidence base for medical interventions for severely malnourished infants U6M is sparse. Our review identifies a specific need for accurate micronutrient profiling and interventional studies of micronutrients and oral fluid management of diarrhoea amongst infants U6M meeting anthropometric criteria for severe malnutrition. Indirect evidence presented in this review may help shape interim policy and programming decisions as well as the future research agenda for the management of infants U6M identified as malnourished. creator: Timothy J. Campion-Smith creator: Marko Kerac creator: Marie McGrath creator: James A. Berkley uri: https://doi.org/10.7717/peerj.9175 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Campion-Smith et al. title: Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria link: https://peerj.com/articles/9861 last-modified: 2020-09-10 description: Dimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton and bacteria, is primarily degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: (1) a recent common ancestor of DmdA and GcvT, (2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and (3) an enzymatic adaptation for utilizing DMSP in marine bacteria prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution between Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA by horizontal gene transfer prior to an environment with higher DMSP. Here, we propose that the ancestor that carried the DMSP demethylation pathway genes evolved in the Archean, and was exposed to a higher concentration of DMSP in a sulfur-rich atmosphere and anoxic ocean, compared to recent Roseobacter eco-orthologs (orthologs performing the same function under different conditions), which should be adapted to lower concentrations of DMSP. creator: Laura Hernández creator: Alberto Vicens creator: Luis E. Eguiarte creator: Valeria Souza creator: Valerie De Anda creator: José M. González uri: https://doi.org/10.7717/peerj.9861 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Hernández et al. title: Consistent administration of cetuximab is associated with favorable outcomes in recurrent/metastatic head and neck squamous cell carcinoma in an endemic carcinogen exposure area: a retrospective observational study link: https://peerj.com/articles/9862 last-modified: 2020-09-10 description: BackgroundThis study aimed to analyze the clinical outcomes associated with patients with recurrent/metastatic head and neck squamous cell carcinoma (RM HNSCC) who received cetuximab-based chemotherapy in a real-world clinical setting.MethodsClinical data were extracted from RM HNSCC patients diagnosed between 2016 and 2019. Kaplan–Meier survival estimates and Cox proportional hazards model were used for survival analyses.ResultsOf 106 RM HNSCC patients (mean age = 55.1 years), 38.7% exhibited recurrent disease and 61.3% had metastatic disease. The majority of patients showed a habit of addictive substance use, including alcohol (67.0%), betel nuts (71.7%), or tobacco (74.5%). The primary tumor sites included the oral cavity (64.1%), hypopharynx (19.8%), and oropharynx (16.0%). The median number of cetuximab cycles for the 106 patients was 11 (2–24). The disease control rate (DCR) was 48.1%, and the overall response rate (ORR) was 28.3%. The median progression-free survival (PFS) and overall survival (OS) were 5.0 and 9.23 months, respectively. Patients treated with more than 11 cycles of cetuximab exhibited a longer median PFS and median OS than did patients treated with less than 11 cycles (median PFS: 7.0 vs. 3.0 months, p < 0.001; OS: 12.43 vs. 4.46 months, p = 0.001). Patients without previous concurrent chemoradiotherapy (CRT) had a better median PFS than did those with previous CRT (6.0 vs. 4.0 months, p = 0.046). Multivariable analysis revealed that perineural invasion and fewer cycles of cetuximab (<11 cycles) were independent risk factors associated with disease progression. In addition, the reduction in treatment cycles of cetuximab and advanced lymph node metastasis were independent prognostic factors predicting poorer overall survival.ConclusionOur study provides important real-world data regarding cetuximab-containing treatment in RM HNSCC. Consistent administration of cetuximab could be associated with more favorable outcomes in RM HNSCC in endemic carcinogen exposure areas. creator: Hui-Ching Wang creator: Pei-Lin Liu creator: Pei-Chuan Lo creator: Yi-Tzu Chang creator: Leong-Perng Chan creator: Tsung-Jang Yeh creator: Hui-Hua Hsiao creator: Shih-Feng Cho uri: https://doi.org/10.7717/peerj.9862 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: A survey of RNA secondary structural propensity encoded within human herpesvirus genomes: global comparisons and local motifs link: https://peerj.com/articles/9882 last-modified: 2020-09-10 description: There are nine herpesviruses known to infect humans, of which Epstein–Barr virus (EBV) is the most widely distributed (>90% of adults infected). This ubiquitous virus is implicated in a variety of cancers and autoimmune diseases. Previous analyses of the EBV genome revealed numerous regions with evidence of generating unusually stable and conserved RNA secondary structures and led to the discovery of a novel class of EBV non-coding (nc)RNAs: the stable intronic sequence (sis)RNAs. To gain a better understanding of the roles of RNA structure in EBV biology and pathogenicity, we revisit EBV using recently developed tools for genome-wide motif discovery and RNA structural characterization. This corroborated previous results and revealed novel motifs with potential functionality; one of which has been experimentally validated. Additionally, since many herpesviruses increasingly rival the seroprevalence of EBV (VZV, HHV-6 and HHV-7 being the most notable), analyses were expanded to include all sequenced human Herpesvirus RefSeq genomes, allowing for genomic comparisons. In total 10 genomes were analyzed, for EBV (types 1 and 2), HCMV, HHV-6A, HHV-6B, HHV-7, HSV-1, HSV-2, KSHV, and VZV. All resulting data were archived in the RNAStructuromeDB (https://structurome.bb.iastate.edu/herpesvirus) to make them available to a wide array of researchers. creator: Ryan J. Andrews creator: Collin A. O’Leary creator: Walter N. Moss uri: https://doi.org/10.7717/peerj.9882 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Andrews et al. title: Evaluation of different culture media to support in vitro growth and biofilm formation of bacterial vaginosis-associated anaerobes link: https://peerj.com/articles/9917 last-modified: 2020-09-10 description: BackgroundBacterial vaginosis (BV) is one of the most common vaginal infections worldwide. It is associated with the presence of a dense polymicrobial biofilm on the vaginal epithelium, formed mainly by Gardnerella species. The biofilm also contains other anaerobic species, but little is known about their role in BV development.AimTo evaluate the influence of different culture media on the planktonic and biofilm growth of six cultivable anaerobes frequently associated with BV, namely Gardnerella sp., Atopobium vaginae, Lactobacillus iners, Mobiluncus curtisii, Peptostreptococcus anaerobius and Prevotella bivia.MethodsA total of nine different culture media compositions, including commercially available and chemically defined media simulating genital tract secretions, were tested in this study. Planktonic cultures and biofilms were grown under anaerobic conditions (10% carbon dioxide, 10% helium and 80% nitrogen). Planktonic growth was assessed by optical density measurements, and biofilm formation was quantified by crystal violet staining.ResultsSignificant planktonic growth was observed for Gardnerella sp., A. vaginae and L. iners in New York City III broth, with or without ascorbic acid supplementation. Biofilm quantification showed high in vitro biofilm growth for Gardnerella sp., P. anaerobius and P. bivia in almost all culture media excluding Brucella broth. Contrary, only New York City III broth was able to promote biofilm formation for A. vaginae, L. iners and M. curtisii.ConclusionsOur data demonstrate that New York City III broth relative to the other tested media is the most conducive for future studies addressing polymicrobial biofilms development as this culture medium allowed the formation of significant levels of single-species biofilms. creator: Aliona S. Rosca creator: Joana Castro creator: Nuno Cerca uri: https://doi.org/10.7717/peerj.9917 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Rosca et al. title: A multi-class classification model for supporting the diagnosis of type II diabetes mellitus link: https://peerj.com/articles/9920 last-modified: 2020-09-10 description: BackgroundNumerous studies have utilized machine-learning techniques to predict the early onset of type 2 diabetes mellitus. However, fewer studies have been conducted to predict an appropriate diagnosis code for the type 2 diabetes mellitus condition. Further, ensemble techniques such as bagging and boosting have likewise been utilized to an even lesser extent. The present study aims to identify appropriate diagnosis codes for type 2 diabetes mellitus patients by means of building a multi-class prediction model which is both parsimonious and possessing minimum features. In addition, the importance of features for predicting diagnose code is provided.MethodsThis study included 149 patients who have contracted type 2 diabetes mellitus. The sample was collected from a large hospital in Taiwan from November, 2017 to May, 2018. Machine learning algorithms including instance-based, decision trees, deep neural network, and ensemble algorithms were all used to build the predictive models utilized in this study. Average accuracy, area under receiver operating characteristic curve, Matthew correlation coefficient, macro-precision, recall, weighted average of precision and recall, and model process time were subsequently used to assess the performance of the built models. Information gain and gain ratio were used in order to demonstrate feature importance.ResultsThe results showed that most algorithms, except for deep neural network, performed well in terms of all performance indices regardless of either the training or testing dataset that were used. Ten features and their importance to determine the diagnosis code of type 2 diabetes mellitus were identified. Our proposed predictive model can be further developed into a clinical diagnosis support system or integrated into existing healthcare information systems. Both methods of application can effectively support physicians whenever they are diagnosing type 2 diabetes mellitus patients in order to foster better patient-care planning. creator: Kuang-Ming Kuo creator: Paul Talley creator: YuHsi Kao creator: Chi Hsien Huang uri: https://doi.org/10.7717/peerj.9920 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Kuo et al. title: KEYLINK: towards a more integrative soil representation for inclusion in ecosystem scale models. I. review and model concept link: https://peerj.com/articles/9750 last-modified: 2020-09-09 description: The relatively poor simulation of the below-ground processes is a severe drawback for many ecosystem models, especially when predicting responses to climate change and management. For a meaningful estimation of ecosystem production and the cycling of water, energy, nutrients and carbon, the integration of soil processes and the exchanges at the surface is crucial. It is increasingly recognized that soil biota play an important role in soil organic carbon and nutrient cycling, shaping soil structure and hydrological properties through their activity, and in water and nutrient uptake by plants through mycorrhizal processes. In this article, we review the main soil biological actors (microbiota, fauna and roots) and their effects on soil functioning. We review to what extent they have been included in soil models and propose which of them could be included in ecosystem models. We show that the model representation of the soil food web, the impact of soil ecosystem engineers on soil structure and the related effects on hydrology and soil organic matter (SOM) stabilization are key issues in improving ecosystem-scale soil representation in models. Finally, we describe a new core model concept (KEYLINK) that integrates insights from SOM models, structural models and food web models to simulate the living soil at an ecosystem scale. creator: Gaby Deckmyn creator: Omar Flores creator: Mathias Mayer creator: Xavier Domene creator: Andrea Schnepf creator: Katrin Kuka creator: Kris Van Looy creator: Daniel P. Rasse creator: Maria J.I. Briones creator: Sébastien Barot creator: Matty Berg creator: Elena Vanguelova creator: Ivika Ostonen creator: Harry Vereecken creator: Laura M. Suz creator: Beat Frey creator: Aline Frossard creator: Alexei Tiunov creator: Jan Frouz creator: Tine Grebenc creator: Maarja Öpik creator: Mathieu Javaux creator: Alexei Uvarov creator: Olga Vindušková creator: Paul Henning Krogh creator: Oskar Franklin creator: Juan Jiménez creator: Jorge Curiel Yuste uri: https://doi.org/10.7717/peerj.9750 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Deckmyn et al. title: Omics approaches in Allium research: Progress and way ahead link: https://peerj.com/articles/9824 last-modified: 2020-09-09 description: BackgroundThe genus Allium (Family: Amaryllidaceae) is an economically important group of crops cultivated worldwide for their use as a vegetable and spices. Alliums are also well known for their nutraceutical properties. Among alliums, onion, garlic, leek, and chives cultivated worldwide. Despite their substantial economic and medicinal importance, the genome sequence of any of the Allium is not available, probably due to their large genome sizes. Recently evolved omics technologies are highly efficient and robust in elucidating molecular mechanisms of several complex life processes in plants. Omics technologies, such as genomics, transcriptomics, proteomics, metabolomics, metagenomics, etc. have the potential to open new avenues in research and improvement of allium crops where genome sequence information is limited. A significant amount of data has been generated using these technologies for various Allium species; it will help in understanding the key traits in Allium crops such as flowering, bulb development, flavonoid biosynthesis, male sterility and stress tolerance at molecular and metabolite level. This information will ultimately assist us in speeding up the breeding in Allium crops.MethodIn the present review, major omics approaches, and their progress, as well as potential applications in Allium crops, could be discussed in detail.ResultsHere, we have discussed the recent progress made in Allium research using omics technologies such as genomics, transcriptomics, micro RNAs, proteomics, metabolomics, and metagenomics. These omics interventions have been used in alliums for marker discovery, the study of the biotic and abiotic stress response, male sterility, organ development, flavonoid and bulb color, micro RNA discovery, and microbiome associated with Allium crops. Further, we also emphasized the integrated use of these omics platforms for a better understanding of the complex molecular mechanisms to speed up the breeding programs for better cultivars.ConclusionAll the information and literature provided in the present review throws light on the progress and potential of omics platforms in the research of Allium crops. We also mentioned a few research areas in Allium crops that need to be explored using omics technologies to get more insight. Overall, alliums are an under-studied group of plants, and thus, there is tremendous scope and need for research in Allium species. creator: Kiran Khandagale creator: Ram Krishna creator: Praveen Roylawar creator: Avinash B. Ade creator: Ashwini Benke creator: Bharat Shinde creator: Major Singh creator: Suresh J. Gawande creator: Ashutosh Rai uri: https://doi.org/10.7717/peerj.9824 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Khandagale et al. title: Assessment of postoperative health functioning after knee arthroplasty in relation to pain catastrophizing: a 6-month follow-up cohort study link: https://peerj.com/articles/9903 last-modified: 2020-09-09 description: BackgroundKnee arthroplasty (KA) is a typically successful surgical procedure commonly performed to alleviate painin participants with end-stage knee osteoarthritis. Despite its beneficial effects, a significant proportion of individuals with KA continue experiencing persistent pain and functional limitations. The purpose of this study was to assess the postoperative outcomes after KA in relation to postoperative pain catastrophizing.MethodsParticipants were recruited at a domiciliary physiotherapy service, using a prospective, observational, hypothesis-generating cohort design. Participants were divided into two groups based on their Pain Catastrophizing Scale (PCS) total score (50th percentile), which resulted in high and low PCS groups. The primary outcome measure was the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC). In addition, quality of life, walking speed, physical performance, range of motion, and pain were measured. Outcome measures were collected at baseline (1 week postoperatively) and at follow-up (1, 3, and 6 months postoperatively).ResultsA total of 60 participants (21 total KA and 39 unicompartmental KA) were recruited. Individuals with a higher degree of pain catastrophizing showed significantly higher WOMAC total scores at every follow-up, indicating poorer health functioning (p < 0.01). Similarly, the high PCS group showed higher WOMAC pain, stiffness and disability subscale scores (p < 0.05), poorer quality of life (p < 0.01), and poorer physical performance (p < 0.05) at every follow-up. In addition, the high PCS group achieved a slower walking speed at baseline and at 3 months follow-up (p < 0.05), and a higher degree of pain at rest, on walking and on knee flexion at every follow-up (p < 0.01, p < 0.05 and p < 0.05, respectively) except for walking pain at 3 months follow-up. No significant differences were observed between groups in range of motion, except for active knee extension at the 6-month follow-up (p < 0.05). Effect size was large at 1 month follow-up in WOMAC total score (r = 0.578) and pain intensity during knee flexion (r = 0.529). Longitudinal analyses revealed different improvement trends during the rehabilitation process between groups, with a lack of significant improvements in the high PCS group between the 3- and 6-month follow-up in WOMAC total score, WOMAC pain, WOMAC disability, quality of life, physical performance, active knee extension and resting pain (p > 0.05).ConclusionThe results of the present study suggest that participants with high postoperative pain catastrophizing might have poorer outcomes during the rehabilitation process after KA. Future work should seek to clarify if this relationship is causal. creator: Marc Terradas-Monllor creator: Mirari Ochandorena-Acha creator: Julio Salinas-Chesa creator: Sergi Ramírez creator: Hector Beltran-Alacreu uri: https://doi.org/10.7717/peerj.9903 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Terradas-Monllor et al.