title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1057 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: A prediction modeling based on SNOT-22 score for endoscopic nasal septoplasty: a retrospective study link: https://peerj.com/articles/9890 last-modified: 2020-09-11 description: BackgroundTo create a nomogram prediction model for the efficacy of endoscopic nasal septoplasty, and the likelihood of patient benefiting from the operation.MethodsA retrospective analysis of 155 patients with nasal septum deviation (NSD) was performed to develop a predictive model for the efficacy of endoscopic nasal septoplasty. Quality of life (QoL) data was collected before and after surgery using Sinonasal Outcome Test-22 (SNOT-22) scores to evaluate the surgical outcome. An effective surgical outcome was defined as a SNOT-22 score change ≥ 9 points after surgery. Multivariate logistic regression analysis was then used to establish a predictive model for the NSD treatment. The predictive quality and clinical utility of the predictive model were assessed by C-index, calibration plots, and decision curve analysis.ResultsThe identified risk factors for inclusion in the predictive model were included. The model had a good predictive power, with a AUC of 0.920 in the training group and a C index of 0.911 in the overall sample. Decision curve analysis revealed that the prediction model had a good clinical applicability.ConclusionsOur prediction model is efficient in predicting the efficacy of endoscopic surgery for NSD through evaluation of factors including: history of nasal surgery, preoperative SNOT-22 score, sinusitis, middle turbinate plasty, BMI, smoking, follow-up time, seasonal allergies, and advanced age. Therefore, it can be cost-effective for individualized preoperative assessment. creator: Xue-ran Kang creator: Bin Chen creator: Yi-sheng Chen creator: Bin Yi creator: Xiaojun Yan creator: Chenyan Jiang creator: Shulun Wang creator: Lixing Lu creator: Runjie Shi uri: https://doi.org/10.7717/peerj.9890 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kang et al. title: Nepenthes maximoides (Nepenthaceae) a new, critically endangered (possibly extinct) species in Sect. Alatae from Luzon, Philippines showing striking pitcher convergence with N. maxima (Sect. Regiae) of Indonesia link: https://peerj.com/articles/9899 last-modified: 2020-09-11 description: Nepenthes maximoides sp. nov. (Sect. Alatae) is described and assessed as Critically Endangered (Possibly Extinct) from Luzon, Philippines and appears unrecorded in 110 years. The spectacular, large, narrowly funnel-shaped upper pitchers, lids with recurved basal and filiform apical appendages, unlike any other species in the Philippines, closely resemble those of N. maxima (Sect. Regiae) of Sulawesi–New Guinea, likely due to convergent evolution. Following recent phylogenomic analysis, sect. Alatae is divided into two, Sect. Alatae sensu stricto of Luzon to Sibuyan (including N. maximoides), and Sect. Micramphorae, expanded and recircumscribed to encompass those species of the southern Visayas, and Mindanao. A key is provided to the six species now recognised in the newly narrowly recircumscribed Sect. Alatae. The number of Nepenthes species recorded from Luzon has increased from two in 2001, to eight in 2020, all but one of which are endemic to that island, and four of which appear to be point endemics. creator: Charles King creator: Martin Cheek uri: https://doi.org/10.7717/peerj.9899 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 King and Cheek title: First report of lionfish prey from Western Florida waters as identified by DNA barcoding link: https://peerj.com/articles/9922 last-modified: 2020-09-11 description: DNA barcoding was used to identify prey fragments recovered from the stomachs of lionfish harvested during the 2016 Sarasota Lionfish Derby. A total of 305 prey fragments were recovered from 50 stomachs (mean = 4.6 per stomach), of which 184 (60.3%) fragments could be identified to either species or genus when Cytochrome Oxidase I (COI) sequences were queried against the Barcode of Life Database. We identified 21 fish prey species which represented fourteen families and accounted for 95.7% of genetically identifiable prey items. The remaining prey items identified corresponded to six crustacean species. The four most common prey taxa in lionfish stomachs were Ptereleotris calliura (24.3%), an unidentified Microgobius species (20.4%), Diplectum formosum (14.3%), and Apogon aurolineatus (12.2%). The most frequently observed crustacean species, Metapenaeopsis goodei, was found in only three stomachs (6.1%). We also report eleven taxa as putative novel lionfish prey species, most of which are common in Florida waters. Sixteen prey items were identified as lionfish (P. volitans); however, it was not definitive whether these detections were due to cross contamination or cannibalization. This represents the first report of lionfish diets from Florida waters in the Eastern Gulf of Mexico based on barcoding efforts. Our results are largely congruent with previous COI barcoding based studies of lionfish diets, indicating these predators to be generalists exhibiting preferences for specific prey traits but with regional differences in their diets. creator: Carlos A. Santamaria creator: James Locascio creator: Taylor M. Greenan uri: https://doi.org/10.7717/peerj.9922 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Santamaria et al. 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.