title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=837 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: New free-living nematode species and records (Chromadorea: Plectida and Desmodorida) from the edge and axis of Kermadec Trench, Southwest Pacific Ocean link: https://peerj.com/articles/12037 last-modified: 2021-09-24 description: One new nematode species is described and two new species records are provided from the edge (6,080 m depth) and axis (7,132 m) of Kermadec Trench, Southwest Pacific. Leptolaimus hadalis sp. nov. is characterised by medium body 587–741 μm long, labial region not offset from body contour, inconspicuous labial sensilla, amphid located 12–19 μm from anterior end, female without supplements, male with four tubular precloacal supplements (alveolar supplements absent), tubular supplements almost straight with dentate tip, arcuate spicules and weakly cuticularized dorsal gubernacular apophyses strongly bent distally. In a previously published ecological survey of Kermadec Trench, L. hadalis sp. nov. was the most abundant species in a core obtained at 8,079 m water depth and third most abundant species in a core obtained at 7,132 m, while only one individual was found at 6,096 m depth, and none at 9,175 m depth (Leduc & Rowden, 2018). Alaimella aff. cincta and Desmodora aff. pilosa are recorded for the first time from the Southwest Pacific region. Prior to the present study, Alaimella had only been recorded from coastal locations and from the Weddell sea to a depth of 2,000 m. The record of Desmodora aff. pilosa at 6,080 m depth is the deepest record of a Desmodora species to date, although unidentified Desmodora specimens have been found as deep as 6,300 m in the South Sandwich Trench. The morphology of the Kermadec Trench Alaimella aff. cincta and Desmodora aff. pilosa specimens bear a strong resemblance to their respective type populations from the Northern Hemisphere, but further morphological and molecular data are required to ascertain whether they in fact represent distinct species. creator: Daniel Leduc uri: https://doi.org/10.7717/peerj.12037 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Leduc title: Quantitative trait locus mapping analysis of multiple traits when using genotype data with potential errors link: https://peerj.com/articles/12187 last-modified: 2021-09-24 description: BackgroundQuantitative trait locus (QTL) analysis aims to locate and estimate the effects of the genes influencing quantitative traits and infer the relationship between gene variants and changes in phenotypic characteristics using statistical methods. Some methods have been developed to map QTLs of multiple traits in the case of no genotype error in a given dataset. However, practical genetic data that people use may contain some potential errors because of the limitations of biotechnology. Common genetic data correction methods can only reduce errors, but cannot calculate the degree of error. In this paper, we propose a QTL mapping strategy for multiple traits in the presence of genotype errors.MethodsThe additive effect, dominant effect, recombination rate, error rate, and other parameters of QTLs can be simultaneously obtained using this new method in the framework of multiple-interval mapping.ResultsOur simulation results show that the accuracy of parameter estimation can be improved by considering the errors of marker genotypes during the analysis of genetic data. Real data analysis also shows that the new method proposed in this paper can map the QTLs of multiple traits more accurately. creator: Liang Tong creator: Ying Zhou creator: Yixing Guo creator: Hui Ding creator: Donghai Ji uri: https://doi.org/10.7717/peerj.12187 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Tong et al. title: Bilateral back squat strength is increased during a 3-week undulating resistance training program with and without variable resistance in DIII collegiate football players link: https://peerj.com/articles/12189 last-modified: 2021-09-24 description: BackgroundOptimizing training adaptations is of the utmost importance for the strength and conditioning professional. The pre-season of any sport is particularly important to ensure preparedness of the athletes. In DIII Collegiate Football pre-season consists of approximately 3 weeks. The abbreviated time of the pre-season increases the importance of optimizing training using safe methods, including alternative loading strategies. The purpose of the current study was to determine if a 3-week variable resistance training VRT during an undulating (UL) resistance training program elicited a greater increase in back squat strength compared to traditional loading methods.Methods and MaterialsForty DIII Football players (age range: 18–25 years) participated in a 3-week UL bilateral back squat (BBS) program. Both groups performed the BBS 3 times per week with a minimum of 24 hours between exercise sessions. The control group (C) (n = 20) (height = 182.3 + 5.1 cm, body mass: pre = 102.8 ± 17.7 kg, post = 104.1 ± 17.8 kg) used traditional loading methods (i.e., Olympic weights only) and the experimental group (E) (n = 20) (height = 180.7 ± 8.0 cm, body mass: pre = 100.3 ± 27.1 kg, post = 101.0 ± 27.7 kg) used traditional loading methods and variable resistance (i.e., resistance bands). The variable resistance accounted for approximately 20% of the total resistance while 80% of the resistance was supplied by traditional loading methods.ResultsWhen all data was pooled, subjects had a significant increase (p < 0.05) in 1-RM BBS from pre (154.2 + 26.1 kg) to post (166.8 + 26.2 kg), with a percent increase of 8.13% at the completion of the 3-week training program. There was no significant difference (p > 0.05) between the C and E groups for muscular strength, muscular power, or vertical jump. Volume-loads were not significantly (p > 0.05) different between groups for any of the weeks (C: Week 1 = 858.1 + 101.3, Week 2 = 588.6 + 69.2, Week 3 = 332.5 + 38.9, Total = 1179.2 + 209.4 vs. E: Week 1 = 835.2 + 179.7, Week 2 = 572.2 + 123.4, Week 3 = 323.5 + 68.8, Total = 1730.9 + 371.8) or for the pre-season as a whole.ConclusionA traditional UL resistance training program and training program with variable resistance are both effective methods at increasing back squat strength during 3 weeks of training. Resistance band variable resistance (VR) does not enhance training effects within a 3-week mesocycle greater than traditional resistance. creator: Jason Sawyer creator: Paul Higgins creator: Paul A. Cacolice creator: Troy Doming uri: https://doi.org/10.7717/peerj.12189 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Sawyer et al. title: Novel real-time PCR based assays for differentiating fall armyworm strains using four single nucleotide polymorphisms link: https://peerj.com/articles/12195 last-modified: 2021-09-24 description: The fall armyworm, Spodoptera frugiperda, is a polyphagous global pest with a preference for gramineous crops such as corn, sorghum and pasture grasses. This species is comprised of two morphologically identical but genetically distinct host strains known as the corn and rice strains, which can complicate pest management approaches. Two molecular markers are commonly used to differentiate between strains, however, discordance between these markers can lead to inconclusive strain identification. Here, we used double digest restriction site associated DNA sequencing to identify diagnostic single nucleotide polymorphisms (SNPs) with alleles unique to each strain. We then used these strain-specific SNPs to develop four real-time PCR based TaqMan assays to rapidly and reliably differentiate between strains and interstrain hybrids. These assays provide a new tool for differentiating between strains in field-collected samples, facilitating future studies on strain population dynamics and interstrain hybridization rates. Understanding the basic ecology of S. frugiperda strains is necessary to inform future management strategies. creator: Ashley E. Tessnow creator: Todd M. Gilligan creator: Eric Burkness creator: Caroline Placidi De Bortoli creator: Juan Luis Jurat-Fuentes creator: Patrick Porter creator: Danielle Sekula creator: Gregory A. Sword uri: https://doi.org/10.7717/peerj.12195 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Tessnow et al. title: Efficacy of 4% articaine vs 2% lidocaine in mandibular and maxillary block and infiltration anaesthesia in patients with irreversible pulpitis: a systematic review and meta-analysis link: https://peerj.com/articles/12214 last-modified: 2021-09-24 description: ObjectiveThe goal of this systematic review and meta-analysis is to determine the performance of 4% Articaine vs. 2% Lidocaine for mandibular and maxillary block and infiltration anaesthesia in patients with irreversible pulpitis (IP).MethodsPubMed/MEDLINE, Cochrane Central Register of Controlled Trials, Web of Science, Google Scholar, and Open Gray were used to conduct a thorough literature search. A manual search of the reference lists of the publications found was also carried out. Two reviewers critically evaluated the papers for inclusion and exclusion criteria, and data extraction was done on the selected publications. The Cochrane Collaboration Tool and the Minors checklist were used to assess the quality of the selected studies for randomised controlled trials (RCTs) and non-randomised studies, respectively. The RevMan software was used to perform a meta-analysis of the pooled data and subgroups according to the technique of anaesthetic solution delivery, as well as a sensitivity analysis (P < 0.05).ResultsA total of twenty-six papers were included in the qualitative synthesis, with twenty-two of them being included in the meta-analysis. There were fifteen studies with a low potential for bias, three with a moderate potential for bias, and seven with a high potential for bias. The combined results of the 19 trials in the tooth level unit revealed that 4% articaine had a success rate 1.37 times greater than 2% lidocaine for mandibular teeth (RR, 1.37; 95% CI [1.17–1.62]; P = 0.0002). For the maxillary buccal infiltration method, the combined results from the three trials revealed that 4% articaine resulted in a success rate 1.06 times greater than 2% lidocaine (RR, 1.06; 95% CI [0.95–1.2]; P = 0.3). Excluding subgroups with a single study in sensitivity analysis for mandibular teeth revealed a substantial improvement in the success rate of the articaine group in treating IP when compared to the lidocaine group.ConclusionThe findings of this meta-analysis back up the claim that articaine is more effective than lidocaine in providing anaesthesia in patients with IP. PROSPERO Registration No.: CRD42020204606 (https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42020204606). creator: Sanjay Miglani creator: Irfan Ansari creator: Swadheena Patro creator: Ankita Mohanty creator: Shahnaz Mansoori creator: Bhoomika Ahuja creator: Mohmed Isaqali Karobari creator: Krishna Prasad Shetty creator: Musab Hamed Saeed creator: Alexander Maniangat Luke creator: Ajinkya M. Pawar uri: https://doi.org/10.7717/peerj.12214 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Miglani et al. title: Locating ligand binding sites in G-protein coupled receptors using combined information from docking and sequence conservation link: https://peerj.com/articles/12219 last-modified: 2021-09-24 description: GPCRs (G-protein coupled receptors) are the largest family of drug targets and share a conserved structure. Binding sites are unknown for many important GPCR ligands due to the difficulties of GPCR recombinant expression, biochemistry, and crystallography. We describe our approach, ConDockSite, for predicting ligand binding sites in class A GPCRs using combined information from surface conservation and docking, starting from crystal structures or homology models. We demonstrate the effectiveness of ConDockSite on crystallized class A GPCRs such as the beta2 adrenergic and A2A adenosine receptors. We also demonstrate that ConDockSite successfully predicts ligand binding sites from high-quality homology models. Finally, we apply ConDockSite to predict the ligand binding sites on a structurally uncharacterized GPCR, GPER, the G-protein coupled estrogen receptor. Most of the sites predicted by ConDockSite match those found in other independent modeling studies. ConDockSite predicts that four ligands bind to a common location on GPER at a site deep in the receptor cleft. Incorporating sequence conservation information in ConDockSite overcomes errors introduced from physics-based scoring functions and homology modeling. creator: Ashley Ryan Vidad creator: Stephen Macaspac creator: Ho Leung Ng uri: https://doi.org/10.7717/peerj.12219 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Vidad et al. title: Vitamin D serum levels and non-melanoma skin cancer risk link: https://peerj.com/articles/12234 last-modified: 2021-09-24 description: BackgroundSkin cancer is one of the common malignancies. There is sufficient evidence that sunlight (ultraviolet radiation) contributes to the development of skin cancer, but there is also evidence that relates adequate serum levels of vitamin D produced on the skin by the action of ultraviolet radiation with the decreased risk of various types of cancers, including skin cancer. The aim of this study was to investigate the association of vitamin D serum levels among patients with non-melanoma skin cancers (basal cell carcinoma and squamous cell carcinoma) and controls.MethodsA prospective observational case-control study was conducted in a sample of 84 subjects in Extremadura (Spain). Forty-one patients with histologically diagnosed basal cell carcinomas and squamous cell carcinomas and 43 healthy controls were randomly chosen to assess whether vitamin D (25(OH)D3) serum level, age and sex were related to non-melanoma skin cancer and to determine the possible risk of this type of skin cancer for these variables.ResultsWhen analysing serum vitamin D levels, we ensured that all our subjects, both cases and controls, had normal or low serum vitamin D levels, even though the samples were taken during months with the highest solar irradiance in our region. It is striking in our results that there was a higher percentage of subjects with deficits of vitamin D who did not have skin cancer (66%) than patients with deficits with these types of skin cancers (34%). When adjusting the model for age and sex, vitamin D values above 18 ng/ml increased the risk of suffering from non-melanoma skin cancer by nearly 7-fold (aOR: 6.94, 95% CI [1.55–31.11], p = 0.01).ConclusionsDespite the controversial data obtained in the literature, our results suggest that lower levels of vitamin D may be related to a reduced incidence of non-melanoma skin cancer. creator: Carolina Morgado-Águila creator: Guadalupe Gil-Fernández creator: Orlando Rafael Dávila-Villalobos creator: Jesús Pérez-Rey creator: Purificación Rey-Sánchez creator: Francisco José Rodríguez-Velasco uri: https://doi.org/10.7717/peerj.12234 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Morgado-Águila et al. title: Pristimantis achupalla sp. n., a new minute species of direct-developing frog (Amphibia, Anura, Strabomantidae) inhabiting bromeliads of the montane forest of the Amazonian Andes of Puno, Peru link: https://peerj.com/articles/11878 last-modified: 2021-09-23 description: We describe a new species of bromeliad-dwelling Pristimantis from primary montane forest (2,225 m a.s.l.) in southern Peru. The type locality is near Thiuni, in the Department of Puno (province of Carabaya) in the upper watershed of a tributary of the Inambari River. Pristimantis achupalla sp. n. is characterized by a snout-vent length of 10.0–12.8 mm in adult males (n = 4), unknown in adult females, and is compared morphologically and genetically with species in the Pristimantis lacrimosus group, and with other similar species of Pristimantis. The new species is characterized by having skin on dorsum and flanks rugose, green brownish color, distinctive scapular folds, subacuminate or acuminate snout profile, upper eyelid bearing two or three subconical tubercles and some rounded tubercles, rostral papilla, flanks light brown to brown, with irregular dark brown marks. creator: Alex Ttito creator: Alessandro Catenazzi uri: https://doi.org/10.7717/peerj.11878 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Ttito and Catenazzi title: A predictive model for the ichnological suitability of the Jezero crater, Mars: searching for fossilized traces of life-substrate interactions in the 2020 Rover Mission Landing Site link: https://peerj.com/articles/11784 last-modified: 2021-09-23 description: Ichnofossils, the fossilized products of life-substrate interactions, are among the most abundant biosignatures on Earth and therefore they may provide scientific evidence of potential life that may have existed on Mars. Ichnofossils offer unique advantages in the search for extraterrestrial life, including the fact that they are resilient to processes that obliterate other evidence for past life, such as body fossils, as well as chemical and isotopic biosignatures. The goal of this paper is evaluating the suitability of the Mars 2020 Landing Site for ichnofossils. To this goal, we apply palaeontological predictive modelling, a technique used to forecast the location of fossil sites in uninvestigated areas on Earth. Accordingly, a geographic information system (GIS) of the landing site is developed. Each layer of the GIS maps the suitability for one or more ichnofossil types (bioturbation, bioerosion, biostratification structures) based on an assessment of a single attribute (suitability factor) of the Martian environment. Suitability criteria have been selected among the environmental attributes that control ichnofossil abundance and preservation in 18 reference sites on Earth. The goal of this research is delivered through three predictive maps showing which areas of the Mars 2020 Landing Site are more likely to preserve potential ichnofossils. On the basis of these maps, an ichnological strategy for the Perseverance rover is identified, indicating (1) 10 sites on Mars with high suitability for bioturbation, bioerosion and biostratification ichnofossils, (2) the ichnofossil types, if any, that are more likely to be present at each site, (3) the most efficient observation strategy for detecting eventual ichnofossils. The predictive maps and the ichnological strategy can be easily integrated in the existing plans for the exploration of the Jezero crater, realizing benefits in life-search efficiency and cost-reduction. creator: Andrea Baucon creator: Carlos Neto de Carvalho creator: Antonino Briguglio creator: Michele Piazza creator: Fabrizio Felletti uri: https://doi.org/10.7717/peerj.11784 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Baucon et al. title: Dietary effects on fitness in captive-reared Hawaiian tree snails link: https://peerj.com/articles/11789 last-modified: 2021-09-23 description: The native terrestrial snail fauna of the Hawaiian Islands faces numerous threats that have led to severe range reductions, population declines, and extinction of species. With the continued declines of many wild populations, a crucial component of preserving Hawaiian terrestrial snail biodiversity is through captive rearing programs, like that implemented by the Hawai‘i Department of Land and Natural Resources Snail Extinction Prevention Program. Rare and endangered tree snails in the family Achatinellidae, which feed on epiphytic microbial communities, are maintained in captivity with a diet that includes native vegetation brought in from nearby forests, as well as a cultured fungus originally isolated from native host trees. Recent mortality events in lab populations have been attributed to wild-gathered vegetation. These events have increased interest in developing a completely manufactured or cultured diet that would eliminate the need for exposure to wild-gathered plants. This study compared survival and egg production in Auriculella diaphana provided with lab-cultured fungus, and those provided with wild vegetation. We compared the number of eggs laid and number of deaths among three treatments: (1) wild collected vegetation only; (2) wild vegetation supplemented with laboratory-cultured fungus; and (3) laboratory cultured fungus only. Mortality did not significantly differ among treatments, but the number of eggs laid was significantly higher in snails provided wild vegetation and cultured fungus (F = 24.998; P < 0.001), compared with those provided with only wild vegetation (t = 1.88, P = 0.032) or only cultured fungus (t = 4.530, P = 0.004). Our results suggest: (1) the existing strain of cultured fungus alone is not sufficient to maintain captive-reared snail populations; (2) the additional energy or calcium provided by the cultured fungus appears to enhance egg reproduction in captive-reared populations; (3) the presence or absence of live vegetation influences snail behavior, including aestivation and egg laying. These results highlight the importance of ongoing research to culture additional species of fungi at a rate that could support captive-reared populations, as the diversity of fungi present in wild epiphytic microbial communities may be important for snail reproductive health. creator: Evan Strouse creator: Melissa R. Price creator: David R. Sischo uri: https://doi.org/10.7717/peerj.11789 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Strouse et al.