title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=923
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Diabetic kidney disease in type 2 diabetes: a review of pathogenic mechanisms, patient-related factors and therapeutic options
link: https://peerj.com/articles/11070
last-modified: 2021-04-19
description: The global prevalence of diabetic kidney disease is rapidly accelerating due to an increasing number of people living with type 2 diabetes. It has become a significant global problem, increasing human and financial pressures on already overburdened healthcare systems. Interest in diabetic kidney disease has increased over the last decade and progress has been made in determining the pathogenic mechanisms and patient-related factors involved in the development and pathogenesis of this disease. A greater understanding of these factors will catalyse the development of novel treatments and influence current practice. This review summarises the latest evidence for the factors involved in the development and progression of diabetic kidney disease, which will inform better management strategies targeting such factors to improve therapeutic outcomes in patients living with diabetes.
creator: Louise Woodhams
creator: Tin Fei Sim
creator: Leanne Chalmers
creator: Bu Yeap
creator: Daniel Green
creator: Markus Schlaich
creator: Carl Schultz
creator: Graham Hillis
uri: https://doi.org/10.7717/peerj.11070
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Woodhams et al.

title: Mycelial compatibility, anastomosis, and nucleus numbers of eight Mexican Hirsutella citriformis strains isolated from Diaphorina citri
link: https://peerj.com/articles/11080
last-modified: 2021-04-19
description: BackgroundAmong entomopathogenic fungi, H. citriformis has been recognized as potential biocontrol agent against the Asian citrus psyllid Diaphorina citri (Hemiptera: Liviidae). Nevertheless, this fungus is poorly characterized. Previous molecular studies have shown high sequence similarities among strains, but significant differences in Diaphorina citri virulence.ObjectiveThe aim of the present study was to determine mycelial compatibility and anastomosis, and nucleus numbers in mycelium and conidia of eight H. citriformis strains isolated from mycosed D. citri adults collected from several Mexican states.MethodsMycelial compatibility and anastomosis evaluation was performed after pairing strains, leading to 36 confrontations, and cultured in chlorate minimum medium to obtain mutants for vegetative compatibility group.ResultsHypha or conidia nuclei were visualized with safranin-O and 3% KOH, and 0.05% trypan blue–lactophenol solution. H. citriformis strains showed compatibly and anastomosis events after confrontation. In addition, they showed one nucleus per conidium and mycelium section. It was not possible to obtain H. citriformis nit mutants from the chlorate concentrations tested.ConclusionsTo date, this is the first report demonstrating mycelial compatibility, anastomosis occurrence, and hyphae and conidia nuclei number among H. citriformis strains.
creator: Orquídea Pérez-González
creator: Ricardo Gomez-Flores
creator: Patricia Tamez-Guerra
uri: https://doi.org/10.7717/peerj.11080
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Pérez-González et al.

title: Elatostema qinzhouense (Urticaceae), a new species from limestone karst in Guangxi, China
link: https://peerj.com/articles/11148
last-modified: 2021-04-19
description: Elatostema qinzhouense L.F. Fu, A.K. Monro & Y.G. Wei, a new species from Guangxi, China is described and illustrated. Morphologically, E. qinzhouense is most similar to E. hezhouense from which it differs by having smaller size of leaf laminae, fewer and smaller staminate peduncle bracts, longer pistillate peduncle bracts and a larger achene. This result is supported by the molecular evidence. The phylogenetic position of the new species within Elatostema is evaluated using three DNA regions, ITS, trnH-psbA and psbM-trnD, for 107 taxa of Elatostema s.l. (including E. qinzhouense). Bayesian inference (BI) and maximum likelihood (ML) analyses each recovered the same strongly supported tree topologies, indicating that E. qinzhouense is a member of the core Elatostema clade and sister to E. hezhouense. Along with the phylogenetic studies, plastid genome and ribosomal DNA (rDNA) sequences of the new species are assembled and annotated. The plastid genome is 150,398 bp in length and comprises two inverted repeats (IRs) of 24,688 bp separated by a large single-copy of 83,919 bp and a small single-copy of 17,103 bp. A total of 113 functional genes are recovered, comprising 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The rDNA is 5,804 bp in length and comprised the 18S ribosomal RNA partial sequence (1,809 bp), internal transcribed spacer 1 (213 bp), 5.8S ribosomal RNA (164 bp), internal transcribed spacer 2 (248 bp) and 26S ribosomal RNA partial sequence (3,370 bp). In addition, the chromosome number of E. qinzhouense is observed to be 2n = 26, suggesting that the species is diploid. Given a consistent relationship between ploidy level and reproductive system in Elatostema, the new species is also considered to be sexually reproducing. Our assessment of the extinction threat for E. qinzhouense is that it is Endangered (EN) according to the criteria of the International Union for Conservation of Nature.
creator: Longfei Fu
creator: Alexandre K. Monro
creator: Tiange Yang
creator: Fang Wen
creator: Bo Pan
creator: Zibing Xin
creator: Zhixiang Zhang
creator: Yigang Wei
uri: https://doi.org/10.7717/peerj.11148
license: https://creativecommons.org/licenses/by-nc/4.0
rights: ©2021 Fu et al.

title: A DNA barcode library for the butterflies of North America
link: https://peerj.com/articles/11157
last-modified: 2021-04-19
description: Although the butterflies of North America have received considerable taxonomic attention, overlooked species and instances of hybridization continue to be revealed. The present study assembles a DNA barcode reference library for this fauna to identify groups whose patterns of sequence variation suggest the need for further taxonomic study. Based on 14,626 records from 814 species, DNA barcodes were obtained for 96% of the fauna. The maximum intraspecific distance averaged 1/4 the minimum distance to the nearest neighbor, producing a barcode gap in 76% of the species. Most species (80%) were monophyletic, the others were para- or polyphyletic. Although 15% of currently recognized species shared barcodes, the incidence of such taxa was far higher in regions exposed to Pleistocene glaciations than in those that were ice-free. Nearly 10% of species displayed high intraspecific variation (>2.5%), suggesting the need for further investigation to assess potential cryptic diversity. Aside from aiding the identification of all life stages of North American butterflies, the reference library has provided new perspectives on the incidence of both cryptic and potentially over-split species, setting the stage for future studies that can further explore the evolutionary dynamics of this group.
creator: Jacopo D’Ercole
creator: Vlad Dincă
creator: Paul A. Opler
creator: Norbert Kondla
creator: Christian Schmidt
creator: Jarrett D. Phillips
creator: Robert Robbins
creator: John M. Burns
creator: Scott E. Miller
creator: Nick Grishin
creator: Evgeny V. Zakharov
creator: Jeremy R. DeWaard
creator: Sujeevan Ratnasingham
creator: Paul D.N. Hebert
uri: https://doi.org/10.7717/peerj.11157
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 D’Ercole et al.

title: Neural network analysis of clinical variables predicts escalated care in COVID-19 patients: a retrospective study
link: https://peerj.com/articles/11205
last-modified: 2021-04-19
description: This study sought to identify the most important clinical variables that can be used to determine which COVID-19 patients hospitalized in the general floor will need escalated care early on using neural networks (NNs). Analysis was performed on hospitalized COVID-19 patients between 7 February 2020 and 4 May 2020 in Stony Brook Hospital. Demographics, comorbidities, laboratory tests, vital signs and blood gases were collected. We compared those data obtained at the time in emergency department and the time of intensive care unit (ICU) upgrade of: (i) COVID-19 patients admitted to the general floor (N = 1203) vs. those directly admitted to ICU (N = 104), and (ii) patients not upgraded to ICU (N = 979) vs. those upgraded to the ICU (N = 224) from the general floor. A NN algorithm was used to predict ICU admission, with 80% training and 20% testing. Prediction performance used area under the curve (AUC) of the receiver operating characteristic analysis (ROC). We found that C-reactive protein, lactate dehydrogenase, creatinine, white-blood cell count, D-dimer and lymphocyte count showed temporal divergence between COVID-19 patients hospitalized in the general floor that were upgraded to ICU compared to those that were not. The NN predictive model essentially ranked the same laboratory variables to be important predictors of needing ICU care. The AUC for predicting ICU admission was 0.782 ± 0.013 for the test dataset. Adding vital sign and blood-gas data improved AUC (0.822 ± 0.018). This work could help frontline physicians to anticipate downstream ICU need to more effectively allocate healthcare resources.
creator: Joyce Q. Lu
creator: Benjamin Musheyev
creator: Qi Peng
creator: Tim Q. Duong
uri: https://doi.org/10.7717/peerj.11205
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Lu et al.

title: Improving the gnomonic approach with the gnomonicM R-package to estimate natural mortality throughout different life stages
link: https://peerj.com/articles/11229
last-modified: 2021-04-19
description: Natural mortality (M) is defined as the rate of loss that occurs in a fish stock due to natural (non-fishing) causes and can be influenced by density-dependent or density-independent factors. Different methods have been used to estimate M, one of these is the gnomonic approach. This method estimates M rates by dividing the life cycle of a species into subunits of time that increase as a constant proportion of the time elapsed from birth up to the initiation of each subdivision. In this study, an improved gnomonic approach is proposed to estimate natural mortality throughout different life stages in marine stocks using the gnomonicM package written in R software. This package was built to require data about (i) the number of gnomonic intervals, (ii) egg stage duration, (iii) longevity, and (iv) fecundity. With this information, it is possible to estimate the duration and natural mortality (Mi) of each gnomonic interval. The gnomonicM package uses a deterministic or stochastic approach, the latter of which assesses variability in M by assuming that the mean lifetime fecundity (MLF) is the main source of uncertainty. Additionally, the gnomonicM package allows the incorporation of auxiliary information related to the observed temporal durations of specific gnomonic intervals, which is useful for calibrating estimates of M vectors. The gnomonicM package, tested via deterministic and stochastic functions, was supported by the reproducibility and verification of the results obtained from different reports, thus guaranteeing its functionality, applicability, and performance in estimating M for different ontogenetic developmental stages. Based on the biological information of Pacific chub mackerel (Scomber japonicus), we presented a new case study to provide a comprehensive guide to data collection to obtain results and explain the details of the application of the gnomonicM package and avoid its misuse. This package could provide an alternative approach for estimating M and provide basic input data for ecological models, allowing the option of using estimates of variable natural mortality across different ages, mainly for life stages affected by fishing. The inputs for the gnomonicM packages are composed of numbers, vectors, or characters depending on whether the deterministic or stochastic approach is used, making the package quick, flexible, and easy to use; this allows users to focus on obtaining and interpreting results rather than the calculation process.
creator: Josymar Torrejón-Magallanes
creator: Enrique Morales-Bojórquez
creator: Francisco Arreguín-Sánchez
uri: https://doi.org/10.7717/peerj.11229
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Torrejón-Magallanes et al.

title: Semidry acid hydrolysis of cellulose sustained by autoclaving for production of reducing sugars for bacterial biohydrogen generation from various cellulose feedstock
link: https://peerj.com/articles/11244
last-modified: 2021-04-19
description: Cellulosic biowastes are one of the cheapest and most abundant renewable organic materials on earth that can be, subsequent to hydrolysis, utilized as an organic carbon source for several fermentation biotechnologies. This study was devoted to explore a semidry acid hydrolysis of cellulose for decreasing the cost and ionic strength of the hydrolysate. For semidry acid hydrolysis, cellulose was just wetted with HCl (0 to 7 M) and subjected to autoclaving. The optimum molar concentration of HCl and period of autoclaving for semidry acid hydrolysis of cellulose were 6 M and 50 min respectively. Subsequent to the semidry acid hydrolysis with a minimum volume of 6 M HCl sustained by autoclaving, the hydrolysate was diluted with distilled water and neutralized with NaOH (0.5 M). The reducing sugars produced from the semidry acid hydrolysis of cellulose was further used for dark fermentation biohydrogen production by Escherichia coli as a representative of most hydrogen producing eubacteria which cannot utilize non-hydrolyzed cellulose. An isolated E. coli TFYM was used where this bacterium was morphologically and biochemically characterized and further identified by phylogenetic 16S rRNA encoding gene sequence analysis. The reducing sugars produced by semidry acid hydrolysis could be efficiently utilized by E. coli producing 0.4 mol H2 mol−1 hexose with a maximum rate of hydrogen gas production of 23.3 ml H2 h−1 L−1 and an estimated hydrogen yield of 20.5 (L H2 kg−1 dry biomass). The cheap cellulosic biowastes of wheat bran, sawdust and sugarcane bagasse could be hydrolyzed by semidry acid hydrolysis where the estimated hydrogen yield per kg of its dry biomass were 36, 18 and 32 (L H2 kg−1 dry biomass) respectively indicating a good feasibility of hydrogen production from reducing sugars prepared by semidry acid hydrolysis of these cellulosic biowastes. Semidry acid hydrolysis could also be effectively used for hydrolyzing non-cellulosic polysaccharides of dry cyanobacterial biomass. The described semidry acid hydrolysis of cellulosic biowastes in this study might be applicable not only for bacterial biohydrogen production but also for various hydrolyzed cellulose-based fermentation biotechnologies.
creator: Fatthy Mohamed Morsy
creator: Medhat Elbadry
creator: Yasser Elbahloul
uri: https://doi.org/10.7717/peerj.11244
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Morsy et al.

title: Intraspecific variability in the filter mesh size of suspension feeding organisms: the case of invasive Ponto-Caspian corophiids (Crustacea: Amphipoda)
link: https://peerj.com/articles/11245
last-modified: 2021-04-19
description: Suspension feeders play pivotal roles in the nutrient cycling of almost all aquatic ecosystems. Since sufficiently large differences in the filter mesh size (FMS) can lead to different food web positions, the inter- and intraspecific variability of this trait might be of community-level importance. The aim of this study was to quantify the range of FMS variation within the three invasive Ponto-Caspian Chelicorophium species based on a large material representing various conditions (1,224 specimens from 40 samples across Central Europe), characterize the components of variation within populations, identify the main factors determining intraspecific differences, and reveal how intraspecific variation affects the FMS overlaps among species. The FMS of the most widespread invader, C. curvispinum, varied within the broadest range (between 2.34–8.28 μm, compared to 2.51–5.97 μm in C. robustum and 1.08–3.23 μm in C. sowinskyi); nevertheless, the contribution of intraspecific plasticity to the invasion success of the species is not evident based on the present study. The within-individual variability of FMS increased with the individual mean of the trait and decreased with body size; however, it showed little differences among samples. The among-individual variation within samples could be partitioned into components related to body size (ontogenetic niche shift/differences among cohorts) and sex (ecological sexual dimorphism) as well as a seemingly random component (individual specialization), varying widely in extent and relative contributions. The FMS of C. curvispinum was significantly larger in the presence of C. sowinskyi than in allopatry, likely reflecting character displacement; however, it did not show further increase when C. robustum was also present. Similar differences could not be observed in C. sowinskyi. The FMS ranges of C. curvispinum and C. robustum never overlapped with that of C. sowinskyi in co-occurrence despite the considerable intraspecific differences among sites, suggesting that their interaction can be seen as a clear case of niche differentiation by food particle size. On the contrary, the strong overlaps observed between C. curvispinum and C. robustum indicate that other factors might play the primary role in their coexistence. The studied species appear to be suitable model organisms for identifying the drivers and mechanisms of FMS variability.
creator: Péter Borza
uri: https://doi.org/10.7717/peerj.11245
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Borza

title: Historical effective population size of North American hoary bat (Lasiurus cinereus) and challenges to estimating trends in contemporary effective breeding population size from archived samples
link: https://peerj.com/articles/11285
last-modified: 2021-04-19
description: BackgroundHoary bats (Lasiurus cinereus) are among the bat species most commonly killed by wind turbine strikes in the midwestern United States. The impact of this mortality on species census size is not understood, due in part to the difficulty of estimating population size for this highly migratory and elusive species. Genetic effective population size (Ne) could provide an index of changing census population size if other factors affecting Ne are stable.MethodsWe used the NeEstimator package to derive effective breeding population size (Nb) estimates for two temporally spaced cohorts: 93 hoary bats collected in 2009–2010 and an additional 93 collected in 2017–2018. We sequenced restriction-site associated polymorphisms and generated a de novo genome assembly to guide the removal of sex-linked and multi-copy loci, as well as identify physically linked markers.ResultsAnalysis of the reference genome with psmc suggested at least a doubling of Ne in the last 100,000 years, likely exceeding Ne = 10,000 in the Holocene. Allele and genotype frequency analyses confirmed that the two cohorts were comparable, although some samples had unusually high or low observed heterozygosities. Additionally, the older cohort had lower mean coverage and greater variability in coverage, and batch effects of sampling locality were observed that were consistent with sample degradation. We therefore excluded samples with low coverage or outlier heterozygosity, as well as loci with sequence coverage far from the mode value, from the final data set. Prior to excluding these outliers, contemporary Nb estimates were significantly higher in the more recent cohort, but this finding was driven by high values for the 2018 sample year and low values for all other years. In the reduced data set, Nb did not differ significantly between cohorts. We found base substitutions to be strongly biased toward cytosine to thymine or the complement, and further partitioning loci by substitution type had a strong effect on Nb estimates. Minor allele frequency and base quality bias thresholds also had strong effects on Nb estimates. Instability of Nb with respect to common data filtering parameters and empirically identified factors prevented robust comparison of the two cohorts. Given that confidence intervals frequently included infinity as the stringency of data filtering increased, contemporary trends in Nb of North American hoary bats may not be tractable with the linkage disequilibrium method, at least using the protocol employed here.
creator: Robert S. Cornman
creator: Jennifer A. Fike
creator: Sara J. Oyler-McCance
creator: Paul M. Cryan
uri: https://doi.org/10.7717/peerj.11285
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Cornman et al.

title: Student health behavior and academic performance
link: https://peerj.com/articles/11107
last-modified: 2021-04-16
description: ObjectiveTo explore the association between health behaviors and habits of university students and academic achievement.ParticipantsSix hundred fourteen undergraduate students at a state university in the United States.MethodsStudents were invited over a 2-year period to participate in an anonymous online survey that asked questions concerning a wide range of health behaviors and habits; participants were asked to report their current grade point average (GPA). Standard Least Squares Models were used to examine differences in self-reported GPA across the different health behaviors and habits, with individuals as replicates.ResultsThe study found positive associations between breakfast consumption, physical activity, and strength training and self-reported GPA, and negative associations between the hours of sleep per night, hours worked per week, fast food and energy drinks consumption, and use of marijuana, alcohol and electronic vaping products.ConclusionsWhile there is an association for some of the studied health behaviors and habits with self-reported GPA, the effect sizes for these health behaviors were low. The significant effect of vaping on GPA as well as the increased use reported in this study indicates that the topic should be explored further. Furthermore, students should be educated on the potential positive and negative effects of health behavior choices to help them make better choices.
creator: Peter R. Reuter
creator: Bridget L. Forster
uri: https://doi.org/10.7717/peerj.11107
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Reuter and Forster