title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=762 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The Female Athlete Triad—the impact of running and type of diet on the regularity of the menstrual cycle assessed for recreational runners link: https://peerj.com/articles/12903 last-modified: 2022-03-02 description: BackgroundThe Female Athlete Triad (FAT) included three interrelated conditions including disordered eating, amenorrhea, and osteoporosis. The American College of Sports Medicine updated the definition of FAT to reflect the interdependence of low energy availability with or without eating disorders. The main aim of the study was to assess the impact of recreational running on potential disturbances in the regularity of women’s menstrual cycles. Additionally, this work compared differences in the menstrual cycle between women runners and women who did not regularly practice sports. The respondents were also asked about the type of diet they consumed.MethodsA total of 360 women took part in the research. This group included 217 runners and 143 control. The authors’ questionnaire was used in the research.ResultsWhen compared to the control group, the runners had an increased frequency of menstrual cycles of <24 days (10.14% vs. 3.50%), fewer typical cycles of 25–31 days (75.58% vs. 86.71%), had fewer regular cycles per year (9.62 vs. 11.22), shorter duration of bleeding (4.79 vs. 5.27 days), and an increased frequency of painless menstruation (23.96% vs. 7.69%). A positive predictor of menstrual cycle disorders was the use of a ‘special diet’ (R:1.67; 95% C:0.47–2.87).ConclusionsThe runners had shorter and less regular monthly cycles and shorter and more often painless menstrual bleeding when compared to the control group. The frequency of menstrual disorders in runners was increased by following a ‘special diet’. The frequency of menstrual cycle disorders in runners, however, did not differ significantly from the control group. creator: Joanna Witkoś creator: Magdalena Hartman-Petrycka uri: https://doi.org/10.7717/peerj.12903 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Witkoś and Hartman-Petrycka title: Development and validation of a multi-parameter nomogram for predicting prostate cancer: a retrospective analysis from Handan Central Hospital in China link: https://peerj.com/articles/12912 last-modified: 2022-03-02 description: BackgroundTo explore the possible predicting factors related to prostate cancer and develop a validated nomogram for predicting the probability of patients with prostate cancer.MethodClinical data of 697 patients who underwent prostate biopsy in Handan Central Hospital from January 2014 to January 2020 were retrospectively collected. Cases were randomized into two groups: 80% (548 cases) as the development group, and 20% (149 cases) as the validation group. Univariate and multivariate logistic regression analyses were performed to determine the independent risk factors for prostate cancer. The nomogram prediction model was generated using the finalized independent risk factors. Decision curve analysis (DCA) and the area under receiver operating characteristics curve (ROC) of both development group and validation group were calculated and compared to validate the accuracy and efficiency of the nomogram prediction model. Clinical utility curve (CUC) helped to decide the desired cut-off value for the prediction model. The established nomogram with Prostate Cancer Prevention Trial Derived Cancer Risk Calculator (PCPT-CRC) and other domestic prediction models using the entire study population were compared.ResultsThe independent risk factors determined through univariate and multivariate logistic regression analyses were: age, tPSA, fPSA, PV, DRE, TRUS and BMI. Nomogram prediction model was developed with the cut-off value of 0.31. The AUC of development group and validation group were 0.856 and 0.797 respectively. DCA exhibits consistent observations with the findings. Through validating our prediction model as well as other three domestic prediction models based on the entire study population of 697 cases, our prediction model demonstrated significantly higher predictive value than all the other models.ConclusionThe nomogram for predicting prostate cancer can facilitate more accurate evaluation of the probability of having prostate cancer, and provide better ground for prostate biopsy. creator: Libin Nan creator: Kai Guo creator: Mingmin Li creator: Qi Wu creator: Shaojun Huo uri: https://doi.org/10.7717/peerj.12912 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Nan et al. title: Physiological stress and higher reproductive success in bumblebees are both associated with intensive agriculture link: https://peerj.com/articles/12953 last-modified: 2022-03-02 description: Free-living organisms face multiple stressors in their habitats, and habitat quality often affects development and life history traits. Increasing pressures of agricultural intensification have been shown to influence diversity and abundance of insect pollinators, and it may affect their elemental composition as well. We compared reproductive success, body concentration of carbon (C) and nitrogen (N), and C/N ratio, each considered as indicators of stress, in the buff-tailed bumblebee (Bombus terrestris). Bumblebee hives were placed in oilseed rape fields and semi-natural old apple orchards. Flowering season in oilseed rape fields was longer than that in apple orchards. Reproductive output was significantly higher in oilseed rape fields than in apple orchards, while the C/N ratio of queens and workers, an indicator of physiological stress, was lower in apple orchards, where bumblebees had significantly higher body N concentration. We concluded that a more productive habitat, oilseed rape fields, offers bumblebees more opportunities to increase their fitness than a more natural habitat, old apple orchards, which was achieved at the expense of physiological stress, evidenced as a significantly higher C/N ratio observed in bumblebees inhabiting oilseed rape fields. creator: Tatjana Krama creator: Ronalds Krams creator: Maris Munkevics creator: Jonathan Willow creator: Sergejs Popovs creator: Didzis Elferts creator: Linda Dobkeviča creator: Patrīcija Raibarte creator: Markus Rantala creator: Jorge Contreras-Garduño creator: Indrikis A. Krams uri: https://doi.org/10.7717/peerj.12953 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Krama et al. title: Influence of Lymphangio vascular (V) and perineural (N) invasion on survival of patients with resected esophageal squamous cell carcinoma (ESCC): a single-center retrospective study link: https://peerj.com/articles/12974 last-modified: 2022-03-02 description: BackgroundLymphangio vascular invasion (LVI) and perineural invasion (PNI) are associated with survival following resection for gastrointestinal cancer. But the relationship between LVI/PNI and survival of esophageal squamous cell carcinoma (ESCC) is still unclear. We aim to demonstrate the prognostic significance of LVI/PNI in ESCC.MethodsA total of 195 ESCC patients underwent curative surgery from 2012 to 2018 was collected in the 2nd Affiliated Hospital of Fujian Medical University. All the patients were divided into four groups based on the status of the neurovascular invasion: (1) neither LVI nor PNI (V0N0); (2) LVI alone (V1N0); (3) PNI alone (V0N1); (4) combined LVI and PNI (V1N1). First, the analysis included the Kaplan-Meier survival estimates with the Log rank test were performed to determine median overall survival (OS) in different groups divided according to the clinical factor, respectively. And the association between OS with multi clinical factors was examined using Cox regression analysis. Next, the risk factors for recurrence in patients with V1N1 were analyzed with univariate and multivariate logistic regression analyses, respectively.ResultsThe cases in V0N0, V1N0, V0N1, and V1N1 groups were 91 (46.7%), 62 (31.8%), 9 (4.6%) and 33 (16.9%), respectively. The OS in the four groups was different (P < 0.001). The 1-, 3- and 5-year OS in V0N0 group was higher than that in V1N1 group, respectively (1-year OS: 93.4% vs 75.8%, 3-year OS: 53.8 % vs 24.2%, 5-year OS: 48.1% vs 10.5%). The OS in stage I-II for patients with V1N1 was significantly lower than that in the other groups (V0N0, V1N0, V0N1) (P < 0.001). The postoperative adjuvant chemotherapy was a significant impact factor of OS for ESCC patients with V1N1 (P = 0.004). Lymphatic invasion and LVI were significantly prognosis factors associated (P = 0.036, P = 0.030, respectively). The ulcerative type is a risk factor for V1N1 occurance (P = 0.040).ConclusionsThe LVI and PNI are important prognosis factors for ESCC patients. ESCC patients with simultaneous lymphangio vascular and perineural invasion (V1N1) showed worse OS than patients with either lymphangio vascular or perineural invasion alone (V1N0 or V0N1) or none (V0N0). In addition, adjuvant chemotherapy may prolong the OS for ESCC patients with V1N1. creator: Chengke Xie creator: Zhiyao Chen creator: Jie Xu creator: Zhiyong Meng creator: Zhijun Huang creator: Jianqing Lin uri: https://doi.org/10.7717/peerj.12974 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Xie et al. title: Reliability and validity of the multi-point method and the 2-point method’s variations of estimating the one-repetition maximum for deadlift and back squat exercises link: https://peerj.com/articles/13013 last-modified: 2022-03-02 description: This study aimed at examining the concurrent validity and reliability of the multi-point method and the two-point method’s variations for estimating the one-repetition maximum (1RM) in the deadlift and squat exercises and to determine the accuracy of which optimal two loads can be used for the two-point method protocol. Thirteen resistance-trained men performed six sessions that consisted of two incremental loading tests (multi-point method: 20–40–60–80–90% and two-point method variations: 40–60%, 40–80%, 40–90%,60–80%, 60–90%) followed by 1RM tests. Both the multi-point method and the two-point method load variations showed reliable results for 1RM estimation (CV < 10%) squat and deadlift exercises. Session-session reliability was found to be low in deadlift (ICC: 0.171–0.335) and squat exercises (ICC: 0.235–0.479) of 40–60% and 60–80% in two-point methods. Deadlift (ICC: 0.815–0.996) and squat (ICC: 0.817–0.988) had high session-to-session reliability in all other methods. Regarding the validity of deadlift exercise, the multipoint method (R2 = 0.864) and two variations of the two-point method (R2 = 0.816 for 40–80%, R2 = 0.732 for 60–80%) showed very large correlations, whereas other two variations of the two-point method (R2 = 0.945 for 40–90%, R2 = 0.914 for 60–90%) showed almost perfect correlations with the actual 1RM. Regarding the validity of squat exercise, the multi-point method (R2 = 0.773) and two variations of the two-point method (R2 = 0.0847 for 60–80%, R2 = 0.705 for 40–90%) showed very large correlations, whereas 40–60% variation showed almost perfect correlation (R2 = 0.962) with the actual 1RM. In conclusion, whereas both the multi-point method and the two-point method load variations showed reliable results, the multiple-point method and most of the two-point methods’ load variations examined in this research provided an accurate (from large-moderate to perfect) estimate of the 1RM. Therefore, we recommend using the multi-point method and especially the two-point methods variations including higher relative loads to estimate 1RM. creator: Onat Çetin creator: Zeki Akyildiz creator: Barbaros Demirtaş creator: Yılmaz Sungur creator: Filipe Manuel Clemente creator: Florin Cazan creator: Luca Paolo Ardigò uri: https://doi.org/10.7717/peerj.13013 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Çetin et al. title: Relationship between the distribution of vegetation and the environment in the coastal embryo dunes of Jalisco, México link: https://peerj.com/articles/13015 last-modified: 2022-03-02 description: BackgroundThe poorly developed soils of the embryo dunes imply little capacity for plant support, however, the adaptation mechanisms of plants respond sensitively to environmental variations, even when these variations are small, which results in a set of specialized habitats and flora that are rarely shared with other terrestrial ecosystems. The coastal dunes of the Mexican Pacific remain vaguely studied, this is why this research explored the relationship between environmental properties and the presence of plant species in the embryo dunes of the coast of Jalisco, Mexico.MethodsTwenty-nine sites were sampled, one or two sites per embryo dune, with a random stratified design. Geomorphological and vegetation data were collected at site. Laboratory determinations included soil color, particle size, organic matter, pH, electrical conductivity, magnetite content, and moisture retention. Statistical analysis included correlation analysis to identify relationships between environmental variables; principal component analysis (PCA) and cluster analysis to group dune sites by environmental properties; canonical correspondence analysis (CCA) to determine a possible significant relationship between the presence of plant species and environmental variables; cluster analysis to group dune sites by presence/absence of plant species and correlate both clusters to validate the relationship between them, the salient aspects of this relationship were described and the spatial distribution of the groups was mapped.ResultsEleven plant species were identified, six of them exclusive to the embryo dunes and the rest ubiquitous. The incipient development of these soils is reflected in a low content of organic matter, silt, clay, and moisture retention, with scattered data on granulometry, electrical conductivity, organic matter, and magnetite. Some significant correlations were found between some environmental properties, and the CCA showed a significant relationship between the presence of plant species and environmental variables (p-value of the Monte Carlo test = 0.026). The cluster analysis of dune sites according to environmental variables and the cluster analysis by presence/absence of plant species produces the formation of five groups of sites with significant environmental differences and five groups of sites with significant floristic differences. A significant connection (r = 0.471, p = 0.01) between the two clustering schemes also evidences the meaningful relationship between the presence of plant species and the environmental characteristics of the embryo dunes of Jalisco, Mexico. Differences in habitat preferences were observed among plant species exclusive to the embryo dunes; thus, Abronia maritima, Uniola pittieri, and Pectis arenaria showed a preference for embryo dunes with poor edaphic conditions, in contrast to Okenia hypogaea, Canavalia rosea, and Scaevola plumieri, which were mostly found in embryo dunes with higher fertility. creator: Héctor Gerardo Frías-Ureña creator: José Ariel Ruiz-Corral creator: Miguel Ángel Macías-Rodríguez creator: Noé Durán creator: Diego Gonzalez creator: Fabio De Albuquerque creator: José Pablo Torres Morán uri: https://doi.org/10.7717/peerj.13015 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Frías-Ureña et al. title: Highly pathogenic avian influenza virus of the A/H5N8 subtype, clade 2.3.4.4b, caused outbreaks in Kazakhstan in 2020 link: https://peerj.com/articles/13038 last-modified: 2022-03-02 description: BackgroundLarge poultry die-offs happened in Kazakhstan during autumn of 2020. The birds’ disease appeared to be avian influenza. Northern Kazakhstan was hit first and then the disease propagated across the country affecting eleven provinces. This study reports the results of full-genome sequencing of viruses collected during the outbreaks and investigation of their relationship to avian influenza virus isolates in the contemporary circulation in Eurasia.MethodsSamples were collected from diseased birds during the 2020 outbreaks in Kazakhstan. Initial virus detection and subtyping was done using RT-PCR. Ten samples collected during expeditions to Northern and Southern Kazakhstan were used for full-genome sequencing of avian influenza viruses. Phylogenetic analysis was used to compare viruses from Kazakhstan to viral isolates from other world regions.ResultsPhylogenetic trees for hemagglutinin and neuraminidase show that viruses from Kazakhstan belong to the A/H5N8 subtype and to the hemagglutinin H5 clade 2.3.4.4b. Deduced hemagglutinin amino acid sequences in all Kazakhstan’s viruses in this study contain the polybasic cleavage site (KRRKR-G) indicative of the highly pathogenic phenotype. Building phylogenetic trees with the Bayesian phylogenetics results in higher statistical support for clusters than using distance methods. The Kazakhstan’s viruses cluster with isolates from Southern Russia, the Russian Caucasus, the Ural region, and southwestern Siberia. Other closely related prototypes are from Eastern Europe. The Central Asia Migratory Flyway passes over Kazakhstan and birds have intermediate stops in Northern Kazakhstan. It is postulated that the A/H5N8 subtype was introduced with migrating birds.ConclusionThe findings confirm the introduction of the highly pathogenic avian influenza viruses of the A/Goose/Guangdong/96 (Gs/GD) H5 lineage in Kazakhstan. This virus poses a tangible threat to public health. Considering the results of this study, it looks justifiable to undertake measures in preparation, such as install sentinel surveillance for human cases of avian influenza in the largest pulmonary units, develop a human A/H5N8 vaccine and human diagnostics capable of HPAI discrimination. creator: Asylulan Amirgazin creator: Alexandr Shevtsov creator: Talgat Karibayev creator: Maxat Berdikulov creator: Tamila Kozhakhmetova creator: Laura Syzdykova creator: Yerlan Ramankulov creator: Alexandr V. Shustov uri: https://doi.org/10.7717/peerj.13038 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Amirgazin et al. title: Lactococcus lactis secreting phage lysins as a potential antimicrobial against multi-drug resistant Staphylococcus aureus link: https://peerj.com/articles/12648 last-modified: 2022-03-01 description: BackgroundStaphylococcus aureus is an opportunistic Gram-positive bacterium that can form biofilm and become resistant to many types of antibiotics. The treatment of multi-drug resistant Staphylococcus aureus (MDRSA) infection is difficult since it possesses multiple antibiotic-resistant mechanisms. Endolysin and virion-associated peptidoglycan hydrolases (VAPGH) enzymes from bacteriophage have been identified as potential alternative antimicrobial agents. This study aimed to assess the ability of Lactococcus lactis NZ9000 secreting endolysin and VAPGH from S. aureus bacteriophage 88 to inhibit the growth of S. aureus PS 88, a MDRSA.MethodEndolysin and VAPGH genes were cloned and expressed in L. lactis NZ9000 after fusion with the SPK1 signal peptide for secretion. The recombinant proteins were expressed and purified, then analyzed for antimicrobial activity using plate assay and turbidity reduction assay. In addition, the spent media of the recombinant lactococcal culture was analyzed for its ability to inhibit the growth of the S. aureus PS 88.ResultsExtracellular recombinant endolysin (Endo88) and VAPGH (VAH88) was successfully expressed and secreted from L. lactis which was able to inhibit S. aureus PS 88, as shown by halozone formation on plate assays as well as inhibition of growth in the turbidity reduction assay. Moreover, it was observed that the spent media from L. lactis NZ9000 expressing Endo88 and VAH88 reduced the viability of PS 88 by up to 3.5-log reduction with Endo88 being more efficacious than VAH88. In addition, Endo88 was able to lyse all MRSA strains tested and Staphylococcus epidermidis but not the other bacteria while VAH88 could only lyse S. aureus PS 88.ConclusionRecombinant L. lactisNZ9000 expressing phage 88 endolysin may be potentially developed into a new antimicrobial agent for the treatment of MDRSA infection. creator: Carumathy Chandran creator: Hong Yun Tham creator: Raha Abdul Rahim creator: Swee Hua Erin Lim creator: Khatijah Yusoff creator: Adelene Ai-Lian Song uri: https://doi.org/10.7717/peerj.12648 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chandran et al. title: Production of single cell oil by Yarrowia lipolytica JCM 2320 using detoxified desiccated coconut residue hydrolysate link: https://peerj.com/articles/12833 last-modified: 2022-03-01 description: Nowadays, the replacement of petro-diesel with biodiesel has raised the concern among the community for the utilization of improper feedstocks and the cost involved. However, these issues can be solved by producing single cell oil (SCO) from lignocellulosic biomass hydrolysates by oleaginous microorganisms. This study introduced Yarrowia lipolytica JCM 2320 with a desiccated coconut residue (DCR) hydrolysate (obtained from the 2% dilute sulphuric acid pretreatment) as a carbon source in generating SCO. However, common inhibitors formed during acid pretreatment of biomass such as five-hydroxymethylfurfural (HMF), furfural, acetic acid and levulinic acid resulting from the sugar degradations may have detrimental effects towards the fermentation process. To visualize the effect of inhibitors on Y. lipolytica, an inhibitory study was conducted by adding 0.5–5.0 g/L of potential inhibitors to the YPD (yeast, peptone and D-glucose) medium. It was found that the presence of furfural at 0.5 g/L would increase the lag phase, which beyond that was detrimental to Y. lipolytica. Furthermore, increasing the five-hydroxymethylfurfural (HMF) concentration would increase the lag phase of Y. lipolytica, whereas, for acetic acid and levulinic acid, it showed a negligible effect. Detoxification was hence conducted to remove the potential inhibitors from the DCR hydrolysate prior its utilization in the fermentation. To examine the possibility of using adsorption resins for the detoxification of DCR hydrolysate, five different resins were tested (Amberlite® XAD-4, Amberlite® XAD-7, Amberlite® IR 120, Amberlite® IRA 96 and Amberlite® IRA 402) with five different concentrations of 1%, 3%, 5%, 10% and 15% (w/v), respectively. At resin concentration of 10%, Amberlite® XAD-4 recorded the highest SCO yield, 2.90 ± 0.02 g/L, whereas the control and the conventional overliming detoxification method, recorded only 1.29 ± 0.01 g/L and 1.27 ± 0.02 g/L SCO accumulation, respectively. Moreover, the fatty acid profile of the oil produced was rich in oleic acid (33.60%), linoleic acid (9.90%), and palmitic acid (14.90%), which indicates the potential as a good biodiesel raw material. creator: Muhammad Fakhri Zainuddin creator: Chong Kar Fai creator: Mohd Shamzi Mohamed creator: Nor ’Aini Abdul Rahman creator: Murni Halim uri: https://doi.org/10.7717/peerj.12833 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zainuddin et al. title: Remarkable genomic diversity among Escherichia isolates recovered from healthy chickens link: https://peerj.com/articles/12935 last-modified: 2022-03-01 description: The genus Escherichia has been extensively studied and it is known to encompass a range of commensal and pathogenic bacteria that primarily inhabit the gastrointestinal tracts of warm-blooded vertebrates. However, the presence of E. coli as a model organism and potential pathogen has diverted attention away from commensal strains and other species in the genus. To investigate the diversity of Escherichia in healthy chickens, we collected fecal samples from antibiotic-free Lohmann Brown layer hens and determined the genome sequences of 100 isolates, 81 of which were indistinguishable at the HC0 level of the Hierarchical Clustering of Core Genome Multi-Locus Sequence Typing scheme. Despite initial selection on CHROMagar Orientation medium, which is considered selective for E. coli, in silico phylotyping and core genome single nucleotide polymorphism analysis revealed the presence of at least one representative of all major clades of Escherichia, except for E. albertii, Shigella, and E. coli phylogroup B2 and cryptic clade I. The most frequent phylogenomic groups were E. coli phylogroups A and B1 and E. ruysiae (clades III and IV). We compiled a collection of reference strains isolated from avian sources (predominantly chicken), representing every Escherichia phylogroup and species, and used it to confirm the phylogeny and diversity of our isolates. Overall, the isolates carried low numbers of the virulence and antibiotic resistance genes typically seen in avian pathogenic E. coli. Notably, the clades not recovered are ones that have been most strongly associated with virulence by other studies. creator: Nicholas M. Thomson creator: Rachel Gilroy creator: Maria Getino creator: Ebenezer Foster-Nyarko creator: Arnoud H.M. van Vliet creator: Roberto M. La Ragione creator: Mark J. Pallen uri: https://doi.org/10.7717/peerj.12935 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Thomson et al.