title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=414 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Cessation of exclusive breastfeeding and predictors among infants aged 0–6 months in Ararso district of the Somali region, Ethiopia. A community-based cross-sectional study link: https://peerj.com/articles/15963 last-modified: 2023-09-25 description: BackgroundExclusive breastfeeding (EBF) is the gold standard of child feeding practice in which the infant only receives breast milk without any additional food or drink, not even water and it lasts up to 6 months after delivery. In the study area, there is a lack of data on the prevalence of cessation of EBF.MethodsCommunity-based cross-sectional study design was used among 292 mothers of infants aged 0–6 months. The data was collected using a pretested structured questionnaire. Bivariate and multivariate logistic regression analyses were carried out. An odds ratio with a 95% confidence interval was used to measure the strength of the association. Statistical significance was declared at P-value <0.05.ResultsThe prevalence of cessation of EBF was 57.3% with 95% CI [50.9–62.6]. This study showed being employed (working outside the home) (AOR = 2.44; 95% CI [1.32–4.53]), being rural residence (AOR = 1.87; 95% CI [1.05–3.32]), and inadequate knowledge of EBF (AOR = 2:02; 95% CI [1.19–3.43]) were independent predictors of cessation of EBF.Conclusion and RecommendationOur data identified a higher prevalence of cessation of EBF in the study area compared to most studies in Ethiopia and elsewhere. Efforts on improving knowledge of the importance of EBF particularly in rural areas and support for breastfeeding-employed women are recommended. creator: Kalid Hassen Ibrahim creator: Abdulkarim Mohammed Ali creator: Zelalem Tafese Wondimagegne uri: https://doi.org/10.7717/peerj.15963 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ibrahim et al. title: Levels of PIVKA-II and alpha-fetoprotein in unresectable hepatocellular carcinoma compared to healthy controls and predictive values of both markers with radiological responses after loco-regional interventions link: https://peerj.com/articles/15988 last-modified: 2023-09-25 description: BackgroundThe significance of the current study was to determine normative levels of PIVKA-II and AFP in patients with unresectable HCC and healthy participants. The second goal was to assess the roles of PIVKA-II and AFP in predicting radiological response after loco-regional therapy.MethodsThis prospective cohort study enrolled consecutive samples of HCC patients and healthy controls. Venous blood samples were obtained at baseline and after interventions to determine serum levels of PIVKA-II and AFP using the chemiluminescent microparticle immunoassay method. Radiologic responses were determined based on the WHO criteria.ResultsFifty-four HCC patients (mean age 58.9 years, 49 males) and 40 healthy controls (mean age 33.5 years, 26 males) were recruited. The median serum levels of PIVKA-II and AFP in HCC vs. healthy controls were 988.4 vs. 24.2 mAU/ml and 13.6 vs. 1.7 ng/ml, respectively (both p < 0.001). With ROC curve analysis, the area under the curve (AUC) for PIVKA-II was 0.95 95% CI [0.90–0.99], and for AFP it was 0.98, 95% CI [0.95–1.0]). The cut-off value for PIVKA-II was 41.4 mAU/ml, and AFP was 4.8 ng/ml. PIVKA-II levels correlated significantly with radiological responses (r = 0.64, p = 0.02) but not AFP (r = 0.09, p = 0.2).ConclusionPIVKA-II and AFP levels are distinctive between unresectable HCC and healthy controls. However, PIVKA-II, not AFP, can predict the radiological response after loco-regional therapy. creator: Norhanan Hamzah creator: Nur Karyatee Kassim creator: Julia Omar creator: Mohd Shafie Abdullah creator: Yeong Yeh Lee uri: https://doi.org/10.7717/peerj.15988 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Hamzah et al. title: An observational study on the adherence to study registrations in German interventional and observational studies from various fields link: https://peerj.com/articles/16015 last-modified: 2023-09-25 description: BackgroundThe registration of studies, especially in the case of clinical trials, is required by the declaration of Helsinki and the policies of various scientific journals. However, numerous analyses have found considerable discrepancies between published articles and accompanying trial registrations. The aim of this study is to assess such discrepancies for a sample of studies with recruiting locations in Germany. Additionally, the association between the adherence to registrations and possible involvement of Coordinating Centers for Clinical Studies (KKS) as well as Universities of Excellence was tested.MethodsFor a sample of 376 interventional or observational study registrations, we found 115 published articles. Subsequently, we searched for discrepancies in the study design, the key inclusion criteria, the interventions, the blinding, and a primary and a secondary outcome.ResultsWe found discrepancies in 26% of all studies, most frequently in the secondary outcomes, where 16.5% of the secondary outcomes per study that were registered in most detail had discrepancies. When running regression models for adherence discrepancies, the only variable that had a statistically significant association with better adherence was registration on ClinicalTrials.gov. The association of potential involvement of a KKS with adherence ratings was positive, too, but statistically insignificant.ConclusionsIn summary, the amount of discrepancies between registrations and published articles remains elevated. creator: Christian Thiele creator: Gerrit Hirschfeld uri: https://doi.org/10.7717/peerj.16015 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Thiele et al. title: Claw shape variation in oribatid mites of the genera Carabodes and Caleremaeus: exploring the interplay of habitat, ecology and phylogenetics link: https://peerj.com/articles/16021 last-modified: 2023-09-25 description: BackgroundClaws are a commonly observed biological adaptation across a wide range of animal groups. They serve different functions and their link to evolution is challenging to analyze. While there are many studies on the comparative anatomy and morphology of claws in reptiles, birds and several arthropods, knowledge about claws of soil-living oribatid mites, is still limited. Recent research on intertidal oribatid mites has shown that claw shape is strongly correlated with microhabitat and is subject to ecological selective pressures. However, the selective constraints shaping claws in terrestrial oribatid mites are still unknown.MethodsIn this study, 300 specimens from 12 different species and two genera were examined. Geometric morphometrics were used to quantify claw length and curvature, and to analyze two-dimensional claw shape. In combination with molecular phylogenetic analyses of investigated populations phylogenetic signal was quantified within genera using Blomberg’s K and random replicates. Additionally, ecological information on the investigated species was gathered from previous studies and compiled into tables.ResultsThe claw shapes of Carabodes species vary moderately, with the three species C. reticulatus, C. rugosior and C. tenuis deviating the most from the others. These three species are only found in a small number of habitats, which may require a more specialized claw shape. Our results show that there is a phylogenetic influence on claw shape in Carabodes but not in Caleremaeus. Additionally, habitat specificity and lifestyle were found to have ecological impact on claw shape in both genera. The present results demonstrate that characteristics of the claws of terrestrial oribatid mites are correlated with ecology, but this correlation is apparently weaker than in intertidal oribatid mites that are prone to strong external forces. creator: Michaela Kerschbaumer creator: Sylvia Schäffer creator: Tobias Pfingstl uri: https://doi.org/10.7717/peerj.16021 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Kerschbaumer et al. title: Phenology and predictors of spring emergence for the Timber Rattlesnake (Crotalus horridus) link: https://peerj.com/articles/16044 last-modified: 2023-09-25 description: Many temperate reptiles survive winter by using subterranean refugia until external conditions become suitable for activity. Determining when to emerge from refugia relies on the ability to interpret when above-ground environmental conditions are survivable. If temperate reptiles rely on specific environmental cues such as temperature to initiate emergence, we should expect emergence phenologies to be predictable using local climatic data. However, specific predictors of emergence for many temperate reptiles, including the Timber Rattlesnake (Crotalus horridus), remain unclear, limiting our understanding of their overwintering phenology and restricting effective conservation and management. Our objectives were to identify environmental cues of spring emergence for C. horridus in Illinois to determine the species’ emergence phenology, and to examine the applicability of identified cues in predicting emergence phenology across the species’ range. We used wildlife cameras and weather station-derived environmental data to observe and predict the daily surface presence of C. horridus throughout the late winter and early spring at communal refugia in west-central and northern Illinois. The most parsimonious model for predicting surface presence included the additive effects of maximum daily temperature, accumulated degree days, and latitude. With a notable exception in the southeastern U.S., the model accurately predicted the average emergence day for eight other populations range wide, emphasizing the importance of temperature in influencing the phenological plasticity observed across the species’ range. The apparent broad applicability of the model to other populations suggests it can be a valuable tool in predicting spring emergence phenology. Our results provide a foundation for further ecological enquiries and improved management and conservation strategies. creator: Andrew C. Jesper creator: Scott A. Eckert creator: Brian J. Bielema creator: Scott R. Ballard creator: Michael J. Dreslik uri: https://doi.org/10.7717/peerj.16044 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Jesper et al. title: Comparative analysis of codon usage patterns and phylogenetic implications of five mitochondrial genomes of the genus Japanagallia Ishihara, 1955 (Hemiptera, Cicadellidae, Megophthalminae) link: https://peerj.com/articles/16058 last-modified: 2023-09-25 description: Japanagallia is a genus of Cicadomorpha in the family of leafhoppers that are plant piercing-sucking insects, and it is difficult to distinguish by morphological characteristics. So far, only one complete mitochondrial genome data has been reported for the genus Japanagallia. Therefore, in order to better understand this group, we assembled and annotated the complete mitochondrial genomes of five Japanagallia species, and analyzed their codon usage patterns. Nucleotide composition analysis showed that AT content was higher than GC content, and the protein-coding sequences preferred to end with A/T at the third codon position. Relative synonymous codon usage analysis revealed most over-represented codon ends with A or T. Parity plot analysis revealed the codon usage bias of mitochondrial genes was influenced by both natural selection and mutation pressure. In the neutrality plot, the slopes of regression lines were < 0.5, suggesting that natural selection was playing a major role while mutation pressure was of minor importance. The effective number of codons showed that the codon usage bias between genes and genomes was low. Correspondence analysis revealed that the codon usage pattern differed among 13 protein-coding genes. Phylogenetic analyses based on three datasets using two methods (maximum likelihood and Bayesian inference), restored the Megophthalminae monophyly with high support values (bootstrap support values (BS) = 100, Bayesian posterior probability (PP) = 1). In the obtained topology, the seven Japanagallia species were clustered into a monophyletic group and formed a sister group with Durgade. In conclusion, our study can provide a reference for the future research on organism evolution, identification and phylogeny relationships of Japanagallia species. creator: Min Li creator: Jiajia Wang creator: Renhuai Dai creator: Guy Smagghe creator: Xianyi Wang creator: Siying You uri: https://doi.org/10.7717/peerj.16058 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Li et al. title: Berberine protects hepatocyte from hypoxia/reoxygenation-induced injury through inhibiting circDNTTIP2 link: https://peerj.com/articles/16080 last-modified: 2023-09-25 description: BackgroundDuring hepatic ischemia-reperfusion injury, the excessive release of inflammatory cytokines can activate the intracellular signal transduction cascade to induce hepatocyte injury. Apoptosis is an important way of cell death after I/R injury. Berberine, a common quaternary ammonium alkaloid, has anti-inflammatory, anti-oxidative stress, and anti-apoptotic effects. An increasing number of studies have revealed the importance of non-coding RNAs, including microRNA, long non-coding RNAs and circular RNAs (circRNAs), as regulators of the effects of berberine.PurposeIn this study, we investigated the mechanism of berberine against liver ischemia-reperfusion injury in vitro.Study Design and MethodsIn this study, hypoxia-reoxygenation (H/R)-treated L02 cells were pretreated with berberine to study the role and mechanism of berberine in resisting hepatic ischemia-reperfusion injury.ResultsThe results show that berberine pre-treatment increased the cell viability of H/R-challenged cells, reduced H/R-induced apoptosis and ROS production, reversed H/R-increased on IL-6, IL-1β, TNF-α, and H/R-decreased IL-10 expression. Mechanically, berberine protect hepatocyte from H/R injury, at least partially, through circDNTTIP2. In addition, circDNTTIP2 can bind to the TATA box of caspase3 promoter, thereby promoting caspase 3-related cell apoptosis and the release of inflammatory cytokines.ConclusionThis study found that berberine has a protective effect on H/R-induced hepatocyte damage by inhibiting a novel circRNA, circDNTTIP2. This study provides potential treatment strategies and treatment targets for liver ischemia-reperfusion injury. creator: Yi Zhu creator: Junhui Li creator: Pengpeng Zhang creator: Bo Peng creator: Cai Li creator: Yingzi Ming creator: Hong Liu uri: https://doi.org/10.7717/peerj.16080 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Zhu et al. title: Habitat suitability of four threatened Himalayan species: Asiatic black bear, common leopard, musk deer, and snow leopard link: https://peerj.com/articles/16085 last-modified: 2023-09-25 description: BackgroundBiodiversity conservation is becoming challenging day by day. For this, it is essential to understand the distribution, habitat, and impact of anthropogenic activities on animals at risk. We assessed the suitable habitats and anthropogenic impacts on Asiatic black bears, common leopards, musk deer, and snow leopards in and outside the protected areas of Gandaki Province, Nepal.MethodsWe collected the presence locations of Asiatic black bears, common leopards, musk deer, and snow leopards based on scats and other signs. We employed the Maximum Entropy (MaxEnt) tool to identify suitable habitats of our studied species and their anthropogenic impacts on them.ResultsThe total suitable habitat of the common leopard was found to be 6,052 km2, followed by the Asiatic black bear (5,819 km2), snow leopard (4,447 km2), and musk deer (1,690 km2) in Gandaki Province. Most of the areas of suitable habitat for common leopards and Asiatic black bears were outside the protected areas, and for musk deer and snow leopards were inside the protected areas. Elevation was the most important variable determining habitat suitability of Asiatic black bear, common leopard, and musk deer, whereas the distance to water was the most important variable determining habitat suitability of snow leopard. Asiatic black bears, common leopards, and musk deer face significant anthropogenic impacts, but snow leopards face some anthropogenic impacts.ConclusionManaging these animals’ habitats inside and outside protected areas is essential. Hence, biodiversity conservation and livelihood opportunities should be balanced in the Himalayas on a win-win basis. creator: Rajesh Malla creator: Saroj Panthi creator: Hari Adhikari creator: Shiva Pariyar creator: Rishi Baral creator: Rukmagat Subedi creator: Bishnu Prasad Adhikari creator: Mahesh Poudel creator: Nischal Sedhai creator: Megharaj Poudel uri: https://doi.org/10.7717/peerj.16085 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Malla et al. title: Exploring the relationship between nutritional intake and menstrual cycle in elite female athletes link: https://peerj.com/articles/16108 last-modified: 2023-09-25 description: This study aimed to examine potential variations in nutritional intake among female athletes, including top-level, throughout the menstrual cycle. A total 122 female athletes participated in the study, documenting their food consumption over a 3-day period. The menstrual status of female athletes was also assessed, and using the survey results, the phase of the menstrual cycle (the follicular, early luteal, or late luteal) during which each meal was recorded was determined. Consequently, the meal records were categorized into the respective three phases. The findings of this study indicated that there were no notable disparities in nutritional intake, encompassing energy, protein, fat, carbohydrate, calcium, iron, and fiber, across the three phases of the menstrual cycle. The results imply that female athletes may experience comparatively smaller variations in nutrient intake related to the menstrual cycle. This could be attributed to the higher energy requirements of female athletes because of their rigorous training. This study underscores the significance of accounting for the population when examining nutrient intake changes associated with the menstrual cycle. creator: Mana Miyamoto creator: Kenichi Shibuya uri: https://doi.org/10.7717/peerj.16108 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Miyamoto and Shibuya title: DeepMethylation: a deep learning based framework with GloVe and Transformer encoder for DNA methylation prediction link: https://peerj.com/articles/16125 last-modified: 2023-09-25 description: DNA methylation is a crucial topic in bioinformatics research. Traditional wet experiments are usually time-consuming and expensive. In contrast, machine learning offers an efficient and novel approach. In this study, we propose DeepMethylation, a novel methylation predictor with deep learning. Specifically, the DNA sequence is encoded with word embedding and GloVe in the first step. After that, dilated convolution and Transformer encoder are utilized to extract the features. Finally, full connection and softmax operators are applied to predict the methylation sites. The proposed model achieves an accuracy of 97.8% on the 5mC dataset, which outperforms state-of-the-art methods. Furthermore, our predictor exhibits good generalization ability as it achieves an accuracy of 95.8% on the m1A dataset. To ease access for other researchers, our code is publicly available at https://github.com/sb111169/tf-5mc. creator: Zhe Wang creator: Sen Xiang creator: Chao Zhou creator: Qing Xu uri: https://doi.org/10.7717/peerj.16125 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Wang et al.