title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=690 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Clinical characteristics and prognostic analysis of multiple primary malignant neoplasms in female patients with breast cancer or genitalia malignancies link: https://peerj.com/articles/13528 last-modified: 2022-06-24 description: BackgroundAs public awareness of health has increased and diagnostic and treatment options have improved, the survival of patients with malignant tumors has continued to extend, and the population has been aging, the number of multiple primary malignant neoplasms has gradually increased in recent years. There are few reports concerning female patients with multiple primary malignant neoplasms of breast cancer or genitalia malignancies. In this study, we aimed to analyze the clinical characteristics and prognosis of multiple primary malignant neoplasms in female patients with breast cancer or genitalia malignancies, as well as further explore the factors that affect the survival.MethodsWe collected clinical data on 80 female patients diagnosed with multiple primary malignant neoplasms of the breast or genitalia, described their clinical features. Furthermore, we calculated the survival and prognostic factors for 52 participants.ResultsIn our study, the prevalence rate of multiple primary malignant neoplasms was 0.66% (367/55404). Corresponding to female patients with multiple primary malignant neoplasms of breast cancer or genitalia malignancies, it was 1.4% (80/5707). the median age of diagnosis for the first tumor was 48 years, and the median age of diagnosis for the second tumor was 52 years. Regarding the interval, 67.57% (50/74) of patients were within five years. Most tumors were located in the breast (44.68%), followed by the uterus (20.21%), the ovary (17.02%), and the cervix (15.96%). The overall 12-, 36-and 60-month survival rates of the patients were 86.4%, 74.3%, and 69.8%. For the female patients, the stage (III–IV) (P = 0.046), non-radical surgery (P = 0.002), and types of the last tumor (breast cancer or genitalia malignancies) (P = 0.019) were associated with the poor prognosis.ConclusionsFemale patients with breast cancer or genital malignancies should pay attention to screening for the second tumor, especially within 4 years after the first tumor diagnosed. Furthermore, during tumor screening, it may be recommended for these patients to focus on colorectal cancer and lung cancer. Compared with previous studies, in addition to clinical staging and types of surgery, we found whether the last tumor was breast cancer or genitalia malignancies should also be considered a prognostic factor. creator: Li Xiao creator: Tiantian Cao creator: Jiali Ou creator: Weijiang Liang uri: https://doi.org/10.7717/peerj.13528 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Xiao et al. title: Contribution of hippocampal BDNF/CREB signaling pathway and gut microbiota to emotional behavior impairment induced by chronic unpredictable mild stress during pregnancy in rats offspring link: https://peerj.com/articles/13605 last-modified: 2022-06-24 description: BackgroundNumerous studies have shown that exposure to prenatal maternal stress (PMS) is associated with various psychopathological outcomes of offspring. The accumulating evidence linking bacteria in the gut and neurons in the brain (the microbiota-gut-brain axis) has been aconsensus; however, there is a lack of research on the involvement mechanism of gut microbiota in the regulation of the BDNF/CREB signaling pathway in the hippocampus of prenatally stressed offspring.MethodsPregnant rats were subjected to chronic unpredictable mild stress (CUMS) to establish the prenatal maternal stress model. The body weight was measured and the behavioral changes were recorded. Offspring were tested to determine emotional state using sucrose preference test (SPT), open-field test (OFT) and suspended tail test (STT). Gut microbiota was evaluated by sequencing the microbial 16S rRNA V3–V4 region, and the interactive analysis of bacterial community structure and diversity was carried out. The expression of hippocampal BDNF, TrkB and CREB mRNA and proteins were respectively measured using RT-PCR and Western blotting.ResultsPrenatal maternal stress increased maternal plasma corticosterone levels, slowed maternal weight gain and caused depression-like behaviors (all P < 0.05). In offspring, prenatal maternal stress increased plasma corticosterone levels (P < 0.05) and emotional behavior changes (depression-like state) were observed (P < 0.05). The species abundance, diversity and composition of the offspring’s gut microbiota changed after the maternal stress during pregnancy (P < 0.05). Compared with the control group’s offspring, the species abundance of Lactobacillaceae was dropped, while the abundance of the Muribaculaceae species abundance was risen. Concurrent, changes in the hippocampal structure of the offspring and decreases in expression of BDNF/CREB signaling were noted (P < 0.05).ConclusionsPrenatal maternal stress leads to high corticosterone status and abnormal emotion behavior of offspring, which may be associated with the abnormal BDNF/CREB signaling in hippocampus of offspring caused by the change of gut microbiota composition. creator: Feng Zhao creator: Kai Wang creator: Yujun Wen creator: Xiaohui Chen creator: Hongya Liu creator: Faqiu Qi creator: Youjuan Fu creator: Jiashu Zhu creator: Suzhen Guan creator: Zhihong Liu uri: https://doi.org/10.7717/peerj.13605 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhao et al. title: Genomics enters the deep learning era link: https://peerj.com/articles/13613 last-modified: 2022-06-24 description: The tremendous amount of biological sequence data available, combined with the recent methodological breakthrough in deep learning in domains such as computer vision or natural language processing, is leading today to the transformation of bioinformatics through the emergence of deep genomics, the application of deep learning to genomic sequences. We review here the new applications that the use of deep learning enables in the field, focusing on three aspects: the functional annotation of genomes, the sequence determinants of the genome functions and the possibility to write synthetic genomic sequences. creator: Etienne Routhier creator: Julien Mozziconacci uri: https://doi.org/10.7717/peerj.13613 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Routhier and Mozziconacci title: Specimen alignment with limited point-based homology: 3D morphometrics of disparate bivalve shells (Mollusca: Bivalvia) link: https://peerj.com/articles/13617 last-modified: 2022-06-24 description: BackgroundComparative morphology fundamentally relies on the orientation and alignment of specimens. In the era of geometric morphometrics, point-based homologies are commonly deployed to register specimens and their landmarks in a shared coordinate system. However, the number of point-based homologies commonly diminishes with increasing phylogenetic breadth. These situations invite alternative, often conflicting, approaches to alignment. The bivalve shell (Mollusca: Bivalvia) exemplifies a homologous structure with few universally homologous points—only one can be identified across the Class, the shell ‘beak’. Here, we develop an axis-based framework, grounded in the homology of shell features, to orient shells for landmark-based, comparative morphology.MethodsUsing 3D scans of species that span the disparity of shell morphology across the Class, multiple modes of scaling, translation, and rotation were applied to test for differences in shell shape. Point-based homologies were used to define body axes, which were then standardized to facilitate specimen alignment via rotation. Resulting alignments were compared using pairwise distances between specimen shapes as defined by surface semilandmarks.ResultsAnalysis of 45 possible alignment schemes finds general conformity among the shape differences of ‘typical’ equilateral shells, but the shape differences among atypical shells can change considerably, particularly those with distinctive modes of growth. Each alignment corresponds to a hypothesis about the ecological, developmental, or evolutionary basis of morphological differences, but we suggest orientation via the hinge line for many analyses of shell shape across the Class, a formalization of the most common approach to morphometrics of shell form. This axis-based approach to aligning specimens facilitates the comparison of approximately continuous differences in shape among phylogenetically broad and morphologically disparate samples, not only within bivalves but across many other clades. creator: Stewart M. Edie creator: Katie S. Collins creator: David Jablonski uri: https://doi.org/10.7717/peerj.13617 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Edie et al. title: Identification of aluminum-activated malate transporters (ALMT) family genes in hydrangea and functional characterization of HmALMT5/9/11 under aluminum stress link: https://peerj.com/articles/13620 last-modified: 2022-06-24 description: Hydrangea (Hydrangea macrophylla (Thunb.) Ser.) is a famous ornamental plant species with high resistance to aluminum (Al). The aluminum-activated malate transporter (ALMT) family encodes anion channels, which participate in many physiological processes, such as Al tolerance, pH regulation, stomatal movement, and mineral nutrition. However, systematic studies on the gene family have not been reported in hydrangea. In this study, 11 candidate ALMT family members were identified from the transcriptome data for hydrangea, which could be divided into three clusters according to the phylogenetic tree. The protein physicochemical properties, phylogeny, conserved motifs and protein structure were analyzed. The distribution of base conservative motifs of HmALMTs was consistent with that of other species, with a highly conserved WEP motif. Furthermore, tissue-specific analysis showed that most of the HmALMTs were highly expressed in the stem under Al treatment. In addition, overexpression of HmALMT5, HmALMT9 and HmALMT11 in yeasts enhanced their tolerance to Al stress. Therefore, the above results reveal the functional role of HmALMTs underlying the Al tolerance of hydrangea. The present study provides a reference for further research to elucidate the functional mechanism and expression regulation of the ALMT gene family in hydrangea. creator: Ziyi Qin creator: Shuangshuang Chen creator: Jing Feng creator: Huijie Chen creator: Xiangyu Qi creator: Huadi Wang creator: Yanming Deng uri: https://doi.org/10.7717/peerj.13620 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Qin et al. title: Deletion of two-component system QseBC weakened virulence of Glaesserella parasuis in a murine acute infection model and adhesion to host cells link: https://peerj.com/articles/13648 last-modified: 2022-06-24 description: The widespread two-component system (TCS), QseBC, involves vital virulence regulators in Enterobacteriaceae and Pasteurellaceae. Here we studied the function of QseBC in Glaesserella parasuis. A ΔqseBC mutant was constructed using a Glaesserella parasuis serovar 11 clinical strain SC1401 by natural transformation. Immunofluorescence was used to evaluate cellular adhesion, the levels of inflammation and apoptosis. The ability of ΔqseBC and ΔqseC mutant strains to adhere to PAM and MLE-12 cells was significantly reduced. Additionally, by focusing on the clinical signs, H&E, and IFA for inflammation and apoptosis, we found that the ΔqseBC mutant weakened virulence in the murine models. Together, these findings suggest that QseBC plays an important role in the virulence of Glaesserella parasuis. creator: Xuefeng Yan creator: Ke Dai creator: Congwei Gu creator: Zehui Yu creator: Manli He creator: Wudian Xiao creator: Mingde Zhao creator: Lvqin He uri: https://doi.org/10.7717/peerj.13648 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yan et al. title: Pocillopora spp. growth analysis on restoration structures in an Eastern Tropical Pacific upwelling area link: https://peerj.com/articles/13248 last-modified: 2022-06-23 description: Coral reefs in Culebra Bay (North Pacific of Costa Rica) are threatened by multiple anthropogenic disturbances including global warming, overfishing, eutrophication, and invasive species outbreaks. It is possible to assist their recovery by implementing ecological restoration techniques. This study used artificial hexagonal steel structures, called “spiders” to compare growth of Pocillopora spp. coral fragments of different sizes. Three initial fragment class sizes were used: 2, 5 and 8 cm, with each class size having 42 initial fragments. Changes in fragment length, width and area were measured monthly from January to December 2020. Results showed an overall survivorship of 70.21%, and no significant differences in survivorship and linear growth rate were detected between class sizes. The linear growth rates are 4.49 ± 1.19 cm year−1, 5.35 ± 1.48 cm year−1 and 3.25 ± 2.22 cm year−1 for the 2, 5 and 8 cm initial class sizes, respectively. Our results do not show significant differences in growth rates between the different initial fragment sizes. However, since small fragments (2 cm) present higher mortality during the first month, we recommend using larger fragments. In addition, coral fragments grew 48% more during the non-upwelling season, which may suggest that it might be more effective and safer to start the restoration efforts during this period. creator: Lisa Combillet creator: Sònia Fabregat-Malé creator: Sebastián Mena creator: José Andrés Marín-Moraga creator: Monica Gutierrez creator: Juan José Alvarado uri: https://doi.org/10.7717/peerj.13248 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Combillet et al. title: Natural selection plays a significant role in governing the codon usage bias in the novel SARS-CoV-2 variants of concern (VOC) link: https://peerj.com/articles/13562 last-modified: 2022-06-23 description: The ongoing prevailing COVID-19 pandemic caused by SARS-CoV-2 is becoming one of the major global health concerns worldwide. The SARS-CoV-2 genome encodes spike (S) glycoprotein that plays a very crucial role in viral entry into the host cell via binding of its receptor binding domain (RBD) to the host angiotensin converting enzyme 2 (ACE2) receptor. The continuously evolving SARS-CoV-2 genome results in more severe and transmissible variants characterized by the emergence of novel mutations called ‘variants of concern’ (VOC). The currently designated alpha, beta, gamma, delta and omicron VOC are the focus of this study due to their high transmissibility, increased virulence, and concerns for decreased effectiveness of the available vaccines. In VOC, the spike (S) gene and other non-structural protein mutations may affect the efficacies of the approved COVID-19 vaccines. To understand the diversity of SARS-CoV-2, several studies have been performed on a limited number of sequences. However, only a few studies have focused on codon usage bias (CUBs) pattern analysis of all the VOC strains. Therefore, to evaluate the evolutionary divergence of all VOC S-genes, we performed CUBs analysis on 300,354 sequences to understand the evolutionary relationship with its adaptation in different hosts, i.e., humans, bats, and pangolins. Base composition and RSCU analysis revealed the presence of 20 preferred AU-ended and 10 under-preferred GC-ended codons. In addition, CpG was found to be depleted, which may be attributable to the adaptive response by viruses to escape from the host defense process. Moreover, the ENC values revealed a higher bias in codon usage in the VOC S-gene. Further, the neutrality plot analysis demonstrated that S-genes analyzed in this study are under 83.93% influence of natural selection, suggesting its pivotal role in shaping the CUBs. The CUBs pattern of S-genes was found to be very similar among all the VOC strains. Interestingly, we observed that VOC strains followed a trend of antagonistic codon usage with respect to the human host. The identified CUBs divergence would help to understand the virus evolution and its host adaptation, thus help design novel vaccine strategies against the emerging VOC strains. To the best of our knowledge, this is the first report for identifying the evolution of CUBs pattern in all the currently identified VOC. creator: Neetu Tyagi creator: Rahila Sardar creator: Dinesh Gupta uri: https://doi.org/10.7717/peerj.13562 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Tyagi et al. title: Intra- and interspecific competition resulting from spatial coexistence among larvae of closely-related caddisflies from the genus Hydropsyche link: https://peerj.com/articles/13576 last-modified: 2022-06-23 description: Caddisfly larvae commonly inhabit freshwater ecosystems, where they often create multi-species aggregations. However, while several strategies have been developed to avoid or reduce inter- and intraspecific interactions, most species choose the same time to seek a suitable place for pupation, which can increase competition. The current study assesses the competitive interactions among larvae (5th instar) of three co-existing Hydropsyche species, viz. H. contubernalis, H. pellucidula, and H. modesta, analysing their direct one-on-one interaction and various morphological features, such as size, weight, and mandibles. More than half of the interspecific conflicts ended with a draw, and 80% of intraspecific interactions with a decisive outcome. In fights between species, H. pellucidula was the most successful, and H. modesta the weakest. Our results confirm that among the larvae, competitive interactions were usually decided by body size, especially that of the head capsule. Although wider head capsule and higher weight were advantageous for ~60% of winning larvae, there were no distinct winning species. The chewing mouthpart turned out to be supportive in the fight: regardless of the species, longer and wider mandibles were significant for winning specimens, but not the distance between mandibles. Hence, acquiring a suitable place for pupation is determined by the possession of certain features enhancing the fighting potential of individual larvae, which does not exclude any species from the possibility of closing the life cycle. Future studies on interactions among caddisfly larvae could include experience in fights, volitional features and stridulation (not tested). creator: Mariusz Tszydel creator: Dagmara Błońska uri: https://doi.org/10.7717/peerj.13576 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Tszydel and Błońska title: Selective effects of exercise on reactive and proactive inhibition in Parkinson’s disease link: https://peerj.com/articles/13628 last-modified: 2022-06-23 description: ObjectivePatients with Parkinson’s disease (PD) have an obvious motor inhibition disorder, which is closely related to their motor symptoms. Although previous studies have shown that exercise can improve their inhibition deficits, the effect of exercise on different types of inhibition (proactive and reactive inhibition) has not been addressed.MethodsWe used a behavioral paradigm combined with a series of questionnaires to explore the effect of long-term exercise on different types of motor inhibition in 59 patients with PD aged 55–75 years. According to the intensity and frequency of exercise, the participants were divided into regular-exercise and no-exercise groups. To obtain the average reference value for inhibition ability at the same age, we also recruited 30 healthy elderly people as controls.ResultsThe main defect in the motor inhibition of PD is reactive inhibition, while proactive inhibition has no obvious differences compared with healthy controls. Additionally, compared with the non-exercise group, PD in the exercise group showed significantly better reaction speeds and reactive control ability, fewer motor symptoms and negative emotions.ConclusionsTaken together, the motor inhibition defects of patients with PD affect only reactive inhibition. In addition, PD with exercise reported fewer negative emotions than that of the non-exercise group, indicating that exercise can relieve negative emotions and improve behavioral symptoms and quality of life in PD to a certain extent. We demonstrate for the first time that exercise has and can improve reactive inhibition in PD patients and has no effect on proactive inhibition. creator: Zhen Wang creator: Yan-Ling Pi creator: Yin Wu creator: Jianing Wei creator: Yuting Li creator: Jian Zhang creator: Zhen Wang uri: https://doi.org/10.7717/peerj.13628 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wang et al.