A modularity analysis helps improving the structure of the International Code of Zoological Nomenclature
Background In a recent work I transformed a complex and integrated text like the International Code of Zoological Nomenclature into a network of interconnected parts of text. This new approach allowed understanding that a continuous body of text cannot accurately reflect the true structure of the Code, and provided a scientific methodology to identify a priori parts that could be affected by future revisions. In this next step, I investigate further the structure of the Code, seeking to use the network in order to identify the various conceptual communities grouping the various articles and other text items of the Code. Methods Using the first version of the network of the Code, I perform a comprehensive modularity analysis in two rounds: the first round aims to identify the fewest and largest communities or modules for the entire network, whereas the second round identifies the sub-modules within each larger module. The potential conflicts between the current structure of the Code and the module composition are evaluated with a parcellation analysis. Results The optimal modularity search identified 10 different modules in the entire network of varying size (ranging from 75 to 200 nodes). Each module can be further divided into smaller modules, that all-together allow describing the 65 conceptual groups of text items in the Code. Parcellation analysis revealed that two-thirds of the current chapters of the Code are in excellent or good accordance with the recovered conceptual modules, whereas the current composition of six chapters is in serious conflict with the conceptual structure of the Code. Discussion Judging only the composition and not the order of appearance of the Articles in the Chapters of the Code, I show that in many cases the current structure of the Code is found to correspond quite well to the concepts presented therein. The most important conflict is found on the provisions related to the various groups of names governed by the Code: family-, genus-, and species-group names. Currently, these provisions are spread out in different Articles in different Chapters, along the entire length of the Code. The modularity analysis suggests that re-organizing the Code in chapters that will deal with all aspects related to a given group (e.g., chapters including information on name formation, availability, typification, and validity for a given group), could potentially improve reader experience and, consequently, the applicability of the Code.
Vlachos (2021) A modularity analysis helps improving the structure of the International Code of Zoological Nomenclature. PeerJ 9:e10815 https://doi.org/10.7717/peerj.10815
Knee replacement outcome predicted by physiotherapists: a prospective cohort study
Background Knee arthroplasty (KA) is commonly used for osteoarthritis of the knee joint and it is a highly successful procedure. Still, KA leaves 20% of patients dissatisfied with their outcome. The purpose of this study was to determine if a prognosis made by physiotherapists at the orthopaedic wards during the first post-operative days could predict the 6- and 12-months outcome of KA. Methods Physiotherapists at two orthopaedic wards in Denmark were asked to predict the 6- and 12-months outcome of the KA patients they have treated post-operatively on a 0–10 scale (10 representing the best prognosis). At 6 and 12 months post-operatively the patients answered the Oxford Knee Score (OKS), EuroQol 5D-3L and Patient Acceptable Symptom State (PASS). Multivariable logistic regression analyses were performed to assess the prediction of PASS and treatment success. We assessed predictive performance by examining measures of calibration and discrimination. Results A total of 361 patients were included. The models for PASS and Treatment Success showed poor to acceptable discriminative values (OR between 1.47 and 1.92 and areas under the curves of 0.62–0.73), however the calibration plots indicated significant uncertainties in the prediction. Conclusion Physiotherapists prognoses of recovery after KA are associated with 6- and 12-months patient reported outcomes and satisfaction but have weak predictive value. This study suggests that physiotherapists’ prognoses may be useful as an additional source of information when identifying patients in need of additional post-operative care.
Henriksen et al. (2021) Knee replacement outcome predicted by physiotherapists: a prospective cohort study. PeerJ 9:e10838 https://doi.org/10.7717/peerj.10838
Hemocyte siRNA uptake is increased by 5′ cholesterol-TEG addition in Biomphalaria glabrata, snail vector of schistosome
Biomphalaria glabrata is one of the snail intermediate hosts of Schistosoma mansoni, the causative agent of intestinal schistosomiasis disease. Numerous molecular studies using comparative approaches between susceptible and resistant snails to S. mansoni infection have helped identify numerous snail key candidates supporting such susceptible/resistant status. The functional approach using RNA interference (RNAi) remains crucial to validate the function of such candidates. CRISPR-Cas systems are still under development in many laboratories, and RNA interference remains the best tool to study B. glabrata snail genetics. Herein, we describe the use of modified small interfering RNA (siRNA) molecules to enhance cell delivery, especially into hemocytes, the snail immune cells. Modification of siRNA with 5′ Cholesteryl TriEthylene Glycol (Chol-TEG) promotes cellular uptake by hemocytes, nearly eightfold over that of unmodified siRNA. FACS analysis reveals that more than 50% of hemocytes have internalized Chol-TEG siRNA conjugated to Cy3 fluorophores, 2 hours only after in vivo injection into snails. Chol-TEG siRNA targeting BgTEP1 (ThioEster-containing Protein), a parasite binding protein, reduced BgTEP1 transcript expression by 70–80% compared to control. The level of BgTEP1 protein secreted in the hemolymph was also decreased. However, despite the BgTEP1 knock-down at both RNA and protein levels, snail compatibility with its sympatric parasite is not affected suggesting functional redundancy among the BgTEP genes family in snail-schistosoma interaction.
Portet et al. (2021) Hemocyte siRNA uptake is increased by 5′ cholesterol-TEG addition in Biomphalaria glabrata, snail vector of schistosome. PeerJ 9:e10895 https://doi.org/10.7717/peerj.10895
MCQ-Balance: a method to monitor patients with balance disorders and improve clinical interpretation of posturography
Background An estimated 20% to 30% of the global population has suffered a vertiginous episode. Among them, 20% do not receive a clear diagnosis. Improved methods, indicators and metrics are necessary to assess the sensory systems related to balance, especially when patients are undergoing treatment for vertiginous episodes. Patients with balance disorders should be monitored for changes at the individual level to gather objective information. In this study, we evaluate the use of the MCQ-Balance (Measure, Classify and Qualify) assessment for examining a patient’s balance progression using tests to measure static balance control and dynamic postural balance with a stabilometric platform. Materials and Methods The MCQ-Balance assessment comprises three stages: (i) measuring the progression of each variable between two separate and consecutive days (called sessions) using the Magnitude-Based Decision analysis; (ii) classifying the progression of the patient’s balance with a score; and (iii) qualifying the progression of the patient’s balance from the resulting scores using a set of rules. This method was applied to 42 patients with balance disorders of peripheral or central origin characterised by vertigo as the cardinal symptom. Balance progression was measured using the MCQ-Balance assessment over the course of three months, and these results were compared with the assessment of a clinical expert. Results The MCQ-Balance assessment showed an accuracy of 83.4% and a Cohen’s Kappa coefficient of 0.752 compared to the assessment of a clinical expert. Conclusion The MCQ-Balance assessment facilitates the monitoring of patient balance and provides objective information that has the potential to improve medical decision making and the adjustment of individual treatment.
De la Torre et al. (2021) MCQ-Balance: a method to monitor patients with balance disorders and improve clinical interpretation of posturography. PeerJ 9:e10916 https://doi.org/10.7717/peerj.10916
Identification of the hub gene BUB1B in hepatocellular carcinoma via bioinformatic analysis and in vitro experiments
Background Hepatocellular carcinoma (HCC) is one of the most commonly diagnosed cancers and the fourth leading cause of cancer-related deaths in the world. Although the treatment of HCC has made great progress in recent years, the therapeutic effects on HCC are still unsatisfactory due to difficulty in early diagnosis, chemoresistance and high recurrence rate post-surgery. Methods In this study, we identified differentially expressed genes (DEGs) based on four Gene Expression Omnibus (GEO) datasets (GSE45267, GSE98383, GSE101685 and GSE112790) between HCC and normal hepatic tissues. A protein–protein interaction (PPI) network was established to identify the central nodes associated with HCC. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the central nodes were conducted to find the hub genes. The expression levels of the hub genes were validated based on the ONCOMINE and Gene Expression Profiling Interactive Analysis (GEPIA) databases. Additionally, the genetic alterations of the hub genes were evaluated by cBioPortal. The role of the hub genes on the overall survival (OS) and relapse survival (RFS) of HCC patients was evaluated by Kaplan-Meier plotter. At last, the mechanistic role of the hub genes was illustrated by in vitro experiments. Results We found the following seven hub genes: BUB1B, CCNB1, CCNB2, CDC20, CDK1, MAD2L1 and RRM2 using integrated bioinformatics analysis. All of the hub genes were significantly upregulated in HCC tissues. And the seven hub genes were associated with the OS and RFS of HCC patients. Finally, in vitro experiments indicated that BUB1B played roles in HCC cell proliferation, migration, invasion, apoptosis and cell cycle by partially affecting mitochondrial functions. Conclusions In summary, we identified seven hub genes that were associated with the expression and prognosis of HCC. The mechanistic oncogenic role of BUB1B in HCC was first illustrated. BUB1B might play an important role in HCC and could be potential therapeutic targets for HCC.
Fu et al. (2021) Identification of the hub gene BUB1B in hepatocellular carcinoma via bioinformatic analysis and in vitro experiments. PeerJ 9:e10943 https://doi.org/10.7717/peerj.10943
Functional analysis of CgWRKY57 from Cymbidium goeringii in ABA response
Background The orchid is one of the top ten Chinese flowers and has high ornamental value and elegant color. However, orchids are vulnerable to abiotic stresses during their growth and development, and the molecular mechanism of the abiotic stress response in orchids is unclear. WRKY proteins belong to a transcription factor family that plays important roles in biotic stress, abiotic stress, growth and development in plants, but little is known about the WRKY family in Cymbidium goeringii. Methods The specific fragment of the CgWRKY57 gene of C. goeringii was analyzed by bioinformatics. The expression of the CgWRKY57 gene of C. goeringii under 4 °C, 42 °C water and ABA stress as well as different tissues was detected by real-time fluorescence quantitative PCR. CgWRKY57 gene was overexpressed in wild type Arabidopsis thaliana by inflorescence infection method, and the function of transgenic lines under ABA stress was analyzed. Results CgWRKY57 was cloned from C. goeringii and found to encode 303 amino acids. The CgWRKY57 protein is an acidic, nonsecreted hydrophilic protein without a signal peptide or transmembrane domain. The CgWRKY57 protein is located to the nucleus and may function intracellularly according to its predicted subcellular localization. A domain analysis and homology comparison showed that the CgWRKY57 protein has a “WRKYGQK” domain and belongs to Group III of the WRKY family, and a phylogenetic analysis demonstrated that CgWRKY57 is closely related to OsWRKY47. CgWRKY57 was expressed in the roots, stems, leaves and floral organs of C. goeringii, and its expression level was highest in the roots according to real-time qPCR analysis. There were significant differences in CgWRKY57 expression under 4 °C, 42 °C ABA and water stress treatments, and its expression changed greatly under ABA stress. The expression of CgWRKY57 in transgenic plants was significantly higher than that in wild type plants under ABA stress, and the root length and germination rate were reduced in transgenic plants compared to wild type plants. Conclusions These results indicate that CgWRKY57 overexpression is responsive to ABA stress, and they provide a foundation for future analyses of the biological functions of the WRKY family in C. goeringii.
Liu et al. (2021) Functional analysis of CgWRKY57 from Cymbidium goeringii in ABA response. PeerJ 9:e10982 https://doi.org/10.7717/peerj.10982
Refining the marine reptile turnover at the Early–Middle Jurassic transition
Even though a handful of long-lived reptilian clades dominated Mesozoic marine ecosystems, several biotic turnovers drastically changed the taxonomic composition of these communities. A seemingly slow paced, within-geological period turnover took place across the Early–Middle Jurassic transition. This turnover saw the demise of early neoichthyosaurians, rhomaleosaurid plesiosaurians and early plesiosauroids in favour of ophthalmosaurid ichthyosaurians and cryptoclidid and pliosaurid plesiosaurians, clades that will dominate the Late Jurassic and, for two of them, the entire Early Cretaceous as well. The fossil record of this turnover is however extremely poor and this change of dominance appears to be spread across the entire middle Toarcian–Bathonian interval. We describe a series of ichthyosaurian and plesiosaurian specimens from successive geological formations in Luxembourg and Belgium that detail the evolution of marine reptile assemblages across the Early–Middle Jurassic transition within a single area, the Belgo–Luxembourgian sub-basin. These fossils reveal the continuing dominance of large rhomaleosaurid plesiosaurians, microcleidid plesiosaurians and Temnodontosaurus-like ichthyosaurians up to the latest Toarcian, indicating that the structuration of the upper tier of Western Europe marine ecosystems remained essentially constant up to the very end of the Early Jurassic. These fossils also suddenly record ophthalmosaurid ichthyosaurians and cryptoclidid plesiosaurians by the early Bajocian. These results from a geographically-restricted area provide a clearer picture of the shape of the marine reptile turnover occurring at the early–Middle Jurassic transition. This event appears restricted to the sole Aalenian stage, reducing the uncertainty of its duration, at least for ichthyosaurians and plesiosaurians, to 4 instead of 14 million years.
Fischer et al. (2021) Refining the marine reptile turnover at the Early–Middle Jurassic transition. PeerJ 9:e10647 https://doi.org/10.7717/peerj.10647
Sensing and processing whisker deflections in rodents
The classical view of sensory information mainly flowing into barrel cortex at layer IV, moving up for complex feature processing and lateral interactions in layers II and III, then down to layers V and VI for output and corticothalamic feedback is becoming increasingly undermined by new evidence. We review the neurophysiology of sensing and processing whisker deflections, emphasizing the general processing and organisational principles present along the entire sensory pathway—from the site of physical deflection at the whiskers to the encoding of deflections in the barrel cortex. Many of these principles support the classical view. However, we also highlight the growing number of exceptions to these general principles, which complexify the system and which investigators should be mindful of when interpreting their results. We identify gaps in the literature for experimentalists and theorists to investigate, not just to better understand whisker sensation but also to better understand sensory and cortical processing.
Burns et al. (2021) Sensing and processing whisker deflections in rodents. PeerJ 9:e10730 https://doi.org/10.7717/peerj.10730
Association between problematic internet use and behavioral/emotional problems among Chinese adolescents: the mediating role of sleep disorders
Background Studies that focus on the relationships of problematic Internet use (PIU), sleep disorders, and behavioral/emotional problems were limited. This study aimed to explore (1) the relationship between PIU and behavioral/emotional problems among Chinese adolescents and (2) whether sleep disorders mediate the relationship between PIU and behavioral/emotional problems. Methods A total of 1,976 adolescents were recruited by cluster sampling from ten secondary schools in Guangzhou between January and April 2019, and 1,956 of them provided valid information (response rate: 98.9% ). Among them, 50.8% were males and the mean age was 13.6±1.5 years, ranging from 11 to 18 years. Data on behavioral/emotional problems, sleep disorders, and PIU were collected using a self-reported questionnaire. Linear regression models and mediation analyses were performed. Results Of the participants, 14.5% (284/1,956) reported moderate to severe PIU, and their average score for total difficulties was significantly higher than the score for average users (14.9±5.5 Vs 9.8±4.7). After adjusting for controlled variables, PIU was further proven to be positively related to elevated levels of behavioral/emotional problems (unstandardized β = 0.16, p < 0.05). In addition, sleep disorders partially mediated the forgoing associations. Conclusions Adolescents with problematic Internet habits were at higher risk of developing behavioral and emotional problems than their normal-use peers, and sleep disorders partially mediated the effect. Close attention and effective guidance for adolescents with PIU and behavioral/emotional problems were recommended for parents and schools.
Wang et al. (2021) Association between problematic internet use and behavioral/emotional problems among Chinese adolescents: the mediating role of sleep disorders. PeerJ 9:e10839 https://doi.org/10.7717/peerj.10839
The click is not the trick: the efficacy of clickers and other reinforcement methods in training naïve dogs to perform new tasks
Background A handheld metal noisemaker known as a “clicker” is widely used to train new behaviors in dogs; however, evidence for their superior efficacy compared to providing solely primary reinforcement or other secondary reinforcers in the acquisition of novel behavior in dogs is largely anecdotal. Methods Three experiments were conducted to determine under what circumstances a clicker secondary reinforcer may result in acquisition of a novel behavior more rapidly or to a higher level compared to other readily available reinforcement methods. In Experiment 1, three groups of 30 dogs each were shaped to emit a novel sit and stay behavior of increasing duration with either the delivery of food alone, a verbal stimulus paired with food, or a clicker with food. The group that received only a primary reinforcer reached a significantly higher criterion of training success than the group trained with a verbal secondary reinforcer. Performance of the group experiencing a clicker as a secondary reinforcer was intermediate between the other two groups, but not significantly different from either. In Experiment 2, three groups of 25 dogs each were shaped to emit a nose targeting behavior and then perform that behavior at increasing distances from the experimenter using the same three methods of positive reinforcement as in Experiment 1. No statistically significant differences between the groups were found. In Experiment 3, three groups of 30 dogs each were shaped to emit a nose-targeting behavior upon an array of wooden blocks with task difficulty increasing throughout testing using the same three methods of positive reinforcement as previously tested. No statistically significant differences between the groups were found. Results Overall, the findings suggest that both primary reinforcement alone as well as a verbal or clicker secondary reinforcer can be used successfully in training a dog to perform a novel behavior, but that no positive reinforcement method demonstrated significantly greater efficacy than any other.
Gilchrist et al. (2021) The click is not the trick: the efficacy of clickers and other reinforcement methods in training naïve dogs to perform new tasks. PeerJ 9:e10881 https://doi.org/10.7717/peerj.10881