A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx)
To be computationally reproducible and efficient, integration of disparate data depends on shared entities whose matching meaning (semantics) can be computationally assessed. For biodiversity data one of the most prevalent shared entities for linking data records is the associated taxon concept. Unlike Linnaean taxon names, the traditional way in which taxon concepts are provided, phylogenetic definitions are native to phylogenetic trees and offer well-defined semantics that can be transformed into formal, computationally evaluable logic expressions. These attributes make them highly suitable for phylogeny-driven comparative biology by allowing computationally verifiable and reproducible integration of taxon-linked data against Tree of Life-scale phylogenies. To achieve this, the first step is transforming phylogenetic definitions from the natural language text in which they are published to a structured interoperable data format that maintains strong ties to semantics and lends itself well to sharing, reuse, and long-term archival. To this end, we developed the Phyloreference Exchange Format (Phyx), a JSON-LD-based text format encompassing rich metadata for all elements of a phylogenetic definition, and we created a supporting software library, phyx.js, to streamline computational management of such files. Together they form a foundation layer for digitizing and computing with phylogenetic definitions of clades.
Vaidya et al. (2022) A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx). PeerJ 10:e12618 https://doi.org/10.7717/peerj.12618
Should the frequency, severity, or both response scales be used for multi-item dental patient-reported outcome measures?
Background The Oral Impacts on Daily Performances (OIDP) index asks the respondents to indicate both, the frequency and severity of the impact. However, it is not clear if the two scaling methods are correlated, and if using one scale is sufficient. The purpose of the study was to investigate the correlation between frequency and severity rating scales of the OIDP instrument, and whether only one of the rating scales can be used instead of both. Methods A battery of patient-reported outcome questionnaires were administered to a consecutive sample of adult dental patients from HealthPartners dental clinics in Minnesota (N = 2,115). Only those who responded to any of the OIDP items were included in the analysis for this study (N = 873). We assessed correlations between the frequency and severity scales for all OIDP items, and for the summary scores of the two OIDP response scales. We additionally fit a categorical structural equation model (SEM) (or an item factor analysis model) and examined the correlation between two latent variables (Frequency and Severity). Results The correlation estimates for all OIDP items were greater than 0.50, indicating large correlations between the frequency and severity scores for each OIDP item. The correlation estimate between the two summary scores was 0.85 (95% CI [0.82–0.86]). When we calculated the correlation coefficient using a latent variable model, the value increased to 0.96 (95% CI [0.93–1.00]). Conclusion Our study findings show that OIDP frequency and severity scores are highly correlated, which indicates the use of one scale only. Based on previous evidence, we recommend applying the frequency rating scale only in research and clinical settings.
Pattanaik et al. (2022) Should the frequency, severity, or both response scales be used for multi-item dental patient-reported outcome measures?. PeerJ 10:e12717 https://doi.org/10.7717/peerj.12717
Dogs and wolves differ in their response allocation to their owner/caregiver or food in a concurrent choice procedure
Dogs and wolves both show attachment-like behaviors to their owners/caregivers, including exploring more in the presence of the owner/caregiver, and greeting the owner/caregiver more effusively after an absence. Concurrent choice studies can elucidate dogs’ and wolves’ relationship to their owners/caregivers by assessing their preference for the owner/caregiver compared to other stimuli. While previous research has used concurrent choice paradigms to evaluate dogs’ and wolves’ preference between humans giving social interaction or humans giving food, no research has explored their preferences for an owner/caregiver compared to food when the food is not delivered by a human. In the current study, we investigated whether dogs and hand-reared wolves preferred their owner/caregiver or food, unassociated with a human, when they had been equally deprived of each stimulus (at least 4 hours). Each canid experienced four trials; we measured first choice and time spent with each alternative. Dogs overall did not show a preference for the owner or food. Wolves, on the other hand, tended to show a preference for food in both measures. We observed a range of individual variation in both measures, although dogs showed more individual variation. The differences we observed between dogs and wolves align with prior research comparing wolf and dog behavior directed towards humans; however, the reasons for this differential responding could be due to a variety of factors beyond phylogeny.
Isernia et al. (2022) Dogs and wolves differ in their response allocation to their owner/caregiver or food in a concurrent choice procedure. PeerJ 10:e12834 https://doi.org/10.7717/peerj.12834
From hair to liver: emerging application of hair follicle mesenchymal stem cell transplantation reverses liver cirrhosis by blocking the TGF-β/Smad signaling pathway to inhibit pathological HSC activation
Liver cirrhosis (LC) involves multiple systems throughout the body, and patients with LC often die of multiple organ failure. However, few drugs are useful to treat LC. Hair follicle mesenchymal stem cells (HF-MSCs) are derived from the dermal papilla and the bulge area of hair follicles and are pluripotent stem cells in the mesoderm with broad prospects in regenerative medicine. As an emerging seed cell type widely used in skin wound healing and plastic surgery, HF-MSCs show considerable prospects in the treatment of LC due to their proliferation and multidirectional differentiation capabilities. We established an LC model in C57BL/6J mice by administering carbon tetrachloride (CCl4) and injected HF-MSCs through the tail vein to explore the therapeutic effects and potential mechanisms of HF-MSCs on LC. Here, we found that HF-MSCs improved liver function and ameliorated the liver pathology of LC. Notably, PKH67-labeled HF-MSCs were detected in the injured liver and expressed the hepatocyte-specific markers cytokeratin 18 (CK18) and albumin (ALB). In addition, in contrast to that in the LC group, the α-SMA expression showed a decreasing trend in the treatment group in vitro and in vivo, indicating that the pathological activation of hepatic stellate cells (HSCs) was inhibited by HF-MSC treatment. Moreover, the levels of transforming growth factor β (TGF-β1) and p-Smad3, a signaling molecule downstream of TGF-β1, were increased in mice with LC, while HF-MSC treatment reversed these changes in vivo and in vitro. Based on these findings, HF-MSCs may reverse LC by blocking the TGF-β/Smad pathway and inhibiting the pathological activation of HSCs, which may provide evidence for the application of HF-MSCs to treat LC.
Liu et al. (2022) From hair to liver: emerging application of hair follicle mesenchymal stem cell transplantation reverses liver cirrhosis by blocking the TGF-β/Smad signaling pathway to inhibit pathological HSC activation. PeerJ 10:e12872 https://doi.org/10.7717/peerj.12872
New observations on test architecture and construction of Jullienella foetida Schlumberger, 1890, the largest shallow-water agglutinated foraminifer in modern oceans
We present new observations on Jullienella foetida Schlumberger, 1890, a giant agglutinated foraminifer with a leaf- or fan-like test reaching a maximum dimension of 14 cm, that is common on some parts of the west African continental shelf. The test wall comprises a smooth, outer veneer of small (<10 µm) mineral grains that overlies the much thicker inner layer, which has a porous structure and is composed of grains measuring several hundreds of microns in size. Micro-CT scans suggest that much of the test interior is filled with cytoplasm, while X-ray micrographs reveal an elaborate system of radiating internal partitions that probably serve to channel cytoplasmic flow and strengthen the test. Jullienella foetida resembles some xenophyophores (giant deep-sea foraminifera) in terms of test size and morphology, but lacks their distinctive internal organization; the similarities are therefore likely to be convergent. Based on micro-CT scan data, we calculated an individual cytoplasmic biomass of 3.65 mg wet weight for one specimen. When combined with literature records of seafloor coverage, this yielded an estimate of >7.0 g wet weight m−2 for the seafloor biomass of J. foetida in areas where it is particularly abundant. The relatively restricted distribution of this species off the north-west African coast at depths above 100 m is probably related to the elevated, upwelling-related surface productivity along this margin, which provides enough food to sustain this high biomass. This remarkable species appears to play an important, perhaps keystone, role in benthic ecosystems where it is abundant, providing the only common hard substrate on which sessile organisms can settle.
Langer et al. (2022) New observations on test architecture and construction of Jullienella foetida Schlumberger, 1890, the largest shallow-water agglutinated foraminifer in modern oceans. PeerJ 10:e12884 https://doi.org/10.7717/peerj.12884
7,8-Dihydroxyflavone protects neurons against oxygen-glucose deprivation induced apoptosis and activates the TrkB/Akt pathway
Background 7,8-dihydroxyflavone (7,8-DHF), a selective agonist of tropomyosin related kinase receptor B (TrkB), is known to exert protective effects in neurodegenerative diseases. However, the role of 7,8-DHF in TrkB signaling after ischemic stroke has remained elusive. Methods In the vitro model of ischemic stroke, we investigated the neuroprotective effect of 7,8-DHF through activation of TrkB signaling. Neurons subjected to oxygen and glucose deprivation/reperfusion were treated with the protein kinase inhibitor K252a and a knockdown of TrkB. Cell counting kit-8 (CCK-8) assay, Flow Cytometric Analysis (FACS), TdT-mediated dUTP nick end labeling (TUNEL) assay were conducted for measuring cell viability and numbers of apoptotic cells. And apoptosis-associated proteins were analyzed by Western blotting. Results Compared with the Control group, OGD/R group revealed lower cell viability by CCK-8 assay FACS and TUNEL assay showed increased rates of neuronal apoptosis. However, 7,8-DHF treatment increased cell viability and reduced neuronal apoptosis. Western blotting indicated upregulated Bax and cleaved caspase-3 and but downregulated Bcl-2 following OGD/R. Whereas 7,8-DHF treatment downregulated Bax and cleaved caspase-3 but upregulated Bcl-2. These changes were accompanied by a significant increase in the phosphorylation of TrkB and Akt following 7,8-DHF administration. However, the administration of K252a and knockdown of TrkB could alleviate those effects. Conclusion Our study demonstrates that activation of TrkB signaling by 7,8-DHF protects neurons against OGD/R injury via the TrkB/Akt pathway, which provides the evidence for the role of TrkB signaling in OGD-induced neuronal damage and may become a potential therapeutic target for ischemic stroke.
Zhou et al. (2022) 7,8-Dihydroxyflavone protects neurons against oxygen-glucose deprivation induced apoptosis and activates the TrkB/Akt pathway. PeerJ 10:e12886 https://doi.org/10.7717/peerj.12886
Morphological characterization and sexual dimorphism of the antennal sensilla in Bactericera gobica Loginova (Hemiptera: Psyllidae)—a scanning and transmission electron microscopic study
Bactericera gobica is the major pest of Goji berry plants and causes severe damage. Psyllids mainly use the antennal sensilla to recognize olfactory cues necessary to find host plants and mates. However, the structure and function of the antenna and the antennal sensilla of B. gobica remains previously unexplored. Here, we identify the external and internal morphology of the antennal sensilla of B. gobica using both scanning electron microscopy (SEM) and transmission electron microscopy (TEM). We found seven types of sensilla on the filiform antennae, including apical setae (LAS, SAS), sensilla basiconica (SB1, SB2), sensilla campaniform (SCA), sensilla chaetica (ChS1, ChS2), cavity sensilla (CvS1, CvS2), antennal rhinaria (AR1, AR2), and sensilla trichodea (ST). Five of these sensilla types—apical setae, sensilla basiconica, sensilla chaetica, cavity sensilla, and antennal rhinaria—may have olfactory functions based on their porous surfaces and internal dendritic outer segments (DOS). We also found several differences between the two sexes of B. gobica in the sensilla array and internal structure. ChS and DOS in the protrusions of AR were more abundant in males than females. Altogether, we comprehensively revealed the fine structure and probable function of B. gobica antennae and identified differences in the distribution and structure between psyllid sexes. Our findings provide important insights for future studies on defining the olfactory function of psyllid antenna using electrophysiological methods.
Ge et al. (2022) Morphological characterization and sexual dimorphism of the antennal sensilla in Bactericera gobica Loginova (Hemiptera: Psyllidae)—a scanning and transmission electron microscopic study. PeerJ 10:e12888 https://doi.org/10.7717/peerj.12888
The coalescent with replication-independent mutations
We develop the mathematical structure of the neutral coalescent with both replication-dependent and replication-independent mutations. This allows us to explain and quantify empirical results that explore differences in genetic diversity in bacterial cultures with different growth rates. We also derive an unbiased and consistent estimator for the replication-independent mutation rate that is based on a comparison of total single nucleotide polymorphism counts for two independent well-mixed cultures with different growth rates. In addition to explaining differences in genetic diversity between well-mixed cultures with different (but constant) growth rates, our coalescent also quantifies the effects of fluctuating growth rates—a situation that can be common in natural populations.
Krone et al. (2022) The coalescent with replication-independent mutations. PeerJ 10:e12926 https://doi.org/10.7717/peerj.12926
Wei2GO: weighted sequence similarity-based protein function prediction
Background Protein function prediction is an important part of bioinformatics and genomics studies. There are many different predictors available, however most of these are in the form of web-servers instead of open-source locally installable versions. Such local versions are necessary to perform large scale genomics studies due to the presence of limitations imposed by web servers such as queues, prediction speed, and updatability of databases. Methods This paper describes Wei2GO: a weighted sequence similarity and python-based open-source protein function prediction software. It uses DIAMOND and HMMScan sequence alignment searches against the UniProtKB and Pfam databases respectively, transfers Gene Ontology terms from the reference protein to the query protein, and uses a weighing algorithm to calculate a score for the Gene Ontology annotations. Results Wei2GO is compared against the Argot2 and Argot2.5 web servers, which use a similar concept, and DeepGOPlus which acts as a reference. Wei2GO shows an increase in performance according to precision and recall curves, Fmax scores, and Smin scores for biological process and molecular function ontologies. Computational time compared to Argot2 and Argot2.5 is decreased from several hours to several minutes. Availability Wei2GO is written in Python 3, and can be found at https://gitlab.com/mreijnders/Wei2GO.
Reijnders (2022) Wei2GO: weighted sequence similarity-based protein function prediction. PeerJ 10:e12931 https://doi.org/10.7717/peerj.12931
Human cytomegalovirus infection and its association with gestational diabetes mellitus during pregnancy
Background Infection is an important risk factor for gestational diabetes mellitus (GDM), while infection of human cytomegalovirus (HCMV) with GDM remains unclear and rarely reported. This study aimed to investigate the association of HCMV infection and serum inflammatory factor levels in pregnancy with GDM. Methods This prospective study included pregnant women who attended at Affiliated Hospital of Qingdao Hospital and Zibo Maternal and Child Health Hospital between December 2018 and August 2020. HCMV specific IgM and serum levels of inflammatory factors, including TNF-α, IL-6, and IL-1β, were analyzed. Results A total of 5,316 pregnant women were included (415 with GDM (107 with HCMV+GDM+ and 308 with HCMV-GDM+) and 4901 GDM-free (759 with HCMV+GDM- and 4142 with HCMV-GDM-)). The prevalence of GDM was 7.81%. The rate of activation of HCMV was 16.29%. Specifically, 107 and 759 women in the GDM and control group exhibited HCMV infection, with positive rates of25.78% and 15.48%, respectively (P < 0.01). TNF-α, IL-6, and IL-1β at 24–28 weeks of gestation were significantly higher in women with GDM and HCMV infection than inthe other groups (all P < 0.01). Multivariable analysis showed that HCMV positive (OR = 1.851; 95% CI [1.425–2.403]; P < 0.001), IL-6 (OR = 1.010; 95% CI [1.002–1.018]; P = 0.013), and IL-1β (OR = 1.410; 95% CI [1.348–1.474]; P < 0.001) were all significantly correlated with GDM. Conclusion This study suggests HCMV infection during pregnancy is an independent risk factor of GDM and could significantly increase its incidence. Further studies are needed to elucidate possible mechanisms underlying associations between HCMV infection and GDM.
Wang et al. (2022) Human cytomegalovirus infection and its association with gestational diabetes mellitus during pregnancy. PeerJ 10:e12934 https://doi.org/10.7717/peerj.12934