Comparison of machine learning approaches for enhancing Alzheimer’s disease classification
Alzheimer’s disease (AD) is a progressive neurodegenerative disorder, accounting for nearly 60% of all dementia cases. The occurrence of the disease has been increasing rapidly in recent years. Presently about 46.8 million individuals suffer from AD worldwide. The current absence of effective treatment to reverse or stop AD progression highlights the importance of disease prevention and early diagnosis. Brain structural Magnetic Resonance Imaging (MRI) has been widely used for AD detection as it can display morphometric differences and cerebral structural changes. In this study, we built three machine learning-based MRI data classifiers to predict AD and infer the brain regions that contribute to disease development and progression. We then systematically compared the three distinct classifiers, which were constructed based on Support Vector Machine (SVM), 3D Very Deep Convolutional Network (VGGNet) and 3D Deep Residual Network (ResNet), respectively. To improve the performance of the deep learning classifiers, we applied a transfer learning strategy. The weights of a pre-trained model were transferred and adopted as the initial weights of our models. Transferring the learned features significantly reduced training time and increased network efficiency. The classification accuracy for AD subjects from elderly control subjects was 90%, 95%, and 95% for the SVM, VGGNet and ResNet classifiers, respectively. Gradient-weighted Class Activation Mapping (Grad-CAM) was employed to show discriminative regions that contributed most to the AD classification by utilizing the learned spatial information of the 3D-VGGNet and 3D-ResNet models. The resulted maps consistently highlighted several disease-associated brain regions, particularly the cerebellum which is a relatively neglected brain region in the present AD study. Overall, our comparisons suggested that the ResNet model provided the best classification performance as well as more accurate localization of disease-associated regions in the brain compared to the other two approaches.
Li et al. (2021) Comparison of machine learning approaches for enhancing Alzheimer’s disease classification. PeerJ 9:e10549 https://doi.org/10.7717/peerj.10549
Characterization and functional analysis of the Hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) gene family in poplar
Hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) divides the mass flux to H, G and S units in monolignol biosynthesis and affects lignin content. Ten HCT homologs were identified in the Populus trichocarpa (Torr. & Gray) genome. Both genome duplication and tandem duplication resulted in the expansion of HCT orthologs in Populus. Comprehensive analysis including motif analysis, phylogenetic analysis, expression profiles and co-expression analysis revealed the divergence and putative function of these candidate PoptrHCTs. PoptrHCT1 and 2 were identified as likely involved in lignin biosynthesis. PoptrHCT9 and 10- are likely to be involved in plant development and the response to cold stress. Similar functional divergence was also identified in Populus tomentosa Carr. Enzymatic assay of PtoHCT1 showed that PtoHCT1 was able to synthesize caffeoyl shikimate using caffeoyl-CoA and shikimic acid as substrates.
Chao et al. (2021) Characterization and functional analysis of the Hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) gene family in poplar. PeerJ 9:e10741 https://doi.org/10.7717/peerj.10741
Genetic structure and historical and contemporary gene flow of Astyanaxmexicanus in the Gulf of Mexico slope: a microsatellite-based analysis
Background Astyanax mexicanus from the river basins of the Gulf of Mexico slope are small freshwater fish that usually live in large groups in different freshwater environments. The group is considered successful due to its high capacity for dispersal and adaptation to different habitats, and the species present high morphological variability throughout their distribution in Mexico. This has produced the most extreme morphotype of the group; the hypogeous or troglobite, which has no eyes or coloration, and is probably the cause of taxonomic uncertainty in the recognition of species across the entire range. Most studies of A. mexicanus have mainly focused on cave individuals, as well as their adjacent surface locations, providing an incomplete evolutionary history, particularly in terms of factors related to dispersal and the potential corridors used, barriers to gene flow, and distribution of genetic variability. The aim of the present study is to determine the population structure and the degree and direction of genetic flow in this complex taxonomic group, incorporating geographic locations not previously included in analyses using microsatellite loci. Our aim is to contribute to the knowledge of the intricate evolutionary history of A. mexicanus throughout most of its range. Methods The present study included a set of several cave and surface locations of A. mexicanus, which have been widely sampled along the Gulf of Mexico slope, in a genetic population analysis using 10 microsatellite loci. Results Ten genetic populations or lineages were identified. In these populations, gene flow was recorded at two time periods. Historical gene flow, both inter and intra-basin, was observed among surface populations, from surface to cave populations, and among cave populations, whereas recording of contemporary gene flow was limited to intra-basin exchanges and observed among surface populations, surface to cave populations, and cave populations.
Pérez-Rodríguez et al. (2021) Genetic structure and historical and contemporary gene flow of Astyanaxmexicanus in the Gulf of Mexico slope: a microsatellite-based analysis. PeerJ 9:e10784 https://doi.org/10.7717/peerj.10784
Phenotype characteristics of gastric epithelial mucus in patients with different gastric diseases: from superficial gastritis to gastric cancer
Background Gastric gland mucin is important for maintaining the basic function of the gastric mucosa, protecting it from foreign substances and reducing the occurrence of gastric diseases. Exploring the phenotype of gastric gland mucus changes during the progression of gastric disease is of great clinical significance. Methods A total of 483 patients with different gastric diseases were collected in this study, including 82 superficial gastritis (SG), 81 atrophic gastritis (AG), 168 dysplasia (GD), and 152 gastric cancer (GC). Mucin staining was performed using HID-ABpH2.5-PAS method and was further grouped according to the mucin coloration. Results The phenotypic characteristics of mucin during disease progression were divided into neutral, acidic, and mucus-free types. Furthermore, acidic mucus can be divided into type I, type II, and type III. The SG group was dominated by neutral mucus (100%), and the AG was dominated by acid mucus (81.48%), which gradually increased with the severity of atrophy (P < 0.05). The GD and GC groups were dominated by mucus-free (43.45%, 78.29%), and as the degree of GD worsened, neutral and acidic mucus gradually decreased and mucus-free increased (P < 0.001). From the SG, AG, GD, and GC progression, neutral and acidic mucus gradually decreased, and mucus- free gradually increased. Acidic mucin revealed that type III (red-brown black) mucin was predominant in AG, GD, and GC, and increased with the degree of AG, GD, as well as the biological behavior of GC. In the lesion adjacent to high-grade GD or GC, type III acid mucin is predominant. Conclusion There were three mucin phenotypes in the process of gastric diseases. With the disease progression, the trend of phenotypic change was that neutral and acidic mucus gradually decreased and mucus-free increased. The appearance of type III mucin suggested a relatively serious phase of gastric diseases and may be a more suitable candidate for follow-up monitoring of patients with GC risk.
Dong et al. (2021) Phenotype characteristics of gastric epithelial mucus in patients with different gastric diseases: from superficial gastritis to gastric cancer. PeerJ 9:e10822 https://doi.org/10.7717/peerj.10822
Comparison of microleakage between different restorative materials to restore marginal gap at crown margin
Background An occurrence of secondary caries around the indirect restoration margin is reported to remain a leading cause of failures. Objective This study aimed to test the interfacial microleakage of conventional glass-ionomer (CGI), resin-modified glass ionomer (RMGI) and Nano-hybrid composite (CR) restorations at a full veneer margin crown. Methods Ninety human extracted molar teeth were divided into three groups (n = 30). Each group was subdivided into three subgroups (n = 10) according to the extent of the structural defects; The structural defect in G1 had a depth of 1.5 mm, width and length at 2 mm and 1 mm intrusion within the crown cervical margin. The corresponding structural defect dimension values for G2 were 2, 5, 4 and 2 mm with defects extending onto the root structure. Meanwhile, G3: structural deficiency of 2 mm depth, 3 mm width and 3 mm length and with 1.5 mm extension into the prepared teeth. These structural defects in each subgroup were restored with CGI, RMGI and CR. Artificial carious lesion formation was induced at the cervical finish line with a demineralizing solution. The artificial carious lesions were restored as per the group distribution. Subsequently, teeth samples were prepared and cemented with Nickel-chromium full coverage restorations utilizing glass-ionomer luting cement. Teeth samples were thermocycled, isolated with nail varnish, and immersed in 0.1% methylene blue for 24 h. The teeth samples were sectioned longitudinally, dye penetration was evaluated with a stereomicroscope. The data were analyzed with Kruskal–Wallis and Mann–Whitney U tests. Results CGI-G1 recorded the highest micro-leakage score at 1.450; while CR-G3 recorded the least score (0.350). At a cementum-restoration interface, CR-G1 (0.850) documented the lowest micro-leakage; RMGI-G3 had a greater value at 1.700. Conclusions The hybrid CR could be effectively used to restore the restoration of a marginal gap around crown margins.
Haralur et al. (2021) Comparison of microleakage between different restorative materials to restore marginal gap at crown margin. PeerJ 9:e10823 https://doi.org/10.7717/peerj.10823
Sheath-tailed bats (Chiroptera: Emballonuridae) from the early Pleistocene Rackham’s Roost Site, Riversleigh World Heritage Area, and the distribution of northern Australian emballonurid species
Sheath-tailed bats (Family Emballonuridae) from the early Pleistocene Rackham’s Roost Site cave deposit in the Riversleigh World Heritage Area, north-western Queensland are the oldest recorded occurrence for the family in Australia. The fossil remains consist of maxillary and dentary fragments, as well as isolated teeth, but until now their precise identity has not been assessed. Our study indicates that at least three taxa are represented, and these are distinguished from other Australian emballonurids based on morphometric analysis of craniodental features. Most of the Rackham’s Roost Site emballonurid remains are referrable to the modern species Taphozous georgianus Thomas, 1915, but the extant species T. troughtoni Tate, 1952 also appears to be present, as well as a very large, as-yet undetermined species of Saccolaimus Temminck, 1838. We identify craniodental features that clearly distinguish T. georgianus from the externally very similar T. troughtoni. Results suggest that the distributions of T. georgianus and T. troughtoni may have overlapped in north-western Queensland since at least the early Pleistocene.
King et al. (2021) Sheath-tailed bats (Chiroptera: Emballonuridae) from the early Pleistocene Rackham’s Roost Site, Riversleigh World Heritage Area, and the distribution of northern Australian emballonurid species. PeerJ 9:e10857 https://doi.org/10.7717/peerj.10857
The Doublesex/Mab-3 domain transcription factor DMD-10 regulates ASH-dependent behavioral responses
The Doublesex/Mab-3 Domain transcription factor DMD-10 is expressed in several cell types in C. elegans, including in the nervous system. We sought to investigate whether DMD-10 is required for normal neuronal function using behavioral assays. We found that mutation of dmd-10 did not broadly affect behavior. dmd-10 mutants were normal in several behavioral assays including a body bends assay for locomotion, egg laying, chemotaxis and response to gentle touch to the body. dmd-10 mutants did have defects in nose-touch responsiveness, which requires the glutamate receptor GLR-1. However, using quantitative fluorescence microscopy to measure levels of a GLR-1::GFP fusion protein in the ventral nerve cord, we found no evidence supporting a difference in the number of GLR-1 synapses or in the amount of GLR-1 present in dmd-10 mutants. dmd-10 mutants did have decreased responsiveness to high osmolarity, which, along with nose-touch, is sensed by the polymodal sensory neuron ASH. Furthermore, mutation of dmd-10 impaired behavioral response to optogenetic activation of ASH, suggesting that dmd-10 promotes neuronal signaling in ASH downstream of sensory receptor activation. Together our results suggest that DMD-10 is important in regulating the frequency of multiple ASH-dependent behavioral responses.
Durbeck et al. (2021) The Doublesex/Mab-3 domain transcription factor DMD-10 regulates ASH-dependent behavioral responses. PeerJ 9:e10892 https://doi.org/10.7717/peerj.10892
Resistance training with different repetition duration to failure: effect on hypertrophy, strength and muscle activation
Background This study investigated the effects of two 14-week resistance training protocols with different repetition duration (RD) performed to muscle failure (MF) on gains in strength and muscle hypertrophy as well as on normalized electromyographic (EMG) amplitude and force-angle relationships. Methods The left and right legs of ten untrained males were assigned to either one of the two protocols (2-s or 6-s RD) incorporating unilateral knee extension exercise. Both protocols were performed with 3–4 sets, 50–60% of the one-repetition maximum (1RM), and 3 min rest. Rectus femoris and vastus lateralis cross-sectional areas (CSA), maximal voluntary isometric contraction (MVIC) at 30o and 90o of knee flexion and 1RM performance were assessed before and after the training period. In addition, normalized EMG amplitude-angle and force-angle relationships were assessed in the 6th and 39th experimental sessions. Results The 6-s RD protocol induced larger gains in MVIC at 30o of knee angle measurement than the 2-s RD protocol. Increases in MVIC at 90o of knee angle, 1RM, rectus femoris and vastus lateralis CSA were not significant between the 2-s and 6-s RD protocols. Moreover, different normalized EMG amplitude-angle and force-angle values were detected between protocols over most of the angles analyzed. Conclusion Performing longer RD could be a more appropriate strategy to provide greater gains in isometric maximal muscle strength at shortened knee positions. However, similar maximum dynamic strength and muscle hypertrophy gains would be provided by protocols with different RD.
Lacerda et al. (2021) Resistance training with different repetition duration to failure: effect on hypertrophy, strength and muscle activation. PeerJ 9:e10909 https://doi.org/10.7717/peerj.10909
A community perspective on the concept of marine holobionts: current status, challenges, and future directions
Host-microbe interactions play crucial roles in marine ecosystems. However, we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help to describe and understand these complex systems. It posits that a host and its associated microbiota with which it interacts, form a holobiont, and have to be studied together as a coherent biological and functional unit to understand its biology, ecology, and evolution. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences. Given the connectivity and the unexplored biodiversity specific to marine ecosystems, a deeper understanding of such complex systems requires further technological and conceptual advances, e.g., the development of controlled experimental model systems for holobionts from all major lineages and the modeling of (info)chemical-mediated interactions between organisms. Here we propose that one significant challenge is to bridge cross-disciplinary research on tractable model systems in order to address key ecological and evolutionary questions. This first step is crucial to decipher the main drivers of the dynamics and evolution of holobionts and to account for the holobiont concept in applied areas, such as the conservation, management, and exploitation of marine ecosystems and resources, where practical solutions to predict and mitigate the impact of human activities are more important than ever.
Dittami et al. (2021) A community perspective on the concept of marine holobionts: current status, challenges, and future directions. PeerJ 9:e10911 https://doi.org/10.7717/peerj.10911
Towards a multi-basin SWAT model for the migration of nutrients and pesticides to Puck Bay (Southern Baltic Sea)
Background This paper analyzes the impact of changes in fertilization on crop yields and the runoff of nutrients from a small agricultural catchment (176 km2) to a shallow bay, using the SWAT model. Puck Bay is part of the Gulf of Gdansk and belongs to the Baltic Sea. The whole area of Puck Bay (364 km2) is protected (Natura 2000) yet despite this it suffers from eutrophication problems due to the relatively minimal depth and difficult water exchange. Methods The paper presents a comparison of the calculated yields and the runoff of nutrients and pesticides in the SWAT model, for a small agricultural coastal catchment. Calculations were made for 13 crop scenarios with weather data from 2011 to 2019. For each crop, an agriculture calendar was made. Two variants of fertilization were considered (autofertilization mode and according to the calendar). The nutrient runoff was calculated depending on the adopted scenario. In addition, the fate of selected pesticides was simulated. Results Depending on the crop, the annual load of NO3into the stream ranged from 0.74 to 3.65 kg ha−1. The annual load of organic phosphorous into the stream was between 0.686 and 3.64 kg ha−1. This is lower than in the majority of EU or Baltic countries. The surface runoff of dissolved Glyphosate was equal to 286 mg ha−1. The annual loads of nutrients from the catchment area are equivalent in both fertilization modes. Regardless of the selected fertilization mode, in addition to the dosage, the form of nutrients is important for the model.
Wielgat et al. (2021) Towards a multi-basin SWAT model for the migration of nutrients and pesticides to Puck Bay (Southern Baltic Sea). PeerJ 9:e10938 https://doi.org/10.7717/peerj.10938