title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=278 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: deepAMPNet: a novel antimicrobial peptide predictor employing AlphaFold2 predicted structures and a bi-directional long short-term memory protein language model link: https://peerj.com/articles/17729 last-modified: 2024-07-19 description: BackgroundGlobal public health is seriously threatened by the escalating issue of antimicrobial resistance (AMR). Antimicrobial peptides (AMPs), pivotal components of the innate immune system, have emerged as a potent solution to AMR due to their therapeutic potential. Employing computational methodologies for the prompt recognition of these antimicrobial peptides indeed unlocks fresh perspectives, thereby potentially revolutionizing antimicrobial drug development.MethodsIn this study, we have developed a model named as deepAMPNet. This model, which leverages graph neural networks, excels at the swift identification of AMPs. It employs structures of antimicrobial peptides predicted by AlphaFold2, encodes residue-level features through a bi-directional long short-term memory (Bi-LSTM) protein language model, and constructs adjacency matrices anchored on amino acids’ contact maps.ResultsIn a comparative study with other state-of-the-art AMP predictors on two external independent test datasets, deepAMPNet outperformed in accuracy. Furthermore, in terms of commonly accepted evaluation matrices such as AUC, Mcc, sensitivity, and specificity, deepAMPNet achieved the highest or highly comparable performances against other predictors.ConclusiondeepAMPNet interweaves both structural and sequence information of AMPs, stands as a high-performance identification model that propels the evolution and design in antimicrobial peptide pharmaceuticals. The data and code utilized in this study can be accessed at https://github.com/Iseeu233/deepAMPNet. creator: Fei Zhao creator: Junhui Qiu creator: Dongyou Xiang creator: Pengrui Jiao creator: Yu Cao creator: Qingrui Xu creator: Dairong Qiao creator: Hui Xu creator: Yi Cao uri: https://doi.org/10.7717/peerj.17729 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhao et al. title: Nocturnal substrate association of four coral reef fish groups (parrotfishes, surgeonfishes, groupers and butterflyfishes) in relation to substrate architectural characteristics link: https://peerj.com/articles/17772 last-modified: 2024-07-19 description: Although numerous coral reef fish species utilize substrates with high structural complexities as habitats and refuge spaces, quantitative analysis of nocturnal fish substrate associations has not been sufficiently examined yet. The aims of the present study were to clarify the nocturnal substrate associations of 17 coral reef fish species (nine parrotfish, two surgeonfish, two grouper and four butterflyfish) in relation to substrate architectural characteristics. Substrate architectural characteristics were categorized into seven types: (1) eave-like space, (2) large inter-branch space, (3) overhang by protrusion of fine branching structure, (4) overhang by coarse structure, (5) uneven structure without large space or overhang, (6) flat and (7) macroalgae. Overall, fishes were primarily associated with three architectural characteristics (eave-like space, large inter-branch space and overhang by coarse structure). The main providers of these three architectural characteristics were tabular and corymbose Acropora, staghorn Acropora, and rock. Species-specific significant positive associations with particular architectural characteristics were found as follows. For the nine parrotfish species, Chlorurus microrhinos with large inter-branch space and overhang by coarse structure; Ch. spilurus with eave-like space and large inter-branch space; Hipposcarus longiceps with large inter-branch space; Scarus ghobban with overhang by coarse structure; five species (Scarus forsteni, S. niger, S. oviceps, S. rivulatus and S. schlegeli) with eave-like space. For the two surgeonfish species, Naso unicornis with overhang by coarse structure; N. lituratus with eave-like space. For the two grouper species, Plectropomus leopardus with eave-like space; Epinephelus ongus with overhang by coarse structure. For the four butterflyfish species, Chaetodon trifascialis with eave-like space and large inter-branch space; C. lunulatus and C. ephippium with large inter-branch space; C. auriga showed no significant associations with any architectural characteristics. Four species (Ch. microrhinos, H. longiceps, S. niger and N. unicornis) also showed clear variations in substrate associations among the different fish size classes. Since parrotfishes, surgeonfishes and groupers are main fisheries targets in coral reefs, conservation and restoration of coral species that provide eave-like space (tabular and corymbose Acropora) and large inter-branch space (staghorn Acropora) as well as hard substrates with coarse structure that provide overhang (rock) should be considered for effective fisheries management in coral reefs. For butterflyfishes, coral species that provide eave-like space (tabular Acropora) and large inter-branch space (staghorn Acropora) should also be conserved and restored for provision of sleeping sites. creator: Atsushi Nanami uri: https://doi.org/10.7717/peerj.17772 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Nanami title: Natural grazing by horses and cattle promotes bird diversity in a restored European alluvial grassland link: https://peerj.com/articles/17777 last-modified: 2024-07-19 description: ContextA challenge in grassland conservation is to maintain both the openness and the heterogeneity of the habitat to support the diversity of their animal communities, including birds—a taxon that is known to be sensitive to disturbance. An increasingly used management tool in European grassland conservation, especially in rewilding projects, is grazing by large herbivores such as horses and cattle. These grazers are believed to create and maintain patchy landscapes that promote diversity and richness of other species, but their influence on birds is often debated by conservationists, who raise concerns about the impact of disturbance by the grazers.ObjectivesOur aim was to examine the relationship between the abundance and species richness of birds across four foraging guilds and the area utilization patterns of Highland cattle and Konik horses in an alluvial grassland in France. We also aimed to examine the influence of land cover and season on the spatial distribution, including abundance and species richness, of different bird guilds present in the grazed area.MethodsWe used GPS-collars on all grazers and recorded their positions on an hourly basis over a study period of 1.5 years, assessing patterns of area usage. We counted birds weekly along three transects to describe their distribution within the grazed area and carried out land-cover surveys to describe the habitat. To assess how species richness and abundance of birds of different guilds were related to grazer density, season, and habitat characteristics, we used GAMM models in a spatially explicit framework. We also compared bird numbers at our main study site with a nearby non-grazed control area.ResultsThe number of birds in the grazed area was about twice the number in the non-grazed control area. Within the grazed area, the abundance of open-area foraging birds increased with increasing grazer density. The number of woodland-foraging birds was also positively correlated with grazer density but less so than open-area foraging birds. The number of individuals in the aerial and wetland bird guilds was not correlated with the density of grazers. Most bird species and individuals were observed on open landscapes scattered with woody patches and waterbodies, and on areas with moderate grazer density.ConclusionsLow-intensity grazing represents a potentially important management tool in creating heterogeneity in alluvial grasslands, thereby promoting suitable habitat for a diverse assemblage of bird species. creator: Lilla Lovász creator: Fränzi Korner-Nievergelt creator: Valentin Amrhein uri: https://doi.org/10.7717/peerj.17777 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Lovász et al. title: Revolutionizing CAD/CAM-based restorative dental processes and materials with artificial intelligence: a concise narrative review link: https://peerj.com/articles/17793 last-modified: 2024-07-19 description: Artificial intelligence (AI) is increasingly prevalent in biomedical and industrial development, capturing the interest of dental professionals and patients. Its potential to improve the accuracy and speed of dental procedures is set to revolutionize dental care. The use of AI in computer-aided design/computer-aided manufacturing (CAD/CAM) within the restorative dental and material science fields offers numerous benefits, providing a new dimension to these practices. This study aims to provide a concise overview of the implementation of AI-powered technologies in CAD/CAM restorative dental procedures and materials. A comprehensive literature search was conducted using keywords from 2000 to 2023 to obtain pertinent information. This method was implemented to guarantee a thorough investigation of the subject matter. Keywords included; “Artificial Intelligence”, “Machine Learning”, “Neural Networks”, “Virtual Reality”, “Digital Dentistry”, “CAD/CAM”, and “Restorative Dentistry”. Artificial intelligence in digital restorative dentistry has proven to be highly beneficial in various dental CAD/CAM applications. It helps in automating and incorporating esthetic factors, occlusal schemes, and previous practitioners’ CAD choices in fabricating dental restorations. AI can also predict the debonding risk of CAD/CAM restorations and the compositional effects on the mechanical properties of its materials. Continuous enhancements are being made to overcome its limitations and open new possibilities for future developments in this field. creator: Hanin E. Yeslam creator: Nadine Freifrau von Maltzahn creator: Hani M. Nassar uri: https://doi.org/10.7717/peerj.17793 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yeslam et al. title: Acute clomipramine exposure elicits dose-dependent surfacing behavior in adult zebrafish (Danio rerio) link: https://peerj.com/articles/17803 last-modified: 2024-07-19 description: Chronic treatment with clomipramine, a tricyclic antidepressant drug, reduces symptoms of obsessive-compulsive disorder (OCD) and can influence the activity of the hypothalamic-pituitary-adrenal axis. However, little is known regarding the effects of acute clomipramine on the immediate expression of stress responses. Serotonergic drugs can elicit surfacing, a behavioral profile potentially related to toxicity in fish, although surfacing has not yet been observed after clomipramine exposure. The present study investigated the impact of acute exposure to clomipramine on basal and stress-induced behaviors in the novel tank test and cortisol levels in mixed-sex, wild-type, adult zebrafish (Danio rerio). The findings show clomipramine-exposed groups (regardless of stress exposure) spent much more time in the top of the novel tank and had significantly less overall motor activity in the behavioral task compared to the fish not exposed to the drug. Then, the dose-dependent effects of acute clomipramine on activity in the surface of the novel tank (top third of the top half) were investigated further. Clomipramine dose-dependently increased surface-dwelling and elicited a dose-dependent hypoactivity in overall motor behavior. There were no statistically significant differences in whole-body cortisol levels in either experiment. Like other serotonin-acting drugs, clomipramine strongly elicited surface-dwelling and depressed motor behavior in adult zebrafish. Additional testing is needed to elucidate whether surfacing represents a toxic state and how serotonin regulates surfacing. creator: Adeel Shafiq creator: Mercedes Andrade creator: Richanne Matthews creator: Alexandria Umbarger creator: Maureen L. Petrunich-Rutherford uri: https://doi.org/10.7717/peerj.17803 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Shafiq et al. title: Bioprospecting of soil-borne microorganisms and chemical dereplication of their anti-microbial constituents with the aid of UPLC-QTOF-MS and molecular networking approach link: https://peerj.com/articles/17364 last-modified: 2024-07-18 description: Due to the emergence of drug-resistant microorganisms, the search for broad-spectrum antimicrobial compounds has become extremely crucial. Natural sources like plants and soils have been explored for diverse metabolites with antimicrobial properties. This study aimed to identify microorganisms from agricultural soils exhibiting antimicrobial effects against known human pathogens, and to highlight the chemical space of the responsible compounds through the computational metabolomics-based bioprospecting approach. Herein, bacteria were extracted from soil samples and their antimicrobial potential was measured via the agar well diffusion method. Methanolic extracts from the active bacteria were analyzed using the liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) technique, and the subsequent data was further analyzed through molecular networking approach which aided in identification of potential anti-microbial compounds. Furthermore, 16S rRNA gene sequencing enabled identification of the active bacterial isolates, where isolate 1 and 2 were identified as strains of Bacillus pumilus, whilst isolate 3 was found to be Bacillus subtilis. Interestingly, isolate 3 (Bacillus subtilis) displayed wide-ranging antimicrobial activity against the tested human pathogens. Molecular networking revealed the presence of Diketopiperazine compounds such as cyclo (D-Pro-D-Leu), cyclo (L-Tyr-L-Pro), cyclo (L-Pro-D-Phe), and cyclo (L-Pro-L-Val), alongside Surfactin C, Surfactin B, Pumilacidin E, and Isarrin D in the Bacillus strains as the main anti-microbial compounds. The application of the molecular networking approach represents an innovation in the field of bio-guided bioprospection of microorganisms and has proved to be an effective and feasible towards unearthing potent antimicrobial compounds. Additionally, the (computational metabolomics-based) approach accelerates the discovery of bioactive compounds and isolation of strains which offer a promising avenue for discovering new clinical antimicrobials. Finally, soil microbial flora could serve an alternative source of anti-microbial compounds which can assist in the fight against emergence of multi-drug resistance bacterial pathogens. creator: Adivhaho Khwathisi creator: Ntakadzeni Edwin Madala creator: Afsatou Ndama Traore creator: Amidou Samie uri: https://doi.org/10.7717/peerj.17364 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Khwathisi et al. title: Automated identification and segmentation of urine spots based on deep-learning link: https://peerj.com/articles/17398 last-modified: 2024-07-18 description: Micturition serves an essential physiological function that allows the body to eliminate metabolic wastes and maintain water-electrolyte balance. The urine spot assay (VSA), as a simple and economical assay, has been widely used in the study of micturition behavior in rodents. However, the traditional VSA method relies on manual judgment, introduces subjective errors, faces difficulty in obtaining appearance time of each urine spot, and struggles with quantitative analysis of overlapping spots. To address these challenges, we developed a deep learning-based approach for the automatic identification and segmentation of urine spots. Our system employs a target detection network to efficiently detect each urine spot and utilizes an instance segmentation network to achieve precise segmentation of overlapping urine spots. Compared with the traditional VSA method, our system achieves automated detection of urine spot area of micturition in rodents, greatly reducing subjective errors. It accurately determines the urination time of each spot and effectively quantifies the overlapping spots. This study enables high-throughput and precise urine spot detection, providing important technical support for the analysis of urination behavior and the study of the neural mechanism underlying urination. creator: Xin Fan creator: Jun Li creator: Junan Yan uri: https://doi.org/10.7717/peerj.17398 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Fan et al. title: Intraspecific variation in the pterosaur Rhamphorhynchus muensteri—implications for flight and socio-sexual signaling link: https://peerj.com/articles/17524 last-modified: 2024-07-18 description: Pterosaurs were the first powered flying vertebrates, with a fossil record that stretches back to about 230 million years before present. Most species are only known from one to three specimens, which are most often fragmentary. However, Rhamphorhynchus muensteri is known from numerous excellent specimens, including multiple specimens with soft tissue preservation. As such, Rhamphorhynchus muensteri is one of the only pterosaurs amenable to analysis for intraspecific variation. It has been previously predicted that elements directly involved in the flight apparatus, such as those of the forelimb, will be more highly constrained in their proportions than other parts of the skeleton. We investigated the degree of variation seen in elements and body parts of Rhamphorhynchus, which represents the best model system among pterosaurs for testing these expectations of intraspecific variation. We recover evidence for high levels of constraint throughout the appendicular and axial elements (head, neck, torso, tail, forelimbs, hindlimbs), suggesting that all were important for flight. We further find that tail variation increases among the largest specimens, suggesting reduced constraint and/or stronger sexual selection on the tail in more mature individuals. creator: Michael B. Habib creator: David WE. Hone uri: https://doi.org/10.7717/peerj.17524 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Habib and Hone title: The prognostic role of lymphocyte-to-monocyte ratio in patients with resectable pancreatic cancer: a systematic review and meta-analysis link: https://peerj.com/articles/17585 last-modified: 2024-07-18 description: ObjectivesThis systematic review and meta-analysis examined whether the lymphocyte-to-monocyte ratio (LMR) can serve as an indicator for predicting the prognosis of patients with resectable pancreatic cancer.Patients and MethodsThis meta-analysis was registered with PROSPERO: CRD42023461260. A systematic literature search was conducted in the PubMed, Embase, Cochrane, and Web of Science databases up to September 2023 to assess whether LMR can predict the prognosis of patients with resectable pancreatic cancer. The outcomes measured included subgroup analyses of overall survival (OS) with hazard ratios (HR) and confidence intervals of geographical region, patient population, and LMR threshold. A sensitivity analysis was also performed for OS and HR and confidence intervals were calculated for recurrence-free survival (RFS).ResultsA total of 14 eligible articles, comprising 4,019 patients, were included in the comprehensive analysis. The results of this comprehensive analysis indicate that LMR is a robust predictor of OS, demonstrating strong prognostic significance (HR = 0.55, 95% CI [0.44–0.69], I2 = 79%, P < 0.00001). This predictive significance extended to various types of pancreatic cancer, such as pancreatic ductal adenocarcinoma (HR = 0.73, 95% CI [0.57–0.93], I2 = 46%, P = 0.01), pancreatic neuroendocrine neoplasms (HR = 0.81, 95% CI [0.66–0.99], P = 0.04) and other subtypes (HR = 0.40, 95% CI [0.22–0.72], I2 = 89%, P < 0.00001), but not to pancreatic head cancer (HR = 0.46, 95% CI [0.16–1.13], I2 = 59%, P = 0.12). LMR retained its predictive value across different regions, including Asia (HR = 0.62, 95% CI [0.47–0.76], I2 = 68%, P < 0.0001), Europe (HR = 0.78, 95% CI [0.67–0.91], I2 = 0%, P = 0.002), and the Americas (HR = 0.14, 95% CI [0.08–0.24], I2 = 0%, P < 0.00001). Notably, both LMR cut-off values greater than or equal to three (HR = 0.62, 95% CI [0.47–0.82], I2 = 67%, P = 0.0009) and less than three (HR = 0.47, 95% CI [0.32–0.69], I2 = 85%, P = 0.0001) exhibited prognostic significance. The sensitivity analysis for OS confirmed the strong predictive value of LMR, whereas LMR did not exhibit predictive significance for RFS (HR = 0.35, 95% CI [0.09–1.32], I2 = 95%, P = 0.12). In both subgroups categorized by Newcastle-Ottawa Scale (NOS) scores of ≥7 (HR = 0.66, 95% CI [0.54–0.80], I2 = 53%, P = 0.04) and <7 (HR = 0.41, CI [0.23–0.72], I2 = 89%, P < 0.00001), LMR was demonstrated to have predictive value.ConclusionDespite the observed heterogeneity and potential biases in the included studies, the findings of this study suggest that LMR may serve as a valuable predictor of OS in patients with resectable pancreatic cancer. creator: Haipeng Li creator: Shang Peng creator: Ran An creator: Nana Du creator: Huan Wu creator: Xiangcheng Zhen creator: Yuanzhi Gao creator: Zhenghong Li creator: Jingting Min uri: https://doi.org/10.7717/peerj.17585 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: A multi-ethnic proteomic profiling analysis in Alzheimer’s disease identifies the disparities in dysregulation of proteins and pathogenesis link: https://peerj.com/articles/17643 last-modified: 2024-07-18 description: BackgroundAlzheimer’s disease (AD) is the most common type of dementia that affects the elderly population. Lately, blood-based proteomics have been intensively sought in the discovery of AD biomarkers studies due to the capability to link external environmental factors with the development of AD. Demographic differences have been shown to affect the expression of the proteins in different populations which play a vital role in the degeneration of cognitive function.MethodIn this study, a proteomic study focused on Malaysian Chinese and Malay prospects was conducted. Differentially expressed proteins (DEPs) in AD patients and normal controls for Chinese and Malays were identified. Functional enrichment analysis was conducted to further interpret the biological functions and pathways of the DEPs. In addition, a survey investigating behavioural practices among Chinese and Malay participants was conducted to support the results from the proteomic analysis.ResultThe variation of dysregulated proteins identified in Chinese and Malay samples suggested the disparities of pathways involved in this pathological condition for each respective ethnicity. Functional enrichment analysis supported this assumption in understanding the protein-protein interactions of the identified protein signatures and indicate that differentially expressed proteins identified from the Chinese group were significantly enriched with the functional terms related to Aβ/tau protein-related processes, oxidative stress and inflammation whereas neuroinflammation was associated with the Malay group. Besides that, a significant difference in sweet drinks/food intake habits between these two groups implies a relationship between sugar levels and the dysregulation of protein APOA4 in the Malay group. Additional meta-analysis further supported the dysregulation of proteins TF, AHSG, A1BG, APOA4 and C4A among AD groups.ConclusionThese findings serve as a preliminary understanding in the molecular and demographic studies of AD in a multi-ethnic population. creator: Mei Sze Tan creator: Phaik-Leng Cheah creator: Ai-Vyrn Chin creator: Lai-Meng Looi creator: Siow-Wee Chang uri: https://doi.org/10.7717/peerj.17643 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Tan et al.