A multi-class classification algorithm based on hematoxylin-eosin staining for neoadjuvant therapy in rectal cancer: a retrospective study
Neoadjuvant therapy (NAT) is a major treatment option for locally advanced rectal cancer. With recent advancement of machine/deep learning algorithms, predicting the treatment response of NAT has become possible using radiological and/or pathological images. However, programs reported thus far are limited to binary classifications, and they can only distinguish the pathological complete response (pCR). In the clinical setting, the pathological NAT responses are classified as four classes: (TRG0-3), with 0 as pCR, 1 as moderate response, 2 as minimal response and 3 as poor response. Therefore, the actual clinical need for risk stratification remains unmet. By using ResNet (Residual Neural Network), we developed a multi-class classifier based on Hematoxylin-Eosin (HE) images to divide the response to three groups (TRG0, TRG1/2, and TRG3). Overall, the model achieved the AUC 0.97 at 40× magnification and AUC 0.89 at 10× magnification. For TRG0, the model under 40× magnification achieved a precision of 0.67, a sensitivity of 0.67, and a specificity of 0.95. For TRG1/2, a precision of 0.92, a sensitivity of 0.86, and a specificity of 0.89 were achieved. For TRG3, the model obtained a precision of 0.71, a sensitivity of 0.83, and a specificity of 0.88. To find the relationship between the treatment response and pathological images, we constructed a visual heat map of tiles using Class Activation Mapping (CAM). Notably, we found that tumor nuclei and tumor-infiltrating lymphocytes appeared to be potential features of the algorithm. Taken together, this multi-class classifier represents the first of its kind to predict different NAT responses in rectal cancer.
Wu et al. (2023) A multi-class classification algorithm based on hematoxylin-eosin staining for neoadjuvant therapy in rectal cancer: a retrospective study. PeerJ 11:e15408 https://doi.org/10.7717/peerj.15408
Fertilizer and herbicide alter nectar and pollen quality with consequences for pollinator floral choices
Background Pollinating insects provide economically and ecologically valuable services, but are threatened by a variety of anthropogenic changes. The availability and quality of floral resources may be affected by anthropogenic land use. For example, flower-visiting insects in agroecosystems rely on weeds on field edges for foraging resources, but these weeds are often exposed to agrochemicals that may compromise the quality of their floral resources. Methods We conducted complementary field and greenhouse experiments to evaluate the: (1) effect of low concentrations of agrochemical exposure on nectar and pollen quality and (2) relationship between floral resource quality and insect visitation. We applied the same agrochemcial treatments (low concentrations of fertilizer, low concentrations of herbicide, a combination of both, and a control of just water) to seven plant species in the field and greenhouse. We collected data on floral visitation by insects in the field experiment for two field seasons and collected pollen and nectar from focal plants in the greenhouse to avoid interfering with insect visitation in the field. Results We found pollen amino acid concentrations were lower in plants exposed to low concentrations of herbicide, and pollen fatty acid concentrations were lower in plants exposed to low concentrations of fertilizer, while nectar amino acids were higher in plants exposed to low concentrations of either fertilizer or herbicide. Exposure to low fertilizer concentrations also increased the quantity of pollen and nectar produced per flower. The responses of plants exposed to the experimental treatments in the greenhouse helped explain insect visitation in the field study. The insect visitation rate correlated with nectar amino acids, pollen amino acids, and pollen fatty acids. An interaction between pollen protein and floral display suggested pollen amino acid concentrations drove insect preference among plant species when floral display sizes were large. We show that floral resource quality is sensitive to agrochemical exposure and that flower-visiting insects are sensitive to variation in floral resource quality.
Russo et al. (2023) Fertilizer and herbicide alter nectar and pollen quality with consequences for pollinator floral choices. PeerJ 11:e15452 https://doi.org/10.7717/peerj.15452
Marine aquaculture as a source of propagules of invasive fouling species
Non-indigenous species tend to colonize aquaculture installations, especially when they are near international ports. In addition to the local environmental hazard that colonizing non-indigenous species pose, they can also take advantage of local transport opportunities to spread elsewhere. In this study, we examined the risk of the spread of eight invasive fouling species that are found in mussel farms in southern Brazil. We used ensemble niche models based on worldwide occurrences of these species, and environmental variables (ocean temperature and salinity) to predict suitable areas for each species with three algorithms (Maxent, Random Forest, and Support Vector Machine). As a proxy for propagule pressure, we used the tonnage transported by container ships from Santa Catarina (the main mariculture region) that travel to other Brazilian ports. We found that ports in the tropical states of Pernambuco, Ceará, and Bahia received the largest tonnage, although far from Santa Catarina and in a different ecoregion. The ascidians Aplidium accarense and Didemnum perlucidum are known from Bahia, with a high risk of invasion in the other states. The bryozoan Watersipora subtorquata also has a high risk of establishment in Pernambuco, while the ascidian Botrylloides giganteus has a medium risk in Bahia. Paraná, a state in the same ecoregion as Santa Catarina is likely to be invaded by all species. A second state in this region, Rio Grande do Sul, is vulnerable to A. accarense, the barnacle Megabalanus coccopoma, and the mussel Mytilus galloprovincialis. Climate change is changing species latitudinal distributions and most species will gain rather than lose area in near future (by 2050). As an ideal habitat for fouling organisms and invasive species, aquaculture farms can increase propagule pressure and thus the probability that species will expand their distributions, especially if they are close to ports. Therefore, an integrated approach of the risks of both aquaculture and nautical transport equipment present in a region is necessary to better inform decision-making procedures aiming at the expansion or establishment of new aquaculture farms. The risk maps provided will allow authorities and regional stakeholders to prioritize areas of concern for mitigating the present and future spread of fouling species.
Lins et al. (2023) Marine aquaculture as a source of propagules of invasive fouling species. PeerJ 11:e15456 https://doi.org/10.7717/peerj.15456
Remimazolam versus propofol for procedural sedation: a meta-analysis of randomized controlled trials
Background To improve patient tolerability and satisfaction as well as minimize complications, procedural sedation has been widely used. Propofol is the most widely used agent for induction of anesthesia and sedation by anesthesiologists. With a different mechanism compared to propofol, remimazolam is a new short-acting GABA-A receptor agonist. It is an ester-based benzodiazepine. This meta-analysis aims to clarify the efficacy and safety of remimazolam versus propofol for procedure sedation. Methods Electronic databases were searched for randomized controlled trials (RCTs) comparing efficacy or safety of remimazolam versus propofol. Meta-analysis were conducted using RStudio with “metafor” package with random-effects model. Results A total of twelve RCTs were included in the meta-analysis. The pooled results demonstrated that patients with remimazolam for procedural sedation had lower risk of bradycardia (OR 0.28, 95% CI [0.14–0.57]), hypotension (OR 0.26, 95% CI [0.22–0.32]), and respiratory depression (OR 0.22, 95% CI [0.14–0.36]). There was no difference in the risk of developing postoperative nausea and vomiting (PONV) (OR 0.65, 95% CI [0.15–2.79]) and dizziness (OR 0.93, 95% CI [0.53–1.61]) between the remimazolam and propofol groups. Using remimazolam for procedural sedation is significantly associated with less injection pain compared to propofol (OR 0.06, 95% CI [0.03–0.13]). Regarding the sedation efficacy, there was no difference in sedation success rate or time to loss of consciousness, recover and discharge between the remimazolam and the propofol groups. Conclusions Based on our meta-analysis, patients receiving procedural sedation with remimazolam had lower risk of bradycardia, hypotension, respiratory depression and injection pain compared with propofol. On the other hand, there was no difference in sedation success rate, risk of PONV, dizziness, time to LOC, recovery and discharge between these two sedatives. PROSPERO registration number CRD42022362950
Chang et al. (2023) Remimazolam versus propofol for procedural sedation: a meta-analysis of randomized controlled trials. PeerJ 11:e15495 https://doi.org/10.7717/peerj.15495
Analysis of brain activation and wave frequencies during a sentence completion task: a paradigm used with EEG in aphasic participants
Aphasia is a language disorder that occurs after brain injury and directly affects an individual’s communication. The incidence of stroke increases with age, and one-third of people who have had a stroke develop aphasia. The severity of aphasia changes over time and some aspects of language may improve, while others remain compromised. Battery task training strategies are used in the rehabilitation of aphasics. The idea of this research is to use electroencephalography (EEG) as a non-invasive method, of electrophysiological monitoring, with a group of aphasic patients in rehabilitation process in a prevention and rehabilitation unit of the person with disabilities of the Unified Health System (SUS), of reference in the state of Bahia-Brazil. In this study, the goal is to analyze brain activation and wave frequencies of aphasic individuals during a sentence completion task, to possibly assist health professionals with the analysis of the aphasic subject’s rehabilitation and task redefinition. We adopted the functional magnetic resonance imaging (fMRI) paradigm, proposed by the American Society for Functional Neuroradiology as a reference paradigm. We applied the paradigm in the group of aphasics with preserved comprehension, right hemiparesis, and left hemisphere injured or affected by stroke. We analyzed four electrodes (F3/F4 and F7/F8) corresponding to the left/right frontal cortex. Preliminary results of this study indicate a more robust activation in the right hemisphere (average of aphasics), with a difference of approximately 14% higher in Theta and Alpha frequencies, with 8% higher in low Beta (BetaL) and with approximately 1% higher in high Beta frequency (BetaH), Gamma frequency was higher by approximately 3% in the left hemisphere of the brain. The difference in electrical activation may be revealing to us a migration of language to the non-language dominant hemisphere. We point to possible evidence suggesting that EEG may be a promising tool for monitoring the rehabilitation of the aphasic subject.
Lima et al. (2023) Analysis of brain activation and wave frequencies during a sentence completion task: a paradigm used with EEG in aphasic participants. PeerJ 11:e15518 https://doi.org/10.7717/peerj.15518
Development of a real-time PCR (qPCR) method for the identification of the invasive paddle crab Charybdis japonica (Crustacea, Portunidae)
Crabs can be transported beyond their native range via anthropogenic-mediated means such as aquarium trade, live seafood trade and shipping. Once introduced into new locations, they can establish persisting populations and become invasive, often leading to negative impacts on the recipient environment and native species. Molecular techniques are increasingly being used as complementary tools in biosecurity surveillance and monitoring plans for invasive species. Molecular tools can be particularly useful for early detection, rapid identification and discrimination of closely related species, including when diagnostic morphological characters are absent or challenging, such as early life stages, or when only part of the animal is available. In this study, we developed a species-specific qPCR assay, which targets the cytochrome c oxidase subunit 1 (CO1) region of the Asian paddle crab Charybdis japonica. In Australia, as well as many parts of the world, this species is considered invasive and routine biosecurity surveillance is conducted to reduce the risk of establishment. Through rigorous testing of tissue from target and non-target species we demonstrate that this assay is sensitive enough to detect as little as two copies per reaction and does not cross amplify with other closely related species. Field samples and environmental samples spiked with C. japonica DNA in high and low concentrations indicate that this assay is also a promising tool for detecting trace amounts of C. japonica eDNA in complex substrates, making it a useful complementary tool in marine biosecurity assessments.
Simpson et al. (2023) Development of a real-time PCR (qPCR) method for the identification of the invasive paddle crab Charybdis japonica (Crustacea, Portunidae). PeerJ 11:e15522 https://doi.org/10.7717/peerj.15522
Follow-up focused on psychological intervention initiated after intensive care unit in adult patients and informal caregivers: a systematic review and meta-analysis
Psychological dysfunction is one of the considerable health-related outcomes among critically-ill patients and their informal caregivers. Follow-up of intensive care unit (ICU) survivors has been conducted in a variety of different ways, with different timing after discharge, targets of interest (physical, psychological, social) and measures used. Of diverse ICU follow-up, the effects of follow-ups which focused on psychological interventions are unknown. Our research question was whether follow-up with patients and their informal caregivers after ICU discharge improved mental health compared to usual care. We published a protocol for this systematic review and meta-analysis in https://www.protocols.io/ (https://dx.doi.org/10.17504/protocols.io.bvjwn4pe). We searched PubMed, Cochrane Library, EMBASE, CINAHL and PsycInfo from their inception to May 2022. We included randomized controlled trials for follow-ups after ICU discharge and focused on psychological intervention for critically ill adult patients and their informal caregivers. We synthesized primary outcomes, including depression, post-traumatic stress disorder (PTSD), and adverse events using the random-effects method. We used the Grading of Recommendations Assessment, Development and Evaluation approach to rate the certainty of evidence. From the 10,471 records, we identified 13 studies (n = 3, 366) focusing on patients and four (n = 538) focusing on informal caregivers. ICU follow-up for patients resulted in little to no difference in the prevalence of depression (RR 0.89, 95% CI [0.59–1.34]; low-certainty evidence) and PTSD (RR 0.84, 95% CI [0.55–1.30]; low-certainty evidence) among patients; however, it increased the prevalence of depression (RR 1.58 95% CI [1.01–2.46]; very low-certainty evidence), PTSD (RR 1.36, 95% CI [0.91–2.03]; very low-certainty evidence) among informal caregivers. The evidence for the effect of ICU follow-up on adverse events among patients was insufficient. Eligible studies for informal caregivers did not define any adverse event. The effect of follow-ups after ICU discharge that focused on psychological intervention should be uncertain.
Yoshihiro et al. (2023) Follow-up focused on psychological intervention initiated after intensive care unit in adult patients and informal caregivers: a systematic review and meta-analysis. PeerJ 11:e15260 https://doi.org/10.7717/peerj.15260
Mineral nutrient variability of potato (Solanum tuberosum L.) tubers with different colors grown in Niksar, Kazova and Artova locations of Tokat Province, Turkey
Potato is one of the most commonly consumed non-grain staple food crops in the world therefore, the mineral nutrient content of the potato is extremely important for human nutrition. The lack of mineral nutrients causes significant health problems, thus, many of these nutrients are often taken as supplements. This study was carried out to investigate the effects of potato flesh color and location on different mineral nutrient contents under Niksar, Kazova and Artova locations in Tokat Province, Turkey, during 2013 and 2014 potato growing seasons. The experimental design in each location was randomized blocks with three replications. In this study, a total of 67 clones (including varieties and advanced breeding selections) with nine white, 10 cream, 30 light yellow, and 18 dark yellow flesh colors were used. Potatoes with cream flesh colors had the highest K (23.81 g kg−1), P (0.31 g kg−1), Mg (1.20 g kg−1), Zn (27.26 mg kg−1), Cu (8.28 mg kg−1) and Mn (7.21 mg kg−1) contents, and the lowest Ca (45.6 mg kg−1) content. The mineral contents (except K and Cu) of potatoes grown in Artova were higher compared to the other two locations. The results clearly suggested that Artova is the most suitable location to produce potatoes with a high mineral composition, and Kazova is suitable to cultivate potatoes with high K and Cu contents. In addition, the knowledge of nutrient rich potato accessions is valuable for developing biofortified potato genotypes.
Karan (2023) Mineral nutrient variability of potato (Solanum tuberosum L.) tubers with different colors grown in Niksar, Kazova and Artova locations of Tokat Province, Turkey. PeerJ 11:e15262 https://doi.org/10.7717/peerj.15262
Systemic effect of calcium silicate-based cements with different radiopacifiers-histopathological analysis in rats
Aim This in vivo study aimed to examine the systemic effects of contemporary calcium silicate cements (CSC) contain different radiopacifiers in rats. Materials & Methods Polyethylene tubes filled with BIOfactor MTA (BIO), Neo MTA Plus (NEO), MTA Repair HP (REP), Biodentine (DENT) and empty tubes (control group) were implanted into the subcutaneous tissues of 80 male Spraque Dawley rats for 7 and 30 days (n = 8). After 7 and 30 day, samples of liver and kidney tissues were submitted to histopathological analysis. Blood samples were collected to evaluate changes in hepatic and renal functions of rats. Wilcoxon and post hoc Dunn Bonferroni tests were used to compare between the 7th and 30th days in order to evaluate the histopathological data. Paired-sample t-test was used to compare laboratory values between the 7th and 30th days, ANOVA analysis and a post hoc Tukey test were used to compare values between groups (p < 0.05). Results On the 7th day, REP, BIO and NEO groups were statistically similar in kidney tissue and the degree of inflammation was found to be significantly higher in these groups compared to the control and DENT groups. On the 30th day, the degree of inflammation of the REP and NEO groups in the kidney tissue was found to be significantly higher than the control, BIO and DENT groups. Although the inflammation in the liver was moderate and mild on the 7th and 30th days, no statistically significant difference was observed between the groups. Vascular congestion was evaluated as mild and moderate in kidney and liver in all groups, and no statistically significant difference was observed between the groups. While there was no statistically significant difference between the groups in the 7th day AST, ALT and urea values, when the creatinine values were compared, the DENT and NEO groups were found to be statistically similar and significantly lower than the control group. On the 30th day, ALT values were statistically similar between the groups. The AST values of the BIO group were found to be significantly higher than the DENT group. While BIO, DENT, NEO and control groups had statistically similar urea values, the REP group was found to be significantly higher than the other groups. The creatinine value of the REP group was significantly higher than the groups other than the control group (p < 0.05). Conclusion CSCs with different radiopacifiers had similar and acceptable effects on the histological examination of the kidneys and liver systemically, and serum ALT, AST, urea, creatinine levels.
Ataş et al. (2023) Systemic effect of calcium silicate-based cements with different radiopacifiers-histopathological analysis in rats. PeerJ 11:e15376 https://doi.org/10.7717/peerj.15376
Characterization of prophages in bacterial genomes from the honey bee (Apis mellifera) gut microbiome
The gut of the European honey bee (Apis mellifera) possesses a relatively simple bacterial community, but little is known about its community of prophages (temperate bacteriophages integrated into the bacterial genome). Although prophages may eventually begin replicating and kill their bacterial hosts, they can also sometimes be beneficial for their hosts by conferring protection from other phage infections or encoding genes in metabolic pathways and for toxins. In this study, we explored prophages in 17 species of core bacteria in the honey bee gut and two honey bee pathogens. Out of the 181 genomes examined, 431 putative prophage regions were predicted. Among core gut bacteria, the number of prophages per genome ranged from zero to seven and prophage composition (the compositional percentage of each bacterial genome attributable to prophages) ranged from 0 to 7%. Snodgrassella alvi and Gilliamella apicola had the highest median prophages per genome (3.0 ± 1.46; 3.0 ± 1.59), as well as the highest prophage composition (2.58% ± 1.4; 3.0% ± 1.59). The pathogen Paenibacillus larvae had a higher median number of prophages (8.0 ± 5.33) and prophage composition (6.40% ± 3.08) than the pathogen Melissococcus plutonius or any of the core bacteria. Prophage populations were highly specific to their bacterial host species, suggesting most prophages were acquired recently relative to the divergence of these bacterial groups. Furthermore, functional annotation of the predicted genes encoded within the prophage regions indicates that some prophages in the honey bee gut encode additional benefits to their bacterial hosts, such as genes in carbohydrate metabolism. Collectively, this survey suggests that prophages within the honey bee gut may contribute to the maintenance and stability of the honey bee gut microbiome and potentially modulate specific members of the bacterial community, particularly S. alvi and G. apicola.
Bueren et al. (2023) Characterization of prophages in bacterial genomes from the honey bee (Apis mellifera) gut microbiome. PeerJ 11:e15383 https://doi.org/10.7717/peerj.15383