bluuebunny/crossref_metadata_2025 huggingface dataset:
A two-stage distributed optimization method for home energy management systems via multi-modal data-driven algorithm
Authors: Cui Feifei , An Dou , Zhao Yingzhuo
Published: November 2023

The home energy management system (HEMS), which utilizes multi-modal data from multiple sensors to generate the knowledge about decision making, is essential to the optimization of home energy management efficiency. Load scheduling based on HEMS can improve the utilization efficiency of multi-modal data and derived knowledge, achieve power supply-demand balance, and reduce users’ electricity costs. This paper proposes a distributed load optimization scheduling method for the load scheduling problem in HEMS based on multi-modal data-driven algorithm. Additionally, a two-stage data-driven optimization method is proposed, including a first-stage optimization model based on minimizing electricity costs and a second-stage optimization model based on minimizing system load fluctuations. In the first stage, cost self-optimization is performed based on energy storage devices. In the second stage, a load optimization instruction is issued by the control center, and each user optimizes the load fluctuations based on the system load data. Compared to centralized control methods, this approach reduces the computational overhead of the control center. Finally, simulation experiments based on load scheduling in the HEMS are conducted. The results of the first optimization stage show that when the battery capacity integrated into the system increases from 3.68 kWh to 6.68 kWh, user costs can be reduced from 57.572 cents to 42.064 cents. It is not only evident that the proposed method can effectively save users on electricity costs, but the introduction of larger capacity batteries also lowers these costs. The second stage of load fluctuation optimization results show that the proposed method can effectively optimize the usage data of a group of users and decrease the absolute peak-valley difference by 8.8%.
A quantitative framework to evaluate urban ecological resilience: broadening understanding through multi-attribute perspectives
Authors: Wang Yongyang , Cai Yanpeng , Xie Yulei , Zhang Pan , Chen Lei
Published: November 2023

Intensive human and economic activities in urban areas have had adverse effects on local resources and ecology, leading to a decline in ecological resilience. Enhancing ecological resilience is crucial for improving the urban ecosystem's ability to withstand and recover from external risks. However, quantitative research on urban ecological resilience remains somewhat ambiguous, with many studies lacking comprehensive assessment methods from multiple perspectives. In this study, we established a comprehensive framework to assess urban ecological resilience based on four regime attributes. The study's results indicated the following key findings: The average urban ecological resilience value exhibited a trend of initially declining and then recovering. Cities proposed different approaches when considering and managing social and ecological relationships during the development process. A significant correlation between urbanization levels and ecological resilience was observed, with urban ecological resilience increasing in areas with low urbanization levels and sharply decreasing in areas with high urbanization levels. The findings from this study provide a specific theoretical foundation for decision-makers involved in urban planning and development strategies.
Tree seedling shade tolerance arises from interactions with microbes and is mediated by functional traits
Authors: Wood Katherine E. A. , Kobe Richard K. , McCarthy-Neumann Sarah
Published: November 2023

Shade tolerance is a central concept in forest ecology and strongly influences forest community dynamics. However, the plant traits and conditions conferring shade tolerance are yet to be resolved. We propose that shade tolerance is shaped not only by responses to light but also by a species’ defense and recovery functional traits, soil microbial communities, and interactions of these factors with light availability. We conducted a greenhouse experiment for three temperate species in the genus Acer that vary in shade tolerance. We grew newly germinated seedlings in two light levels (2% and 30% sun) and controlled additions of microbial filtrates using a wet-sieving technique. Microbial filtrate treatments included: <20 µm, likely dominated by pathogenic microbes; 40-250 µm, containing arbuscular mycorrhizal fungi (AMF); combination, including both filtrate sizes; and sterilized combination. We monitored survival for nine weeks and measured fine root AMF colonization, hypocotyl phenolics, stem lignin, and stem+root nonstructural carbohydrates (NSC) at three-week intervals. We found that differences in seedling survival between low and high light only occurred when microbes were present. AMF colonization, phenolics, and NSC generally increased with light. Phenolics were greater with <20 µm microbial filtrate, suggesting that soil-borne pathogens may induce phenolic production; and NSC was greater with 40-250 µm filtrate, suggesting that mycorrhizal fungi may induce NSC production. Across species, microbe treatments, and light availability, survival increased as phenolics and NSC increased. Therefore, shade tolerance may be explained by interactions among soil-borne microbes, seedling traits, and light availability, providing a more mechanistic and trait-based explanation of shade tolerance and thus forest community dynamics.
Water, power, homeland: restoring and re-storying the Eklutna River
Authors: Middleton Manning Beth Rose
Published: November 2023

Beginning in 1929, the Eklutna River in Southcentral Alaska was largely de-watered for hydropower production without the consent of the Eklutna Dena'ina. The hydropower projects were implemented in two waves—first in 1929 by a private developer and then in 1951 by the Bureau of Reclamation. In 1991, a Fish and Wildlife Agreement between the utilities, the State of Alaska, and federal agencies called for study of the impacts of the hydroelectric projects on fish and wildlife, and development of a mitigation plan by 2024. This paper examines the process and partners involved in advocating for restoration of the Eklutna, building on the documented importance of tribal leadership in dam removals, and centering three factors that are underrepresented in the current analyses of alternative management approaches to the Eklutna: the context of the Eklutna as a Dena'ina place; the egregious and ongoing Indigenous environmental injustice of seizing Eklutna water; and the praxis of Dena'ina-led efforts to find a balance of uses of this highly valued Dena'ina watershed.
Study on mechanical properties and microstructure of steel-polypropylene fiber coal gangue concrete
Authors: Li Jiuyang , Chen Li , Luo Jingwei , Zhu Yuepeng , Fan Xinmei , Hu Guangchao
Published: November 2023

Incorporating coal gangue into the concrete matrix can realize the utilization of solid waste and reduce the use of natural aggregate. To improve the mechanical properties of coal gangue concrete, this paper designs four-level and four-factor orthogonal tests with coal gangue ceramide substitution rate, coal gangue ceramide sand substitution rate, steel fiber content, and polypropylene fiber content as independent variables. Through multidimensional data analysis of the test results, The main and secondary factors of compressive strength of hybrid fiber coal gangue concrete from strong to weak are the replacement rate of coal gangue ceramic sand, the replacement rate of coal gangue ceramic grain, the content of steel fiber and the content of polypropylene fiber. The optimal content is 30% coal gangue ceramic particle, 25∼30% coal gangue ceramic sand, 0.75∼1% steel fiber, and 0.2% polypropylene fiber. The grey prediction model GM (1, 5) is obtained, which can predict the concrete strength well within the range selected in this paper. The influence of fiber and coal gangue on the microstructure was studied by scanning electron microscopy, and the influence law of interfacial transition zone on the strength of concrete was explored, which provided a theoretical basis for the study of solid waste utilization of coal gangue.
The man, the plant, and the insect: shooting host specificity determinants in Serratia marcescens pangenome
Authors: Shikov Anton E. , Merkushova Anastasiya V. , Savina Iuliia A. , Nizhnikov Anton A. , Antonets Kirill S.
Published: November 2023

Introduction

Serratia marcescens is most commonly known as an opportunistic pathogen causing nosocomial infections. It, however, was shown to infect a wide range of hosts apart from vertebrates such as insects or plants as well, being either pathogenic or growth-promoting for the latter. Despite being extensively studied in terms of virulence mechanisms during human infections, there has been little evidence of which factors determine S. marcescens host specificity. On that account, we analyzed S. marcescens pangenome to reveal possible specificity factors.

Methods

We selected 73 high-quality genome assemblies of complete level and reconstructed the respective pangenome and reference phylogeny based on core genes alignment. To find an optimal pipeline, we tested current pangenomic tools and obtained several phylogenetic inferences. The pangenome was rich in its accessory component and was considered open according to the Heaps’ law. We then applied the pangenome-wide associating method (pan-GWAS) and predicted positively associated gene clusters attributed to three host groups, namely, humans, insects, and plants.

Results

According to the results, significant factors relating to human infections included transcriptional regulators, lipoproteins, ABC transporters, and membrane proteins. Host preference toward insects, in its turn, was associated with diverse enzymes, such as hydrolases, isochorismatase, and N-acetyltransferase with the latter possibly exerting a neurotoxic effect. Finally, plant infection may be conducted through type VI secretion systems and modulation of plant cell wall synthesis. Interestingly, factors associated with plants also included putative growth-promoting proteins like enzymes performing xenobiotic degradation and releasing ammonium irons. We also identified overrepresented functional annotations within the sets of specificity factors and found that their functional characteristics fell into separate clusters, thus, implying that host adaptation is represented by diverse functional pathways. Finally, we found that mobile genetic elements bore specificity determinants. In particular, prophages were mainly associated with factors related to humans, while genetic islands-with insects and plants, respectively.

Discussion

In summary, functional enrichments coupled with pangenomic inferences allowed us to hypothesize that the respective host preference is carried out through distinct molecular mechanisms of virulence. To the best of our knowledge, the presented research is the first to identify specific genomic features of S. marcescens assemblies isolated from different hosts at the pangenomic level.
A self-amplifying RNA vaccine provides protection in a murine model of bubonic plague
Authors: Shattock Robin John , Andrianaivoarimanana Voahangy , McKay Paul F. , Randriantseheno Lovasoa Nomena , Murugaiah Valarmathy , Samnuan K. , Rogers Paul , Tregoning John S. , Rajerison Minoarisoa , Moore Kristoffer M. , Laws Thomas Robert , Williamson E. Diane
Published: November 2023

Mice were immunized with a combination of self-amplifying (sa) RNA constructs for the F1 and V antigens of Yersinia pestis at a dose level of 1 μg or 5 μg or with the respective protein sub-units as a reference vaccine. The immunization of outbred OF1 mice on day 0 and day 28 with the lowest dose used (1 μg) of each of the saRNA constructs in lipid nanoparticles protected 5/7 mice against subsequent sub-cutaneous challenge on day 56 with 180 cfu (2.8 MLD) of a 2021 clinical isolate of Y. pestis termed 10-21/S whilst 5/7 mice were protected against 1800cfu (28MLD) of the same bacteria on day 56. By comparison, only 1/8 or 1/7 negative control mice immunized with 10 μg of irrelevant haemagglutin RNA in lipid nanoparticles (LNP) survived the challenge with 2.8 MLD or 28 MLD Y. pestis 10-21/S, respectively. BALB/c mice were also immunized with the same saRNA constructs and responded with the secretion of specific IgG to F1 and V, neutralizing antibodies for the V antigen and developed a recall response to both F1 and V. These data represent the first report of an RNA vaccine approach using self-amplifying technology and encoding both of the essential virulence antigens, providing efficacy against Y. pestis. This saRNA vaccine for plague has the potential for further development, particularly since its amplifying nature can induce immunity with less boosting. It is also amenable to rapid manufacture with simpler downstream processing than protein sub-units, enabling rapid deployment and surge manufacture during disease outbreaks.
Xerophilic fungi contaminating historically valuable easel paintings from Slovenia
Authors: Zalar Polona , Graf Hriberšek Daša , Gostinčar Cene , Breskvar Martin , Džeroski Sašo , Matul Mojca , Novak Babič Monika , Čremožnik Zupančič Jerneja , Kujović Amela , Gunde-Cimerman Nina , Kavkler Katja
Published: November 2023

Historically valuable canvas paintings are often exposed to conditions enabling microbial deterioration. Painting materials, mainly of organic origin, in combination with high humidity and other environmental conditions, favor microbial metabolism and growth. These preconditions are often present during exhibitions or storage in old buildings, such as churches and castles, and also in museum storage depositories. The accumulated dust serves as an inoculum for both indoor and outdoor fungi. In our study, we present the results on cultivable fungi isolated from 24 canvas paintings, mainly exhibited in Slovenian sacral buildings, dating from the 16th to 21st centuries. Fungi were isolated from the front and back of damaged and undamaged surfaces of the paintings using culture media with high- and low-water activity. A total of 465 isolates were identified using current taxonomic DNA markers and assigned to 37 genera and 98 species. The most abundant genus was Aspergillus, represented by 32 species, of which 9 xerophilic species are for the first time mentioned in contaminated paintings. In addition to the most abundant xerophilic A. vitricola, A. destruens, A. tardicrescens, and A. magnivesiculatus, xerophilic Wallemia muriae and W. canadensis, xerotolerant Penicillium chrysogenum, P. brevicompactum, P. corylophilum, and xerotolerant Cladosporium species were most frequent. When machine learning methods were used to predict the relationship between fungal contamination, damage to the painting, and the type of material present, proteins were identified as one of the most important factors and cracked paint was identified as a hotspot for fungal growth. Aspergillus species colonize paintings regardless of materials, while Wallemia spp. can be associated with animal fat. Culture media with low-water activity are suggested in such inventories to isolate and obtain an overview of fungi that are actively contaminating paintings stored indoors at low relative humidity.
Stability of soil bacteria in undisturbed soil and continuous maize cultivation in Northern Thailand
Authors: Arunrat Noppol , Sansupa Chakriya , Sereenonchai Sukanya , Hatano Ryusuke
Published: November 2023

Rotational shifting cultivation (RSC) in Northern Thailand serves the dual purpose of ensuring food security and meeting economic goals through maize cultivation. However, the research question remains: Does the dynamics of soil bacterial communities differ between maize monoculture and RSC fields with continuous fallow throughout the season? Therefore, the objective of this study was to investigate and compare the variation of soil bacterial communities in maize monoculture and fallow RSC fields. A continuous 5-year fallow field (undisturbed soil; CF-5Y) and a continuous 5-year maize cultivation field (M-5Y) in Mae Chaem District, Chiang Mai Province, Northern Thailand, were selected due to their similarities in microclimate, topography, and the 5-year duration of different field activities. Over the span of a year, we collected soil samples from the surface layer (0–2 cm depth) at both sites. These collections occurred at 3-month intervals, starting from March 2022 (summer season) and followed by June (rainy season), September (rainy season), December (winter season), and March 2023 (summer season). Soil bacterial diversity and composition were analyzed using 16S rRNA gene-based metagenomic analysis. The results found that undisturbed soil over a 5-year period exhibited more stability in the richness and diversity of bacteria across seasons compared with M-5Y. Notably, fertilizer application and tillage practices in M-5Y can enhance both the diversity and richness of soil bacteria. In terms of bacterial abundance, Proteobacteria prevailed in CF-5Y, while Actinobacteria dominated in M-5Y. At the genus level, Candidatus Udaeobacter dominated during the summer and winter seasons in both CF-5Y and M-5Y sites. Interestingly, during the rainy season, the dominant genus shifted to Bacillus in both CF-5Y and M-5Y fields. The soil bacterial community in M-5Y was strongly influenced by organic matter (OM) and organic carbon (OC). In contrast, in CF-5Y, there was no correlation between soil properties and the soil bacterial community, likely due to the lower variation in soil properties across seasons. β-Glucosidase was the dominant enzyme in both CF-5Y and M-5Y sites, and it showed a positive correlation with OM and OC. Further studies should continue to investigate soil bacteria dynamics, considering the changes in land management practices.
Lipidomic landscape of lipokines in adipose tissue derived extracellular vesicles
Authors: Zhang Yan , Dong Tingyan , Wang Muyao
Published: November 2023

Introduction: Adipose tissue-derived extracellular vesicles (EVs-AT) are recognized as critical mediators of metabolic alterations in obesity-related diseases. However, few studies have focused on the role of lipids within EVs-AT in the development of obesity-related diseases.

Methods: In this study, we performed a targeted lipidomic analysis to compare the lipidome of EVs secreted by inguinal white adipose tissue (EVs-iWAT), epididymal white adipose tissue (EVs-eWAT), and interscapular brown adipose tissue (EVs-BAT) in lean and obese mice.

Results: We uncovered a comprehensive lipidomic map, revealing the diversity and specific lipid sorting in EVs-iWAT, EVs-eWAT, and EVs-BAT in obesity. Biological function analyses suggested that lipids encapsulated within EVs-AT of obese individuals might correlate with metabolism, pro-inflammatory response, and insulin resistance. These effects were particularly pronounced in EVs-eWAT and EVs-BAT.

Conclusion: Our findings indicated that EVs-AT serves as novel carriers for lipokines, thereby mediating the biological functions of EVs-AT. This study holds promise for the identification of new biomarkers for obesity-related diseases and the development of new strategies to combat metabolic diseases.
Sex differences in the neuronal transcriptome and synaptic mitochondrial function in the cerebral cortex of a multiple sclerosis model
Authors: Itoh Noriko , Itoh Yuichiro , Stiles Linsey , Voskuhl Rhonda
Published: November 2023

Introduction

Multiple sclerosis (MS) affects the cerebral cortex, inducing cortical atrophy and neuronal and synaptic pathology. Despite the fact that women are more susceptible to getting MS, men with MS have worse disability progression. Here, sex differences in neurodegenerative mechanisms are determined in the cerebral cortex using the MS model, chronic experimental autoimmune encephalomyelitis (EAE).

Methods

Neurons from cerebral cortex tissues of chronic EAE, as well as age-matched healthy control, male and female mice underwent RNA sequencing and gene expression analyses using RiboTag technology. The morphology of mitochondria in neurons of cerebral cortex was assessed using Thy1-CFP-MitoS mice. Oxygen consumption rates were determined using mitochondrial respirometry assays from intact as well as permeabilized synaptosomes.

Results

RNA sequencing of neurons in cerebral cortex during chronic EAE in C57BL/6 mice showed robust differential gene expression in male EAE compared to male healthy controls. In contrast, there were few differences in female EAE compared to female healthy controls. The most enriched differential gene expression pathways in male mice during EAE were mitochondrial dysfunction and oxidative phosphorylation. Mitochondrial morphology in neurons showed significant abnormalities in the cerebral cortex of EAE males, but not EAE females. Regarding function, synaptosomes isolated from cerebral cortex of male, but not female, EAE mice demonstrated significantly decreased oxygen consumption rates during respirometry assays.

Discussion

Cortical neuronal transcriptomics, mitochondrial morphology, and functional respirometry assays in synaptosomes revealed worse neurodegeneration in male EAE mice. This is consistent with worse neurodegeneration in MS men and reveals a model and a target to develop treatments to prevent cortical neurodegeneration and mitigate disability progression in MS men.
Health-related quality of life after otologic surgical treatment for chronic otitis media: systematic review
Authors: Schouwenaar Esther M. M. , Hellingman Catharine A. , Waterval Jérôme J.
Published: November 2023

Objective

This systematic review aims to describe the impact of otologic surgery as a treatment for chronic otitis media (COM) on the Health-Related Quality of Life (HRQoL) of adult patients.

Methods

A literature search was performed in PubMed, Scopus, Embase, and Web of Science until May 2023. Prospective studies including adult patients with COM (cholesteatoma) who underwent canal wall up mastoidectomy, canal wall down mastoidectomy, or tympanoplasty without mastoidectomy, with pre- and postoperative HRQoL measurements, were considered eligible. Questionnaire validation studies were excluded. The risk of bias and study quality were evaluated with a Quality Assessment Tool (for before-after studies with no control group). To assess the change in HRQoL, pre- and postoperative HRQoL values and absolute changes were extracted, synthesized, and presented in tables. Standardized mean differences (SMD) were calculated to enhance comparisons.

Results

Of the 720 studies identified, 16 met the inclusion criteria of this review. Different questionnaires were used throughout the studies. The CES and COMOT-15 were used in five studies and the ZCMEI-21 and COMQ-12 in three studies. All studies indicated statistically significant improvement in HRQoL from pre- to postoperative, measured with disease-specific HRQoL questionnaires. General HRQoL questionnaires did not show significant improvement. Calculated SMDs ranged from 0.24 to 6.99.

Discussion and conclusion

Included studies had low (n = 10) to high (n = 6) risk of bias and poor (n = 4), fair (n = 7) or good (n = 5) study quality. Surgical treatment positively impacts the HRQoL of adult COM patients with and without cholesteatoma. However, the clinical relevance of the reported changes is unknown due to the lack of minimal clinically important differences (MCID) or cut-off values in each questionnaire. Therefore, further research regarding the MCIDs of each questionnaire is needed. Future research should also report preoperative chief symptoms and indications for surgery to improve individual patient counseling.
Effectiveness of rehabilitation intervention in persons with Friedreich ataxia
Authors: Paparella Gabriella , Stragà Cristina , Vavla Marinela , Pesenti Nicola , Merotto Vasco , Martorel Gian A. , Zalunardo Sara , Armellin Maria , Comiotto Jimmy , Martinuzzi Andrea
Published: November 2023

Introduction

The relevance of rehabilitation in progressive neurological disorders, such as Friedreich’s Ataxia (FRDA), has yet to be convincingly proven. FRDA is characterized by ataxia, loss of gait, scoliosis, cardiomyopathy, dysarthria and dysphagia, with reduced life expectancy. The disease onset is usually in adolescence, leading to progressive disability. Omaveloxolone has been recently approved as the first pharmacological treatment for FRDA in adults and adolescents aged 16 years and older. Regarding non-pharmacological therapies, neurorehabilitation is a valuable aid in addressing the symptoms and in maintaining the residual functioning. We performed a prospective observational cohort study to evaluate the efficacy of inpatient rehabilitation (IR) for people with FRDA.

Methods

A total of 42 individuals (29 adults and 13 children) with FRDA were recruited. There were 27 ambulant and 15 non-ambulant participants. The patients underwent IR of 3 and 4 weeks in children and adults, respectively. The IR treatment was designed to be applied within a multidisciplinary setting, so FRDA patients underwent, in addition to physiotherapy, also occupational therapy, practical manual activities and psychological support aiming to enhance transferable skills useful in the activities of daily living. The primary outcome was the Scale for the Assessment and Rating of Ataxia (SARA). Other measures were: Friedreich Ataxia Rating Scale (FARS) and Nine Hole Peg Test (NHPT). Furthermore, we used the 6 Minute Walk Test (6MWT), the Timed Up and Go (TUG) and the Berg Balance Scale (BBS) only on ambulant subjects. Outcomes were evaluated at baseline and at the end of the treatment.

Results

We report that the IR significantly improves motor performance and ataxia symptoms in patients with FRDA. Our study shows significant functional improvement in all the outcome measures used, except for NHPT bilaterally. FARS and SARA scores post-IR are significatively reduced when compared (p < 0.001).

Discussion

We demonstrate that IR programs in FRDA can provide a meaningful clinical improvement in terms of outcome measures. These findings could be useful when approaching progressive neurological disorders.
Listening effort and fatigue among cochlear implant users: a scoping review
Authors: Philips Cato , Jacquemin Laure , Lammers Marc J. W. , Mertens Griet , Gilles Annick , Vanderveken Olivier M. , Van Rompaey Vincent
Published: November 2023

Introduction

In challenging listening situations, speech perception with a cochlear implant (CI) remains demanding and requires high levels of listening effort, which can lead to increased levels of listening-related fatigue. The body of literature on these topics increases as the number of CI users rises. This scoping review aims to provide an overview of the existing literature on listening effort, fatigue, and listening-related fatigue among CI users and the measurement techniques to evaluate them.

Methods

The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) Statements were used to conduct the scoping review. The search was performed on PubMed, Scopus, and Web of Science to identify all relevant studies.

Results

In total, 24 studies were included and suggests that CI users experience higher levels of listening effort when compared to normal hearing controls using scales, questionnaires and electroencephalogram measurements. However, executing dual-task paradigms did not reveal any difference in listening effort between both groups. Uncertainty exists regarding the difference in listening effort between unilateral, bilateral, and bimodal CI users with bilateral hearing loss due to ambiguous results. Only five studies were eligible for the research on fatigue and listening-related fatigue. Additionally, studies using objective measurement methods were lacking.

Discussion

This scoping review highlights the necessity for additional research on these topics. Moreover, there is a need for guidelines on how listening effort, fatigue, and listening-related fatigue should be measured to allow for study results that are comparable and support optimal rehabilitation strategies.
An open-source nnU-net algorithm for automatic segmentation of MRI scans in the male pelvis for adaptive radiotherapy
Authors: Lorenzen Ebbe Laugaard , Celik Bahar , Sarup Nis , Dysager Lars , Christiansen Rasmus Lübeck , Bertelsen Anders Smedegaard , Bernchou Uffe , Agergaard Søren Nielsen , Konrad Maximilian Lukas , Brink Carsten , Mahmood Faisal , Schytte Tine , Nyborg Christina Junker
Published: November 2023

Background

Adaptive MRI-guided radiotherapy (MRIgRT) requires accurate and efficient segmentation of organs and targets on MRI scans. Manual segmentation is time-consuming and variable, while deformable image registration (DIR)-based contour propagation may not account for large anatomical changes. Therefore, we developed and evaluated an automatic segmentation method using the nnU-net framework.

Methods

The network was trained on 38 patients (76 scans) with localized prostate cancer and tested on 30 patients (60 scans) with localized prostate, metastatic prostate, or bladder cancer treated at a 1.5 T MRI-linac at our institution. The performance of the network was compared with the current clinical workflow based on DIR. The segmentation accuracy was evaluated using the Dice similarity coefficient (DSC), mean surface distance (MSD), and Hausdorff distance (HD) metrics.

Results

The trained network successfully segmented all 600 structures in the test set. High similarity was obtained for most structures, with 90% of the contours having a DSC above 0.9 and 86% having an MSD below 1 mm. The largest discrepancies were found in the sigmoid and colon structures. Stratified analysis on cancer type showed that the best performance was seen in the same type of patients that the model was trained on (localized prostate). Especially in patients with bladder cancer, the performance was lower for the bladder and the surrounding organs. A complete automatic delineation workflow took approximately 1 minute. Compared with contour transfer based on the clinically used DIR algorithm, the nnU-net performed statistically better across all organs, with the most significant gain in using the nnU-net seen for organs subject to more considerable volumetric changes due to variation in the filling of the rectum, bladder, bowel, and sigmoid.

Conclusion

We successfully trained and tested a network for automatically segmenting organs and targets for MRIgRT in the male pelvis region. Good test results were seen for the trained nnU-net, with test results outperforming the current clinical practice using DIR-based contour propagation at the 1.5 T MRI-linac. The trained network is sufficiently fast and accurate for clinical use in an online setting for MRIgRT. The model is provided as open-source.
Handgrip strength assessment at baseline in addition to bone parameters could potentially predict the risk of curve progression in adolescent idiopathic scoliosis
Authors: Lau Rufina Wing Lum , Cheuk Ka Yee , Hung Vivian Wing Yin , Yu Fiona Wai Ping , Tam Elisa Man Shan , Wong Lyn Lee Ning , Zhang Jiajun , Lee Wayne Yuk Wai , Cheng Jack Chun Yiu , Lam Tsz Ping , Lau Adam Yiu Chung
Published: November 2023

Introduction

Adolescent idiopathic scoliosis (AIS) is characterized by deranged bone and muscle qualities, which are important prognostic factors for curve progression. This retrospective case–control study aims to investigate whether the baseline muscle parameters, in addition to the bone parameters, could predict curve progression in AIS.

Methods

The study included a cohort of 126 female patients diagnosed with AIS who were between the ages of 12 and 14 years old at their initial clinical visit. These patients were longitudinally followed up every 6 months (average 4.08 years) until they reached skeletal maturity. The records of these patients were thoroughly reviewed as part of the study. The participants were categorized into two sub-groups: the progressive AIS group (increase in Cobb angle of ≥6°) and the stable AIS group (increase in Cobb angle <6°). Clinical and radiological assessments were conducted on each group.

Results

Cobb angle increase of ≥6° was observed in 44 AIS patients (34.9%) prior to skeletal maturity. A progressive AIS was associated with decreased skeletal maturity and weight, lower trunk lean mass (5.7%, p = 0.027) and arm lean mass (8.9%, p < 0.050), weaker dominant handgrip strength (8.8%, p = 0.027), deranged cortical compartment [lower volumetric bone mineral density (vBMD) by 6.5%, p = 0.002], and lower bone mechanical properties [stiffness and estimated failure load lowered by 13.2% (p = 0.005) and 12.5% (p = 0.004)]. The best cut-off threshold of maximum dominant handgrip strength is 19.75 kg for distinguishing progressive AIS from stable AIS (75% sensitivity and 52.4% specificity, p = 0.011).

Discussion

Patients with progressive AIS had poorer muscle and bone parameters than patients with stable AIS. The implementation of a cut-off threshold in the baseline dominant handgrip strength could potentially be used as an additional predictor, in addition to bone parameters, for identifying individuals with AIS who are at higher risk of experiencing curve progression.
S-Net: a multiple cross aggregation convolutional architecture for automatic segmentation of small/thin structures for cardiovascular applications
Authors: Mu Nan , Lyu Zonghan , Rezaeitaleshmahalleh Mostafa , Bonifas Cassie , Gosnell Jordan , Haw Marcus , Vettukattil Joseph , Jiang Jingfeng
Published: November 2023

With the success of U-Net or its variants in automatic medical image segmentation, building a fully convolutional network (FCN) based on an encoder-decoder structure has become an effective end-to-end learning approach. However, the intrinsic property of FCNs is that as the encoder deepens, higher-level features are learned, and the receptive field size of the network increases, which results in unsatisfactory performance for detecting low-level small/thin structures such as atrial walls and small arteries. To address this issue, we propose to keep the different encoding layer features at their original sizes to constrain the receptive field from increasing as the network goes deeper. Accordingly, we develop a novel S-shaped multiple cross-aggregation segmentation architecture named S-Net, which has two branches in the encoding stage, i.e., a resampling branch to capture low-level fine-grained details and thin/small structures and a downsampling branch to learn high-level discriminative knowledge. In particular, these two branches learn complementary features by residual cross-aggregation; the fusion of the complementary features from different decoding layers can be effectively accomplished through lateral connections. Meanwhile, we perform supervised prediction at all decoding layers to incorporate coarse-level features with high semantic meaning and fine-level features with high localization capability to detect multi-scale structures, especially for small/thin volumes fully. To validate the effectiveness of our S-Net, we conducted extensive experiments on the segmentation of cardiac wall and intracranial aneurysm (IA) vasculature, and quantitative and qualitative evaluations demonstrated the superior performance of our method for predicting small/thin structures in medical images.
Resolving an inconsistency in the estimation of the energy for excitation of cardiac muscle contraction
Authors: Han June-Chiew , Pham Toan , Taberner Andrew J. , Loiselle Denis S. , Tran Kenneth
Published: November 2023

In the excitation of muscle contraction, calcium ions interact with transmembrane transporters. This process is accompanied by energy consumption and heat liberation. To quantify this activation energy or heat in the heart or cardiac muscle, two non-pharmacological approaches can be used. In one approach using the “pressure-volume area” concept, the same estimate of activation energy is obtained regardless of the mode of contraction (either isovolumic/isometric or ejecting/shortening). In the other approach, an accurate estimate of activation energy is obtained only when the muscle contracts isometrically. If the contraction involves muscle shortening, then an additional component of heat associated with shortening is liberated, over and above that of activation. The present study thus examines the reconcilability of the two approaches by performing experiments on isolated muscles measuring contractile force and heat output. A framework was devised from the experimental data to allow us to replicate several mechanoenergetics results gleaned from the literature. From these replications, we conclude that the choice of initial muscle length (or ventricular volume) underlies the divergence of the two approaches in the estimation of activation energy when the mode of contraction involves shortening (ejection). At low initial muscle lengths, the heat of shortening is relatively small, which can lead to the misconception that activation energy is contraction mode independent. In fact, because cardiac muscle liberates heat of shortening when allowed to shorten, estimation of activation heat must be performed only under isometric (isovolumic) contractions. We thus recommend caution when estimating activation energy using the “pressure-volume area” concept.
Comprehensive and evolutionary analysis of Spodoptera litura-inducible Cytochrome P450 monooxygenase gene family in Glycine max elucidate their role in defense
Authors: Yadav Manisha , Panwar Ruby , Rustagi Anjana , Chakraborty Amrita , Roy Amit , Singh Indrakant K. , Singh Archana
Published: November 2023

Plants being sessile organisms and lacking both circulating phagocytic cells and somatic adaptive immune response, have thrived on various defense mechanisms to fend off insect pests and invasion of pathogens. CYP450s are the versatile enzymes, which thwart plants against insect pests by ubiquitous biosynthesis of phytohormones, antioxidants, and secondary metabolites, utilizing them as feeding deterrents and direct toxins. Therefore, a comprehensive analysis of biotic stress-responsive CYPs from Glycine max was performed to ascertain their function against S. litura-infestation. Phylogenetic analysis and evolutionary studies on conserved domains and motifs disclosed the evolutionary correspondence of these GmCYPs with already characterized members of the CYP450 superfamily and close relatedness to Medicago truncatula. These GmCYPs were mapped on 13 chromosomes; they possess 1-8 exons; they have evolved due to duplication and are localized in endoplasmic reticulumn. Further, identification of methyl-jasmonate, salicylic acid, defense responsive and flavonoid biosynthesis regulating cis-acting elements, their interaction with biotic stress regulating proteins and their differential expression in diverse types of tissues, and during herbivory, depicted their responsiveness to biotic stress. Three-dimensional homology modelling of GmCYPs, docking with heme cofactor required for their catalytic activity and enzyme-substrate interactions were performed to understand the functional mechanism of their action. Moreover, to gain insight into their involvement in plant defense, gene expression analysis was evaluated, which revealed differential expression of 11 GmCYPs upon S. litura-infestation, 12 GmCYPs on wounding while foliar spray of ethylene, methyl-jasmonate and salicylic acid differentially regulated 11 GmCYPs, 6 GmCYPs, and 10 GmCYPs respectively. Our study comprehensively analysed the underlying mechanism of GmCYPs function during S. litura-infestation, which can be further utilized for functional characterization to develop new strategies for enhancing soybean resistance to insect pests.
Transcriptomics and metabolomics reveal the primary and secondary metabolism changes in Glycyrrhiza uralensis with different forms of nitrogen utilization
Authors: Chen Ying , Bai Yu , Zhang ZhengRu , Zhang YuanFan , Jiang Yuan , Wang ShangTao , Wang YanJun , Sun Zhirong
Published: November 2023

The roots and rhizomes of Glycyrrhiza uralensis Fisch. represent the oldest and most frequently used herbal medicines in Eastern and Western countries. However, the quality of cultivated G. uralensis has not been adequate to meet the market demand, thereby exerting increased pressure on wild G. uralensis populations. Nitrogen, vital for plant growth, potentially influences the bioactive constituents of plants. Yet, more information is needed regarding the effect of different forms of nitrogen on G. uralensis. G. uralensis seedlings were exposed to a modified Hoagland nutrient solution (HNS), varying concentrations of nitrate (KNO3), or ammonium (NH4)2SO4. We subsequently obtained the roots of G. uralensis for physiology, transcriptomics, and metabolomics analyses. Our results indicated that medium-level ammonium nitrogen was more effective in promoting G. uralensis growth compared to nitrate nitrogen. However, low-level nitrate nitrogen distinctly accelerated the accumulation of flavonoid ingredients. Illumina sequencing of cDNA libraries prepared from four groups—treated independently with low/medium NH4+ or NO3- identified 364, 96, 103, and 64 differentially expressed genes (DEGs) in each group. Our investigation revealed a general molecular and physiological metabolism stimulation under exclusive NH4+ or NO3- conditions. This included nitrogen absorption and assimilation, glycolysis, Tricarboxylic acid (TCA) cycle, flavonoid, and triterpenoid metabolism. By creating and combining putative biosynthesis networks of nitrogen metabolism, flavonoids, and triterpenoids with related structural DEGs, we observed a positive correlation between the expression trend of DEGs and flavonoid accumulation. Notably, treatments with low-level NH4+ or medium-level NO3- positively improved primary metabolism, including amino acids, TCA cycle, and glycolysis metabolism. Meanwhile, low-level NH4+ and NO3- treatment positively regulated secondary metabolism, especially the biosynthesis of flavonoids in G. uralensis. Our study lays the foundation for a comprehensive analysis of molecular responses to varied nitrogen forms in G. uralensis, which should help understand the relationships between responsive genes and subsequent metabolic reactions. Furthermore, our results provide new insights into the fundamental mechanisms underlying the treatment of G. uralensis and other Glycyrrhiza plants with different nitrogen forms.
Candidate genes for field resistance to cassava brown streak disease revealed through the analysis of multiple data sources
Authors: Ferguson Morag E. , Eyles Rodney P. , Garcia-Oliveira Ana Luísa , Kapinga Fortunus , Masumba Esther A. , Amuge Teddy , Bredeson Jessen V. , Rokhsar Daniel S. , Lyons Jessica B. , Shah Trushar , Rounsley Steve , Mkamilo Geoffrey
Published: November 2023

Cassava (Manihot esculenta Crantz) is a food and industrial storage root crop with substantial potential to contribute to managing risk associated with climate change due to its inherent resilience and in providing a biodegradable option in manufacturing. In Africa, cassava production is challenged by two viral diseases, cassava brown streak disease (CBSD) and cassava mosaic disease. Here we detect quantitative trait loci (QTL) associated with CBSD in a biparental mapping population of a Tanzanian landrace, Nachinyaya and AR37-80, phenotyped in two locations over three years. The purpose was to use the information to ultimately facilitate either marker-assisted selection or adjust weightings in genomic selection to increase the efficiency of breeding. Results from this study were considered in relation to those from four other biparental populations, of similar genetic backgrounds, that were phenotyped and genotyped simultaneously. Further, we investigated the co-localization of QTL for CBSD resistance across populations and the genetic relationships of parents based on whole genome sequence information. Two QTL on chromosome 4 for resistance to CBSD foliar symptoms and one on each of chromosomes 11 and 18 for root necrosis were of interest. Of significance within the candidate genes underlying the QTL on chromosome 4 are Phenylalanine ammonia-lyase (PAL) and Cinnamoyl-CoA reductase (CCR) genes and three PEPR1-related kinases associated with the lignin pathway. In addition, a CCR gene was also underlying the root necrosis-resistant QTL on chromosome 11. Upregulation of key genes in the cassava lignification pathway from an earlier transcriptome study, including PAL and CCR, in a CBSD-resistant landrace compared to a susceptible landrace suggests a higher level of basal lignin deposition in the CBSD-resistant landrace. Earlier RNAscope®in situ hybridisation imaging experiments demonstrate that cassava brown streak virus (CBSV) is restricted to phloem vessels in CBSV-resistant varieties, and phloem unloading for replication in mesophyll cells is prevented. The results provide evidence for the involvement of the lignin pathway. In addition, five eukaryotic initiation factor (eIF) genes associated with plant virus resistance were found within the priority QTL regions.
CRISPR-enabled investigation of fitness costs associated with the E198A mutation in β-tubulin of Colletotrichum siamense
Authors: Cosseboom Scott D. , Agarwal Chiti , Hu Mengjun
Published: November 2023

Introduction

Understanding fitness costs associated with fungicide resistance is critical to improve resistance management strategies. E198A in b-tubulin confers resistance to the fungicide thiophanate-methyl and has been widely reported in several plant pathogens including Colletotrichum siamense.

Method

To better understand potential fitness costs associated with the resistance, a ribonucleoprotein (RNP) complex mediated CRISPR/Cas9 system was used to create a point mutation (E198A) through homology directed repair (HDR) in each of the sensitive (E198) C. siamense isolates collected from strawberries, raspberries, and peaches. The RNP complex was delivered into fungal protoplasts using polyethylene glycol-mediated (PEG) transfection.

Results

The transformation efficiency, the proportion of transformants of sensitive parental isolates containing the E198A mutation, averaged 72%. No off-target mutations were observed when sequences similar to the b-tubulin target region with a maximum of four mismatch sites were analyzed, suggesting that the CRISPR/Cas9 system used in this study was highly specific for genome editing in C. siamense. Of the 41 comparisons of fitness between mutant and wild type isolates through in vitro and detached fruit assays, mutant isolates appeared to be as fit (24 of 41 comparisons), if not more fit than wild-type isolates (10 of 41 comparisons).

Discussion

The use of CRISPR/Cas9 to evaluate fitness costs associated with point mutations in this study represents a novel and useful method, since wild-type and mutant isolates were genetically identical except for the target mutation.
Volunteers’ growth mindset and continuance intention: what are the roles of nostalgia and positive emotions?
Authors: Cho Heetae , Lee Hyun-Woo , Kim Taehee
Published: November 2023

This study examined the cognitive and affective aspects of volunteering experiences by focusing on the relationships between volunteers’ growth mindset, nostalgia, positive emotions, and their intention to continue volunteering. A total of 364 responses were collected from volunteers who had volunteered within the past 5 years. Results showed that the growth mindset had a positive effect on nostalgia, which in turn positively affected valenced emotions toward volunteering. Nostalgia and volunteers’ positive emotions positively influenced their intention to continue volunteering. All indirect effects via nostalgia were significant. This study lays the groundwork to identify the role of nostalgia in volunteerism and contributes to extending the literature on growth mindset and mindset theory.