bluuebunny/crossref_metadata_2025 huggingface dataset:
Coordinating upper limbs for octave playing on the piano via neuro-musculoskeletal modeling
Authors: Wang Huijiang , Nonaka Tetsushi , Abdulali Arsen , Iida Fumiya
Published: September 2023

Understanding the coordination of multiple biomechanical degrees of freedom in biological organisms is crucial for unraveling the neurophysiological control of sophisticated motor tasks. This study focuses on the cooperative behavior of upper-limb motor movements in the context of octave playing on the piano. While the vertebrate locomotor system has been extensively investigated, the coherence and precision timing of rhythmic movements in the upper-limb system remain incompletely understood. Inspired by the spinal cord neuronal circuits (central pattern generator, CPG), a computational neuro-musculoskeletal model is proposed to explore the coordination of upper-limb motor movements during octave playing across varying tempos and volumes. The proposed model incorporates a CPG-based nervous system, a physiologically-informed mechanical body, and a piano environment to mimic human joint coordination and expressiveness. The model integrates neural rhythm generation, spinal reflex circuits, and biomechanical muscle dynamics while considering piano playing quality and energy expenditure. Based on real-world human subject experiments, the model has been refined to study tempo transitions and volume control during piano playing. This computational approach offers insights into the neurophysiological basis of upper-limb motor coordination in piano playing and its relation to expressive features.
Quantifying the relative contributions of climate change and ENSO to flood occurrence in Bangladesh
Authors: Uddin Shahab , Revel Menaka , Modi Prakat , Yamazaki Dai
Published: September 2023

Bangladesh is highly vulnerable to flood hazards, and its flood risk is projected to increase with global warming. In addition to climate change, internal climate variation, such as the El Niño–Southern Oscillation (ENSO), influences flooding in many rivers worldwide. However, the impact of internal climate variability on flooding in Bangladesh remains unclear due to the limited observations. Here, we assess the impacts of ENSO and climate change on flood occurrence in Bangladesh using a large-ensemble climate simulation dataset and a global river model (CaMa-Flood). After separating 6000 years of simulation (100-member ensemble river simulations for 1950–2010) into El Niño, La Niña, and neutral years, we calculated the extent to which each ENSO stage increased flood occurrence probability relative to the neutral state using the fraction of attributable risk method. In addition, we estimated the impact of historical climate change on past flood occurrence through a comparison of simulations with and without historical global warming. Under the no-global-warming climate, La Niña increased the occurrence probability of a 10 year return period flood at Hardinge Bridge on the Ganges River by 38% compared to neutral years. The influence of La Niña or El Niño state on flood occurrence probability in the Brahmaputra River at Bahadurabad station is negligible. Historical global warming increased the occurrence of flooding in the Ganges River, the Brahmaputra River, and their confluence by 59%, 44%, and 55%, respectively. The impact of ENSO on flood occurrence probability decreased in the historical simulation, likely due to the conflation of ENSO and climate change signals, and no significant correlation between ENSO and flood occurrence was detected when only small-ensemble simulations were used. These findings suggest that the use of large-ensemble climate simulation datasets is essential for precise attribution of the impacts of internal climate variability on flooding in Bangladesh.
Research advances in mechanisms of climate change impacts on soil organic carbon dynamics
Authors: Guo Yadong , Zeng Zhenzhong , Wang Junjian , Zou Junyu , Shi Zhou , Chen Songchao
Published: September 2023

Soil, as the largest terrestrial carbon pool, has garnered significant attention concerning its response to global warming. However, accurately estimating the stocks and dynamics of soil organic carbon (SOC) remains challenging due to the complex and unclear influence mechanisms associated with biogeochemical processes in above- and belowground ecosystems, as well as technical limitations. Therefore, it is imperative to facilitate the integration of models and knowledge and promote dialogue between empiricists and modelers. This review provides a concise SOC turnover framework to understand the impact of climate change on SOC dynamics. It covers various factors such as warming, precipitation changes, elevated carbon dioxide, and nitrogen deposition. The review presents impact mechanisms from the perspective of organismal traits (plants, fauna, and microbes), their interactions, and abiotic regulation. Although valuable insights have been gained regarding SOC inputs, decomposition, and stabilization under climate change, there are still knowledge gaps that need to be addressed. In the future, it is essential to conduct systematic and refined research in this field. This includes standardizing the organismal traits most relevant to SOC, studying the standardization of SOC fractions and their resistance to decomposition, and focusing on the interactions and biochemical pathways of biological communities. Through further investigation of biotic and abiotic interactions, a clearer understanding can be attained regarding the physical protection, chemical stability, and biological driving mechanisms of SOC under climate change. This can be achieved by integrating multidisciplinary knowledge, utilizing novel technologies and methodologies, increasing in-situ experiments, and conducting long-term monitoring across multi-scales. By integrating reliable data and elucidating clear mechanisms, the accuracy of models can be enhanced, providing a scientific foundation for mitigating climate change.
Measuring Sloping Floor of Heritage Building Using Point Cloud Data from LiDAR Survey
Authors: Shahrin Muhammad Shahir bin , Said Shahrul Yani , Latif Zulkiflee Abd , Harun Siti Norlizaiha , Sulaiman Mohd Sabere
Published: September 2023

Heritage building restoration and preservation work relies heavily on a thorough inspection of building condition survey. One of the building dilapidations that may occur in a heritage building, is sloping floor defect where the floor is uneven, or slanting towards a specific direction. In this case study, a sloping floor defect was identified at Ipoh Town Hall, Perak which require further investigation. Using conventional methods to survey the sloping floor in building surveying will require more time and manpower. Instead, this paper explores LiDAR scanning methods to measure and identify sloping floor defects. R programming techniques are applied to analyse the point cloud results from the LiDAR survey to assess the sloping floor defect in greater detail.
Assessment of Difference in Structure from Motion for Stockpile Volume Estimation using UAV Approach
Authors: Halim Ahmad Eizat Abdul , Rahman Abdul Aziz Ab , Maulud Khairul Nizam Abdul , Nekmat Muhammad Salihin , Mukhlisin Muhammad
Published: September 2023

The software for processing the photogrammetry software is increasingly capable of producing a high-quality 3D model DEM, DSM, and DTM from an aerial photo and measuring the volume of material. Nowadays, UAV technology has been rapidly used for stockpile volume calculation for the mining and construction industry. The purpose of this study is to compare image processing for the stockpile volume calculation using three different software for the UAV with the conventional method GPS as a reference. The result obtained using GPS is processed using CIVIL3D and act as a base measurement of the stockpile volume to compare result obtain from photogrammetry software which is Pix4D, Agisoft, and SimActives Correlator3D. The analysis of this study compared 3D model for volume calculation from a photo image for each photogrammetry software selected and obtained the result volume calculation for photogrammetry with the accuracy achieving below 3% error from the referenced volume of the stockpile. 12 GCP were placed around the study area to test the difference between the numbers of GCP processing for the volume stockpile results. The image acquisition is taken at 10 meter altitude and 20 meter altitude using UAV Phantom 4 pro and set with Pix4Dcapture circular mission. The processing method is SfM in the 3 photogrammetric selected that have 4 types of processing for each software, 10 meter altitude and 20 meter altitude with 4 GCP and 12 GCP. 12 results of the 3D model and volume of the stockpile was obtained. As for the volume results, the Pix4D 10 meter 4 GCP result obtained the closest volume to the reference. The point cloud generated is also stable based on the cloud compare volume density result. Overall, the study can conclude that not only the altitude of flight affected, and the type of software used is affecting the number of point clouds generated but also the number of GCP.
Marine Habitat Mapping using Multibeam Echosounder Survey and Underwater Video Observations: A Case Study from Tioman Marine Park
Authors: Muhamad Muhammad Abdul Hakim , Hasan Rozaimi Che , Said Najhan Md , Said Mohd Shahmy Mohd , Razali Raiz
Published: September 2023

In recent years, there has been an increasing trend of utilizing high-resolution multibeam echosounder (MBES) datasets and supervised classification via machine learning to create marine habitat maps. The purpose of current study was threefold: (1) to extract bathymetric and backscatter derivatives from a multibeam dataset, (2) to measure the correlation between bathymetric and backscatter derivatives, and (3) to generate a marine habitat map using the Random Forest (RF). Tioman Marine Park (TMP), which is situated Southeast China Sea. MBES surveyed area are encompassed an area of 406 km² and served as the location for the study. Based on results and analysis, fourteen (14) derivative were derived from bathymetry map and backscatter mosaic. The second step involved integrating variables and a total of 152 of habitat ground-truth data were used, derived from underwater imageries, and sediment samples, into an RF model to generate a map of the marine habitat. Based on marine habitat map, six habitat classes including sand, rock, gravel and sand, coral rubble, coral and rock, and coral were classified. The distribution of coral habitat was found to be correlated with the depth of the bathymetry in the shallow water region. Therefore, the study has reached the conclusion that the integration between MBES derivatives, ground-truth data, and RF machine learning algorithm is an effective in classifying the distribution of marine habitats, specifically the coral habitat.
Conceptual Framework for Maximizing Service Catchment Area Between Rail Transit and Feeder Service Using Spatial Temporal Regression Technique
Authors: Halim Maisarah Abdul , Rosni Nur Aulia , Tsong Teh Bor
Published: September 2023

The move towards a more sustainable transport mode is crucial in the Klang Valley by incorporating feeder services to rail network stations. Feeder services will complement the expanding rail transits network and deliver connectivity for areas not covered within rail stations. Past literatures found that feeder services were ineffective during rail breakdown as feeder service was not going or stopping to where it was intended to. Feeder service can be allocated more effectively if we have better idea of targeted service area. Urban planners now have access to a variety of urban analytics because of technological advancements and the rise of smart cities. Data generated are produced across numerous locations and at diverse time scales, providing a significant possibility for data mining to uncover insightful information when both space and time are considered. This study will attempt to assess the community’s accessibility to rail transit through feeder service in Klang Valley. In achieving this a conceptual framework is developed within the objectives of this study which are firstly, to identify built environment factors that influence ridership around transit stations. Secondly, to determine the spatial -temporal relationship between built environment and transit ridership of feeder service and rail transits. Next, the station-level spatial and temporal variability of ridership data between feeder service to rail network is examined. Finally, as the main finding of this study, a framework in maximizing a service catchment transportation service for feeder service and rail transit will be developed. In doing that, the conceptual framework approach is by addressing numerical analytical technique in geographic data, by using spatial temporal regression. This study aspires to provide planning departments and transit agencies with useful guidance to execute targeted policies and develop a sustainable and efficient feeder service coverage area to support rail transits by looking at both spatial and temporal scales.
Analyzing the Impact of Land Surface Temperature Due to Urbanization Using Landsat 8 Satellite Image
Authors: Idris Muhammad Ajmal A’imullah Bin , Hashim Nurhanisah , Khalid Nafisah
Published: September 2023

Over the past years, global warming has become one of the enormous issues the world has faced. Malaysia is also not excluded from this worldwide problem. Due to rapid urbanization and deforestation, the temperature is getting warmer day by day. One of the dangerous effects that can be occurred were heatwaves. This phenomenon can even cause death due to heatstroke. This study aims to analyse the temporal changes in Land Surface Temperature due to Land Cover changes using multispectral Landsat 8 satellite images. The study area is Puncak Alam, Selangor where thermal images and landcover classification images were produced. By using Landsat 8 TIRS, analysing the land surface temperature of the study area can be achieved. The output was landcover classification images using Support Vector Machine algorithm and thermal images for year 2014 and 2021. From the result, it can be analysed that, the study area had been experiencing deforestation due to urbanization over the years. This causes an increase in land surface temperature in 2021 compared to 2014. The increase in land surface temperature percentage was obvious in class range 20°C to 25°C to a hotter range of 27.5°C to 32.5°C by almost 15% to 30% increase. The forest and urban area which show the most deforestation area has experienced an increase in land surface temperature to 27.5°C - 30°C by 44%.
Coastlines estimation and erosion rate assessment in Tuba Island, Langkawi using remotely-sensed digital imageries analysis
Authors: Adnan Nor Aizam , Norazman Najiehah , Maulud Khairul Nizam , Mokhtar Ernieza Suhana , Yusoff Zaharah Mohd
Published: September 2023

Malaysia’s coastline is constantly exposed to ocean threats, resulting in coastal erosion and sea-level rise. Pulau Tuba’s is a part of Pulau Langkawi which known as a popular tourist destination in Malaysia. This study focuses on using remote sensing and Geographical Information System (GIS) tools to examine changes along the coastline of Pulau Tuba, Langkawi, during a six-year period. In this research, changes to the coastline were analyzed using Sentinel-2 imagery from 2016 to 2021, as a result of the comparison of coastline extraction methods. Coastline extraction methods used in this study include 3x3-5x5 and 7x7 edge detection filtering techniques. Image classifier of Maximum Likelihood (ML) and Support Vector Machine (SVM) were also used to quantify the estimated coastlines length. Digital Shoreline Analysis System (DSAS) was used to calculate coastline erosion rate from Sentinel-2 images. The comparison between method to extract coastline revealed that the best window size of edge detection image filtering method is 7x7 and SVM outperform MLC classifier. The erosion rate as estimated from DSAS statistical calculation also highlighted that come parts along the Pulau Tuba coastlines experiencing alarming rate of coastal erosion. The authority needs to plan for soft and hard structure to mitigate the impact of coastal erosion in the future.
The seasonal Antarctic sea ice concentration anomalies related to the Atlantic Niño index
Authors: Yu Lejiang , Zhong Shiyuan , Vihma Timo , Sui Cuijuan , Sun Bo
Published: September 2023

Antarctic sea ice concentration anomalies (ASICA) have been found to be linked to sea surface temperature anomalies in tropical oceans. However, it is not clear whether and how ASICA is linked to the Atlantic Niño mode (ANM). This study demonstrates a significant relationship between ASICA and ANM. The relationships vary by season, with a peak in austral winter and a secondary one in spring. Significant sea ice anomalies associated with a positive phase of ANM are mostly negative in austral winter and spring, and mostly positive in austral summer and autumn. This teleconnection is established by atmospheric wavetrains that are excited over the tropical southwestern Pacific and Indian Oceans and the southern Atlantic Oceans and propagate over the Southern Ocean. These wavetrains induce anomalous near-surface circulations, which generate dynamic and thermodynamic forcing on sea ice, resulting in the observed ASICA patterns. The absence of El Niño Southern Oscillation weakens the connection.
Becky Thatcher’s Literary Half-life: Appropriating Mark Twain’s Good Girl
Authors: Shannon Edward A
Published: September 2023

Mark Twain’s Becky Thatcher features very little in The Adventures of Tom Sawyer and Adventures of Huckleberry Finn. She mostly vanishes after Tom Sawyer, and even in that novel she speaks fewer than a thousand words of dialogue. She disappears from Twain’s work almost completely after Huckleberry Finn, where she receives a single mention. An insignificant character to academics, Becky appears in the scholarly record little more than she had in Twain’s fiction. This essay explores Becky Thatcher’s outsized role in cinematic, literary, and other adaptations across the twentieth and twenty-first centuries. Becky Thatcher’s literary half-life extends to clothing racks and gift shops, as well as in cinematic and literary adaptations and appropriations. These transformations map racial and sexual anxieties of several American generations. Minor though she may seem, Becky looms large in films, fiction, restaurants, tourist attractions, and all the ephemera produced from the marketing of successful fictional characters in a capitalist media landscape.
Hidradenitis suppurativa: new insights into disease mechanisms and an evolving treatment landscape
Authors: Krueger James G , Frew John , Jemec Gregor B E , Kimball Alexa B , Kirby Brian , Bechara Falk G , Navrazhina Kristina , Prens Errol , Reich Kristian , Cullen Eva , Wolk Kerstin
Published: September 2023

Hidradenitis suppurativa (HS), also known as acne inversa, is a chronic disabling and debilitating inflammatory disease with a high unmet medical need. The prevalence of HS reported in most studies is 1–2%, although it is likely to be under-reported and estimates vary globally owing to variance in data collection methods, ethnicity, geographical location and under-diagnosis. HS is characterized by persistent, painful cutaneous nodules, abscesses and draining tunnels commonly affecting the axillary, anogenital, inguinal and perianal/gluteal areas. Over time, chronic uncontrolled inflammation results in irreversible tissue destruction and scarring. Although the pathophysiology of HS has not been fully elucidated, the tumour necrosis factor (TNF)-α and interleukin (IL)-17 pathways have an important role, involving multiple cytokines. Currently, treatment options include topical medications; systemic therapies, including repeated and/or rotational courses of systemic antibiotics, retinoids and hormonal therapies; and various surgical procedures. The anti-TNF-α antibody adalimumab is currently the only biologic approved by both the US Food and Drug Administration and the European Medicines Agency for HS; however, its efficacy varies, with a clinical response reported in approximately 50% of patients in phase III trials. HS is a rapidly evolving field of discovery, with a diverse range of agents with distinct mechanisms of action currently being explored in clinical trials. Several other promising therapeutic targets have recently emerged, and agents targeting the IL-17 and Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathways are the most advanced in ongoing or completed phase III clinical trials. Alongside limited therapeutic options, significant challenges remain in terms of diagnosis and disease management, with a need for better treatment outcomes. Other unmet needs include significant diagnostic delays, thus missing the therapeutic ‘window of opportunity’; the lack of standardized outcome measures in clinical trials; and the lack of established, well-defined disease phenotypes and biomarkers.
Machine learning to predict outcomes following endovascular abdominal aortic aneurysm repair
Authors: Li Ben , Aljabri Badr , Verma Raj , Beaton Derek , Eisenberg Naomi , Lee Douglas S , Wijeysundera Duminda N , Forbes Thomas L , Rotstein Ori D , de Mestral Charles , Mamdani Muhammad , Roche-Nagle Graham , Al-Omran Mohammed
Published: September 2023

Background

Endovascular aneurysm repair (EVAR) for abdominal aortic aneurysm (AAA) carries important perioperative risks; however, there are no widely used outcome prediction tools. The aim of this study was to apply machine learning (ML) to develop automated algorithms that predict 1-year mortality following EVAR.

Methods

The Vascular Quality Initiative database was used to identify patients who underwent elective EVAR for infrarenal AAA between 2003 and 2023. Input features included 47 preoperative demographic/clinical variables. The primary outcome was 1-year all-cause mortality. Data were split into training (70 per cent) and test (30 per cent) sets. Using 10-fold cross-validation, 6 ML models were trained using preoperative features with logistic regression as the baseline comparator. The primary model evaluation metric was area under the receiver operating characteristic curve (AUROC). Model robustness was evaluated with calibration plot and Brier score.

Results

Some 63 655 patients were included. One-year mortality occurred in 3122 (4.9 per cent) patients. The best performing prediction model for 1-year mortality was XGBoost, achieving an AUROC (95 per cent c.i.) of 0.96 (0.95–0.97). Comparatively, logistic regression had an AUROC (95 per cent c.i.) of 0.69 (0.68–0.71). The calibration plot showed good agreement between predicted and observed event probabilities with a Brier score of 0.04. The top 3 predictive features in the algorithm were 1) unfit for open AAA repair, 2) functional status, and 3) preoperative dialysis.

Conclusions

In this data set, machine learning was able to predict 1-year mortality following EVAR using preoperative data and outperformed standard logistic regression models.
Unlocking the secret diversity of Anadenanthera: insights from molecular genetics of four evolving species
Authors: Mangaravite Érica , da Silveira Thamyres Cardoso , Vinson Christina Cleo , Bueno Marcelo Leandro , Silva Roberta dos Santos , Carniello Maria Antonia , Veldman Joseph W , Garcia Magali Gonçalves , de Oliveira Luiz Orlando
Published: September 2023

The understanding of genetic diversity and evolutionary relationships within the genus Anadenanthera Speg. (Fabaceae) is limited. Brenan’s classification recognized four species, but Altschul’s classification currently recognizes only two species, each with two varieties. Both classifications were based solely on morphology. We analysed molecular data from 283 specimens using 12 SSRs and 186 specimens using ITS sequence data. The results showed that neither SSR-based genotyping nor ITS-based phylogeny supported Altschul’s classification. Instead, they provided evidence of four reproductively isolated taxa and a single clade corresponding to one of Altschul’s varieties. Additionally, ecological niche modelling (ENM) investigated the influence of past climate on the geographic distribution of Anadenanthera. The ENM results suggest that the ‘varieties’ may have occupied different regions of South America with distinct paleoclimates. On the basis of these findings, the authors suggest recognizing four species, as per Brenan’s original classification.
“We are disposable”: precarity, mobility, and inequity in higher education’s gig academy
Authors: Stewart Nicole K , Adams Philippa R , Bin Quader Shams
Published: September 2023

The COVID-19 pandemic amplified inequities for contingent scholars in the neoliberal gig academy. In this article, we document the struggles of three early career scholars, all contingent instructors, researchers, or both, working at multiple institutions in higher education (HE). Through critical collaborative autoethnography we follow our experiences through the pandemic with a focus on the ‘return to campus’ semester in fall 2021. We forge a critique and activist stance against the structural problem of precarity in HE using our dialogues and vignettes to highlight our experiences around precarity, mobility, and systemic inequities.
Characterizing brain stage-dependent pupil dynamics based on lateral hypothalamic activity
Authors: Takahashi Kengo , Sobczak Filip , Pais-Roldán Patricia , Yu Xin
Published: September 2023

Pupil dynamics presents varied correlation features with brain activity under different vigilant levels. The modulation of brain dynamic stages can arise from the lateral hypothalamus (LH), where diverse neuronal cell types contribute to arousal regulation in opposite directions via the anterior cingulate cortex (ACC). However, the relationship of the LH and pupil dynamics has seldom been investigated. Here, we performed local field potential (LFP) recordings at the LH and ACC, and whole-brain fMRI with simultaneous fiber photometry Ca2+ recording in the ACC, to evaluate their correlation with brain state-dependent pupil dynamics. Both LFP and functional magnetic resonance imaging (fMRI) data showed various correlations to pupil dynamics across trials that span negative, null, and positive correlation values, demonstrating brain state-dependent coupling features. Our results indicate that the correlation of pupil dynamics with ACC LFP and whole-brain fMRI signals depends on LH activity, suggesting a role of the latter in brain dynamic stage regulation.
Differences in atrial substrate localization using late gadolinium enhancement-magnetic resonance imaging, electrogram voltage, and conduction velocity: a cohort study using a consistent anatomical reference frame in patients with persistent atrial fibrillation
Authors: Nairn Deborah , Eichenlaub Martin , Müller-Edenborn Björn , Huang Taiyuan , Lehrmann Heiko , Nagel Claudia , Azzolin Luca , Luongo Giorgio , Figueras Ventura Rosa M , Rubio Forcada Barbara , Vallès Colomer Anna , Westermann Dirk , Arentz Thomas , Dössel Olaf , Loewe Axel , Jadidi Amir
Published: September 2023

Aims

Electro-anatomical voltage, conduction velocity (CV) mapping, and late gadolinium enhancement (LGE) magnetic resonance imaging (MRI) have been correlated with atrial cardiomyopathy (ACM). However, the comparability between these modalities remains unclear. This study aims to (i) compare pathological substrate extent and location between current modalities, (ii) establish spatial histograms in a cohort, (iii) develop a new estimated optimized image intensity threshold (EOIIT) for LGE-MRI identifying patients with ACM, (iv) predict rhythm outcome after pulmonary vein isolation (PVI) for persistent atrial fibrillation (AF).

Methods and results

Thirty-six ablation-naive persistent AF patients underwent LGE-MRI and high-definition electro-anatomical mapping in sinus rhythm. Late gadolinium enhancement areas were classified using the UTAH, image intensity ratio (IIR >1.20), and new EOIIT method for comparison to low-voltage substrate (LVS) and slow conduction areas <0.2 m/s. Receiver operating characteristic analysis was used to determine LGE thresholds optimally matching LVS. Atrial cardiomyopathy was defined as LVS extent ≥5% of the left atrium (LA) surface at <0.5 mV. The degree and distribution of detected pathological substrate (percentage of individual LA surface are) varied significantly (P < 0.001) across the mapping modalities: 10% (interquartile range 0–14%) of the LA displayed LVS <0.5 mV vs. 7% (0–12%) slow conduction areas <0.2 m/s vs. 15% (8–23%) LGE with the UTAH method vs. 13% (2–23%) using IIR >1.20, with most discrepancies on the posterior LA. Optimized image intensity thresholds and each patient’s mean blood pool intensity correlated linearly (R2 = 0.89, P < 0.001). Concordance between LGE-MRI-based and LVS-based ACM diagnosis improved with the novel EOIIT applied at the anterior LA [83% sensitivity, 79% specificity, area under the curve (AUC): 0.89] in comparison to the UTAH method (67% sensitivity, 75% specificity, AUC: 0.81) and IIR >1.20 (75% sensitivity, 62% specificity, AUC: 0.67).

Conclusion

Discordances in detected pathological substrate exist between LVS, CV, and LGE-MRI in the LA, irrespective of the LGE detection method. The new EOIIT method improves concordance of LGE-MRI-based ACM diagnosis with LVS in ablation-naive AF patients but discrepancy remains particularly on the posterior wall. All methods may enable the prediction of rhythm outcomes after PVI in patients with persistent AF.
Introduction to accounting
Authors: Scott Peter
Published: September 2023

This chapter explores why a knowledge of accounting and its integral role in all organizations are of vital importance for a career in business. It looks into the three key accounting statements to provide a working knowledge of how these are put together and how to interpret the information they present. It considers how accounting is a valuable tool for planning for the future and for evaluating outcomes. The chapter illustrates the difference between the two branches of accounting: financial accounting and management accounting, and their roles. What accounting does not do, and the limitations of accounting information, are also discussed.
Business organizations and the financing of business
Authors: Scott Peter
Published: September 2023

This chapter deals with the different features of each type of business organization and the advantages and disadvantages of each format. It presents the different methods each type adopts in order to finance their operations and the requirements that each different financing method imposes. The chapter also considers the features of ordinary and preference share capital and how cash is raised from issuing shares of stock. Moreover, it shows how bonus issues and rights issues work. Finally, it examines how limited companies make dividend distributions and whether they have the capacity to make such distributions.
Relevant costs, marginal costing and short-term decision making
Authors: Scott Peter
Published: September 2023

This chapter expands the analysis of costs to enable use of the costing information in making decisions that will be valid in the short-term (a period of one year or less). This analysis will be used to show which costs are relevant in short-term decision-making situations, and which costs are not. The chapter begins with the definition of contribution. It shows the distinction between fixed and variable costs to determine the costs that are relevant and those that are irrelevant in making short-term decisions. It also illustrates break-even analysis and determination of the margin of safety. Lastly, it shows the use of marginal costing and contribution analysis to make a range of decisions aimed at maximizing short-term profitability.
Immunodeficiencies
Authors: Juris Stephen
Published: September 2023

This chapter outlines the problems that occur when the immune system function is impaired. It discusses what happens if the immune system cannot function properly, noting immunodeficiency as an inability of an arm of the immune system to function which can be caused by a variety of factors. The lack of an immune cell or an immune cell function results in increased likelihood of infection with pathogens that are normally combated by that cell or cell function. The chapter explores examples of immunodeficiencies of the innate and adaptive immune systems and the problems that result. It reviews the three general types of immunodeficiencies: primary immunodeficiencies, secondary immunodeficiencies, and combined immunodeficiencies.
Innate Immunity
Authors: Juris Stephen
Published: September 2023

This chapter explores the many mechanisms that the innate immune system employs to combat pathogens. It looks at the ways in which the innate immune system uses physical and chemical barriers to stave off infection and how it employs innate immune cells to seek out and destroy pathogens. It also analyzes how the innate immune system uses a variety of effector functions to efficiently clear infections. The chapter covers the action of innate immune cells and the use of soluble signaling molecules which function to increase the effectiveness of the innate immune response and facilitate pathogen destruction. It cites Salmonella as an example of an ingested pathogen that the immune system fights using a variety of physical and chemical barriers.
Development of T Lymphocytes
Authors: Juris Stephen
Published: September 2023

This chapter explores the process of T-cell development, reviewing how lymphocytes use the elegant mechanism of somatic recombination to produce a diverse set of receptors responsible for recognizing foreign antigens. It investigates when somatic recombination occurs during lymphocyte development and the means by which these events produce a functioning lymphocyte receptor. It also emphasizes how T cells must produce a cell-surface T-cell receptor to function properly in an adaptive immune response and engage with a peptide presented via an MHC molecule by an antigen-presenting cell. The chapter shows that the production of a T cell is autoreactive or capable of recognizing and combating tissue, which is a major problem that could occur during recombination events. It points out how T-cell receptors must be tested to ensure they cannot bind too tightly to MHC-self-peptide complexes.
Immunoglobulins and B-Cell Diversity
Authors: Juris Stephen
Published: September 2023

This chapter examines the role of immunoglobulins in preventing infections. It discusses how the humoral arm of the adaptive immune system relies on the action of B cells through the action of immunoglobulins, which are important players in the adaptive immune system. It also describes immunoglobulins as proteins that serve as the B-cell receptor and B-cell effector functions. The chapter reviews the somatic recombination of the immunoglobulin loci of B cells that occurs via the same mechanism as T-cell receptor recombination and employ V(D)J recombinase and other key proteins involved in somatic recombination. It outlines five different immunoglobulin isotypes that have specific effector functions that play a role in pathogen destruction and removal: IgM, IgD, IgA, IgG, IgE.
Pathogen Evasion of the Immune System
Authors: Juris Stephen
Published: September 2023

This chapter reviews mechanisms the body uses to combat pathogens and the mechanisms pathogens use to evade immune responses. It highlights the evolutionary arms race between the immune system, which is an efficient weapon against many pathogens that have evolved elaborate mechanisms to survive immune system defenses. It also explains how pathogens use a variety of mechanisms to subvert or evade the immune system hiding from immune system cells, blocking or disrupting the immune response, downregulating immune system activity, and using superantigens to induce a nonspecific immune response. The chapter looks at bacterial pathogens that can reside intracellularly by inducing phagocytosis and then halting the phagocytic process before they are digested by the phagocyte. It also looks at pathogens that can express superantigens that induce a nonspecific lymphocyte response.
Development of B Lymphocytes
Authors: Juris Stephen
Published: September 2023

This chapter explores the other arm of the adaptive immune system, namely, the humoral arm of adaptive immunity. It focuses on B-2 B cells, which make up the majority of B cells responsible for combating infections through activation at secondary lymphoid tissues. It also covers the B-cell development in mice and humans which follows similar patterns during fetal development. These eventually develop in the liver where B-1 B cells are produced to protect pleural and peritoneal cavities and in the bone marrow. The chapter shows how hematopoietic stem cells must receive proper signals to transition to specific lymphoid progenitor cell lineages and ultimately become common lymphoid progenitor cells that can receive B-cell-specific differentiation signals. It discusses the development of B cells that require proper rearrangement of a light chain locus to transition from small pre-B cells to immature B cells.
Review of Molecular Biology
Authors: Momand Jamil , Mccurdy Alison , Heubach Silvia , Warter-Perez Nancy
Published: September 2023

This chapter offers an overview of molecular biology. It presents the essential biology vocabulary for understanding bioinformatics, then introduces the important molecule, the p53 protein (sometimes referred to as ‘p53’, for short), which plays a significant role in preventing cancer. The chapter also discusses the relationship between genes, transcripts, proteins, and some functions carried out by proteins. It then examines how DNA alterations can lead to protein alterations that affect protein function. The chapter next explains the one-letter code for nucleotides and amino acids. Towards the end, the chapter looks at the term ‘sequence alignment’. It also investigates how the first experiment demonstrating the relationship between a mutation and a disease was carried out.
Transcript and Protein Expression Analysis
Authors: Momand Jamil , Mccurdy Alison , Heubach Silvia , Warter-Perez Nancy
Published: September 2023

This chapter highlights the history of gene expression regulation and analysis. It illustrates the methods to measure transcript levels with an emphasis on microarrays and RNA-sequencing, then explicates the nature of proteomics. The chapter further considers the fundamentals of microarray technique, its power, and its limitations as well as the principle of RNA-seq analysis. It also analyses the concept of heatmaps and their use in analysis of microarray expression data. The chapter then moves to highlight the theoretical basis of two-dimensional gel electrophoresis in the separation of proteins. It describes how mass spectrometry is used to identify proteins isolated from 2D-gels. Next, the chapter concludes by examining the peptide mass spectrometry data and software to identify proteins. It then considers the power and limitations of current techniques used for proteome analysis.
Information Organisation and Sequence Databases
Authors: Momand Jamil , Mccurdy Alison , Heubach Silvia , Warter-Perez Nancy
Published: September 2023

This chapter talks about the major public databases that are repositories for sequence data. It describes in detail one of these databases, GenBank, the grandparent of all nucleic acid sequence databases. GenBank is the database that stores the vast amounts of DNA and RNA-sequence data crucial for bioinformatics research. The chapter also looks into Reference Sequence (RefSeq), a database that contains natural (wild-type) sequences, and Protein Knowledge Database (UniProtKB), a well-annotated database focused on the protein products of the genes found in GenBank. Ultimately, the chapter explores the basic organization of a gene or, in other words, how the sequence segments are arranged. The chapter also discusses the method of adding more variability to messenger RNAs and their protein products known as alternative splicing. It then reviews the nomenclature associated with gene organization and alternative splicing to deepen our understanding of bioinformatics and genomics and their applications.
Lipid Metabolism
Authors: McKee Trudy , McKee James R.
Published: September 2023

This chapter outlines the unique role lipids play in living organisms as a result of their hydrophobic structures. Lipids serve as highly efficient and compact energy storage molecules, essential components of biological membranes, and as diverse molecules that have signalling or protective functions. The chapter focuses on the metabolism of the major classes of lipids, that is, how they are synthesized and degraded and how these processes are regulated, emphasizing the central metabolite in lipid metabolism: acetyl-CoA. The chapter covers the metabolism of cholesterol, which plays a prominent role in cardiovascular disease. It explores the metabolism of the major lipid classes: fatty acids, triacylglycerols, phospholipids, and isoprenoids, and reviews the synthesis of the ketone bodies and several metabolic control mechanisms.
Photosynthesis
Authors: McKee Trudy , McKee James R.
Published: September 2023

This chapter considers oxygenic photosynthesis as the most important biochemical process on earth. With a few minor exceptions, photosynthesis is the only mechanism by which an external abiotic source of energy is harnessed by the living world, and it is the source of O2, which sustains all aerobic organisms. It explains photosynthesis as the light-driven biochemical mechanism whereby CO2 is incorporated into organic molecules, such as glucose. The chapter refers to captured light energy that is used to synthesise adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide phosphate (NADPH), which drive the process. The reducing power of NADPH is necessary as a strong electron donor is required to reduce the fully oxidised, low-energy carbon atoms in CO2 to the carbon units of organic molecules.
Nitrogen Metabolism II: Degradation
Authors: McKee Trudy , McKee James R.
Published: September 2023

This chapter deals with the metabolism of nitrogen-containing molecules, such as proteins and nucleic acids, that differs significantly from that of carbohydrates and lipids. Whereas the latter molecules can be stored and mobilized when needed for biosynthetic reactions or for energy generation, there is no nitrogen-storing molecule. The chapter elaborates how organisms must constantly replenish their supply of usable nitrogen to replace organic nitrogen that is lost in catabolism. It mentions the turnover of protein and nucleic acids, which is one of the most obvious aspects of cellular renovation and is a process that results in the continuous flow of nitrogen atoms through living organisms. Living organisms recycle organic nitrogen into a variety of metabolites before the element is reconverted to its inorganic form.
Meta-analysis
Authors: Baker Daniel H.
Published: September 2023

This chapter discusses the significance of meta-analysis as a method for combining the results of several studies computationally. The simplest way to conduct a meta-analysis is by averaging the effect sizes from a bunch of studies that measure the same thing. The main outcome of a meta-analysis is an aggregate estimate of effect size, which is used to determine whether a real effect exists on the balance of evidence. The chapter also considers the tools and designs used for meta-analysis, such as ordinal scales, continuous data, and forest plots. It explains how to conduct a meta-analysis and calculate and convert effect sizes in R.
Multidimensional scaling and k-means clustering
Authors: Baker Daniel H.
Published: September 2023

This chapter covers two multivariate statistical techniques called k-means clustering and multidimensional scaling (MDS). It shows how both methods can be used together as the algorithms involved are used to try to find the best solution without knowing any ground truth group or category labels. K-means clustering aims to partition multivariate data into several clusters, such that observations within a given cluster are more similar to each other than other cluster observations.The chapter further notes that the purpose of multidimensional scaling is to reduce complex multivariate data sets to a smaller number of dimensions to facilitate graphical representation. The chapter also discusses the multidimensional scaling in R.
Climate Oscillations and Climate Change
Authors: Levinton Jeffrey S.
Published: September 2023

This chapter provides an overview of the issue of climate change and its form under oscillations and longer-term trends. Climate changes in the ocean on spatial scales from the size of an entire ocean to that of the world ocean. Warming causes extinctions at the low-latitude end of species ranges, enough to rearrange biogeography. Moreover, the crucial side-product of climate change is the increase of carbon dioxide, which ultimately results in the acidification of the ocean. The chapter discusses the differences between El Niño-Southern Oscillation (ENSO), the North Atlantic Oscillation (NAO), and Pacific Decadal Oscillation (PDO). It also looks at the science surrounding the greenhouse effect and greenhouse gases.
Physiological Development and Epigenetics
Authors: Hill Richard W. , Cavanaugh Daniel J. , Anderson Margaret
Published: September 2023

This chapter focuses on the physiological development and epigenetics of animals. It highlights how the physiology of immature animals always differs from adults. It also considers hermoregulation and brain development as aspects of physiology that undergo postnatal development. Even though their importance is not exclusive for development, phenotypic plasticity and epigenetics have intimate connections with development; phenotype plasticity refers to the ability of an animal to express two or more genetically controlled phenotypes. Epigenetics considers the modifications of gene expression which are transmitted during gene replication. The chapter details the major mechanisms of epigenetic marking: DNA methylation and covalent modification of histone proteins.
Nutrition, Feeding, and Digestion
Authors: Hill Richard W. , Cavanaugh Daniel J. , Anderson Margaret
Published: September 2023

This chapter considers the notion and correlation between nutrition, feeding, and digestion. Nutrition is the study of the chemical compounds that compose and synthesise the bodies of animals. Proteins and lipids are the major components of the body and these allow further understanding of animal nutrition. The chapter defines digestion as the breakdown of food molecules by enzyme action into smaller chemical components, while absorption refers to the entry of molecules into the living tissues of an animal from outside those tissues. The chapter also details the nutritional physiology in longer time frames, while referencing the developmental and clock-driven changes.
Control of Movement
Authors: Hill Richard W. , Cavanaugh Daniel J. , Anderson Margaret
Published: September 2023

This chapter discusses neural control and coordination of movement, particularly the in terms of generation of motor behaviours such as walking, swimming, and flying. It explains that the neural control of skeletal muscle is the basis of animal behaviour, referencing how neural circuits produce relatively simple patterns of motor output to generate behavioural elements. Most animal behaviour consists of sequences of effector actions that result from sequences of motor output of the nervous system. Vertebrate spinal reflexes compensate for circumstance and initiate movement, while the neural generation of rhythmic behaviour involves a central pattern generator (CGP). The chapter then details the interaction of brain areas in movement control.