bluuebunny/crossref_metadata_2025 huggingface dataset:
Umbrella systematic review of potential quality indicators for the detection of dysplasia and cancer at upper gastrointestinal endoscopy
Authors: Kamran Umair , Abbasi Abdullah , Umar Nosheen , Tahir Imran , Brookes Matthew J , Rutter Matt , McCord Mimi , Adderley Nicola J , Dretzke Janine , Trudgill Nigel
Published: September 2023

Background and study aims Upper gastrointestinal (UGI) endoscopy lacks established quality indicators. We conducted an umbrella systematic review of potential quality indicators for the detection of UGI cancer and dysplasia.

Methods Bibliographic databases were searched up to December 2021 for systematic reviews and primary studies. Studies reporting diagnostic accuracy, detection rates or the association of endoscopy or endoscopist-related factors with UGI cancer or dysplasia detection were included. AMSTAR2 and JBI checklists were used to assess systematic review and primary study quality. Clinical heterogeneity precluded meta-analysis and findings are summarized narratively.

Results Eight systematic reviews and nine primary studies were included. Image enhancement, especially narrow band imaging, had high diagnostic accuracy for dysplasia and early gastric cancer (pooled sensitivity 0.87 (95% CI 0.84–0.89) and specificity 0.97 (0.97–0.98)). Higher detection rates with longer endoscopy examination times were reported in three studies, but no difference was observed in one study. Endoscopist biopsy rate was associated with increased gastric cancer detection (odds ratio 2.5; 95% confidence interval [CI] 2.1–2.9). Early esophageal cancer (0.17% vs 0.14%, P=0.04) and gastric cancer (0.16% vs 0.12%, P=0.02) detection rates were higher with propofol sedation compared to no sedation. Endoscopies performed by trained endoscopists on dedicated Barrett’s surveillance lists had higher detection rates (8% vs 3%, P<0.001). The neoplasia detection rate during diagnostic endoscopies for Barrett’s esophagus was 7% (95% CI 4%-10%).

Conclusions Image enhancement use, longer examination times, biopsy rate and propofol sedation are potential quality indicators for UGI endoscopy. Neoplasia detection rate and dedicated endoscopy lists are additional potential quality indicators for Barrett’s esophagus
Lateral Crural Repositioning: Implications on Nasal Function
Authors: Toriumi Dean M. , Cristel Robert T.
Published: September 2023

There are many concepts for surgical management of the nasal tip with varying outcomes on esthetics and nasal function. Nasal tip surgery can influence nasal function based on how the techniques can alter lateral wall integrity. A retrospective chart review of rhinoplasty patients undergoing lateral crural strut grafting (LCSG) with and without repositioning from 2009 to 2017 of the primary author (D.M.T.) was performed. Preoperative and postoperative Nasal Obstruction Symptom Evaluation (NOSE) scores were analyzed. In our study, 832 subjects were evaluated. The mean preoperative NOSE score of all subjects was 35.48. The longest follow-up mean was 652.07 days with a mean NOSE score of 7.07 (p < 0.0001). In the LCSG group, the mean preoperative NOSE score was 22.97. The longest follow-up mean was 583.29 days with a mean NOSE score of 7.22 (p < 0.0001). In the LCSG with repositioning group, the mean preoperative NOSE score was 43.42. The longest follow-up mean was 692.36 days with a mean NOSE score of 7.60 (p < 0.0001). LCSGs with or without repositioning improves nasal function showing significant improvement in NOSE scores. The use of these techniques require adhering to several technical points to maximize outcomes and to avoid deformity.
The Impact of Parkinson's Disease on Social Communication: An Exploratory Questionnaire Study
Authors: Sharma Saryu , Fleck Kimberly , Winslow Sherri , Rothermich Kathrin
Published: September 2023

Individuals with Parkinson's disease (PD) often show breakdown in the production and interpretation of aspects of social communication. However, there is no current method of assessment for evaluating social communication dysfunction in individuals with PD. The aim of this study was to develop a self-report questionnaire for individuals with PD to identify their social communication skills, and further recognize the impact of PD on social communication. Fifty-one individuals with Parkinson's disease answered 28 survey questions. These questions pertained to emotional expression and perception, social communication, sarcasm/humor, and pragmatic skills. Exploratory factor analysis and reliability analysis were conducted to identify items loading onto the factors and to check the internal consistency of the items. Individuals with PD reported changes in emotional expression and perception, social communication, sarcasm and humor, and pragmatic skill domains post-PD diagnosis. No correlations were found between age or time since diagnosis and emotional expression, social communication, sarcasm, and humor. This study provides self-reported evidence that individuals with PD experience social communication challenges. Future research should further quantify these challenges, study their impact on daily communicative functioning, and use the results to develop social communication interventions that improve the quality of life for persons with PD.
Liver and mesenteric hydatid cyst in a child
Authors: Vutukuru Sravanthi , Peters Nitin James , Mewara Abhishek , Kaur Simran , Samujh Ram
Published: September 2023

Hydatid disease, though endemic in the sub-Himalayan region of the subcontinent, is relatively rare in the pediatric age group. The simultaneous existence of hydatid in two or more organs is very rare, seen only in 5 to 13% of patients. We report an 11-year-old patient, who presented with painless progressive abdomen distension over 6 months. Imaging studies revealed a large cystic lesion occupying majority of the abdomen. The patient was diagnosed to have a hydatid cyst of the liver and mesentery, with multiple daughter cysts intraoperatively. Excision of the cyst was done and the patient is doing well on postoperative follow-up of 1 year.
Inferiorly Based Fasciocutaneous Flaps In Leg - Our Experience
Authors: Jena Dr. Subrat Kumar , Ray Dr. Falguni , Nayak Dr. Mrs. Bijaylakhmi , Das Dr. Binay Kumar
Published: September 2023

Inferiorly based fasciocutaneous flaps have emerged as an ideal material for the defects in lower leg and foot. We have used this flap in eleven patients since 1986 through 1989. The flaps have proved to be reliable over difficult areas of ankle and foot, either multistaged distant flaps or free flaps are the other alternative. Here inferiorly based fasciocutaneous flaps offer a much simpler and safer answer.
Extensor Digitorum Brevis Manus Muscle - A Diagnostic Red Herring
Authors: Tewari Vinay K , Tandon Pradeep
Published: September 2023

Extensor digitorum brevis muscle is an atavistic muscle occurring rarely in the dorsum of hand. The anomaly is so rare that it is usually diagnosed as a ganglion. In the case presented one hand was explored and the presence of the muscle on the other side was confirmed by electromyography.
A Comparative Study of Some Treatment Modalities in Cutaneous Haemangiomas
Authors: Jain P , Sinha J K
Published: September 2023

151 children with cutaneous haemangiomas were treated using different treatment modalities and the results were compared. Intralesional triamcinolone was found to be the safest and most effective in strawberry lesions. Cavernous lesions in our study responded best to 50% dextrose injections. A combined approach of oral prednisolone and triamcinolone injections was found to be very useful for mixed lesions.
Pectoralis Major Flap In 77 Head And Neck Reconstructions
Authors: Khazanchi Dr. R.K. , Shukla Dr. N.K. , Nanda Dr. R.
Published: September 2023

77 patients with head and neck excisional defect are treated by use of Pectoralis major myo cu-taneous, myocutaneous with skin paddle, and composite, incorporating rib. Results are presented.
Composite control of anti-drone platform for stable tracking under disturbance
Authors: Gao Wenrui , Cui Huimin
Published: September 2023

First, focused on the complex problem that a U-shaped tracking frame is unreachable to obtain the pointing angles of an unmanned aerial vehicle target, a novel coordinate transformation method is proposed in this paper. The fixed transformation relationship between the intermediate links is deduced by establishing a unified coordinate system, simplifying the algorithm conversion process, and saving computing resources and time. Furthermore, the accuracy of the proposed method has been verified in both aspects of theory and experiment. Then, in order to achieve smooth motion performance between target pointing strategy and stable tracking strategy, a mode switching method based on hysteresis intervals is developed. Compared with the traditional single-point threshold method, the switching method overcomes the high frequency jitter problem. The experimental results validate the consistency between practical effects and theoretical expectations. Finally, to improve the disturbance rejection performance of the platform, a composite control method integrating the information from the gyroscope and circular grating is proposed. The corresponding control scheme and the compensation principle are conceived and explained. The experimental results show the anti-interference performance of the proposed composite control method is five times that of the closed-loop method based on the gyroscope speed signal and two times that of the disturbance observer control method.
Dependence of photocatalytic activity on the direction of the intrinsic dipole in GaOI-based Janus structures
Authors: Li Manting , Zhou Mengshi , Min Jiewen , Zhang Chunxiao , Tang Chao , Zhong Jianxin
Published: September 2023

In Janus photocatalysts, intrinsic dipole (P) plays an important role in the separation of photogenerated carriers and photocatalytic activity for water splitting. However, effectively switching the direction of the P vector between different surfaces is still an open issue. Based on first-principles calculation, we find that the P vector relies on charge distribution, while the distribution of the conduction band maximum-distributed reduction reaction surfaces (Sc) and valence band minimum-distributed oxidation surfaces (Sv) depends on the orbital hybridization in GaOI-based Janus. The direction of the P vector can be switched between Sc and Sv by substituting a metal or halogen atomic layer. The P vector in the direction from Sc to Sv releases bandgap limitation, broadens the light absorption range, and improves high carriers’ mobility and solar-to-hydrogen efficiency (STH) efficiency, while the P vector pointing from Sv to Sc hinders the photocatalytic activity of GaOI-based Janus. Based on the investigation of STH efficiency and redox reactions, GaInOI is found to be a potential photocatalyst for overall water splitting. The stability of the Janus is studied by ab initio molecular dynamics and phonon diffusion spectrum. Current work proposes that switching the direction of the P vector between Sv and Sc is a potential route to regulate the band structure, optical absorption, and photocatalytic activity in GaOI-based Janus.
Two-phase flow and morphology of the gas–liquid interface for bubbles or droplets in different microchannels
Authors: Chen Cheng , Jing Zefeng , Feng Chenchen , Zou Xupeng , Qiao Mingzheng , Xu Donghai , Wang Shuzhong
Published: September 2023

Two-phase interface fluid, bubble or droplet, has shown broad application potential in oil and gas field development, contaminated soil remediation, and medical treatment. These applications are particularly concerned about the flow characteristics of the two-phase fluid in different channels. Herein, we summarize and analyze the research progress in the flow of bubbles (or droplets) in different channels, mainly including simple, Y-junction/T-junction, and obstructed microchannels. At present, there is no systematic theory about the structure and mechanical evolution of the two-phase interface fluid, and therefore, the comprehensive study is still insufficient. Especially, current studies on the breakup of the two-phase interface in bifurcated channels mainly focus on a few of specific perspectives and a general conclusion is not achieved. In addition, to systematically verify the mechanism of bubble (or droplet) breakup, extensive studies on the three-dimensional physical model of bubbles (or droplets) are needed. Furthermore, we have also sorted out the involved influencing factors, as well as the prediction models for bubble (or droplet) breakup and retention in different channels, and in the end, we provide suggestions for the potential research and development of the two-phase interface fluid.
Intruder-free cumulant-truncated driven similarity renormalization group second-order multireference perturbation theory
Authors: Li Shuhang , Misiewicz Jonathon P. , Evangelista Francesco A.
Published: September 2023

Accurate multireference electronic structure calculations are important for constructing potential energy surfaces. Still, even in the case of low-scaling methods, their routine use is limited by the steep growth of the computational and storage costs as the active space grows. This is primarily due to the occurrence of three- and higher-body density matrices or, equivalently, their cumulants. This work examines the effect of various cumulant truncation schemes on the accuracy of the driven similarity renormalization group second-order multireference perturbation theory. We test four different levels of three-body reduced density cumulant truncations that set different classes of cumulant elements to zero. Our test cases include the singlet–triplet gap of CH2, the potential energy curves of the XΣg+1 and AΣu+3 states of N2, and the singlet–triplet splittings of oligoacenes. Our results show that both relative and absolute errors introduced by these cumulant truncations can be as small as 0.5 kcal mol−1 or less. At the same time, the amount of memory required is reduced from O(NA6) to O(NA5), where NA is the number of active orbitals. No additional regularization is needed to prevent the intruder state problem in the cumulant-truncated second-order driven similarity renormalization group multireference perturbation theory methods.
On the electronic structure and spin–orbit coupling of BiB from photoelectron imaging of cryogenically-cooled BiB− anion
Authors: Gao Han-Wen , Choi Hyun Wook , Hui Jie , Chen Wei-Jia , Kocheril G. Stephen , Wang Lai-Sheng
Published: September 2023

We report a study on the electronic structure and chemical bonding of the BiB molecule using high-resolution photoelectron imaging of cryogenically cooled BiB− anion. By eliminating all the vibrational hot bands, we can resolve the complicated detachment transitions due to the open-shell nature of BiB and the strong spin–orbit coupling. The electron affinity of BiB is measured to be 2.010(1) eV. The ground state of BiB− is determined to be 2Π(3/2) with a σ2π3 valence electron configuration, while the ground state of BiB is found to be 3Σ−(0+) with a σ2π2 electron configuration. Eight low-lying spin–orbit excited states [3Σ−(1), 1Δ(2), 1Σ+(0+), 3Π(2), 3Π(1), 1Π(1)], including two forbidden transitions, [3Π(0−) and 3Π(0+)], are observed for BiB as a result of electron detachment from the σ and π orbitals of BiB−. The angular distribution information from the photoelectron imaging is found to be critical to distinguish detachment transitions from the σ or π orbital for the spectral assignment. This study provides a wealth of information about the low-lying electronic states and spin–orbit coupling of BiB, demonstrating the importance of cryogenic cooling for obtaining well-resolved photoelectron spectra for size-selected clusters produced from a laser vaporization cluster source.
ZnO/ZnS core–shell quantum dots with enhanced ultraviolet fluorescence and low cytotoxicity for cell imaging
Authors: Chen Yuhang , Xue Qi , Luo Weiguo , Sun Yu , Li Ming , Hang Tao
Published: September 2023

Zinc oxide quantum dots (ZnO QDs) have gained wide attention due to their wide excitation spectrum, large Stokes shift, adjustable photoluminescence (PL) spectrum, and excellent biocompatibility. However, low fluorescence intensity and poor stability restrict their further applications. In this work, zinc sulfide (ZnS) as a surface modifier, ZnO/ZnS core–shell QDs with type-I core–shell structure and particle size of 5 nm were prepared via sol–gel method. Transmission electron microscope characterization demonstrates the core–shell structure and spherical morphology of the as-synthesized ZnO/ZnS QDs. The PL spectra show that ultraviolet fluorescence has been greatly enhanced. The maximum fluorescence intensity of ZnO/ZnS core–shell QDs increases by 5288.6% compared with that of bare ZnO QDs. The PL quantum yield increases from 9.53% to 30.95%. After being stored for three weeks, the fluorescence performance can be well retained. Furthermore, the cytotoxicity tests confirm the excellent biocompatibility of ZnO/ZnS core–shell QDs, demonstrating they are good candidates for cell imaging.
FSE-Net: feature selection and enhancement network for mammogram classification
Authors: Liao Caiqing , Wen Xin , Qi Shuman , Liu Yanan , Cao Rui
Published: September 2023

Objective. Early detection and diagnosis allow for intervention and treatment at an early stage of breast cancer. Despite recent advances in computer aided diagnosis systems based on convolutional neural networks for breast cancer diagnosis, improving the classification performance of mammograms remains a challenge due to the various sizes of breast lesions and difficult extraction of small lesion features. To obtain more accurate classification results, many studies choose to directly classify region of interest (ROI) annotations, but labeling ROIs is labor intensive. The purpose of this research is to design a novel network to automatically classify mammogram image as cancer and no cancer, aiming to mitigate or address the above challenges and help radiologists perform mammogram diagnosis more accurately. Approach. We propose a novel feature selection and enhancement network (FSE-Net) to fully exploit the features of mammogram images, which requires only mammogram images and image-level labels without any bounding boxes or masks. Specifically, to obtain more contextual information, an effective feature selection module is proposed to adaptively select the receptive fields and fuse features from receptive fields of different scales. Moreover, a feature enhancement module is designed to explore the correlation between feature maps of different resolutions and to enhance the representation capacity of low-resolution feature maps with high-resolution feature maps. Main results. The performance of the proposed network has been evaluated on the CBIS-DDSM dataset and INbreast dataset. It achieves an accuracy of 0.806 with an AUC of 0.866 on the CBIS-DDSM dataset and an accuracy of 0.956 with an AUC of 0.974 on the INbreast dataset. Significance. Through extensive experiments and saliency map visualization analysis, the proposed network achieves the satisfactory performance in the mammogram classification task, and can roughly locate suspicious regions to assist in the final prediction of the entire images.
Flexible capacitive and piezoresistive pressure sensors based on screen-printed parylene C/polyurethane composites in low-pressure range
Authors: Kurnaz Sedat , Ozturk Ozgür , Mehmet Ali Hazar , Guduloglu Utku , Yilmaz Nurdane , Cicek Osman
Published: September 2023

The use of polymers to fabricate flexible pressure sensors as an alternative to conventional pressure sensors has led to the development of physiological monitoring of human body and the electronic skin. In particular, the fabrication of flexible capacitive and piezoresistive sensors using a variety of materials and the investigation of their electromechanical properties are further developments in these fields. Herein, parylene C is synthesized via chemical vapor deposition method. Pressure-sensitive inks are prepared with a composite of parylene C, polyurethane, polymethylmethacrylate, and activated carbon at certain weight ratios. Flexible capacitive and piezoresistive pressure sensors are fabricated by the screen printing method. The sensitivity, detection limit, linearity range, and response/relaxation time, which define the capacitive and piezoresistive properties are investigated and presented in this paper. The sensitivities of the flexible capacitive and piezoresistive pressure sensors are 0.124 kPa−1 and 0.074 kPa−1 in the pressure range of 0.07–1.39 kPa. This study enables parylene C to be used in the composite structure and shows that it can be used not only as a protective layer but also in flexible pressure sensor applications. It also ensures that the design of the flexible capacitance pressure sensor can measure low pressure with high sensitivity compared to the flexible piezoresistive pressure sensor.
Cap-DiBiL: an automated model for crop water requirement prediction and suitable crop recommendation in agriculture
Authors: Munaganuri Ravi Kumar , Rao Yamarthi Narasimha
Published: September 2023

In this technological era, several approaches used to provide the information about suitable crop recommendation means which is crop is suitable for soil. Some of approaches depends on the IoT smart agricultural-devices to gather information from surrounding area. However, several collection of data are used to predict the crops details but it not efficient to provide better performance. Therefore, the proposed model uses various techniques to improve the performance efficiently. Some steps involved in the proposed model as data pre-processing, feature extraction, feature selection, water requirement prediction and recommendation. Initially, the collected IoT data from dataset are pre-processed using data normalization, missing value imputation and one-hot encoding. Then, extract the features from pre-processed data using Gated Residual autoencoder (GRA) model, whereas optimal features are selected using Chaotic Northern Goshawk Optimization (ChaNgo) algorithm. Based on the farmland details, the crop water requirement prediction and suitable crop recommendation due to the market price are carried out using a novel hybrid deep learning model called Channel capsule-assisted stacked dilated Bi-LSTM (Cap-DiBiL). The channel capsule network predicts the crop water requirement and stacked dilated Bi-LSTM is used for suitable crop recommendations such as millets, rice and other crops. Then the proposed model analyses the performance and compares it with several existing techniques to prove the proposed model’s enhancement. The proposed model improved the accuracy as 98.18% for predicting the crop water requirement and crop recommendation. The performance of proposed model for Precision, Recall and F1 score also enhanced as 98.31%, 98.18% and 98.20%.
A sharp bound for the resurgence of sums of ideals
Authors: Kien Do , Nguyen Hop , Thuan Le
Published: September 2023

We prove a sharp upper bound for the resurgence of sums of ideals involving disjoint sets of variables, strengthening work of Bisui–Hà–Jayanthan–Thomas [Collect. Math. 72 (2021), pp. 605–614]. Complete solutions are delivered for two conjectures proposed by these authors. For given real numbers

a
a

and

b
b

, we consider the set

R
e
s
(
a
,
b
)

Res(a,b)

of possible values of the resurgence of

I
+
J

I+J

where

I
I

and

J
J

are ideals in disjoint sets of variables having resurgence

a
a

and

b
b

, respectively. Some questions and partial results about

R
e
s
(
a
,
b
)

Res(a,b)

are discussed.
Revolutionizing dermatology residency: artificial intelligence for knowledge and clinical milestones assessment
Authors: Ramachandran Vignesh , Jairath Neil , Cheraghlou Shayan , Pahalyants Vartan
Published: September 2023

Artificial intelligence can be adapted and used to augment resident education in order to assess clinical milestones in real-time, providing powerful insights for educators and trainees alike. Further research on integrating such technology into our models of learning fosters the growth of our specialty and trainees’ aptitudes.
Outcomes of patients with atrial fibrillation on oral anticoagulation with and without heart failure: the ETNA-AF-Europe registry
Authors: Schnabel Renate B , Ameri Pietro , Siller-Matula Jolanta M , Diemberger Igor , Gwechenberger Marianne , Pecen Ladislav , Manu Marius Constantin , Souza José , De Caterina Raffaele , Kirchhof Paulus
Published: September 2023

Aims

Heart failure (HF) is a risk factor for major adverse events in atrial fibrillation (AF). Whether this risk persists on non-vitamin K antagonist oral anticoagulants (NOACs) and varies according to left ventricular ejection fraction (LVEF) is debated.

Methods and results

We investigated the relation of HF in the ETNA-AF-Europe registry, a prospective, multicentre, observational study with an overall 4-year follow-up of edoxaban-treated AF patients. We report 2-year follow-up for ischaemic stroke/transient ischaemic attack (TIA)/systemic embolic events (SEE), major bleeding, and mortality. Of the 13 133 patients, 1854 (14.1%) had HF. Left ventricular ejection fraction was available for 82.4% of HF patients and was <40% in 671 (43.9%) and ≥40% in 857 (56.1%). Patients with HF were older, more often men, and had more comorbidities. Annualized event rates (AnERs) of any stroke/SEE were 0.86%/year and 0.67%/year in patients with and without HF. Compared with patients without HF, those with HF also had higher AnERs for major bleeding (1.73%/year vs. 0.86%/year) and all-cause death (8.30%/year vs. 3.17%/year). Multivariate Cox proportional models confirmed HF as a significant predictor of major bleeding [hazard ratio (HR) 1.65, 95% confidence interval (CI): 1.20–2.26] and all-cause death [HF with LVEF <40% (HR 2.42, 95% CI: 1.95–3.00) and HF with LVEF ≥40% (HR 1.80, 95% CI: 1.45–2.23)] but not of ischaemic stroke/TIA/SEE.

Conclusion

Anticoagulated patients with HF at baseline featured higher rates of major bleeding and all-cause death, requiring optimized management and novel preventive strategies. NOAC treatment was similarly effective in reducing risk of ischaemic events in patients with or without concomitant HF.
Ratio analysis 1:profitability, efficiency and performance
Authors: Scott Peter
Published: September 2023

This chapter presents ratio analysis, the most commonly used technique in evaluating financial statements. It exposes the importance and advantages of using ratios to evaluate the profitability, efficiency, performance, liquidity, and long-term financial stability. It begins with the discussion of profitability ratios, how they are calculated and their interpretation. Next, it delves into the calculation of efficiency ratios and shows how this helps to explain changes in profitability changes. Then it examines performance ratios and explains what this means to shareholders. Finally, it explores benchmarking, comparing one entity’s ratios against other company’s in the same industry.
Standard costing and variance analysis
Authors: Scott Peter
Published: September 2023

This chapter considers the use of the technique of standard costing and how the analysis of divergences from the standard can be used to identify problems requiring management’s attention. It begins with the definition of standard costing and variance analysis. Then it progresses to the calculation of the standard cost. Moreover, it also provides the calculation of various variances including usage variances, rate variances, and price variances, among others. There is also a discussion of the function of standard costing as an accounting control device. As well as this, the chaopter points out that variances are merely an indication of a problem that requires further management investigation to establish and rectify the causes.
Capital investment appraisal
Authors: Scott Peter
Published: September 2023

This chapter discusses capital investment appraisal, or the determination as to whether new investments will be worthwhile, and whether they will generate more cash than they originally cost. It starts by defining capital investment and explains why businesses undertake capital investment appraisal when making long-term investment decisions. The chapter then introduces the four main capital investment appraisal techniques and their application to capital investment decisions. Moreover, it likewise explores the advantages and limitations of each of the four main capital investment appraisal techniques. At the end of the chapter, the concept of the time value of money is expounded.
Molecular Evolution
Authors: Momand Jamil , Mccurdy Alison , Heubach Silvia , Warter-Perez Nancy
Published: September 2023

This chapter addresses molecular evolution, which explains the diversity of sequences and how mutations get passed to progeny. It seeks to understand the reason why mutations are the drivers of evolution. The chapter also describes the types of mutations, including point mutation, indel, repeat expansion, partial gene duplication, and whole gene duplication. It looks into mutations acquired during cancer progression and mutations acquired during evolution. The chapter then shifts to distinguish the terms homolog, ortholog, and paralog and how they arise during evolution. It also demonstrates how exon shuffling can account for the modular nature of proteins. Finally, the chapter presents the difference between vertical and horizontal gene transfer. It then examines how a DNA-binding domain within TP53 gene is often mutated in human cancers.
Basic Local Alignment Search Tool (Blast) and Multiple Sequence Alignment
Authors: Momand Jamil , Mccurdy Alison , Heubach Silvia , Warter-Perez Nancy
Published: September 2023

This chapter look at the topic of pairwise sequence comparison by describing the Basic Local Alignment Search Tool (BLAST). It discusses multiple sequence alignment programs with an emphasis on the first popular program of this class–Cluster Alignment Weighted (ClustalW). In the 1990s, advances in DNA sequencing technology led to a significant expansion of the number of sequences deposited in databases. The chapter examines the logic of how BLAST aligns a query sequence with a subject sequence from a database. It emphasizes the significant advantages of BLAST over other sequence alignment programs: its increased speed and its use of a statistical measurement, the E-value, to assess the significance of the similarity score. The chapter then shifts to look into major BLAST programs available through NCBI. It then analyses the logic of how ClustalW aligns multiple sequences, then considers other multiple sequence alignment programs.
Genomics
Authors: Momand Jamil , Mccurdy Alison , Heubach Silvia , Warter-Perez Nancy
Published: September 2023

This chapter displays genomics analysis with an emphasis on next-generation sequencing (NGS), and annotation of bacterial genomes. It uncovers the underlying principles of dideoxy sequencing and selected next-generation sequencing technologies. The chapter also examines the theory of polymerase chain reaction (PCR) and the general categories of DNA that constitute the human genome (the genomic landscape). The chapter then shifts to investigate how DNA fingerprinting is performed and the degree of synteny shared between genomes. It reviews the whole genome shotgun strategy approach to genome sequencing, then examines how gene prediction software programs predict and annotate genes in genomes. Finally, the chapter describes the haplotype, the HapMap Project, and the significance of the HapMap project. It then looks into the benefits and concerns of having knowledge of personal genome data.
Introduction
Authors: Momand Jamil , McCurdy Alison , Heubach Silvia , Warter-Perez Nancy
Published: September 2023

This introductory chapter provides a definition of bioinformatics and a brief exploration of the origins of the term. The chapter then provides examples of the application of bioinformatics in society, academia, and the workplace. Finally, the chapter raises the importance of bioinformatics and its application to genomics.
Living Cells
Authors: McKee Trudy , McKee James R.
Published: September 2023

This chapter talks about cells, which are the structural units of all living organisms. The human body represents a remarkable illustration of the diversity of cells as it contains about 200 types. This great variation reflects the variety of functions that cells can perform. However, no matter what their shape, size, or species, cells are also amazingly similar. The chapter shows how cells are surrounded by a membrane that separates them from their environment. It explains that they are composed of the same types of molecules. The chapter reviews the structural hierarchy of life on earth and argues that it extends from the biosphere to biomolecules. Cells are considered the basic unit of life, since they are the smallest entities that are actually alive.
Carbohydrates
Authors: McKee Trudy , McKee James R.
Published: September 2023

This chapter discusses carbohydrates, which are an important source of rapid energy production for living cells,the structural building blocks of cells, and the components of numerous metabolic pathways. The chapter refers to sugar polymers linked to proteins and lipids which, it states, are now recognized as a high-density coding system. Their vast structural diversity is exploited by living organisms to produce the immense informational capacity required for living processes. The chapter describes the structures and chemistry of typical carbohydrate molecules found in living organisms. Carbohydrates are the most abundant biomolecules in nature and are a direct link between solar energy and the chemical bond energy of living organisms.
Carbohydrate Metabolism
Authors: McKee Trudy , McKee James R.
Published: September 2023

This chapter reviews the crucial roles carbohydrates play in the metabolic processes of living organisms as they serve as energy sources and structural elements in living cells. It looks at the role of carbohydrates in energy production, focusing on its synthesis, degradation, and storage as the monosaccharide glucose is a prominent energy source in almost all living cells. The term metabolism is used to describe the thousands of enzyme-catalysed biochemical reactions that sustain life in living organisms. The chapter analyses how biochemical reactions are spatially and temporally organised into complex, interconnected networks. It classifies all biochemical reaction pathways into three major categories: signal transduction pathways, genetic regulatory pathways, and core metabolic pathways.
Lipids and Membranes
Authors: McKee Trudy , McKee James R.
Published: September 2023

This chapter describes lipids as naturally occurring water-insoluble substances that perform a stunning array of functions in living organisms. It presents some lipids that are vital energy reserves and others that are the primary structural components of biological membranes. Other lipid molecules act as hormones, antioxidants, pigments, or vital growth factors and vitamins. The chapter describes the structures and properties of the major lipid classes found in living organisms as well as the structural and functional properties of biomembranes. It also looks at the structure and function of each major type of lipid and investigates lipoproteins, complexes of protein and lipid that transport lipids in animals. It finishes with an overview of membrane structure and function.
Genetic Information
Authors: McKee Trudy , McKee James R.
Published: September 2023

This chapter describes all living organisms as information-processing systems. Their ultimate source of information is encoded in the nucleotide base sequence of DNA. As biochemists have searched ever more deeply into the mysteries of genetic information storage and transmission, how DNA is replicated, and gene expression is controlled, they have transformed all of the life sciences. The chapter cites the knowledge and technologies that were acquired during this pursuit and that have provided an understanding of the intricacies of living processes that is still unfolding. It also reviews the instructions required to produce a certain type of organization that must be stably stored to safeguard their accuracy and availability for use. Information must also be converted into a form that can be utilized.
Protein Synthesis
Authors: McKee Trudy , McKee James R.
Published: September 2023

This chapter considers proteins as the most dynamic, numerous, and varied class of biomolecules, where in the uniqueness of each cell type is caused almost entirely by the proteins it produces. It is not surprising, therefore, that a relatively large amount of cellular energy is used in protein synthesis. The chapter describes the synthesis of proteins as a regulated process which is the result of their strategic importance in the cellular economy. It then turns to protein synthesis, which is the process in which genetic information encoded in the nucleic acids is translated into the 20 standard amino acid alphabet of polypeptides. In addition to translation, protein synthesis includes the processes of posttranslational modification and targeting.
Introduction to the R environment
Authors: Baker Daniel H.
Published: September 2023

This chapter introduces the R programming language, which is freely available for all major operating systems. It explains the significance of Rstudio in the development of the core R language. RStudio has several customizable options to improve accessibility through the sections of Preferences and Appearance. Moreover, the help function is a great way of finding out more about a specific R function. The chapter then discusses the examples of R syntax for fundamental programming concepts such as scripts, data objects, functions, packages, conditional statements, and loops. It presents a table of the useful core R functions and their respective description.
Statistical tests as linear models
Authors: Baker Daniel H.
Published: September 2023

This chapter examines the R implementations of statistical tests commonly taught in introductory statistics courses. Statistical tests have been developed by different people at different times. Such tests include the t-test and the Analysis of Variance (ANOVA). The clearest way to demonstrate the model comparison approach is by starting with linear regression and then applying the same logic to other situations. The chapter elaborates on the assumptions of linear models, citing how the key assumption of parametric statistics is that the data are normally distributed. It explains the necessity of checking whether the variances are equivalent for each group for tests comparing different data groups.
Structural equation modelling
Authors: Baker Daniel H.
Published: September 2023

This chapter looks into structural equation modelling (SEM), which is a technique that allows the further understanding of relationships between different variables. SEM is primarily achieved through the creation of a model that specifies how the variables are connected, and how they relate to latent variables that cannot be measured directly through path analysis. Latent variables often range between factors such as intelligence, belief, political leanings, personality, and quality of life. Moreover, researchers often use SEM to operate multiple correlations between several different pairs of variables. The chapter considers the four stages of SEM: model specification, model identification, model evaluation, and model modification. It also explains how to conduct the SEM in R.
Multivariate pattern analysis
Authors: Baker Daniel H.
Published: September 2023

This chapter covers the process of multivariate pattern analysis. Multivariate pattern analysis is widely used to analyse MRI recordings of brain activity through a subset of machine learning. Machine learning methods also have substantial promise in the area of personalized medicine and automated diagnosis. The ethical issues with machine learning and classification revolve around the reality that any algorithm could be biased by the prejudices of those who constructed them. The chapter also considers object identification algorithms and dictation software which convert speech to text as prominent examples of machine learning methods. It explains how to carry out multivariate pattern analysis in R using the Classification And Regression Training (Caret) package.
Signal detection theory
Authors: Baker Daniel H.
Published: September 2023

This chapter argues that the signal detection theory is the foundation of modern psychophysical studies of perception and memory. Signal detection theory refers to the method of formalizing how humans and other systems make decisions under uncertainty, which primarily revolves around the fluctuation of information being used to make decisions over time. The theory is also applied to recent artificial intelligence (machine learning) research. The chapter references the practice of chicken sexing while looking at the approach of signal detection theory. It notes the growing interest in Type II signal detection theory wherein participants make confident judgements about their performance before elaborating the process of calculating meta-d' in R.
The Open Sea
Authors: Levinton Jeffrey S.
Published: September 2023

The chapter elaborates on the distributions and adaptations of the open sea. Biological and physical processes throughout the depth-time-space gradients of the deep sea operate over a very large range of time and space scales. The chapter discusses the physical processes that disperse plankton and behavior, which cause aggregations of plankton and the attraction of plankton feeders to plankton. The chapter also looks into the oceanographic conditions which result in ocean-scale movements of predators at the top of food webs. Moreover, some interactions of processes regulate spatial differences in phytoplankton abundance and relate these on many spatial scales to consumers.
Processes in the Water Column
Authors: Levinton Jeffrey S.
Published: September 2023

This chapter covers the processes in the water column in relation to plankton. It discusses the importance and interaction of various factors in plankton dynamics. Water motion is important for phytoplankton growth in all parts of the ocean, but its influence is best introduced in correlation with the spring phytoplankton increase. Moreover, animal grazing affects phytoplankton abundance. The chapter explains that temporal changes, driven by seasonal cycles of nutrient supply, light, and turbulence, are also major drivers of plankton abundance. It shows that zooplankton can aggregate by swimming, but a local phytoplankton patch is a balance between population growth and dispersal by turbulence.
The Shallow Coastal Subtidal
Authors: Levinton Jeffrey S.
Published: September 2023

This chapter focuses on a series of shallow, coastal subtidal environments. It shows how grass beds, rocky reefs, kelp forest systems, and coral reefs are the most productive and diverse subtidal benthic environments. The habitats are dominated by highly productive benthic primary producers, which also contribute to the structural habitat and qualify as ecosystem engineers. The chapter notes how coral reefs and nearby environments showcase remarkable mutualisms and species which develop strong defences despite the intensity of predation. It looks into coral reef restoration and describes how this involves the establishment of marine protected areas, the restoration of predators and grazers, and the direct transplant of coral species decimated by disturbance and disease.
Biodiversity and Conservation of the Ocean
Authors: Levinton Jeffrey S.
Published: September 2023

This chapter looks at the notion of biodiversity and the conservation of the ocean. It explores patterns of biological diversity from the broader perspectives of evolution, extinction, and biogeography. Regional variation in geography and climate influences the origin of species, and also the degree of geographic structuring of the world into assemblages of species. The chapter then elaborates on factors of diversity, speciation, extinction, and biography in the ocean. It explains how many marine invasions are facilitated by human transport, referencing the subsequent local extinctions and homogenization of marine biot after the introduction of new species. Thus, conservation genetics play a role in identifying both species and genetically distinct populations.
Environmental Impacts of Industrial Activities and Human Populations
Authors: Levinton Jeffrey S.
Published: September 2023

This chapter highlights the environmental impacts of industrial activities and human populations. It examines how the Industrial Revolution and the sudden flowering of New York City brought along major habitat deterioration. Industrial activities have been adding greenhouse gases to the atmosphere since the nineteenth century. Moreover, complex interactions of human impacts often make it difficult to understand the role of various pollutants in degrading the marine environment. The chapter then looks into the impact of toxic substances on humans and marine life, which references the sources of sewage, nonpoint coastal sources, and atmospheric deposition. Moreover, global climate change only adds another layer of stress to the entire oceanic system.
The Lives of Mammals in Frigid Places
Authors: Hill Richard W. , Cavanaugh Daniel J. , Anderson Margaret
Published: September 2023

This chapter covers the interrelation of food, energy, and temperature with reference to the lives of mammals in frigid regions. Reindeer, as a species, are probably the most adapted of all inland mammals to cold exposure. At birth, reindeer calves must thermoregulate on their own from the moment of their birth or they will die. Body size is a principal determinant of the ways animals relate to a frigid environment. The chapter then discusses hibernation as a winter strategy while highlighting the key role of brown fat in hibernation. It considers the notion of social hibernation, which is the intersection of sociobiology and hibernation physiology.
Neurons
Authors: Hill Richard W. , Cavanaugh Daniel J. , Anderson Margaret
Published: September 2023

This chapter discusses the electrical basis of neuronal function and shows how this correlates to the ability of neurons to generate and propagate electrical signals. It references the neurons of squids, cockroaches, jellyfish and humans to show how the cellular mechanisms of neuronal signalling are similar in all animals. Stimulation of a neuron results in a local change in membrane potential at the site of stimulation. Depending on the nature of the stimulus, the response can be either a membrane depolarisation or hyperporalisation. The chapter also considers the range of physiological control processes and the contrasting functions of neuronal and hormonal modes of integration. It notes the passive electrical properties of neurons and the propagation of action potentials.
Synapses
Authors: Hill Richard W. , Cavanaugh Daniel J. , Anderson Margaret
Published: September 2023

This chapter features the characteristics of a synapse, which is a specialised site of communication between a neuron and another neuron or an effector. Synapses have diverse actions either chemically or electrically, as befits their functional importance. Additionally, synaptic action can be fast or slow, and it can mediate transmission or modulate the plastic properties of the synapse itself. The chapter provides an overview of the presynaptic and postsynaptic mechanisms of chemical synapses, including the regulation of neurotransmitter release. It notes how chemical neurotransmission depends on the ability of presynaptic terminals to release neurotransmitters in response to incoming action potentials.