bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cellular investigations in the diagnosis of lymphoid malignancy
Authors: Campbell A C 
Published: November 2023

Abstract
In many cases of lymphoid malignancy the diagnosis is readily made on the basis of well-established clinical and histological criteria. However, the recognition over the past 20 years of the several pathways of lymphoid cell ontogeny, and stages of differentiation within those pathways, has led to an increasing use of immunological methods of cell characterization in the diagnosis and classification of such malignancies. The application of immunophenotyping to lymphoid cells in blood, bone marrow, or tissue biopsies sometimes offers mere confirmation of a diagnosis which is clear on the basis of other criteria. For example, the diagnosis of multiple myeloma can generally be established on the basis of paraprotein characterization in serum and urine, bone marrow cellular morphology, and radiological findings. Formal demonstration of monoclonality among the bone marrow plasmacytoid cells is not usually an essential investigation. In other groups of diseases, immunophenotyping is crucial to diagnosis, classification, prognosis, and treatment. Acute lymphoblastic leukaemias are classified according to their T- or B-cell lineage and differentiation stage; these can only be established by immunological characterization of surface or internal markers. Some poorly differentiated tumours can only be identified as lymphomas by staining of biopsy sections for T- or B-cell antigens.
Allergy
Authors: Haeney M 
Published: November 2023

Abstract
In Western countries, allergic diseases affect over 15% of the population but are of variable severity: thus some patients have an occasional mild reaction, some suffer life-long debilitating allergic disease while, more rarely, some react with severe or fatal anaphylactic shock. The reasons for this variability are unknown. By common usage, ‘allergy’ has come to mean a disadvantageous immune response to extrinsic antigens. With the introduction of the Gell and Coombs classification of hypersensitivity reactions, the term ‘allergy’ was restricted further, becoming almost synonymous with hypersensitivity of the immediate IgE type (Type I hypersensitivity). In this situation, antigen specific lgE, already attached to mast cell membranes, combines with antigen to trigger release of preformed mast cell mediators stored in secretory granules: these include histamine, lysosomal enzymes, and proteases, neutrophil and eosinophil chemotactic factors and heparin. Other mediators are newly generated metabolites of arachidonic acid derived via two enzyme pathways; one leads to production of prostaglandins and thromboxane, the other to leukotriene formation.
Concepts of molecular pathogenesis
Authors: Oldstone Michael B A 
Published: November 2023

Abstract
Pathology is the study of disease and pathogenesis is the study of the mechanism(s) by which disease occurs. In general viruses cause disease by two distinct ways. First, according to their styles of replication and viral products made or host factors induced, viruses directly damage a cell. Hence, viruses directly destroy a cell by shutting down its protein synthesis, by manufacturing products toxic to the cell or by perturbing membranes either internal (i.e. lysosomal, endosomal) or external (i.e. plasma). Disturbance of internal membranes can result in release of a stable of enzymes potentially autolytic and thus dangerous to the cell. Disturbance of the plasma membrane can lead to cell-cell fusion, formation of giant syncytia and cell lysis or improper passage of ions and fluids causing cell distortion and death. Viruses may also affect cells directly by altering a cell’s function without lysing the cell. This more subtle effect causes disease but does not cause cell lysis. According to this scenario the virus infects differentiated cells (i.e. neurons, lymphocytes, endocrine cells, etc.), and alters their synthesis of neurotransmitters, lymphokines, immunoglobulins, hormones, etc. In contrast to the other mechanisms mentioned previously whereby the end result is destruction of the infected cell, in this instance the architecture and morphology of the infected cell appears normal by light and high resolution microscopy or by assay of cell growth efficiency, total cell RNA, DNA or protein synthesis. Because less than the usual amount of the differentiated product is made, i.e. insulin, growth hormone, ablation of specific anti-viral cytotoxic T lymphocyte function and/or immunoglobulin production, homeostasis can be imbalanced and disease produced (diabetes, growth retardation, viral persistence).
Caged molecules activated by light
Authors: Walker Jeffery W 
Published: November 2023

Abstract
This chapter deals with practical aspects in the use of light activated ‘caged’ molecules in studies of cellular regulation. The term ‘caged’ was originally coined by Kaplan et al. (1) to describe the unique properties of a l(2-nitrophenyl)ethyl ester of ATP which was called caged ATP. This ATP analogue permitted a biological system to be pre-equilibrated with ATP in an inactive form. The system could then be activated by rapidly converting caged ATP to ATP using near-UV irradiation. Successful application of caged ATP to studies of ATP-requiring reactions has led to the development of compounds for investigating other biochemical processes. A summary of biological molecules that have been derivatized with similar photolabile protecting groups to render them inactive and photosensitive can be found in Table 1. The structure of one compound, caged inositol 1,4,5-trisphosphate (InsP3), and its photolysis reaction are illustrated in Scheme .
The Use of Fluorescent Indicators for Measurements of Cytosolic-Free Calcium Concentration in Cell Populations and Single Cells
Authors: Thomas Andrew P , Ville Fernando Dela 
Published: November 2023

Abstract
Introduction The development of fluorescent indicators of free Ca2+ ion concentration which could be loaded into cells in a non-disruptive manner initiated a revolution in studies of cellular Ca2+ homeostasis. This revolution has been led primarily by R. Y. Tsien and co-workers, who first popularized quin-2 for studies of cytosolic-free Ca2+ ([Ca2+]i) and have since contributed a series of additional Ca2+-sensitive dyes with a number of improved properties (1-5). Indicators for measurements of other ions, including Mg2+, Na+, K+, and H+ have also been developed, and new dyes continue to be introduced.
The Use of Electrodes to Study Cellular Ca2+; Metabolism
Authors: Orchard C H , Boyett M R , Fry, C H , Hunter M 
Published: November 2023

Abstract
1. Introduction The importance of electrodes in the study of cellular Ca2+ hardly needs emphasizing. Electrodes can be used to monitor Ca2+ flux across cell membranes and to monitor the concentration of Ca2+ both in the cell cytoplasm and in the extracellular space. Electrodes can also be used to manipulate intracellular Ca2+. Thus, electrodes have contributed a great deal to our understanding of cellular Ca2+ metabolism. The length of a chapter such as this raises two main problems. First, the equipment used in the manufacture and use of electrodes varies in detail from manufacturer to manufacturer. We have, therefore, not concentrated on the details of using one particular brand of equipment but have given such information as should enable the reader to understand, and use effectively, any brand of equipment. Second, limitation of space precludes detailed discussion. We have, therefore, cited references that give further detail for the interested reader. We would particularly recommend the books by Purves (1), Thomas (2), and Thomas (3), and one by various authors (4).
Calmodulin
Authors: Means Anthony R , Bagchi Indrani C , Vanberkum, Mark F A , Rasmussen Colin D 
Published: November 2023

Abstract
1. Introduction A variety of mechanisms exist to maintain intracellular Ca2+ homeostasis (1). The markable regulation of this ion has evolved in a manner so that Ca2+ serves as the only intracellular second messenger of its class. Along with cyclic AMP, Ca2+ controls a wide variety of intracellular processes. Analogous to cyclic AMP, Ca2+ most frequently executes its regulatory roles after binding with high affinity to intracellular Ca2+ binding proteins. Calmodulin is the primary example of such a receptor protein owing to its ubiquitous nature and wide ranging effects. Calmodulin utilizes a linear sequence of 12 amino acids to bind Ca2+ (2). The three-dimensional structure formed to co-ordinate Ca2+ has been called an ‘E-F hand’ or ‘calmodulin-fold’ (3). A superfamily of proteins utilizes this configuration to bind Ca2+ but calmodulin is the only member that subserves such a plethora of functions. About 30 enzymes and structural proteins have been identified that bind calmodulin with high affinity (4). The Ca2+ calmodulin complex can also regulate the intracellular concentration of other second messengers such as cyclic AMP and inositoltrisphosphate (IP3). Isoforms of adenylyl cyclase and phosphodiesterase are calmodulin-dependent and the enzyme that phosphorylates IP3 also utilizes calmodulin as a regulatory subunit. Thus it is not surprising that calmodulin is an essential protein and disruption of the single gene in yeast and fungi is lethal (5).
Phosphorothioate based double-stranded plasmid mutagenesis
Authors: Olsen David B , Eckstein Fritz 
Published: November 2023

Abstract
The ability to specifically modify a nucleotide sequence has facilitated many detailed studies of structure function relationships of DNA and proteins (1-3). To this end oligonucleotide-directed mutagenesis using single-stranded DNA vectors has become almost routine (see refs 4-7 and Chapters 1 to 3 in this volume). The high mutational yields using these well-established methods allow for a rather facile screening of the altered genotype. One of the limitations of MB-based procedures is that the gene of interest must be sub cloned into one of the M13 vectors described by Messing (8). Alternatively, sub cloning may be avoided if the gene is present in a phagemid vector which is a plasmid which contains an origin of replication for single stranded phage [(9); see Chapters I and 2}. However, working with these constructs sometimes requires special experience in order to obtain single stranded DNA suitable for mutagenesis.
Random chemical mutagenesis and the non-selective isolation of mutated DNA sequences in vitro
Authors: Walton Catherine , Booth R Kim , Stockley Peter G 
Published: November 2023

Abstract
This chapter illustrates examples of the types of problems to which random in vitro chemical mutagenesis lends itself. It outlines the most frequently used techniques of chemical mutagenesis, and describes in full experimental detail the two chemical treatments which are the simplest to apply and which generate the most nearly random distribution of mutations. The use of denaturing gradient gel electrophoresis to separate nucleic acids differing by as little as a single base-pair is also described in detail. Routine molecular biology techniques used in the construction of clones of DNA fragments and in the generation of single-stranded DNA for mutagenesis and sequencing are adequately documented elsewhere (1).
Immunogold labelling techniques
Authors: Hyatt Alex D 
Published: November 2023

Abstract
Over the past one to two decade the IGS method has been applied to the detection of micro-organisms, cell surface-associated and intracellular antigens. The techniques utilized in these applications include negative contrast immunoelectron microscopy (NCIEM), pre- and post-embedding TGS, freeze-fracture immunoelectron microscopy, and scanning immunoelectron microscopy (STEM). lt is beyond the scope of this chapter to discuss each IGS technique which has been utilized over the past decade, thus only the more popular IGS procedures which can be performed in routine electron microscopy laboratorie will be covered. It is therefore the aim of this chapter to present laboratory protocols for NCIEM. pre- and post-IGS of plastic sections, SIEM, and briefly the labelling of cryosections. These protocols will be based on methods which have been successfully implemented in this and other laboratories.
Freeze-fracture techniques
Authors: Kawa Seizo Fuji 
Published: November 2023

Abstract
Freeze-fracture techniques were developed originally to prepare cellular ultrastructures in a frozen-hydrated and living state for electron microscopy (I). The replicas made from freeze-fractured biological specimens have provided a new three-dimensional ultrastructure of cells (2). Since the elegant proof by Branton and his co-workers (3) that the freeze-fracture technique reveals the macromolecular organization of the hydrophobic interior of bilayer membranes, the technique has been extensively used in the field of biological science and has made a major contribution to our understanding of biological ultrastructure. (For nomenclature of freeze-fractured membranes, see ref. 4.)
Negative staining
Authors: Harris Robin , Horne Robert 
Published: November 2023

Abstract
The fundamental concept of negative staining is rather old and extremely simple, yet, as with many microscopical specimen preparation techniques, there are numerous subtleties, intricacies, and technical hazards which have to be carefully observed by the user. Gross visual examples of ‘negative staining’ are calcified fossils within dark-brown/black mud, stone and clearglass particles of varying shape surrounded by dye or ink solution, the shape of which is made visible in a ‘negative’ sense. In descriptive terms for transmission electron microscopy (TEM), salts containing heavy metal atoms, which have the property of drying from aqueous solution as an amorphous ‘glass’ rather than a crystalline layer, can surround and permeate small biological particles.
Transmission electron microscopy of vitrified biological macromolecular assemblies
Authors: Stewart Murray 
Published: November 2023

Abstract
There have been a number of recent reviews of the transmission electron microscopy of frozen-hydrated biological material (1-5) to which the reader is directed for a comprehensive discus ion of many aspelh of the method. This chapter provides an introduction to the methods and description of the freezing techniques and electron microscopy procedures that are employed. It first discusses the theoretical background to freezing before progressing to a description of the methods used Lo prepare thin vitrified films containing biological macromolecules.
Introduction
Authors: Vincent Julian F V 
Published: November 2023

Abstract
Particularly for the neophyte, it is very easy (and common!) to think that because you have obtained some numbers, then you have done some science and have gained respectability. In biomechanics it is very easy not only to do the ‘wrong’ experiment (e.g. measure shear stiffness when tensile strength is the important parameter) but to confuse a number of independent parameters and end up with data but no understanding. This is probably because the study of materials science is by no means easy. As Jim Gordon has so elegantly said (1, 2) there is a great tendency, temptation even, to dismiss the study of materials as trivial. This response is well known as the first stage in the acceptance of an idea. In reality the problems are remarkably subtle and difficult to solve, probably because so many of the parameters of materials science are intertwined and difficult to unravel.
Fracture
Authors: Vincent Julian F V 
Published: November 2023

Abstract
To survive, the organism must have mechanisms for resisting fracture (the initiation and propagation of cracks) in order to withstand the mechanical effects of wind, water, and gravity, to grow in such a way that bits do not fall off or split open unannounced, to resist attack from other animals, and to chew food. An organism may also cease to be able to carry the loads that it must do in order to survive, due to structural failure. This may involve fracture but also involves other forms of deformation, both elastic (i.e. recoverable) and plastic (i.e. permanent) .
The Physical Chemistry of Protein Crystallization
Authors: Mikol V , Giege R 
Published: November 2023

Abstract
Of all the different aspects of protein crystallization, the physics of crystal growth and its understanding have been the most neglected. Indeed, the growing of protein crystals is often believed to occur more through serendipity than as the result of a rational approach. This chapter will try to dispute this well established belief. More knowledge on the fundamentals of crystal growth should make it possible to develop easy and convenient assays for defining optimal conditions for protein crystallization. Undoubtedly, the understanding of crystallization from a physicochemical point of view has received more attention recently and crystallization is slowly emerging from its veil of mystery. Using the physicochemical concepts of small molecule crystal growth (1), this chapter will go through all the steps of crystallization: nucleation, growth, cessation of growth, and characterization of crystals. It does not deal with the preliminary X-ray structure analysis reviewed in Chapter 12. Firstly, a brief summary of the basic physical concepts underlying each step is given. This provides a simple theoretical base for the biomacromolecule crystal grower. Then the main results obtained from physical studies on each stage and practical applications are presented.
Electromyography
Authors: Gans Carl 
Published: November 2023

Abstract
Animals move. Much of their locomotor activity, as well as feeding, drinking, ventilation, defence, and mating involve forces and movements that commonly are generated by mmcular action. Hence, studies of the functional morphology of animal behaviours, of the biomechanics of their musculoskeletal systems and of their control characteristics commonly require information about the time and magnitude of muscular action. Electromyography is the premier technique for generating this information. (In the literature, variants of the terms electromyography and electromyogram, are commonly abbreviated as EMG and EMGs. This convenient usage is followed in the present text.)
Hydrostatic skeletons and muscular hydrostats
Authors: Kier William m. 
Published: November 2023

Abstract
A hydrostatic skeleton is a fluid mechanism that provides a means by which contractile elements may be antagonized (1). Hydrostatic skeletons occur in a remarkable variety of organisms with examples not only from invertebrates but also from vertebrates. A hydrostatic skeleton is typically considered to include a liquid-filled cavity surrounded by a muscular wall reinforced with connective tissue fibres. This form of hydrostatic skeleton is seen, for example, in cnidarian polyps, holothuroid echinoderms, echinoderm water vascular systems, many molluscan bodies and organs and annelid, sipunculid, ncmcrtean, and nematode worms (for reviews see refs. 1-7). Comparison of a variety of hydrostatic skeletal support systems shows that the extent and volume of the liquid-filled cavity is variable. In particular, recent work bas identified a number of hydrostatic skeletons, termed muscular hydroslah, that consist of a tightly packed three-dimensional array for muscle fibres (8, 9). Examples of muscular hydrostats include the arms and tentacles, fins, suckers and mantles of cephalopod molluscs, a variety of molluscan structures, the tongues of many mammals and lizards. and the trunk of the elephant.
Circulatory structure and mechanics
Authors: Shadwick R E 
Published: November 2023

Abstract
Thischapter describes techniques to investigate the structure and biomechanical characteristics of animal circulatory systems, with a focus on the viscoelastic properties of the arterial wall. These include quantification of connective tissue components, mechanical characterization of vascular ti;,sue by in vitro and in vivo methods, calculation of vascular impedance and wave velocity from vessel elasticity, and assessing in vivo pressure-flow dynamics. For further details of hacmodynamic principles and analysis the reader should consult the excellent monographs by McDonald (1), Milnor (2), and Fung (3).
Patch-clamp analysis of gap junctional currents
Authors: Veenstra R D , Brink P R 
Published: November 2023

Abstract
The difficulty in recording gap junction channel currents and gating activity can largely be attributed to the specialized location of this ion channel. While virtually all other ion channels are single membrane structures which permit the passage of ions between the extracellular space and the cytoplasm or between the cytoplasm and an internal organellar compartment, gap junctions link the cytoplasms of two adjacent cells. Hence, the direct measurement of junctional currents requires the ability to independently control the membrane voltage of each member of a coupled pair of cells or direct voltage-clamp recording from gap junction membranes. The two-cell voltage-clamp approach was first accomplished using two microelectrodes impaled into each cell, one for passing current and one for recording voltage (1). The two-microelectrode voltage-clamp technique is well suited for use with cells of large diameter (above 20 µ,m), while the patch-clamp technique offers the advantage of requiring only a single electrode for intracellular current injection and voltage recording from small diameter cells (below 20 µ,m) (2). The use of the double whole-cell recording (DWCR) procedure for quantitative analysis of macroscopic and single-channel gap junctional currents is now widespread and has yielded valuable new information about channel conductances and the regulation of electrical coupling in a variety of tissues (3).
Electrophysiological assessment of epithelia
Authors: Karnaky Karl J 
Published: November 2023

Abstract
Epithelia separate two different environments which they help create and maintain by an assortment of ion transport mechanisms. These mechanisms include the tight junction, one of the hallmarks of epithelia (1). The selective and changeable permeability of the tight junction helps confer unique signatures to the secretions and absorbates of epithelia (2). Electrophysiological techniques applied to epithelia can define actively and passively transported ions. In addition, with these techniques the researcher can reveal the rate of ion transport, the direction of net ionic movement, the identity of transporting cells in heterogeneous epithelia, and, possibly, the identity of ions passing through the paracellular pathway.
Bivariate regression
Authors: Fry John C 
Published: November 2023

Abstract
All biologists will use regression analysis between two variables at one time or another and all statistical packages have commands for performing bivariate or simple linear regression. Whole books have been written about regression analysis, but many are mathematically complex and impenetrable for most biologists. The easiest text I have found is by Chatterjee and Price (1). For more detail Sokal and Rohlf (2) and Rawlings (3) are also useful. These texts should be consulted by readers requiring longer or different explanations. As in Chapter 1, I will use examples analyzed with four statistical packages Minitab, SPSS/PC+ Systat, and Stat graphics. However, in this chapter almost all my sample output will be from Minitab. I will only provide sample output from the other packages when Minitab does not provide the necessary procedures. All four packages and many more besides provide excellent facilities for bivariate regression analysis.