bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neurobiology
Authors: Thomas James h. , Lockery Shawn 
Published: November 2023

Abstract
The nervous system of C. elegans is simple and uniquely well described. There are 302 neurons in the adult hermaphrodite that fall into 118 classes based on morphology and other characters (1). These neurons are interconnected by about 5000 chemical synapses and 600 gap junctions. The structure of each neuron is nearly invariant from animal to animal and the cell bodies are invariantly positioned so that each neuron can be identified in vivo (2). Despite its small size and simplicity, this nervous system regulates a wide variety of behaviours. These include several mechanosensory responses, many chemosensory responses, thermotaxis, complex responses to food, locomotion, feeding, egg laying, defecation, and male mating. Neurons that control most of these behaviours have been identified, and in many cases they use identified transmitters and act in defined circuits.
Molecular biology
Authors: Johnstone Iain L 
Published: November 2023

Abstract
This chapter deals with some of the common, molecular biological methods essential for general aspects of gene characterization. It includes the purification of DNA, RNA, and some simple, protein extraction methods useful for Western blot analyses. Because much of what is discussed here is not specific to the nematode and extensive coverage is available in other texts (1), I have emphasized the modifications to those more general methods relevant to working with the worm. The availability of the genome sequence makes an immense body of data available to any researcher. It is an extremely valuable resource which, for many of us in the field, has resulted in a great reduction in the amount of general molecular biology performed in the laboratory. However, it is important to avoid complacency and remember that most of the genes indicated by the genome project are predictions, and that the different aspects of such predictions, e.g. intron/exon organization and gene endpoints, must be con firmed experimentally. This is particularly important when considering the construction of reporter gene fusions and the interpretation of expression patterns so obtained (see Chapter 9). The predictions, around the start of genes in particular, are not always accurate. In this post genome sequence era, in addition to confirming predicted data, general molecular methods are still necessary for many purposes including the analysis of gene expression and gene function, as well as for investigating the nature of mutant strains.
Synthesis of combinatorial libraries using the portioning-mixing procedure
Authors: Furka Árpad , Hamaker Linda K , Petersonꝉ Mark L 
Published: November 2023

Abstract
Combinatorial chemistry is a young, yet intensely popular branch of science. Beginning in the 1980s, several innovative synthetic methods were published (1-7) which radically changed the theory and practice of designing and preparing new substances for pharmaceutical research and other areas of application. The field of combinatorial chemistry evolved as a result of these new approaches and has revolutionized the way scientists think about drug discovery. Combinatorial processes have since spread outside of pharmaceutical research and are gradually expanding to other areas of chemistry including catalysis and materials science. One of the first and most influential combinatorial synthetic methods was the portioning-mixing (split-mix) procedure (3, 8, 9) (see also Chapters 2 and 3).
Positionally addressable parallel synthesis on continuous membranes
Authors: Wenschuh Holger , Gausepohlꝉ Heinrich , Germeroth Lothar , Ulbricht╪ Mathias , Matuschewski§ Heike , Karmer* Achim , Volkmer-Engert* Rudolf , Heine* Niklas , Ast* Thomas , Scheme* Drik , Schneider-Mergener* Jens 
Published: November 2023

Abstract
Spatially addressable high-throughput solid phase synthesis of large arrays of compounds has generated intense interest over the past few years (1). Besides parallel synthesis on resin beads (see Chapters 1-3), polymeric pins and chips (see Chapter 4), SPOT synthesis using continuous membrane supports has been shown to be an efficient solid phase synthetic alternative. The development of this approach was fuelled by the need for a facile and economical complement to the classical solid phase synthesis procedures with increased flexibility and amenability to miniaturization and automation (2).
Regulation of cytoskeletal proteins by inositol lipids
Authors: Flanagan Lisa A , Janmey Paul A 
Published: November 2023

Abstract
Since the initial finding that phosphatidylinositol bisphosphate (PtdIns(4,5)P2) regulates the affinity of profilin for actin and promotes actin assembly from profilin–actin complexes in vitro (1), a variety of inositol lipids have emerged as potential regulators of different forms of cytoskeletal assembly in vivo. At the same time, the recognition and availability of different inositol lipid species and identification of PtdIns(4,5)P2-binding sequences in proteins have confirmed in many cases the biochemical specificity of these protein–lipid interactions. This chapter aims to synthesize recent studies of phosphoinositide effects on cytoskeletal proteins to suggest how these lipids may trigger cytoskeletal changes in response to cellular signals.
Physiological functions of phosphatidylinositol transfer proteins
Authors: Rivas Marcos P , Li Xinmin , Bankaitis Vytas A 
Published: November 2023

Abstract
Eukaryotic cells organize their interior by establishing and maintaining a diverse set of intracellular organelles. These organelles represent membrane-enclosed structures that function to compartmentalize physically the multitude of biochemical machines dedicated to the execution of specific cellular functions. This compartmentation function is reflected by the unique sets of resident proteins and by the lipid compositions that comprise each individual organelle. That cells would evolve elaborate mechanisms to maintain unique lipid compositions in the various organelle membranes is not a difficult concept to grasp. A more challenging problem is the elucidation of how the biochemical compartmentation of lipids is maintained in the face of robust membrane trafficking pathways that should act to randomize lipid distribution. As a result, the problem of how specific organelles maintain their signature lipid compositions is a complex one. It involves issues of where lipid synthesis and degradation reactions are localized, how these metabolic processes are coordinated, and how cells regulate and execute lipid sorting and transport reactions.
Genes, genomes, and chips
Authors: Schena Mark 
Published: November 2023

Abstract
This chapter provides an overview of the microarray or biochip field, describing biological framework, historical perspective, applications, and future trends. Microarray assays are summarized and compared to traditional approaches. Methodological underpinnings of biochips are emphasized. The information content of the genome is carried hereditarily as deoxyribonucleic acid (DNA). The size and composition of a given genomic sequence determines the form and function of the resultant organism. In general, genomic complexity is proportional to the complexity of the organism. Relatively simple organisms such as bacteria have genomes in the 1– 5 million base (megabase) range while mammalian genomes including human are approximately 3000 megabases; genomes from organisms of intermediate complexity such as worms and insects are typically 100– 200 megabases.
Antisense oligonucleotide scanning arrays
Authors: Elder John k. , Johnson Martin 
Published: November 2023

Abstract
Antisense oligonucleotides are short DNA sequences, typically between 15-25 nucleotides, that can bind to a complementary mRNA target by Watson-Crick base pairing and selectively inhibit the expression of the target gene from among the 80000 or so estimated to be present in a typical mammalian cell (1, 2). This, in principle, makes possible the rational design of DNA-based therapeutic drugs for specific inhibition of any gene of known sequence. Antisense oligonucleotide drugs are currently in advanced stages of clinical trials for viral diseases and cancer (3, 4). Antisense oligonucleotides are also a useful tool in biological studies of gene function. A major issue in antisense development is the selection of those reagents that work effectively. The ability to bind to the target mRNA influences the efficacy of an oligonucleotide as an antisense reagent. Oligonucleotides targeted to regions separated by only a few bases can have markedly different antisense effects (5). There is compelling evidence that the presence of secondary structure in mRNA influences the formation of intermolecular heteroduplexes between the mRNA and the antisense oligonucleotide (5, 6). Computer programs such as mfold (7), designed to predict secondary structure of RNAs, have a limited utility in the selection of antisense oligonucleotides (5, 8); empirical selection of those reagents that can form stable heteroduplexes with the target mRNA is more effective.
Applications for analysis of contractile functions in dividing and migrating tissue culture cells
Authors: Fishkind Douglas J , Romenskaia Irina , Bao Yun , Manubay Christine M 
Published: November 2023

Abstract
The cytoskeleton is composed of a dynamic network of filament systems that form the scaffolding and machinery responsible for spatially and temporally integrating a variety of cell functions. In addition to maintaining cell shape and polarity, cytoskeletal polymers orchestrate a variety of cell movements, including intracellular transport, chromosome segregation, cell locomotion, and cell division. Such activities result from the direct interaction of polymer systems such as actin filaments and microtubules that combine with a vast array of complementary binding proteins and molecular motors to transduce mechanochemical energy into active force production. The exquisite sensitivity and timing of such events is controlled in turn by a complex network of signalling molecules that co-operatively function to stimulate and regulate productive interactions leading to force generation and mechanical transduction (1).
Cell shape control and mechanical signalling through the cytoskeleton
Authors: Goldmann Wolfgang H , Alonso Jose Luis , Bojanowski Krzysztof , Brangwynne Clifford , Chen Christopher S , Chicurel Marina E , Dike Laura , Huang Sui , Lee Kyung-Mi , Maniotis Andrew , Mannix Robert , Mcnamee Helen , Meyer Christian J , Naruse Keiji , Parker Kevin Kit , Plopper George , Polte Thomas , Wang Ning , Yan Li , Ingber Donald E 
Published: November 2023

Abstract
For the past twenty years, our group has explored the possibility that cells and tissues use a form of architecture, known as ‘tensegrity’, to control their shape and to transduce mechanical signals into changes in biochemistry and gene expression (1-5). The importance of the tensegrity paradigm is that it predicts that the form and function of living cells are controlled through changes in mechanical interactions between cells and their underlying extracellular matrix (ECM) adhesions that, in turn, alter cytoskeletal and nuclear structure inside the cell (1-6).
Assessment of DNA damage in apoptosis
Authors: Yoshida Akira , Shao Rong-Guang , Pommier Yves 
Published: November 2023

Abstract
Apoptosis is morphologically characterized by early cell shrinkage, chromatin condensation, nuclear fragmentation, cell surface blebbing, and membrane bound apoptotic bodies (1) and these changes are described in Chapter 2. One of the most extensively studied biochemical events in apoptosis is chromatin fragmentation by endonuclease activation. DNA double-strand cleavage occurs in the linker regions between nucleosomes, and produces DNA fragments that are multiples of approximately 185 base pairs (bp) (2-4). These fragments can readily be demonstrated by agarose gel electrophoresis as DNA ladders, and this method has been widely used to detect and define apoptosis. In contrast, necrosis is accompanied by random DNA breakdown, with diffuse smear in agarose gels. The appearance of the nucleosomal DNA ladder in agarose gels is an important biochemical hallmark of apoptosis, although several investigators have observed apoptosis with no detectable intemucleosomal DNA digestion (5, 6).
Analysis of cell death by flow and laser-scanning cytometry
Authors: Darzynkiewicz Zbigniew , Bedner Elzbieta , Li Xun 
Published: November 2023

Abstract
Flow cytometry, by providing the possibility of rapid, accurate, and unbiased measurements of a variety of cell components on a cell by cell basis, has become an indispensable methodology in the analysis of cell death (see reviews in refs 1-6). One area of application of flow cytometry is in studies of the mechanism of cell death.
Cell-mediated cytotoxicity and cell death receptors
Authors: Naval Javier , Anel Alberto 
Published: November 2023

Abstract
T cell-mediated cytotoxicity in short time assays (3-4 h) is achieved through two main mechanisms. A first mechanism, Ca2+ dependent, requires the action of the pore-forming protein perforin and a subfamily of serine proteases named granzymes or fragmentins (1). The second mechanism, which is Ca2+ independent for its execution, requires the expression of Fas (Apo-1/CD95) at the target cell surface (2), and of the Fas ligand (FasL) at the effector cell surface (3).
Methods of measuring Bcl-2 family proteins and their functions
Authors: Reed John C , Xie Zhihua , Kitada Shinichi , Zapata Juan M , Xu Qunli , Schendel Sharon , Krajewska Maryla , Krajewski Stanislaw 
Published: November 2023

Abstract
Bcl-2 family proteins play critical roles in the regulation of programmed cell death and apoptosis (reviewed in refs 1-4). Changes in the levels or bioactivities of these proteins are associated with a variety of physiological processes where cell death occurs, including fetal development, haematopoietic and immune cell differentiation, oogenesis, mammary gland involution, and normal cell turnover in the epidermis, gut, and several other tissues. Moreover, pathological alterations in the expression of Bcl-2 family proteins have been documented in cancer, autoimmunity, immunodeficiency, heart failure, stroke, and other diseases (reviewed in refs 5-9). Consequently, methods for assessing the relative levels and bioactivities of Bcl-2 family proteins can be of interest to scientists in a board range of disciplines.
Scaling-up of animal cell cultures
Authors: Griffiths Bryan 
Published: November 2023

Abstract
Small scale culture of cells in flasks of up to 1 litre volume (175 cm2 surface area) is the best means of establishing new cell lines in culture, for studying cell morphology and for comparing the effects of agents on growth and metabolism. However, there are many applications in which large numbers of cells are required, for example extraction of a cellular constituent (109 cells can provide 7 mg DNA); to produce viruses for vaccine production (typically 5 X 1010 cells per batch) or other cell products (interferon, plasminogen activator, interleukins, hormones, enzymes, erythropoietin, and antibodies); and to produce inocula for even larger cultures. Animal cell culture is a widely used production process in biotechnology, with systems in operation at scales over 10 000 litres. This has been achieved by graduating from multiples of small cultures, an approach which is tedious, labour-intensive, and expensive, to the use of large ‘unit process’ systems. Although unit processes are more cost-effective and efficient, achieving the necessary scale-up has required a series of modifications to overcome limiting factors such as oxygen limitation, shear damage, and metabolite toxicity. One of the aims of this chapter is to describe these limitations, indicate at what scale they are likely to occur, and suggest possible solutions. This theme has to be applied to cells that grow in suspension and also to those that will only grow when attached to a substrate (anchorage-dependent cells). Another aspect of scale-up that will be discussed is increasing unit cell density 50- to 100-fold by the use of cell immobilization and perfusion techniques.
Development of serum-free media
Authors: Karmiol Severin 
Published: November 2023

Abstract
The removal of serum or other undefined components from cell culture medium involves a multifaceted approach. This is mainly due to the interactive nature of cell culture systems. Cell culture systems require various components: basal nutrients, a set of supplements that convey information, such as growth factors, mitogens, hormones, and cytokines, and for anchorage-dependent cells, a substrate. In designing any cell culture system attention must be paid to all these components and their interactions.
Senescence, apoptosis and necrosis
Authors: Kill Ian R , Faraghert† Richard G A 
Published: November 2023

Abstract
Populations of cells which will divide forever in culture (continuous cell lines) differ from those which cease to expand after several weeks or months of growth (finite cell lines). The end of the proliferative lifespan of a cell culture has been loosely termed as either its ‘senescence’ or its ‘death’. These states are distinct biochemical entities and the causes of any failure to thrive in a cell population may involve both processes. TI1e purpose of this chapter is to describe methods for studying senescence, apoptosis, and necrosis.
Morphogenesis of skin epithelia
Authors: Coulombe Pierre A , McGowan Kevin 
Published: November 2023

Abstract
By virtue of its strategic location at the surface of the body, the skin has multiple functions that define in many ways the relationship that the whole organism has with its external environment (1−4). The epithelial compartment of the skin acts as a barrier that restricts the exchange of water-soluble compounds, prevents the entry of infectious micro-organisms, filters out harmful ultraviolet irradiation, and contributes to immunological surveillance. In addition, epithelial specializations such as the hair and nail contribute significantly to thermal insulation, tactile sensation, sexual behaviours, and, in some cases, flight (feathers) and natural defence (claws). These various epithelial compartments lie over, or in some cases are embedded within, a connective tissue known as the dermis. Through its rich vascularization and innervation and a complex extracellular matrix, the dermis makes essential contributions to the properties and functions of skin. The regulation of cutaneous blood flow represents an important homeostatic mechanism for the regulation of body heat, and the afferent and efferent innervation of the skin are an integral part of sensory perception (3, 4). More relevant to this text, however, the dermis is the source of instructions that play essential roles in the morphogenesis and the homeostasis of mature skin tissue (5−13).
Kinetic modeling for biosensors
Authors: Bartlett Philip N , Toh Chee-Seng 
Published: November 2023

Abstract
The purpose of a kinetic model of a biosensor is to identify the key experimental factors (such as the rates of reactions, rates of mass transport, loading of the bio-recognition component, etc.), which determine the response, or output, of the sensor and to then provide a link between these key experimental factors and the concentration of the analyte and the sensor response. Thus, modeling provides a mathematical description of the physical processes occurring within the system. By applying kinetic modeling to enzyme electrodes and biosensors, we can derive a number of advantages. It is clear that several different kinetic processes are involved in the overall functioning of any enzyme electrode or biosensor.
Specific cell types and their requirements
Authors: Sato J Denry , Barnes David W 
Published: November 2023

Abstract
Although attempts at maintaining tissue explants in vitro have been reported since 1907, the beginning of the modern era of cell culture was marked by the establishment of the first cell lines, the mouse L-cell fibroblast line and the human HeLa cervical adenocarcinoma line, and by initial studies to determine the nutritional requirements of cells in culture (1–3). However, it was not until the 1960s that functional differentiated mammalian cell lines were first established from transplantable tumours (4, 5) following the realization that measures had to be taken to prevent the routine overgrowth of differentiated cells by fibroblasts in culture (6). A wide range of normal, immortalized, and transformed cell types can now be maintained or propagated in vitro (7–13). In general, normal cells, which may divide slowly or intermittently in vivo, exhibit a reduced capacity to proliferate in vitro in comparison with their partially or fully transformed counterparts. Furthermore, cells that cease dividing in vivo after undergoing terminal differentiation, such as neurons, skeletal muscle cells, and adipocytes, do not proliferate in vitro. However, as the growth requirements of individual cell types become more explicitly defined and as the interactions between cells and their environments are better understood, cells are able to survive longer or proliferate to a greater extent in culture. Although cells in culture, particularly continuous cell lines, may not display all the properties of differentiated cells in vivo, strides are being made towards the goal of being able to investigate physiologically relevant properties of specialized cells in completely defined culture environments.
Finding Volunteers for Partnerships
Authors: Sherr Michael E 
Published: November 2023

Abstract
Social work practice with volunteers begins with a simple need social workers must find volunteers to develop partnerships. But finding volunteers is a process that takes time and effort. It requires the application of basic helping skills, such as building rapport; reflective listening; and expressing warmth, genuineness, and appreciation for others. Just as social workers learn to be conscious and deliberate in how they develop and maintain trusting relationships in clinical practice, they must do the same in strategically developing a diverse network of genuine relationships with people who may become volunteer partners. This chapter will assist social workers in developing a strategic network of genuine relationships that can lead to fruitful volunteer partnerships.
Understanding Ethics
Authors: Strom-Gottfried Kim 
Published: November 2023

Abstract
On January 2, 2002, the last day of his school’s winter break, twelve year old J. Daniel Scruggs hanged himself with a necktie in the bedroom closet of the small apartment he shared with his mother and nineteen-year-old sister. Six days earlier, the Department of Children and Families had dismissed allegations of neglect against Daniel’s mother due to a lack of evidence.
Ethical and Clinical Decision Making
Authors: Strom-Gottfried Kim 
Published: November 2023

Abstract
When asked what process they use for resolving dilemmas, professionals often respond,”I trust my gut.” Sometimes gut-level decisions are the result of an internalized, almost automatic ethical decision-making strategy honed over years of use until it develops into a reflexive response to addressing dilemmas (Gladwell, 2005). In other cases, though, intuition is a fly-by-the-seat-of-your-pants enterprise, where decisions are independent, inconsistent, ungrounded, and unexamined (Gambrill, 1997). This is a hazardous approach, as it raises questions about the quality of the decisions that result and the efficacy of the social worker who reacts without forethought or consultation.
Individual-vs.-Community Dilemmas
Authors: Strom-Gottfried Kim 
Published: November 2023

Abstract
Individual-vs.-community dilemmas are in essence conflict-of-interest problems. These dilemmas pit the well-being of one person against that of a collective (a family, class, or community, for example). This category can also include situations in which the decision maker is torn between one person’s needs and interests and those of another individual. As such, it can also involve dilemmas in which the decision maker’s own interests are part of the equation.