bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrating Phenotypic Plasticity When Death Is on the Line Insights from Predator-Prey Systems
Authors: Relyea Rick A 
Published: November 2023

Abstract
Environmental heterogeneity is the norm of nature. As a result, many organisms have evolved the ability to alter their phenotypes to track changing environments and improve their fitness. During the past century, investigators have studied phenotypic plasticity with a primary focus on single traits (see dis¬ cussion in Schlichting and Pigliucci 1998). This has provided us with an excellent collection of case studies that have documented the species that possess plastic traits, the types of traits that are plastic, and the types of environments that induce the trait changes. This focus on single traits has extended to models of plasticity evolution, primarily because single-trait models are considerably easier to handle mathematically than are multi-trait models (Levins 1963; Via and Lande 1985, 1987; Lively 1986; van Tienderen 1991; Gomulkiewicz and Kirkpatrick 1992; Moran 1992; Padilla and Adolph 1996). However, while the focus of theoretical and empirical work has been largely on single traits, it is becoming increasingly clear that we need to examine multiple traits and determine how they work together in producing an integrated organism. In this chapter, I argue that while it requires more time, money, and energy to examine multiple traits, it is imperative that we do so if we wish to understand the evolution and ecology of phenotypic plasticity.
Second- and Higher-Order Harmonic Generation
Authors: Boyd Robert W 
Published: November 2023

Abstract
Second-harmonic generation is the prototypical nonlinear optical process. Its discovery by Franken et al. (1961) is often taken as the birth of the field of nonlinear optics. Even today, this process is extremely important for various applications, including shifting the output frequency of lasers, as a diagnostic tool to determine the surface properties of various materials, and for use in nonlinear optical microscopy.
Multiphoton Polarization Microscopy
Authors: Sun Yen , Lo Wen , Su Jiunn Wen , Lin Sung-Jan , Jee, Shiou-Hwa , Dong Chen-Yuan 
Published: November 2023

Abstract
By analyzing the polarization or anisotropy using steady-state or time-resolved methods, orientation information or dynamics of molecular systems can be investigated (Lakowicz, 1999). The natural extension of polarization spectroscopy is to implement polarizationresolved analysis in conjunction with optical microscopy. In this approach, spatially specific orientation information with submicron resolution can be obtained from biological specimens. A number of experimental approaches have been implemented using polarization microscopy techniques such as confocal polarization microscopy and modulated polarization microscopy (Axelrod, 1989; Massoumian et al., 2003; Wilson & Juskaitis, 1995). With the implementation of different forms of polarization microscopy, many studies in the biological and medical sciences have also been conducted. For example, collagen imaging, corneal microscopy, and the dynamics of cytoskeleton are a few examples in which polarization-resolved microscopy has been readily applied (AsiyoVogel et al., 1997; Gitirana & Trindade, 2000; Kuhn et al., 2001). In addition, polarization microscopy has been used to measure the orientation of single chromophores and quantum dots (Chung et al., 2003; Empedocles et al., 1999). Time-resolved polarization microscopy has also been used to probe dynamic phenomena inside cells such as the cytoplasmic viscosity (Fushimi & Verkman, 1991).
Two-Photon Förster Resonance Energy Transfer (FRET) Microscopy
Authors: Chen Ye , Wallrabe, Horst , Periasamy Ammasi 
Published: November 2023

Abstract
Recent technological advances in fluorophores and detectors have made it feasible to apply Förster (fluorescence) energy transfer (FRET) in biomedical research (Clegg, 1996; Day, 1998; Kraynov et al., 2000; Ludwig et al., 1992; Periasamy, 2001; Periasamy & Day, 2005; Sekar & Periasamy, 2003; Wallrabe & Periasamy, 2005). Light microscopy FRET can provide spatial and temporal distribution of protein associations in single living cells, compared to other methods described in the literature (Guo et al., 1995). There are problems involved in using light microscopy methods to localize protein molecules, such as spectral bleedthrough or cross-talk. In principle, the bleedthrough signal is the same for one-photon (1p) or two-photon (2p) FRET microscopy; choosing the right FRET pairs and conducting qualitative and quantitative FRET data processing have been described extensively in the literature (Wallrabe & Periasamy, 2005). In this chapter we will address these issues and correction methodologies, in addition to the theory of FRET. To illustrate these methodologies, we will use transiently transfected GHFT1-5 live cells expressing cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP) fused to the transcription factor CCAAT/enhancer binding protein alpha (C/EBPα ). We will also explain the problems associated with various techniques, including wide-field, confocal, and multiphoton FRET microscopy.
Photobleaching and Recovery with Nonlinear Microscopy
Authors: Brown Edward , Majewska, Ania , Jain Rakesh K 
Published: November 2023

Abstract
Fluorescence recovery after photobleaching (FRAP), or fluorescence photobleaching recovery (FPR), describes a family of related techniques that measure transport properties of fluorescently labeled molecules. This is done by monitoring the evolution of a fluorescence signal after a spatially localized population of fluorophores is bleached by light. The classical FRAP experiment with one-photon excitation uses a focused laser beam to bleach a disk-shaped region of fluorescently labeled molecules in a thin sample such as a cell membrane or a lamellipodium (Fig. 26.1) (Axelrod et al., 1976). The same laser beam, greatly attenuated, generates fluorescence signal from that region as unbleached fluorophores diffuse in. The recovery in fluorescence signal is recorded by a photomultiplier tube (PMT) or similar detector, producing a fluorescence-versus-time curve (Fig. 26.2). Simple analytical formulas can often fit the fluorescence recovery curve, with the recovery time revealing the two-dimensional diffusion coefficient of the fluorescent molecule, and the extent of fluorescence recovery revealing the fraction of fluorophores that are mobile. More complex analysis with multiple diffusion coefficients can be used if the dynamics of the system warrant (Feder et al., 1996; Periasamy & Verkman, 1998). The three-dimensional hourglass profile of a focused laser beam (Born & Wolf, 1980) renders analytical solutions difficult unless the sample is relatively thin along the optical axis of the laser beam. Therefore, conventional one-photon FRAP is often limited to analysis of diffusion in thin two-dimensional systems such as cell membranes, where the intersection of the membrane with the laser beam produces a simple disk of photobleaching. In spite of this limitation, conventional one-photon FRAP has provided extensive insight into myriad cellular processes involving lateral membrane diffusion (Brown et al., 2005; Reits & Neefjes, 2001).
Immunology Based on Nonlinear Optical Microscopy
Authors: Parker Ian , Cahalan Michael D 
Published: November 2023

Abstract
The immune system is probably the most disseminated and mobile system in our bodies. Its component parts (largely individual cells) are in continuous circulation, endlessly surveying peripheral tissues for possible infection, and returning to mount defenses. A key part of the immune response involves cell–cell interactions: for example, the presentation of antigensby dendritic cells(DCs) to T cellswithin lymph nodes. Until recently, studies of these interactions have been constrained by methodological limitations, and two distinct lines of investigation have dominated the field: (i) in vivo experiments that examine the behavior of populations of cells in living animals during an immune response and (ii) in vitro experiments utilizing individual cells in artificial environments. However, the immune response is the sum of many complex and dynamic individual cellular behaviors that are shaped by a host of environmental factors. Whereas in vivo experiments maintain this natural environment, they cannot resolve the behaviors of individual cells. This approach can be termed “snapshot immunology,” as it has previously been limited to histologically fixed preparations or to analysis of cells taken from an animal at a particular time. Conversely, in vitro experiments provide information at subcellular and molecular levels and with realtime single-cell monitoring, but they cannot adequately recapitulate the complexity and dynamics of intact tissue environments.
The Reference Data Sets
Authors: Journel André G , Kyriakidis Phaedon C 
Published: November 2023

Abstract
To provide a demonstration of the methodology proposed for prediction of recoverable reserves, one would like to have access to a large, exhaustive data set including the sample data used for prediction and those used for selection, as well as the actual grades of all SMUs considered. Unfortunately, such information related to a real mining operation is rarely (if ever) available. Only very large operations with computerized track records of all drilling, sampling, and actual recovery characteristics could provide exhaustive data sets; even there, true SMU grades always remain unknown.
Simulation of Recovery: Application
Authors: Journel André G , Kyriakidis Phaedon C 
Published: November 2023

Abstract
In this chapter, the simulation approach proposed in Chapter II is applied to the evaluation of reserves associated with the two reference data sets introduced in Chapter IV. Only a sparse set of sample grades is retained for the task of evaluating recoverable reserves (30 samples out of the reference total of 286 x 286 = 81796 values). The missing information is simulated in stead of being estimated; the difference between the many possible simulated grade realizations provides a measure of uncertainty regarding the spatial distribution of recoverable reserves.
High Adventure
Authors: Hillary Sir Edmund 
Published: November 2023

Abstract
Fear lives among Everest’s mighty ice-fluted faces and howls across its razor-sharp crags. Gnawing at reason and enslaving minds, it has killed many and defeated countless others. But in 1953, Edmund Hillary and Tenzing Norgay stared into its dark eye and did not waver. On May 29, they pushed spent bodies and aching lungs past the achievable to pursue the impossible. At a terminal altitude of 29,028 feet, they stood triumphant atop the highest peak in the world. With nimble words and a straightforward style, New Zealand mountaineering legend Hillary recollects the bravery and frustration, the agony and glory that marked his Everest odyssey. From the 1951 expedition that led to the discovery of the Southern Route, through the grueling Himalayan training of 1952, and on to the successful 1953 expedition led by Colonel John Hunt, Hillary conveys in precise language the mountain’s unforgiving conditions. In explicit detail he recalls an Everest where chaotic icefalls force costly detours, unstable snow ledges promise to avalanche at the slightest misstep, and brutal weather shifts from pulse-stopping cold to fiendish heat in mere minutes. In defiance of these torturous conditions, Hillary remains enthusiastic and never hesitates in his quest for the summit. Despite the enormity of his and Norgay’s achievement, he regards himself, Norgay, and the other members of his expedition as hardworking men, not heroes. And while he never would have reached the top without practiced skill and technical competence, his thrilling memoir speaks first to his admiration of the human drive to explore, to understand, to risk, and to conquer.
Weak Selection on Noncoding Gene Features
Authors: Chen Ying , Stephan Wolfgang 
Published: November 2023

Abstract
The neutral theory of molecular evolution proposed that most of the variation observed at the molecular level is due to neutral mutations and random genetic drift, rather than positive Darwinian selection (Kimura 1983). However, as more protein sequence data became available, it was clear that the strictly neutral theory fails to explain two major observations, namely, the generation-time effect and the narrow range of heterozygosities. It was observed that the rate of protein evolution is roughly constant per year, rather than per generation as expected by the strictly neutral theory. Furthermore, the estimates of effective population sizes (N,) based on heterozygosity data tend to fall into a relatively narrow range for diverse groups of organisms which were thought to have very different population sizes (Ohta & Gillespie 1996). These findings were later explained by a modified version of the neutral theory, the nearly neutral theory of Tomoko Ohta. Ohta proposed that deleterious mutations with selection coefficients (s) around 1/N, might be quite common among amino acid substitutions.
Evolution of Eukaryotic Genome Structure
Authors: Petrov Dmitri , Wendel Jonathan F 
Published: November 2023

Abstract
The discipline of molecular evolution has until recent years focused on understanding patterns and processes of evolutionary change at the level of individual nucleotides, amino acids, and genes. Emerging from the fields of population genetics and evolutionary theory, and enabled by the advent of molecular biology, the nascent discipline of molecular evolution spawned a seemingly endless series of novel insights into the molecular nature of genetic variation and the fundamental forces that are responsible for molecular evolutionary change. Thus, within the span of a couple of decades, our understanding of the evolution of genes, mutational biases, natural selection, and genetic drift was dramatically enhanced. Notwithstanding these many advances, evolutionary processes operating at scales above that of individual genes were largely inaccessible until the last decade or so. These processes operate at the level of the whole genome, shaping assemblages of interacting and coevolving genes, influencing the size and structure of the genome, and, ultimately, affecting its function. Although beyond the scope of traditional molecular evolutionary studies, the exploration of genome-wide processes has in recent years been advanced by an explosion in genome sequencing efforts and in other relevant technologies.
Evolution of Multidomain Proteins
Authors: Patthy Laszlo 
Published: November 2023

Abstract
Although there is evidence that folded proteins occur frequently among randomly generated amino acid sequences (Davidson & Sauer 1994) it seems much easier to remodel replicas of old protein folds than to invent new folds from scratch. Accordingly, it is generally accepted that creation of the first folded proteins was a rate-limiting step in the appearance of protein-based life and that most extant proteins have arisen from a limited number of ancestral protein folds by divergence. In fact, it has been suggested that the majority of proteins belong to less than 1000 types of protein folds (Brenner et al. 1997). Although more recent analyses suggest that the total number of distinct folds is higher (Coulson & Moult 2002; Koonin et al. 2002), the fact remains that the majority of proteins arose from a surprisingly small number of ancestral protein folds.
Genotype-Environment Interactions and Evolution
Authors: Scheiner Samuel M 
Published: November 2023

Abstract
The link between genotype and phenotype is complex and that complexity can have profound effects on the course and nature of evolution. Chapters 15 and 16 described how the developmental system can control evolutionary outcomes. But developmental systems do not operate in isolation. All individuals are embedded in an environment. That environment plays two roles in determining the course of evolution: it determines which phenotypes are most fit (natural selection) and it interacts with the genome to determine the phenotype.
Population Bottlenecks and Founder Effects
Authors: Meffert Lisa Marie 
Published: November 2023

Abstract
Patterns of geographic variation arise from the combined effects of migration, selection, mutation, and genetic drift. One measure of the evolutionary potential for such geographic differentiation is the level of additive genetic variance (i.e., the linear resemblance between relatives, hereafter denoted VA; see Roff, Ch. 18 of this volume; Cheverud, Ch. 19 of this volume). Migration has relatively straightforward effects that increase genetic variation within populations. In contrast, directional selection should exhaust VA for fitness traits, with the residual genetic variance hidden within the nonadditive components of genetic variance (see below) and maintained by some balance between selection and mutation (see Roff, Ch. 18 of this volume). Genetic drift, however, can have less predictable effects on levels of VA, particularly in the cases of bottleneck or founder events (i.e., involving severe reductions in population size). In a purely additive genetic model (i.e., no nonadditive genetic effects), a population bottleneck should reduce VA, on average, by l/2Ne, where Ne is the number of founders. Models that address nonadditive genetic effects, however, have shown that bottlenecks can increase VA, in contrast to purely additive theory (Goodnight 1988; Cheverud & Routman 1996; and see below).
How to Critically Evaluate Alternative Explanations of Life Events: The Case of Van Gogh’s Ear
Authors: Runyan William McKinley 
Published: November 2023

Abstract
Late Sunday evening December 23, 1888, Vincent Van Gogh, then 35 years old, cut off the lower half of his left ear and took it to a brothel, where he asked for a prostitute named Rachel and handed the ear to her, asking her to “keep this object carefully. “ How is this extraordinary event to be accounted for? Over the years, a variety of explanations have been proposed, and more than a dozen of them will be sketched below. What sense can be made of such a variety of interpretations? Is one of them uniquely true, are all of them true in some way, or, perhaps, are none of them true? And how can we know? This incident is examined in order to explore the problem of alternative explanations in the study of lives (Allport, 1961, 1965; Hogan, 1976; Murray et al., 1938; Runyan, 1978, 1980a, 1980b; White, 1963, 1975) and to contribute to a growing literature on the logic and methodology of psychobiographical studies (e.g., Anderson, 1981; Crosby, 1979; Elms, 1976; Gedo, 1972; George, 1971; Glad, 1973; Izenberg, 1975; Lifton & Olson, 1974; Mack, 1971; Mazlish, 1968; Meyer, 1972). The discussion is intended to raise basic issues encountered in applying personality theories to the life of a single individual, whether a historical figure, a research subject, or a clinical patient.
Osama Bin Laden: The Sum of All Fears
Authors: Dennis Anthony J 
Published: November 2023

Abstract
Few would seriously dispute the impact Osama Bin Laden has had on world events since September 11, 2001. Whether one considers him a terrorist, a megalomaniac and mass murderer, or a populist hero and one of the most holy and devout followers of Islam alive today, Osama Bin Laden has left (and continues to leave) an indelible mark on human history that undoubtedly will be debated, analyzed, and discussed for de-cades and even centuries to come. Biographers of Bin Laden face several significant challenges. First, because of the heinous nature of his terrorist acts, and his call for the use of weapons of mass destruction against Western civilians, Osama Bin Laden has become for many who are his intended targets a two-dimensional portrait of evil personified rather than a flesh-and-blood human being. The American media, in particular, has a tendency to portray Bin Laden as a cardboard caricature of a terrorist rather than as a psychologically complex individual acting out of motives he genuinely believes to be laudable. This sort of “pathographizing “ precludes genuine understanding.
DNA Packaging in Double-Stranded DNA Phages
Authors: Anderson Paul J Jardine Dwight L 
Published: November 2023

Abstract
Imagine trying to stuff a string more than 6mm long into a sphere that is fifty nanometers in diameter. The hole in the sphere that the string must enter is only twice as wide as the string itself. The string is stiff, with a persistence length on the order of 50 nm. It is also negatively charged and self-repulsive. The string must be organized such that it can be pulled out easily, so no knots or tangles are permitted. When the sphere is full, the string will have a near crystalline density. You have several minutes to complete this task. This difficult feat is the challenge presented to dsDNA phages during DNA packaging, a pivotal event in the assembly cascade.
The T1-Like Bacteriophages
Authors: Kropinski Gregory J German Rajeev Misra andrew M 
Published: November 2023

Abstract
Although T1 got its initial fame from its use, in 1943, by Salvador Luria and Max Delbruck in their landmark fluctuation test (64), an entirely different reason has resulted in its notoriety since then. This phage’s resistance to desiccation results in its persistence for weeks in an aerosol which in turn created a real nightmare for laboratories engaged in research employing E. coli K-12 strains. It was not uncommon to hear cries from laboratory workers that their overnight bacterial cultures contained only floating debris. This was the result of an onslaught by T1. Laboratories were quarantined for days until the airborne count of T1 vanished. Bacterial geneticists have had T1-resistant E. coli tonA mutants since the 1940s, and as a result many laboratories protected against unwanted invasion of T1 by introducing nullton A alleles into their E. coli strain collection. Even today T1 maintains its bad reputation because it remains a problem, particularly in laboratories that only casually use E. coli strains for experiments involving cloning, protein overproduction, and analysis of genomic libraries. Because of this, almost all commercially available transformation-competent E. coli cells now contain a tonA mutation. Despite the knowledge of T1-mediated calamities, many laboratories continue to work with E. coli strains that are not tonA.
Bacteriophage N4
Authors: Rothman-denes Krystyna M Kazmierczak lucia B 
Published: November 2023

Abstract
Bacteriophage N4 is a lytic phage specific for Escherichia coli K-12 strains originally isolated from the sewers of Genoa (80). N4 is unique in: (i) the use of three different DNA-dependent RNA polymerases during its growth cycle, (ii) a virion-encapsidated RNA polymerase (N4 vRNAP) that is injected into the host cell upon infection, (iii) the use of single-stranded DNA binding proteins as transcriptional activators, (iv) the presence of 30 extensions at each end of its linear genome, and (v) a lysis-inhibited infection cycle. The N4 virion particle, as visualized by electron microscopy, consists of an icosahedral head 70 nm in diameter connected by a base plate to a small noncontractile tail, and a number of short tail fibers originating from the junction between the head and the tail (figure 21-1A) (82). The virion particle is composed of a single linear double-stranded DNA molecule and, as determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis, 10 proteins (25). The major component of the virion is the coat protein, a 48 kDa polypeptide. Also present is a virion-encapsidated phagecoded, DNA-dependent RNA polymerase (vRNAP) that is responsible for transcription of phage early genes (24).