bluuebunny/crossref_metadata_2025_split huggingface dataset:
Challenges in structural molecular biology: genomics in three dimensions
Authors: Janin Joël 
Published: November 2023

Abstract
Challenges are the daily bread of science. Research is all about creating new knowledge, new ways of understanding and mastering the world around us. Structural molecular biology is even more so, as a relatively new and fast moving field of investigation. Its specific aim is to give a description of biological macromolecules and their assemblies at the atomic level, and to relate their structure to the many elaborate functions they perform in cells and organisms. The founding example, arguably still the best example of a structure that explains a function, is the DNA double helix discovered by Jim Watson and Francis Crick in 1953 (Watson and Crick 1953). Their discovery entirely changed biology, and the consequences are still far from exhausted. A few years after the double helix, Max Perutz and John Kendrew found the haemoglobin structure (Perutz et al. 1959) and established X-ray crystallography as the major tool for determining macromolecular structures at the atomic level. At the end of this century, crystallography has been joined by electron microscopy and high resolution nuclear magnetic resonance (NMR). The three techniques have different capacities and limitations, they complement each other and, together, they strive to meet new challenges. One of these is to tackle larger and larger objects and to make structural biology progress upwards from the angstrom (A) scale of the atom to the micrometre (pm) scale of cells, where optical microscopy can take over. In specific cases, X-ray crystallography almost reaches there, as it has succeeded in solving the atomic structure of viruses nearly 1000 A, or 0.1 pm, in diameter. Still, viruses are best studied by the very powerful combination of crystallography and electron microscopy pioneered by Aaron Klug (1983) and now extended to macromolecular assemblies such as the ribosome or the cell membrane. In general, large structures are being approached by crystallography in parallel with other techniques, among which near-field microscopies may become important contributors in coming years.
Data collection and reduction methods
Authors: Leslie A G W 
Published: November 2023

Abstract
This chapter describes modern methods for collecting and processing X-ray diffraction data from macromolecules. The first five sections deal with practical aspects of data collection, with Section 2.1 focusing primarily on laboratory sources. Complementary information on synchrotron radiation instrumentation is given in the next chapter by Fourme et al. (Chapter 3). The final section deals with the computational aspects of integrating diffraction intensities and merging and scaling the data. More detailed accounts of many of these topics can be found in Carter and Sweet (1997) and Sawyer et al. (1993).
X-ray microscopy
Authors: Buckley C J 
Published: November 2023

Abstract
Monochromatic X-rays interact with specimens in a very different way than light, infrared radiation or electrons. The highly specific interaction of these X-rays provides for elemental and chemical state analysis of samples in a range of environments including the wet state. The short wavelength of X-rays places the fundamental limit of spatial resolution more than two orders of magnitude smaller than that of light. However, microscopy using X-rays has only recently been possible. The current advances in this area are due to the emergence of high resolution X-ray optics and X-ray sources with sufficient brilliance. Due to the availability of these resources, it is likely that the next few years will see a considerable expansion in the use of X-ray microscopy to tackle problems in the biological and material sciences.
The fundamentals of electrochemistry
Authors: Bond A M 
Published: November 2023

Abstract
Electrochemistry is regarded as a mature scientific discipline, having a distinguished two-hundred-year-old history (Table 1.1). Electrochemistry giants such as Faraday and Nernst are well known to all students of chemistry. Furthermore, important applied devices based on electrochemical technology have been in widespread use by the general public throughout the twentieth century. An obvious example of an electrochemical ‘product’ that has been well known for generations is the lead-acid battery used in motor vehicles (Section 6.3).
Product operator formalism
Authors: Freeman Ray 
Published: November 2023

Abstract
For those who aspire to lead the spins a merry dance by inventing new pulse sequences, the most valuable tool of all is, without doubt, the product operator treatment.1-5 Whereas the vector model is based firmly on geometry, the product operator treatment relies on algebra, but this has been distilled from the full density operator theory in a manner that avoids the unwieldy nature of density operators applied to multispin systems. Once the basic rules of this algebra have been assimilated, we can adopt several shorthand notations that retain the essential physics without the need to write out all the explicit equations. The beauty of the scheme is that it retains the intuitive geometrical analogies characteristic of the vector model, so that we can focus our attention on the new spin physics while taking the formal¬ ism for granted.
Spin echoes
Authors: Freeman Ray 
Published: November 2023

Abstract
One of the most versatile tools available to the NMR spectroscopist is the spin echo experiment.1 Not only does it pervade the fields of solid- and liquid-state NMR, ESR, and magnetic resonance imaging, but it has acted as a catalyst for the invention of a host of new physical techniques introduced over the last four decades. Today we take it for granted that nuclear spins can be manipulated in much the same way that a conjuror performs tricks with a pack of cards, but if we examine the origin of these ideas we see that it was the spin echo experiment that inspired these fascinating studies in spin choreography. This chapter will restrict itself to the theme of spin echoes in high resolution liquid-phase NMR where the impact of this idea has been extremely influential.
Broadband decoupling
Authors: Freeman Ray 
Published: November 2023

Abstract
The recording of 13C spectra without C-H spin-spin splitting is a widespread and routine operation in high resolution spectroscopy, going under the name of broadband decoupling. It is perhaps useful at this stage to clear up some semantic points. There is a distinction between a splitting, which is an observable in the high resolution spectrum, and coupling, which is a physical interaction between two nuclear spins carried through the valence electrons in the molecule. A double resonance experiment may modify the splitting but it certainly does not change the spin-spin coupling constant. Evidence for this assertion is provided by the fact that broadband decoupling sequences are very effective in promoting the liquid-phase Hartmann-Hahn effect,1-3 where the coupling is responsible for the coherence transfer(§ 1.4.5). Strong continuous irradiation of a particular spin species also causes saturation, but this has nothing to do with decoupling, as we can test by switching off the irradiation-the spin-spin splittings are restored immediately but the saturation persists for times of the order of the spin-lattice relaxation time.
Two-dimensional spectroscopy
Authors: Freeman Ray 
Published: November 2023

Abstract
Imagine for a moment that an extraterrestrial civilization is monitoring life on Earth through a satellite-based telescope and doing its best to make sense of the observations. Some of our sporting activities might well pose a considerable challenge to their understanding. One bewildering observation would be in athletics-the relay race. Several runners go around an approximately oval track but they inexplicably stop when they meet a second group of athletes who, after a short period of confusion, then set off at full speed. What is going on? The telescope in question is limited in resolution and misses some details of the changeover but it is clear that the net result is a high degree of correlation between the colours worn by the fastest runners in the first stage and those of the leading runners in the second.
The ecological theory of adaptive radiation
Authors: Schluter Dolph 
Published: November 2023

Abstract
What causes adaptive radiation, elevated rates of speciation together with correlated divergence of phenotype and use of environment? In this chapter I review the body of ideas that make up the ‘ecological theory’ of adaptive radiation. This theory holds that adaptive radiation is ultimately the outcome of divergent natural selection stemming from environments and resource competition. The theory was built mainly by Simpson (1944,1953), Lack (1947), and Dobzhansky (1951), but it brought together views of many other naturalists back to Darwin. It survives to the present as the last major synthesis of ideas to explain the processes driving ecological diversification of lineages.
General introduction
Authors: Ricard-Blum Sylvie , Dublet * Bernard , der Rest Michel van 
Published: November 2023

Abstract
The name collagen was first given, in the early nineteenth century, to the substance from animal tissues that gives rise to glue upon boiling. It was later discovered that collagen is a fibrous protein and that it assembles into fibrils that appear striated when observed using electron microscopy. These collagen fibrils are responsible for the tensile strength of connective tissues. Study of the molecules responsible for the formation of striated fibrils revealed that these molecules are formed of a large triple helical domain in which three polypeptide chains wind around each other in a unique way (Fig. 1) to form a rod-like structure that favours lateral interactions between adjacent collagen molecules. The triple helical domain is characterized by a repetitive (Gly-Xaa-Yaa),, amino-acid sequence, with Xaa and Yaa being frequently proline and hydroxyproline residues, respectively. In the late 1960s and early 1970s, it was discovered that different types of collagen molecules could be extracted from tissues. The first three collagen types that were described (types I, II and III) are very closely related molecules that participate in the formation of striated fibrils.
The coming of multicellular organisms
Authors: Williams R J P , Silva J J R Fraústo Da 
Published: November 2023

Abstract
Given the time when multicellular organisms first appeared (Table 14.l), less than a billion years ago, it is likely that a considerable level of dioxygen in the atmosphere was necessary to generate both their external structure (Fig. 14.1) and some new internal features of their cells. The special internal features are not present in single cell aerobic eukaryotes, but clearly multicellular organisms are derived from these organisms.
Parasites and host population dynamics
Authors: Tompkins D M , Dobson A P , Arneberg P , Begon M E , Cattadori I M , Greenman J V , Heesterbeek J A P , Hudson P J , Newborn D , Pugliese A , Rizzoli A P , á R Ros , Rosso F , Wilson K 
Published: November 2023

Abstract
The role that parasites have in influencing the dynamics of their host population has been a central question in the study of wildlife diseases (Kennedy 1975; Grenfell and Dobson 1995). Ecologists and wildlife managers have typically assumed that the answer to this question is ‘No’, believing that para-sites are normally benign, specialized predators that live in a delicate balance with their hosts (Lack 1954). Whilst epidemic outbreaks of disease may cause massive host mortalities, they were explained as cases where environmental factors had disturbed the careful balance and thus rationalized as unusual exceptions to the general rule of no impact. It was even frequently argued that parasites were unlikely to impact on host population dynamics because if their actions led to the death of the host, then the parasite would also die. Theoretical and empirical evidence is now available that highlights the fallacy of this view. Since the lifetime reproductive success of parasites does not depend upon survival alone, but on the interactions between survival, reproduction, and transmission which determine the parasites ability to establish breeding offspring in new hosts, parasites can indeed have highly detrimental effects on their hosts (Box 3.1).
Tools of green chemistry
Authors: Anastas Paul T , Warner John C 
Published: November 2023

Abstract
As the environmental and health effects of a chemical or chemical process have begun to be considered at the design stages, the approaches and the development of techniques have been quite diverse. Since the types of chemicals and the types of transformations are so varied, so too are the green chemistry solutions that have been proposed. These, however, can be broken down into several categories.
With alternative synthetic design, we look not at the ultimate molecule but at the synthetic pathway used to create it. By modifying the synthesis, we can arrive at the same final product, yet reduce or eliminate toxic starting materials, by-products, and wastes. Two of the main components of chemical synthesis are feed stocks and reaction conditions: either or both of these may be changed to produce alternative (and improved) chemical syntheses.
Examples of green chemistry
Authors: Anastas Paul T , Warner John C 
Published: November 2023

Abstract
There have been significant accomplishments in the area of using environmentally benign feedstocks for the manufacture of a wide variety of chemical products. Many products have traditionally been made from feed stocks that contain characteristics of concern, including toxicity, are depleting of natural resources, and/or are generated via methods that can result in environmental damage. With advances in biotechnology, biocatalysis, and biosynthesis, the use of biologically based fcedstocks has been demonstrated as a technologically viable alternative to petroleum feedstocks for a number of chemical processes.
Polymers are a very important class of compounds that have broad applications and a wide array of properties that can be exploited. The starting materials for polymers, their monomeric precursors, can run the full range of hazards like any other discreet chemical substances. One approach to using more environmentally benign starting materials for polymers is through the use of polysaccharides as the feedstock. Polysaccharide feedstocks have several advantages which make them appealing from a green chemistry perspective.
Renal and adrenal anatomy
Authors: Redman John F , Greene Graham F 
Published: November 2023

Abstract
The mental picture that emerges when the word anatomy appears in regard to the human anatomy is often that of pungent cadaveric body parts and monochromatic tones of brown. The anatomy as presented in this chapter should be thought of in the context of a living person in whom the vasculature is actually conveying blood and the nerves transmitting impulses and the organs moving with respiration or palpation. Structures easily visualized and under- stood when widely exposed in the laboratory can be maddeningly elusive when visualized through a limited incision. Further, the expected morphology becomes distorted and obscured by tumor growth, edema, hemorrhage, or inflammation. The knowledge of normal structures and especially relationships are therefore vital in interpreting images and performing surgery.
Staging of renal cell carcinoma
Authors: stuart Wolf J 
Published: November 2023

Abstract
Although RCC is increasingly detected incidentally with cross- sectional radiographic imaging, clinical clues to the presence of RCC are still useful. Additionally, aspects of the history and physical examination may lead to the consideration of advanced disease. The most common presenting symptom of RCC is hematuria, noted in 35 per cent of patients in a review of patients presenting with RCC between 1970 and 1986 (Dinney et al. 1992). In this series, in which only 10 per cent of tumors were found incidentally, 27 per cent of patients reported flank pain. Pain is thought to be due to compression or infiltration of surrounding tissue, obstruction of the collecting system or ureter, or acute expansion of the renal mass to hemorrhage.
Hereditary renal cell carcinoma and the von Hippel–Lindau gene
Authors: Maranchie Jodie K , Linehan W Marston 
Published: November 2023

Abstract
Renal cell carcinoma (RCC) represents 3 per cent of adult cancers and occurs most commonly in the sixth and seventh decades of life. It is responsible for over 12 000 deaths per year in America (Boring et al. 1994). For nearly two decades, investigators have attempted to unravel the mysteries of renal cell carcinoma (RCC) by examining families that carry a predisposition for kidney tumors. Families have been identified that carry a predilection for each of the common histologic subtypes of RCC. Large lineages have permitted identification of precise defects that lead to malignant transformation in both familial and sporadic kidney cancer. Through a better understanding of the genetics and biochemistry of renal malignancy we hope to develop new therapeutic strategies for RCC prevention, treatment, and cure.
Preclinical animal models for the investigation of biological approaches to the therapy of neuroblastoma
Authors: Wigginton Jon M 
Published: November 2023

Abstract
Neuroblastoma (NBL) is the most common extracranial solid tumor among children (Young and Miller 1975) and the most common neoplasm overall among infants less than 1 year of age. It accounts for approximately 8–10 per cent of all childhood cancers. Several aspects of the biology and/or clinical presentation of neuroblastoma are predictive of patient outcome, and have facilitated the development of risk-based strategies for patient management. Although age and stage are among the most import- ant prognostic indicators (Breslow and McCann 1971, Evans et al. 1987), other factors that have been reported to be associated with adverse prognosis in patients with neuroblastoma include elevation of serum ferritin concentrations, presence of unfavorable histology, amplification of the Nzmyc oncogene, diploid DNA content, deletions of the short arm of chromosome 1, over- expression of the multidrug resistance-associated protein (MRP), low expression of the cellular adhesion molecule CD44, low-level expression of TrkA, and increased tumor vascularity (Castleberry 1997, Katzenstein and Cohn 1998; Matthay 1997).
Prognostic indicators: localized disease
Authors: Bruno Dieter , Paulson David F 
Published: November 2023

Abstract
Although renal cell carcinoma (RCC) comprises only 2 per cent of adult cancers, it is the third most common genitourinary malignancy with an incidence of 28 800 new cases in 1998 and an associated mortality of 11 300 lives (Parker et al. 1997). The classic triad of gross hematuria, flank pain, and a palpable mass has been used to describe the presentation of RCC; however, historically only 10 per cent of patients present in this fashion (Jayson and Sanders 1998; Figlin 1999). The modern advent of computerized tomography (CT) and ultrasound has revolutionized the diagnosis of RCC with incidentally detected tumors being the rule rather than the exception (Storkel et al. 1989; Engelmann et al. 1988).
Evaluation of the renal mass and the role of renal biopsy
Authors: Shah Ojas , S.Taneja Samir 
Published: November 2023

Abstract
The evaluation of the renal mass has changed dramatically in recent years, largely due to the availability of imaging modalities such as ultrasound, computerized tomography (CT), and magnetic resonance imaging (MRI). In addition to enhancing our ability to evaluate known renal masses, these imaging techniques have changed the means by which most tumors are diagnosed. The number of tumors incidentally noted on radiologic examination for unrelated symptoms has increased with the increasing use of advanced radiologic imaging over the last 40 years (Rodriguez et al. 1995) (see Table 21.1). As such, our evaluation of the renal mass is very different from what it was 20 years ago. In this chapter, we discuss the important aspects of renal mass evaluation including a review of available diagnostic imaging modalities, differential diagnosis, and the role of invasive diagnostic techniques.
Laparoscopic radical nephrectomy
Authors: Chan David Y , Kavoussi Louis R 
Published: November 2023

Abstract
Radical nephrectomy is the standard of care for the management of renal tumors (Robson 1963). Over the years, technical modifications have focused on extent of dissection and addressed issues such as the removal of the ipsilateral adrenal gland and the role of lymphadenectomy (Sagalowsky et al. 1994; Sandock et al. 1997; Giuliani et al. 1990; Johnsen and Hellsten 1997; Kardar et al. 1998). Nephron-sparing or partial nephrectomy has also altered the management of small (&lt; 4 cm) renal cell carcinoma (Novick et al. 1991; Polascik et al. 1995; Duque et al. 1998; Van Poppel et al. 1998; Wunderlich et al. 1998; Hafez et al. 1998). However, all these studies validate the point that surgical extirpation remains the only curative procedure for localized renal cell carcinoma (RCC).
Immunologic therapy for renal cell carcinoma
Authors: Pantuck Allan J , Zisman, Amnon , Belldegrun Arie 
Published: November 2023

Abstract
Conventional therapy for metastatic renal cell carcinoma (RCC) is associated with a poor response rate and few patients are long- term survivors. Patients with advanced disease have an average survival of less than a year from the time of diagnosis (Elson et al. 1988). Although quite controversial and being challenged by recent studies, traditionally it has been felt that nephrectomy does not benefit survival when metastases are present (deKernion et al. 1978) and the objective response rate to conventional chemotherapy is only 6 per cent and of very short duration (Yagoda et al. 1995). However, up to 1–5 per cent of RCC patients will experience spontaneous tumor regression, mainly involving their pulmonary metastases (Papac 1996).
Natural history and prognostic factors associated with metastatic renal cell carcinoma
Authors: Hoffman David M J , Figlin Robert A 
Published: November 2023

Abstract
With approximately 38 500 new cases and 16 600 deaths expected in the US in the year 2002, renal cell carcinoma (RCC) is the seventh leading cause of cancer, accounting for 3 per cent of malignancies in men (Greenlee et al. 2000). Males are affected twice as frequently as females, with RCC most commonly developing in the fifth and sixth decades of life. There has been a steady increase in the incidence of RCC since the 1970s, which is only partly explained by incidentally discovered tumors found by widespread use of modern imaging techniques (Chow et al. 1999). Worldwide mortality is predicted to exceed 100 000 in 2000 (Motzer et al. 1996).
The surgical management of congenital adrenal hyperplasia
Authors: Rucker G Bino , Poppas Dix P 
Published: November 2023

Abstract
Congenital adrenal hyperplasia (CAH) is an enzymatic defect of steroid synthesis transmitted in an autosomal recessive pattern. CAH refers to a group of disorders that manifest with varying degrees of physical stigmata including virilization of female patients. The degree of stigmata differs according to the under- lying enzyme deficit altering cortisol formation in the adrenal gland. The most commonly encountered defect is that of the 21-hydroxylase enzyme. Our attention will be focused on the surgical management of the virilized female with 21-hydroxylase deficiency since this is the most common type of CAH patient encountered (New and Newfield 1997).