bluuebunny/crossref_metadata_2025 huggingface dataset:
Parameter study for the burst mode of accretion in massive star formation
Authors: Meyer D M-A , Vorobyov E I , Elbakyan V G , Eislöffel J , Sobolev A M , Stöhr M
Published: November 2020

It is now a widely held view that, in their formation and early evolution, stars build up mass in bursts. The burst mode of star formation scenario proposes that the stars grow in mass via episodic accretion of fragments migrating from their gravitationally unstable circumstellar discs, and it naturally explains the existence of observed pre-main-sequence bursts from high-mass protostars. We present a parameter study of hydrodynamical models of massive young stellar objects (MYSOs) that explores the initial masses of the collapsing clouds (Mc = 60–$200\, \rm M_{\odot }$) and ratio of rotational-to-gravitational energies (β = 0.005–0.33). An increase in Mc and/or β produces protostellar accretion discs that are more prone to develop gravitational instability and to experience bursts. We find that all MYSOs have bursts even if their pre-stellar core is such that β ≤ 0.01. Within our assumptions, the lack of stable discs is therefore a major difference between low- and high-mass star formation mechanisms. All our disc masses and disc-to-star mass ratios Md/M⋆ > 1 scale as a power law with the stellar mass. Our results confirm that massive protostars accrete about $40\, -\, 60{{\ \rm per\ cent}}$ of their mass in the burst mode. The distribution of time periods between two consecutive bursts is bimodal: there is a short duration ($\sim 1\, -\, 10~\rm yr$) peak corresponding to the short, faintest bursts and a long-duration peak (at $\sim 10^{3}\, -\, 10^{4} \rm yr$) corresponding to the long, FU-Orionis-type bursts appearing in later disc evolution, i.e. around $30\, \rm kyr$ after disc formation. We discuss this bimodality in the context of the structure of massive protostellar jets as potential signatures of accretion burst history.
Diversification of Fungal Chitinases and Their Functional Differentiation in Histoplasma capsulatum
Authors: Goughenour Kristie D , Whalin Janice , Slot Jason C , Rappleye Chad A
Published: November 2020

Chitinases enzymatically hydrolyze chitin, a highly abundant and utilized polymer of N-acetyl-glucosamine. Fungi are a rich source of chitinases; however, the phylogenetic and functional diversity of fungal chitinases are not well understood. We surveyed fungal chitinases from 373 publicly available genomes, characterized domain architecture, and conducted phylogenetic analyses of the glycoside hydrolase (GH18) domain. This large-scale analysis does not support the previous division of fungal chitinases into three major clades (A, B, C) as chitinases previously assigned to the “C” clade are not resolved as distinct from the “A” clade. Fungal chitinase diversity was partly shaped by horizontal gene transfer, and at least one clade of bacterial origin occurs among chitinases previously assigned to the “B” clade. Furthermore, chitin-binding domains (including the LysM domain) do not define specific clades, but instead are found more broadly across clades of chitinases. To gain insight into biological function diversity, we characterized all eight chitinases (Cts) from the thermally dimorphic fungus, Histoplasma capsulatum: six A clade, one B clade, and one formerly classified C clade chitinases. Expression analyses showed variable induction of chitinase genes in the presence of chitin but preferential expression of CTS3 in the mycelial stage. Activity assays demonstrated that Cts1 (B-I), Cts2 (A-V), Cts3 (A-V), Cts4 (A-V) have endochitinase activities with varying degrees of chitobiosidase function. Cts6 (C-I) has activity consistent with N-acetyl-glucosaminidase exochitinase function and Cts8 (A-II) has chitobiase activity. These results suggest chitinase activity is variable even within subclades and that predictions of functionality require more sophisticated models.
Divergent molecular profile of PIK3CA gene in arsenic-associated bladder carcinoma
Authors: Basu Mukta , Chakraborty Balarko , Ghosh Sabnam , Samadder Sudip , Dutta Sankhadeep , Roy Anup , Pal Dilip Kumar , Ghosh Amlan , Panda Chinmay Kumar
Published: November 2020

The activation of PIK3CA in bladder carcinoma (BlCa) with its recurrent mutations in exon 9 and 20 were well reported. But the association of arsenic on the activation of the pathway is not well elucidated. Therefore, we aimed to analyse the effect of arsenic on the genetic (copy number variation/mutation) and expression profiles of PIK3CA in primary BlCa samples. Infrequent amplification (16%) of the PIK3CA locus was observed, with higher frequency among the arsenic-high (AsH) than arsenic-low (AsL) samples. Frequent (54%) tumour-specific mutations in exon 9 and 20 of PIK3CA were observed in the BlCa samples with prevalent (47%) C>T transition mutations. Exon 9 and 20 harboured 48% and 73% of the total mutations, respectively, with 37% in E542K/E545K and 25% of the mutation in H1047Y/R. Though mutation frequency in AsH and AsL was found to be comparable, we observed some arsenic-specific mutation at c.1633G>A, c.1634A>C (E545K) and c.2985C>T and c.3130G>T mutations, as well as prevalent transverse mutations of A>C and G>T in AsH group. Furthermore, 73% of the BlCa samples showed overexpression (mRNA/protein) of PIK3CA with genetic alterations (amplification/mutation), significantly (P = 0.01) higher in AsH group. However, 36% of the samples showed overexpressed PIK3CA, independent of mutation or amplification, signifying a transcriptional upregulation of PIK3CA gene. Therefore, the expression status of NFκB, a transcription factor of PIK3CA, was assessed and found to be significantly correlated with the overexpression of PIK3CA (mRNA/protein) in AsH group. Similarly, the expression pattern of pAKT1 (Thr 308) was also found to be significantly correlated with PIK3CA overexpression. Finally, AsH patients with the overexpression of PIK3CA or NFκB had the worst overall survival, signifying a strong impact of arsenic on this pathway and outcome of the patients. Thus, our study showed that the arsenic-associated differential molecular profile of PIK3CA/AKT1/NFkB in BlCa has an important role in the molecular pathogenesis of the disease.
Open Targets Platform: supporting systematic drug–target identification and prioritisation
Authors: Ochoa David , Hercules Andrew , Carmona Miguel , Suveges Daniel , Gonzalez-Uriarte Asier , Malangone Cinzia , Miranda Alfredo , Fumis Luca , Carvalho-Silva Denise , Spitzer Michaela , Baker Jarrod , Ferrer Javier , Raies Arwa , Razuvayevskaya Olesya , Faulconbridge Adam , Petsalaki Eirini , Mutowo Prudence , Machlitt-Northen Sandra , Peat Gareth , McAuley Elaine , Ong Chuang Kee , Mountjoy Edward , Ghoussaini Maya , Pierleoni Andrea , Papa Eliseo , Pignatelli Miguel , Koscielny Gautier , Karim Mohd , Schwartzentruber Jeremy , Hulcoop David G , Dunham Ian , McDonagh Ellen M
Published: November 2020

The Open Targets Platform (https://www.targetvalidation.org/) provides users with a queryable knowledgebase and user interface to aid systematic target identification and prioritisation for drug discovery based upon underlying evidence. It is publicly available and the underlying code is open source. Since our last update two years ago, we have had 10 releases to maintain and continuously improve evidence for target–disease relationships from 20 different data sources. In addition, we have integrated new evidence from key datasets, including prioritised targets identified from genome-wide CRISPR knockout screens in 300 cancer models (Project Score), and GWAS/UK BioBank statistical genetic analysis evidence from the Open Targets Genetics Portal. We have evolved our evidence scoring framework to improve target identification. To aid the prioritisation of targets and inform on the potential impact of modulating a given target, we have added evaluation of post-marketing adverse drug reactions and new curated information on target tractability and safety. We have also developed the user interface and backend technologies to improve performance and usability. In this article, we describe the latest enhancements to the Platform, to address the fundamental challenge that developing effective and safe drugs is difficult and expensive.
cola: an R/Bioconductor package for consensus partitioning through a general framework
Authors: Gu Zuguang , Schlesner Matthias , Hübschmann Daniel
Published: November 2020

Classification of high-throughput genomic data is a powerful method to assign samples to subgroups with specific molecular profiles. Consensus partitioning is the most widely applied approach to reveal subgroups by summarizing a consensus classification from a list of individual classifications generated by repeatedly executing clustering on random subsets of the data. It is able to evaluate the stability of the classification. We implemented a new R/Bioconductor package, cola, that provides a general framework for consensus partitioning. With cola, various parameters and methods can be user-defined and easily integrated into different steps of an analysis, e.g., feature selection, sample classification or defining signatures. cola provides a new method named ATC (ability to correlate to other rows) to extract features and recommends spherical k-means clustering (skmeans) for subgroup classification. We show that ATC and skmeans have better performance than other commonly used methods by a comprehensive benchmark on public datasets. We also benchmark key parameters in the consensus partitioning procedure, which helps users to select optimal parameter values. Moreover, cola provides rich functionalities to apply multiple partitioning methods in parallel and directly compare their results, as well as rich visualizations. cola can automate the complete analysis and generates a comprehensive HTML report.
Prevalence and Risk Factors for Mycobacterium tuberculosis Infection Among Adolescents in Rural South Africa
Authors: Mzembe Themba , Lessells Richard , Karat Aaron S , Randera-Rees Safiyya , Edwards Anita , Khan Palwasha , Tomita Andrew , Tanser Frank , Baisley Kathy , Grant Alison D
Published: November 2020

Background

We aimed to estimate the prevalence of and explore risk factors for Mycobacterium tuberculosis infection among adolescents in a high tuberculosis (TB) and human immunodeficiency virus (HIV) prevalence setting.

Methods

A cross-sectional study of adolescents (10–19 years) randomly selected from a demographic surveillance area (DSA) in rural KwaZulu-Natal, South Africa. We determined M tuberculosis infection status using the QuantiFERON-TB Gold-plus assay. We used HIV data from the DSA to estimate community-level adult HIV prevalence and random-effects logistic regression to identify risk factors for TB infection.

Results

We enrolled 1094 adolescents (548 [50.1%] female); M tuberculosis infection prevalence (weighted for nonresponse by age, sex, and urban/rural residence) was 23.0% (95% confidence interval [CI], 20.6–25.6%). Mycobacterium tuberculosis infection was associated with older age (adjusted odds ratio [aOR], 1.37; 95% CI, 1.10–1.71, for increasing age-group [12–14, 15–17, and 18–19 vs 10–11 years]), ever (vs never) having a household TB contact (aOR, 2.13; 95% CI, 1.25–3.64), and increasing community-level HIV prevalence (aOR, 1.43 and 95% CI, 1.07–1.92, for increasing HIV prevalence category [25%–34.9%, 35%–44.9%, ≥45% vs <25%]).

Conclusions

Our data support prioritizing TB prevention and care activities in TB-affected households and high HIV prevalence communities.
Foole’s Gold
Authors: Rickard David
Published: November 2020

This classic opening gambit at the stereotypical drinks party always throws me. I have been a professor at a university for most of my life, so the easiest answer is that I teach. This is true, but it disguises the reality that much of my waking time has been concerned with research. If I admit this, then it becomes necessary to explain what I actually research. One of my pet subjects is pyrite. But if I let on that I research pyrite, my interlocutors look at me as though I am one of those wonderful beings who haunt the bowels of natural history museums as world experts on a rare species of toad. As with toads, most people in the world have heard of pyrite. They know it is a mineral or stone, and most know that it is also called fool’s gold, a familiar theme of moral tales and nursery stories. So the idea of someone studying pyrite is not altogether the stuff of IgNobel prizes. Within the time limits imposed by decent conversation I cannot explain that pyrite is the mineral that made the modern world. I cannot refer them to a book about it since there has not been one published about pyrite since 1725. This book is an attempt to rectify the situation. In it I contend that pyrite has had a disproportionate and hitherto unrecognized influence on developing the world as we know it today. This influence extends from human evolution and culture, through science and industry, to ancient, modern, and future Earth environments and the origins and evolution of early life on the planet. The book is aimed at making the subject accessible to the general reader. It is not a scientific monograph, since these handle only the science and are really directed at the converted: the high priests of the cathedral of science and technology and their aspirant novices. It is also not aimed at being a textbook in the conventional sense: textbooks are generally aimed at specific academic courses and ultimately pave the way for the students to understand the monographs.
The Use of Self
Authors: Fox Raymond
Published: November 2020

This monograph presents recent advances in neural network (NN) approaches and applications to chemical reaction dynamics. Topics covered include: (i) the development of ab initio potential-energy surfaces (PES) for complex multichannel systems using modified novelty sampling and feedforward NNs; (ii) methods for sampling the configuration space of critical importance, such as trajectory and novelty sampling methods and gradient fitting methods; (iii) parametrization of interatomic potential functions using a genetic algorithm accelerated with a NN; (iv) parametrization of analytic interatomic potential functions using NNs; (v) self-starting methods for obtaining analytic PES from ab inito electronic structure calculations using direct dynamics; (vi) development of a novel method, namely, combined function derivative approximation (CFDA) for simultaneous fitting of a PES and its corresponding force fields using feedforward neural networks; (vii) development of generalized PES using many-body expansions, NNs, and moiety energy approximations; (viii) NN methods for data analysis, reaction probabilities, and statistical error reduction in chemical reaction dynamics; (ix) accurate prediction of higher-level electronic structure energies (e.g. MP4 or higher) for large databases using NNs, lower-level (Hartree-Fock) energies, and small subsets of the higher-energy database; and finally (x) illustrative examples of NN applications to chemical reaction dynamics of increasing complexity starting from simple near equilibrium structures (vibrational state studies) to more complex non-adiabatic reactions. The monograph is prepared by an interdisciplinary group of researchers working as a team for nearly two decades at Oklahoma State University, Stillwater, OK with expertise in gas phase reaction dynamics; neural networks; various aspects of MD and Monte Carlo (MC) simulations of nanometric cutting, tribology, and material properties at nanoscale; scaling laws from atomistic to continuum; and neural networks applications to chemical reaction dynamics. It is anticipated that this emerging field of NN in chemical reaction dynamics will play an increasingly important role in MD, MC, and quantum mechanical studies in the years to come.
Assembling Life
Authors: Deamer David W.
Published: November 2020

In Assembling Life, David Deamer addresses questions that are the cutting edge of research on the origin of life. For instance, how did non-living organic compounds assemble into the first forms of primitive cellular life? What was the source of those compounds and the energy that produced the first nucleic acids? Did life begin in the ocean or in fresh water on terrestrial land masses? Could life have begun on Mars? The book provides an overview of conditions on the early Earth four billion years ago and explains why fresh water hot springs are a plausible alternative to salty seawater as a site where life can begin. Deamer describes his studies of organic compounds that were likely to be available in the prebiotic environment and the volcanic conditions that can drive chemical evolution toward the origin of life. The book is not exclusively Earth-centric, but instead considers whether life could begin elsewhere in our solar system. Deamer does not propose how life did begin, because we can never know that with certainty. Instead, his goal is to understand how life can begin on any habitable planet, with Earth so far being the only known example.
Bioenergetics and Primitive Metabolic Pathways
Authors: Deamer David W.
Published: November 2020

It seems inescapable that at some point primitive cells incorporated chemical reactions related to what we now call metabolism. In all life today, metabolic reactions are driven by sources of chemical or photochemical energy, and each step is catalyzed by enzymes and regulated by feedback systems. There have been multiple proposals for the kinds of reactions that could have been incorporated into early life, but so far there is little consensus about a plausible way for metabolism to begin. This chapter will briefly review the main ideas that are familiar to chemists as solution chemistry but then ask a new question from the epigraph: how can reactions in bulk aqueous solutions be captured in membranous compartments? This question is still virtually unexplored, but I can offer some ideas in the hope of guiding potentially fruitful approaches. Because metabolism is such a complex process, it is helpful to use bullet points to help clarify the discussion. The first is a list of questions that guide the discussion, the second is list of facts to keep in mind, and the third is a list of assumptions that introduce the argument. Questions to be addressed: What are the primary metabolic reactions used by life today? What reactions can occur in prebiotic conditions that are related to metabolism? How can potential nutrient solutes cross membranes in order to support metabolism? How could metabolic systems become incorporated into primitive cellular life? Metabolism can be defined as the activity of catalyzed networks of intracellular chemical reactions that alter nutrient compounds available in the environment into a variety of compounds that are used by living systems. Most of the reactions are energetically downhill, so there is an intimate association between the energy sources available to life and the kinds of reactions that can occur. Here is a summary of energy sources used by life today: Light is by far the most abundant energy source, totaling 1360 watts per square meter as infrared and visible wavelengths. Chemical energy in the form of reduced carbon compounds is made available by photosynthesis.
American Medical Schools and the Practice of Medicine
Authors: Rothstein William G.
Published: November 2020

In this extensively researched history of medical schools, William Rothstein, a leading historian of American medicine, traces the formation of the medical school from its origin as a source of medical lectures to its current status as a center of undergraduate and graduate medical education, biomedical research, and specialized patient care. Using a variety of historical and sociological techniques, Rothstein accurately describes methods of medical education from one generation of doctors to the next, illustrating the changing career paths in medicine. At the same time, this study considers medical schools within the context of the state of medical practice, institutions of medical care, and general higher education. The most complete and thorough general history of medical education in the United States ever written, this work focuses both on the historical development of medical schools and their current status.
Gödel's Incompleteness Theorems
Authors: Smullyan Raymond M.
Published: November 2020

Kurt Godel, the greatest logician of our time, startled the world of mathematics in 1931 with his Theorem of Undecidability, which showed that some statements in mathematics are inherently "undecidable." His work on the completeness of logic, the incompleteness of number theory, and the consistency of the axiom of choice and the continuum theory brought him further worldwide fame. In this introductory volume, Raymond Smullyan, himself a well-known logician, guides the reader through the fascinating world of Godel's incompleteness theorems. The level of presentation is suitable for anyone with a basic acquaintance with mathematical logic. As a clear, concise introduction to a difficult but essential subject, the book will appeal to mathematicians, philosophers, and computer scientists.
Vibration-Rotation Spectra of Gaseous Molecules
Authors: Goody R. M. , Yung Y. L.
Published: November 2020

In this chapter we discuss the characteristics of absorption by gaseous constituents of the earth’s atmosphere. This is a complex topic and atmospheric investigators may be disturbed by the idea that weather and climate might be affected by details of the kind we shall discuss. But, as yet, we lack criteria as to what is important and what is not, leaving little alternative to developing a general understanding of the field. A full description of the atmospheric absorption spectrum involves the intensities, state dependence, and detailed line profiles of 105 to 106 lines of 20 or more different chemical species. Given the capabilities of modern computers, it is possible to store, retrieve, and manipulate such data and this is the method of choice for purposes such as the identification of lines in high-resolution spectra. One of a number of current attempts to assemble an up-to-date archive of molecular data is the Air Force Geophysics Laboratory (AFGL) magnetic tape. Not only does this tape provide an economical means of access to the best data from a vast literature, but it also provides a convenient international standard atmosphere. Two numerical climate models, both using the AFGL data, cannot attribute their differences to the radiation data employed. We shall, therefore, address the subject of molecular spectroscopy in the general context of the AFGL tape and many of our illustrations are composed from the tape in preference to seeking out observed spectra. As will be apparent by the end of this chapter, it may sometimes take an expert to distinguish between the two. Figure 3.1 offers an overview of the atmospheric absorption spectrum. The six gases considered are the most important radiators, although climate studies often involve more and rarer species. All six gases are minor species (and therefore in dilute mixtures with nitrogen and oxygen) and are very simple molecules (methane is the most complex). Figure 3.1 shows no visible or ultraviolet spectra. The missing features are mainly electronic bands of oxygen and ozone; they will not be treated in this chapter since they are more complex theoretically but easier to handle empirically than the bands shown in Fig. 3.1.
The Equilibrium Constant
Authors: Anderson Greg M. , Crerar David A.
Published: November 2020

Consider a chemical reaction, involving any number of reactants and products and any number of phases, which may be written where Mi represents the chemical formulae of the reaction constituents and Vi represents the stoichiometric coefficients, negative for reactants and positive for products. An example would be where, if MI is SiO2(s), M2 is H2O, and M3 is H4SiO4(ag), and v1 = —I, i/2 = —2, and V3 = 1 , the reaction is Now let's recall (from Chapter 3) what we mean by an equation such as (13.3). If there are no constraints placed on the system containing M1, M2, and M3 other than T and P (or T and V; U and V; S and P; etc.) then M1, M2, and M3 react until they reach an equilibrium state characterized by a minimum in the appropriate energy potential as indicated by expressions like dGT,p = 0. A corollary of this equilibrium relationship, to be fully developed in the next chapter, is that the sums of the chemical potentials of the reactants and products must be equal. In the example, this would be or or in general terms, No notation is necessary for the phases involved because μ must be the same in every phase in the system. However, if more than the minimum two constraints apply to the system, then any equilibrium state achieved will be in our terms a metastable state, (14.25) does not apply, and the difference in chemical potential between products and reactants is not zero. In our example, a solution might be supersaturated with H4SIO4 but prevented from precipitating quartz by a nucleation constraint, so that μ H4SiO4 — μ SiO2 ~ 2 μ H2o > 0.
Tactile Displays
Authors: Kaczmarek Kurt A. , Bach-Y-Rita Paul
Published: November 2020

The average adult has approximately 2m2 of skin (Gibson, 1968), about 90% hairy, and remainder smooth or glabrous. Although the glabrous areas are more sensitive than the hairy, both types are highly innervated with sensory receptors and nerves (Sinclair, 1981). Tactile displays have utilized both glabrous and hairy skin, the type selected being relative to the sensory display needs of the various investigators. There are several advantages for selecting the skin as the sensory surface to receive information. (1) It is accessible, extensive in area, richly innervated, and capable of precise discrimination. Further, when the skin of the forehead or trunk is used, the tactile display system does not interfere materially with motor or other sensory functions. (2) The skin shows a number of functional similarities to the retina of the eye in its capacity to mediate information. Large parts of the body surface are relatively flat, and the receptor surfaces of the skin, like the retina, are capable of mediating displays in two spatial dimensions as well as having the potential for temporal integration (summation over time). Thus, there is generally no need for complex topological transformation or for temporal coding of pictorial information for direct presentation onto the accessible areas of the skin, although temporal display factors have been explored with the goal of transmitting spatial information across the skin more quickly than is possible with present systems (Kaczmarek et al., 1984; Bach-y-Rita and Hughes, 1985; Kaczmarek et al., 1985; Loomis and Lederman, 1986). Spatial patterns learned visually can be identified factually, and vice versa (Epstein et al., 1989; Hughes et al., 1990). (3) Certain types of sensory inhibition, including the Mach band phenomenon and other examples of lateral inhibition originally demonstrated for vision, are equally demonstrable in the skin (Bekesy, 1967). (4) Finally, there is evidence that the skin normally functions as an exteroceptor at least in a limited sense: Katz noted that to some extent both vibration and temperature changes can be felt at a distance (Krueger, 1970). For example, a blind person can “feel” the approach of a warm cylinder at three times the distance required by the sighted individual (Krueger, 1970).
The Causes and Consequences of Geographic Variation in Antipredator Behavior: Perspectives from Fish Populations
Authors: Margurran Anne E.
Published: November 2020

Predators are extremely effective agents of selection. After all, if an individual member of a prey species does not survive long enough to reproduce, it will have lost its chance (kin selection considerations apart) to bequeath its genes to future generations. It is not surprising, therefore, that many cases of population difference have been attributed to geographic variation in risk. These population differences can take a variety of forms and may, for example, involve modifications to morphology or to life-history traits. The correlation between armor and predation in the three-spined stickleback, Gasterosteus aculeatus, is one case that has been well documented (see Reimchen 1994 for a review and discussion), while another is the association between reproductive allotment and risk (Reznick and Endler 1982) and male color pattern and risk (Endler 1980) in the Trinidadian guppy, Poecilia reticulata. However, such adaptations can be futile if they are not accompanied by effective antipredator behavior. For instance, a cryptic color pattern confers no advantage if its holder chooses the “wrong” background or behaves in a conspicuous manner. Behavior is also flexible in a way that life histories or morphology may not be, and it allows moment-to-moment changes in response as risk increases or decreases. Because it is such an important weapon in the evolutionary arms race, antipredator behavior provides important insights into the causes and consequences of natural selection. Some of the best examples of geographically variable antipredator responses occur in populations of freshwater fish (see, e.g., Bell and Foster 1994). The predation regime of these populations is relatively easy to classify—at least in terms of the presence and absence of predatory species—and the distribution of key predators can explain much of the documented variation in antipredator behavior (see p. 140). Covariance in predation regime and antipredator responses is compelling evidence for natural selection. Moreover, because predation regimes can change (or be manipulated) over relatively short periods of time, there is an opportunity to record heritable changes in antipredator responses—in other words, to watch evolution in action.
Thinking Like a River
Authors: Worster Donald
Published: November 2020

When we drive by a modern farm, we still expect to see green plants sprouting from the earth, bearing the promise of food or cooking oil or a cotton shirt. Pulling up one of those plants, we are still prepared to find dirt clinging to its roots. Even in this age of high-tech euphoria, agriculture remains essentially a matter of plants growing in the soil. But another element besides soil has always been a part of the farmer’s life-water. Farming is not only growing crops on a piece of land, it is also growing crops in water. I don’t mean a hydroponics lab. I mean that the farmer and his plants inescapably are participants in the natural cycle of water on this planet. Water is a more volatile, uncertain element than soil in the agricultural equation. Soil naturally stays there on the farm, unless poor management intervenes, whereas water is by nature forever on the move, falling from the clouds, soaking down to roots, running off in streams to the sea. We must farm rivers and the flow of water as well as fields and pastures if we are to continue to thrive. But it has never been easy to extract a living from something so mobile and elusive, so relentless and yet so vulnerable as water. If there is to be a long-term, sustainable agriculture in the United States or elsewhere, farmers must think and act in accord with the flow of water over, under, through, and beyond their farms. Preserving the fertility of the soil resource is critical to sustaining it, of course, but not more so than maintaining the quality of water. In many ways, the two ideals are one. And their failure is one, as when rain erodes the topsoil and creeks and rivers suffer. But there are differences between those two resources, differences we must understand and respect. Unlike soil, water cannot be “built.” It can be lost to the farmer, or it can be diverted, polluted, misused, or over-appropriated, but it can never be deepened or enhanced as soil can be.
Liquids and Solutions at Interfaces
Authors: Fawcett W. Ronald
Published: November 2020

When the properties of liquids and solutions are considered, attention is normally focused on the bulk of the phase, and the properties of the system at its boundaries are ignored. Significant effects are associated with the region near the surface of a liquid phase and an understanding of these is an important part of solution chemistry. As a simple example, consider a beaker of pure water at room temperature in a closed inert environment. As has been seen in the consideration of liquid structure, the properties of water are strongly influenced by hydrogen bonding between neighboring molecules, and to a lesser extent by dipole–dipole interactions. As an observer at the molecular level, one would find that the molecules near the boundaries of the water phase have different properties. There are two boundaries in this system, the water | air interface and the water | glass interface. At the water | air interface, the important feature is the termination of intermolecular interactions, so that molecules must adjust to an environment where the number of nearest neighbors is reduced. At the water | glass interface, water molecules meet the components of glass, a supercooled liquid with silicon dioxide as the major component. Interaction between water and silicon dioxide is different from interaction among water molecules. It is clear that the molecular environment at these interfaces is very different than it is in the bulk. As a result, local properties are different. Now imagine that the water in the beaker is dispersed as a fog, that is to say, as many very small droplets for which the ratio of surface area to volume is much larger than for the water in the beaker. It is obvious that the thermodynamic properties of the fog, a colloidal system, are very different from those of the water as a macrosystem in a beaker. In order to create the fog considerable work must be done to form a system with a much larger surface area. This means that the Gibbs energy of a fog containing the same number of water molecules as the beaker of water is much higher.
Geochemical Reaction Modeling
Authors: Bethke Craig M.
Published: November 2020

Geochemical reaction modeling plays an increasingly vital role in several areas of geoscience, from environmental geochemistry and petroleum geology to the study of geothermal and hydrothermal fluids. This book provides an up-to-date overview of the use of numerical methods to model reaction processes in the Earth's crust and on its surface. Early chapters develop the theoretical foundations of the field, derive a set of governing equations, and show how numerical methods can be used to solve these equations. Other chapters discuss the distribution of species in natural waters; methods for computing activity coefficients in dilute solutions and in brines; the complexation of ions into mineral surfaces; the kinetics of precipitation and dissolution reactions; and the fractionation of stable isotopes. Later chapters provide a large number of fully worked calculation examples and case studies demonstrating the modeling techniques that can be applied to scientific and practical problems. Students in a variety of specialties from low-temperature geochemistry to groundwater hydrology will benefit from the wealth of information and practical applications this book has to offer.
Geochemical Kinetics
Authors: Bethke Craig M.
Published: November 2020

To this point we have measured reaction progress parametrically in terms of the reaction progress variable ξ, which is dimensionless. When in Chapter 11 we reacted feldspar with water, for example, we tied reaction progress to the amount of feldspar that had reacted and expressed our results along that coordinate. Studying reactions in this way is in many cases perfectly acceptable. But what if we want to know how much time it took to reach a certain point along the reaction path? Or, when modeling the reaction of granite with rainwater, how can we set the relative rates at which the various minerals in the granite dissolve? In such cases, we need to incorporate reaction rate laws from the field of geochemical kinetics. The differences between the study of thermodynamics and kinetics might be illustrated (e.g., Lasaga, 198la) by the analogy of rainfall on a mountain. On the mountaintop, the rainwater contains a considerable amount of potential energy. With time, it flows downhill, losing energy (to be precise, losing hydraulic potential, the mechanical energy content of a unit mass of water; Hubbert, 1940), until it eventually reaches the ocean, its lowest possible energy level. The thermodynamic interpretation of the process is obvious: the water seeks to minimize its energy content. But how long will it take for the rainfall to reach the ocean? The rain might enter a swift mountain stream, flow into a river, and soon reach the sea. It might infiltrate the subsurface and migrate slowly through deep aquifers until it discharges in a distant valley, thousands of years later. Or, perhaps it will find a faster route through a fracture network or flow through an open drill hole. There are many pathways, just as there are many mechanisms by which a chemical reaction can proceed. Clearly, the questions addressed by geochemical kinetics are more difficult to answer than are those posed in thermodynamics. In geochemical kinetics, the rates at which reactions proceed are given (in units such as moles/sec or moles/yr) by rate laws, as discussed in the next section. Kinetic theory can be applied to study reactions among the species in solution.
Never-Ending Learning
Authors: Turkanis Carolyn Goodman , Bartlett Leslee
Published: November 2020

In the OC, teachers, parents, and administrators continually try to articulate the overarching principles of learning as a community that guide our everyday practices and underlie natural variations across individuals and classrooms. The principles are enacted in varying ways in the specific practices across classrooms, as variations on the theme that makes up the common thread of the philosophy. The everyday practices that support the philosophy vary according to teacher style and experience, classroom grade levels, and the unique interests and needs of members of the classroom community. For example, some years different teachers experiment with the schedules in their classrooms, arranging all literacy activities in one time block or encouraging varying types of activities within any time block. But such variations in everyday practices are still built around the philosophical principle of purposeful learning activities, as all classrooms support literacy learning with classic and current children's literature that is of interest in their class. The specific types of activities vary across the grade levels to adapt to the interests and growing skills of the students. Teachers and parents continually examine how everyday practices in the different classrooms fit with the OC philosophy. The common principles that tie our classes together not only provide coherence to the way we do things but also underlie many of the issues with which we continue to struggle in philosophical discussions. That is natural, since a community of learners is a work in progress. The common philosophy has developed from and is understood by working together and having innumerable discussions about the way we do things. The variations in practices still must remain true to the core principles in order for the school to remain a coherent community of learners. On occasion, differences in interpretation of the philosophy by particular individuals have been great enough to raise concern. At such times, the teachers observe and reflect to come to consensus on how to support the learning of the people involved. With this process, people usually come to understand and embrace the philosophy; sometimes they realize that another learning situation would be more appropriate for them.
Nonlinear and Mixed-Integer Optimization
Authors: Floudas Christodoulos A.
Published: November 2020

Filling a void in chemical engineering and optimization literature, this book presents the theory and methods for nonlinear and mixed-integer optimization, and their applications in the important area of process synthesis. Other topics include modeling issues in process synthesis, and optimization-based approaches in the synthesis of heat recovery systems, distillation-based systems, and reactor-based systems. The basics of convex analysis and nonlinear optimization are also covered and the elementary concepts of mixed-integer linear optimization are introduced. All chapters have several illustrations and geometrical interpretations of the material as well as suggested problems. Nonlinear and Mixed-Integer Optimization will prove to be an invaluable source--either as a textbook or a reference--for researchers and graduate students interested in continuous and discrete nonlinear optimization issues in engineering design, process synthesis, process operations, applied mathematics, operations research, industrial management, and systems engineering.
Mixed-Integer Nonlinear Optimization
Authors: Floudas Christodoulos A.
Published: November 2020

This chapter presents the fundamentals and algorithms for mixed-integer nonlinear optimization problems. Sections 6.1 and 6.2 outline the motivation, formulation, and algorithmic approaches. Section 6.3 discusses the Generalized Benders Decomposition and its variants. Sections 6.4, 6.5 and 6.6 presents the Outer Approximation and its variants with Equality Relaxation and Augmented Penalty. Section 6.7 discusses the Generalized Outer Approximation while section 6.8 compares the Generalized Benders Decomposition with the Outer Approximation. Finally, section 6.9 discusses the Generalized Cross Decomposition. A wide range of nonlinear optimization problems involve integer or discrete variables in addition to the continuous variables. These classes of optimization problems arise from a variety of applications and are denoted as Mixed-Integer Nonlinear Programming MINLP problems. The integer variables can be used to model, for instance, sequences of events, alternative candidates, existence or nonexistence of units (in their zero-one representation), while discrete variables can model, for instance, different equipment sizes. The continuous variables are used to model the input-output and interaction relationships among individual units/operations and different interconnected systems. The nonlinear nature of these mixed-integer optimization problems may arise from (i) nonlinear relations in the integer domain exclusively (e.g., products of binary variables in the quadratic assignment model), (ii) nonlinear relations in the continuous domain only (e.g., complex nonlinear input-output model in a distillation column or reactor unit), (iii) nonlinear relations in the joint integer-continuous domain (e.g., products of continuous and binary variables in the scheduling/ planning of batch processes, and retrofit of heat recovery systems). In this chapter, we will focus on nonlinearities due to relations (ii) and (iii). An excellent book that studies mixed-integer linear optimization, and nonlinear integer relationships in combinatorial optimization is the one by Nemhauser and Wolsey (1988). The coupling of the integer domain with the continuous domain along with their associated nonlinearities make the class of MINLP problems very challenging from the theoretical, algorithmic,and computational point of view. Apart from this challenge, however, there exists a broad spectrum of applications that can be modeled as mixed-integer nonlinear programming problems.
The Ecology, Exploitation and Conservation of River Turtles
Authors: Moll Don , Moll Edward O.
Published: November 2020

The underlying theme of this book is that a widespread, taxonomically diverse group of animals, important both from ecological and human resource perspectives, remains poorly understood and in delcine, while receiving scant attention from the ecological and conservation community. This volume proposes a comprehensive overview of the world's river turtles' ecology, conservation, and management. It begins with a categorization of taxa which inhabit flowing water habitats followed by information on their evolutionary and physical diversity and biogeography. Within the framework of ecology, the authors discuss the composition of river turtle communities in different types of lotic habitats and regions, population dynamics, movements, reproductive characteristics and behavior, predators, and feeding relationships. In a conservation and management section, the authors identify and evaluate the nature and intensity of factors which threaten river turtle survival--almost all of which involve direct human exploitation or indirect effects of human induced habitat alteration and degradation. They then list and evaluate the various schemes which have been proposed or employed to halt declines and restore populations, and make recommendations for future management plans for specific species and regions. In closing, they state their viewpoint concerning future research directions and priorities, and an evaluation of future prospects for survival of the world's river turtle species.
Logical Reasoning with Diagrams
Authors: Allwein Gerard , Barwise Jon
Published: November 2020

One effect of information technology is the increasing need to present information visually. The trend raises intriguing questions. What is the logical status of reasoning that employs visualization? What are the cognitive advantages and pitfalls of this reasoning? What kinds of tools can be developed to aid in the use of visual representation? This newest volume on the Studies in Logic and Computation series addresses the logical aspects of the visualization of information. The authors of these specially commissioned papers explore the properties of diagrams, charts, and maps, and their use in problem solving and teaching basic reasoning skills. As computers make visual representations more commonplace, it is important for professionals, researchers and students in computer science, philosophy, and logic to develop an understanding of these tools; this book can clarify the relationship between visuals and information.
Grand Teton Tour
Authors: Smith Robert B. , Siegel Lee J.
Published: November 2020

Because winter snows close roads in both Grand Teton and Yellowstone national parks, the driving tours in this chapter and the next are intended for use only from late spring through early fall. You may wish to do only parts of each tour and so we have not shown cumulative trip mileage in these tour guides. Instead, we provide cumulative mileage only from one stop to the next, and for points of interest between them. This chapter’s tour of Grand Teton National Park totals 82 miles, excluding mileage to the optional aerial tramway ride. The intent of these two chapters is to provide a three-day driving tour, including one day in Grand Teton and two in Yellowstone. However, you easily may extend the tour to five days or even longer if you choose a leisurely pace or decide to make optional hikes and stops. The three-day tour outlined in these chapters starts in the town of Jackson, Wyoming. Our tour includes the following suggestions: • On day I, make the Teton tour, perhaps beginning or ending with the optional tramway ride detailed at the end of this chapter. Spend the night either in Jackson or find accommodations closer to Yellowstone, such as at Colter Bay Village or other campgrounds and lodgings in northern Grand Teton National Park. • On day 2, enter Yellowstone’s south entrance and drive the loop road clockwise to Madison Junction, then spend the night at West Yellowstone, Montana. If you arrive at West Yellowstone by early to mid-afternoon, you still will have time to make the optional tour to the Hebgen Lake earthquake area, although the visitor center there closes in the late afternoon. • On day 3, either start with the optional side trip to the Hebgen Lake earthquake area, or proceed from West Yellowstone, Montana, back into Yellowstone National Park, continuing the tour at Madison Junction. Some visitors may choose to drive part or all of these tours in a direction opposite to the one we use here. For that reason, we also provide reverse mileage between each stop and the sights between stops.