cssi/SciSciGPT-SciSciNet huggingface dataset:
Understanding the Time Scales of the Tropospheric Circulation Response to Abrupt CO2 Forcing in the Southern Hemisphere: Seasonality and the Role of the Stratosphere

AbstractThis study examines the time scales of the Southern Hemisphere (SH) tropospheric circulation response to increasing atmospheric CO2 concentrations in models from phase 5 of the Coupled Model Intercomparison Project (CMIP5). In response to an abrupt quadrupling of atmospheric CO2, the midlatitude jet stream and poleward edge of the Hadley circulation shift poleward on the time scale of the rising global-mean surface temperature during the summer and fall seasons but on a much more rapid time scale during the winter and spring seasons. The seasonally varying time scales of the SH circulation response are closely tied to the meridional temperature gradient in the upper troposphere–lower stratosphere and, in particular, to temperatures in the SH polar lower stratosphere. During summer and fall, SH polar lower-stratospheric temperatures cool on the time scale of warming global surface temperatures, as the lifting of the tropopause height with tropospheric warming is associated with cooling at lower-str...
Synthesis and Activity of a New Series of Antileishmanial Agents

We have determined that tetrahydroindazoles such as 1 show potent activity against Leishmania donovani, the causative agent of leishmaniasis. While the Hsp90 activity and anticancer properties of 1 have previously been explored, we present here our efforts to optimize their activity against L. donovani via the synthesis of novel analogues designed to probe the hydrophobic pocket of the protozoan Hsp90 orthologue, specifically through the auspices of functionalization of an amine embedded into the scaffold.
Interplay of structure, elasticity, and dynamics in actin-based nematic materials

Achieving control and tunability of lyotropic materials has been a long-standing goal of liquid crystal research. Here we show that the elasticity of a liquid crystal system consisting of a dense suspension of semiflexible biopolymers can be manipulated over a relatively wide range of elastic moduli. Specifically, thin films of actin filaments are assembled at an oil-water interface. At sufficiently high concentrations, one observes the formation of a nematic phase riddled with [Formula: see text] topological defects, characteristic of a two-dimensional nematic system. As the average filament length increases, the defect morphology transitions from a U shape into a V shape, indicating the relative increase of the material's bend over splay modulus. Furthermore, through the sparse addition of rigid microtubule filaments, one can gain additional control over the liquid crystal's elasticity. We show how the material's bend constant can be raised linearly as a function of microtubule filament density, and present a simple means to extract absolute values of the elastic moduli from purely optical observations. Finally, we demonstrate that it is possible to predict not only the static structure of the material, including its topological defects, but also the evolution of the system into dynamically arrested states. Despite the nonequilibrium nature of the system, our continuum model, which couples structure and hydrodynamics, is able to capture the annihilation and movement of defects over long time scales. Thus, we have experimentally realized a lyotropic liquid crystal system that can be truly engineered, with tunable mechanical properties, and a theoretical framework to capture its structure, mechanics, and dynamics.
Flugschriften als Leitmedien reformatorischer Öffentlichkeit

Innerhalb der Forschung zur Geschichte der deutschen Reformation besteht seit langerem Konsens daruber, dass die Formulierung und Popularisierung einer neuen, die Entstehung konfessionell distinkter Kirchen begrundenden Theologie als erstes europaisches Medienereignis zu gelten hat.
A Decadal Revisiting of the Assessment of Pilot Control Interfaces for Unmanned Aircraft Systems

Unmanned Aircraft System (UAS) control design is critical for mitigating the negative human factors effects associated with operating the aircraft remotely, such as latency in the transfer of information and loss of sensory information. With this in mind, we conducted a systematic review of the human factors UAS literature to identify control automation and input devices with the objective of modernizing the seminal Williams (2007) assessment of UAS control interfaces. We also identified compatible automation-input device pairs, and characterized the literature based on the control strategies. The characterization of the literature reflected our identified compatibilities between the levels of control and input devices. Generally, the levels of UAS control identified by Williams (2007) are still prevalent in the literature, but we identified two levels that he did not account for in his taxonomy, including guided manual control (similar to LNAV/VNAV guidance in manned aircraft) and objective control (in w...
The Behavior of Transforms

A recurring theme of our subject is the effort to say which functions on Γ belong to the Fourier-Stie1tjes transform space B(Γ), and which do not—what the transforms can do, and what they cannot do. The question is a deep one. The known characterizations are neither subtle nor powerful. Indeed, it appears that the property of being a transform is not truly reducible. This Chapter treats three aspects of transform behavior. Our three topics, which may be read independently, are as follows.
The Guilty Mother

> The December 2017 issue of Pediatrics featured the first and second place articles from the First Annual SOPT Advocacy Essay Competition, which focused on the effects and management of toxic stress. The Editorial Board of the SOPT Monthly Feature is pleased to continue this discussion on toxic stress with the following article by Dr Paul E. George. In the article, he poignantly describes the numerous challenges faced by undocumented immigrants and advocates for several key solutions to mitigate the severe effects of toxic stress associated with immigration. > > Catherine Spaulding, MD, Editor, Pediatrics , SOPT Monthly Feature “ This patient is an adorable 5 y/o F with spina bifida, complicated by paraplegia, bilateral Grade 3 reflux, admitted with a urinary tract infection and infected urachal cyst, status post drain placement, currently on IV antibiotics. ” The sign out for Anayansi was perfect. This little girl with giant hazel eyes and curly, black hair, whose lack of English didn’t stop her from talking with anyone in her hospital room, certainly fit the “adorable” description. Yet Anayansi did not garner the most attention on rounds; rather, the gaze of the team members kept drifting toward her mother, or more specifically, toward the conspicuous ankle monitor and charger that confined her to the corner of the room while we discussed her daughter. “I wonder what she did?” whispered my coresident as we left. A simple question with a bitter answer. Anayansi’s mother was born outside of the United States. Knowing her daughter would not receive the medical care she needed in her home country, she left with her 2 young … Address correspondence to Paul E. George, MD, Baylor College of Medicine, Texas Children’s Hospital, 6621 Fannin St, Houston, TX 77054. E-mail: george.paul.e{at}gmail.com
Discontinuous Hamiltonian Monte Carlo for discrete parameters and discontinuous likelihoods

Hamiltonian Monte Carlo has emerged as a standard tool for posterior computation. In this article, we present an extension that can efficiently explore target distributions with discontinuous densities. Our extension in particular enables efficient sampling from ordinal parameters though embedding of probability mass functions into continuous spaces. We motivate our approach through a theory of discontinuous Hamiltonian dynamics and develop a corresponding numerical solver. The proposed solver is the first of its kind, with a remarkable ability to exactly preserve the Hamiltonian. We apply our algorithm to challenging posterior inference problems to demonstrate its wide applicability and competitive performance.
Systemic Lupus Erythematosus Lymphadenopathy

Systemic lupus erythematosus (SLE) lymphadenopathy is lymph node enlargement associated with SLE, an autoimmune disease characterized by increased numbers of autoreactive CD4-positive T-cells and dysregulation of the adaptive immune system resulting in multiorgan damage from autoantibodies and immune complexes. The disease has wide prevalence but tends to occur more commonly in non-white females during the second to fourth decades of life. The etiology of SLE remains unknown. Overall, SLE is much more common in women, with a 3–1 female-to-male ratio before puberty, rising to 9–1 in patients of reproductive age. The disease also can be exacerbated during pregnancy. These findings suggest a role for female hormones and particularly estrogen in SLE pathogenesis. Estrogen receptors are expressed intracellularly in many immune cells including lymphocytes, monocytes, and dendritic cells. Via these receptors, estrogen may promote a TH2 cytokine environment and promote survival of autoreactive B- and T-cells. Other data point to genetic predisposition and environmental factors playing a role in disease pathogenesis.
Interference Between Greenleaf Manzanita (Arctostaphylos Patula) and Ponderosa Pine (Pinus Ponderosa)

Shrubs which usually occur on forested sites following a serious disturbance are believed to compete with newly planted conifers, thus restricting tree growth. When studying competition, it is important to recognize the importance of total plant density, proportions between species, and their spatial relationships. Several experimental designs (additive, substitutive, and systematic) have been used to study competition. In 1980 a substitutive experiment was established to examine the interaction between seedling ponderosa pine and sprouting greenleaf manzanita. This design considers all three factors since spatial arrangement and total density are held constant and proportion between species is varied. After the first growing season shrubs dramatically inhibited tree growth. Soil moisture was found to be the limiting factor for maximum tree growth when ponderosa pine occurred in association with greenleaf manzanita.
Reproductive Factors Affecting the Course of Affective Illness in Women

Women are at higher risk than men to develop depressive episodes during the reproductive years. Furthermore, women are vulnerable to depressions associated with oral contraceptives, abortion, the premenstrual period, the puerperium, and menopause. The phenomenology and the biologic mechanisms involved in these illnesses perhaps should be viewed in the context of other manifestations of the link between depression and female reproductive functions. For example, women are especially vulnerable to a rapid cycling form of affective illness and to hypothyroidism, an associated factor for this form of affective disorder. The postpartum period is also associated with impaired thyroid function, and there are reports of the induction of rapid cycles of mood following the termination of pregnancy. Thus, alterations in thyroid hormones may be a feature of both postpartum and rapid cycling forms of affective disorder in women. A previous history of a postpartum depression places a woman at a high risk for the development of a subsequent puerperal episode. Also, difficulties during pregnancy may predispose a woman to the development of other reproductive-related depressions. The role reproductive hormones play in this possible sensitization phenomenon needs to be examined in order to understand the relationship of depression to the female reproductive cycle.
Modern Neural Networks Generalize on Small Data Sets

In this paper, we use a linear program to empirically decompose fitted neural networks into ensembles of low-bias sub-networks. We show that these sub-networks are relatively uncorrelated which leads to an internal regularization process, very much like a random forest, which can explain why a neural network is surprisingly resistant to overfitting. We then demonstrate this in practice by applying large neural networks, with hundreds of parameters per training observation, to a collection of 116 real-world data sets from the UCI Machine Learning Repository. This collection of data sets contains a much smaller number of training examples than the types of image classification tasks generally studied in the deep learning literature, as well as non-trivial label noise. We show that even in this setting deep neural nets are capable of achieving superior classification accuracy without overfitting.
Investigation of the Electronic Structure of Aryl-Bridged Dinuclear U(III) and U(IV) Compounds

A family of dinuclear bis(Tp*) (Tp* = hydrotris(3,5-dimethylpyrazolyl)borate) uranium compounds with conjugated organic linkers was synthesized to explore possible electronic communication between ...
Label-free assessment of preimplantation embryo quality by the Fluorescence Lifetime Imaging Microscopy (FLIM)-phasor approach

Introduction The standard non-invasive method to assess embryo quality and viabilityrelies on the visual inspection of embryo morphology according to predefined criteria. Development of more quantitative and objective means for assessing embryo qualitythat are simpler, safer, and faster could provide significant advantages in assistedreproduction. We have applied the phasor-FLIM (Fluorescence Lifetime Imaging Microscopy) approach to preimplantation mouse embryos. FLIM produces an imagebased on the differences in the exponential decay rate of the fluorescence from afluorescent sample. We apply non- invasive phasor-FLIM to identify endogenousfluorescent biomarkers (metabolic signatures) of preimplantation embryos for embryoquality assessment. Material and Methods Fluorescent lifetimes of endogenous fluorescent species arecollected at various stages of preimplantation development. At each developmentalstage, the mouse embryo displays a characteristic phasor-FLIM signature. Collectively,these signatures define a unique graphical metabolic trajectory (defined as D-trajectory), indicating the dynamic metabolic states of embryos during preimplantationdevelopment. We test whether the major components responsible for the shifts in the Dtrajectoryis intracellular NADH changes by altering its energy metabolism. Second, wedetermine the optimum laser power to examine the effect on the developmentalprogression of embryos until the blastocyst stage. Third, we test whether the uniquelifetime distribution patterns of an embryo cultured under altered physiological statescan be detected by the changes in spectroscopic distributions of phasor-FLIM. Lastly,we define an EVI (Embryo Viability Index) to distinguish preimplantation embryo qualityusing the Distance analysis (DA) program. Results We have defined a unique graphical metabolic trajectory that correlates with energy metabolism and embryo development. The intrinsic lifetime trajectory of preimplantation embryos cultured in nutrient-compromised media deviates from the normal lifetime distribution, demonstrating that the lifetime trajectory can detect metabolic changes in developing embryos. Lastly, we have identified a combination of mathematical parameters that are statistically different between healthy and unhealthy preimplantation embryos based on machine learning information. The phasor-FLIM approach identifies healthy embryos at the early compaction stage with over 85% accuracy. Conclusions The phasor-FLIM approach provides an objective, non-invasive, and quantitative method to assess the quality of preimplantation mammalian embryos. Our future goal is to apply the technology for the reproductive biology of human and other mammals.
Management of Dyslipidemia

An estimated 16 million adults in the United States have coronary heart disease (CHD), which accounts for more deaths than any single cause or group of causes of death in the United States (1). Atherosclerosis is a complex, multifactorial disease. Over the course of the past five decades, numerous prospective observational cohort studies have established beyond any doubt that risk for atherosclerotic disease is driven by a number of risk factors, which include dyslipidemia, hypertension, insulin resistance and diabetes mellitus, obesity, cigarette smoking, and age (2–6). The greater the burden of risk factors, the higher the likelihood for developing such manifestations of atherosclerosis as coronary artery disease (CAD), carotid artery disease, and peripheral arterial disease. Atherosclerotic disease is unequivocally associated with increased risk for myocardial infarction, stroke, renal artery disease and renal insufficiency, claudication and lower extremity amputation, and death. Progressive accumulation of lipid in arterial walls is a cardinal structural manifestation of atherosclerotic disease. Arresting this process of lipid infiltration and retention is an important goal in modern cardiovascular medicine.
Atomistic mechanisms of crack nucleation and propagation in amorphous silica

This paper presents an atomistic understanding of the nanoscale processes that govern crack nucleation and propagation in amorphous silica using a combination of theoretical calculations and molecular dynamics simulations with the ReaxFF potential. We show that both crack nucleation and propagation are governed by chainlike nanoscale virial stress-fibers formed by an intricate mixture of Si and O atoms. The stress-fibers are of a few nanometers in length, aligned parallel to the loading direction, and spatially localized at the evolving crack front at the nucleating site or a propagating crack tip. They form and break continuously during the crack nucleation and propagation process and are responsible for localizing stress at the crack nucleation site or propagating crack front. As soon as the stress-fibers reach a critical density the material starts nucleating cracks or leads to the propagation of initial crack. Additionally, the virial stress fields in the domain is highly heterogeneous and species-dependent---and the O and Si atoms play fundamentally distinct roles throughout the deformation process. With increased loading, heterogeneity in virial stress for the Si atoms goes up, whereas for the O atoms it goes down. Furthermore, from the virial and Hardy estimates of atomic stress, it is found that the stress field emanating from the crack tip decays as $1/r$. Also, presence of holes or pores within the interaction distance of a crack tip intensifies the stress state of the stress-fibers near the crack front leading to an improved effective toughness compared to the situation where the pore is far from the crack tip. Nucleation and propagation of cracks are strictly mediated by a complex admixture of localized bond rupture processes across a set of interacting stress-fibers. The details of the atomistic process regulating the underlying mechanisms are undetectable from the macroscopic stress-strain data.
Apparent Genetic Rescue of Adult Shank3 Exon 21 Insertion Mutation Mice Tempered by Appropriate Control Experiments

SHANK3 (ProSAP2) is among the most common genes mutated in autism spectrum disorders (ASD) and is the causative gene in Phelan-McDermid syndrome (PMS). We performed genetic rescue of Shank3 mutant phenotypes in adult mice expressing a Shank3 exon 21 insertion mutation (Shank3G ). We used a tamoxifen-inducible Cre/loxP system (CreTam ) to revert Shank3G to wild-type (WT) Shank3+/+ We found that tamoxifen treatment in adult Shank3GCreTam+ mice resulted in complete rescue of SHANK3 protein expression in the brain and appeared to rescue synaptic transmission and some behavioral differences compared to Shank3+/+CreTam+ controls. However, follow-up comparisons between vehicle-treated, WT Cre-negative mice (Shank3+/+CreTam- and Shank3+/+CreTam+) demonstrated clear effects of CreTam on baseline synaptic transmission and some behaviors, making apparently positive genetic reversal effects difficult to interpret. Thus, while the CreTam tamoxifen-inducible system is a powerful tool that successfully rescues Shank3 expression in our Shank3G/G reversible mutants, one must exercise caution and use appropriate control comparisons to ensure sound interpretation.
An Orienting Theory for Implementing Advanced Manufacturing Technologies

Technological innovation is arguably the key competitive challenge of the 1990s. Our paper suggests that the selection and evaluation processes for advanced manufacturing technology should anticipate potential implementation problems as part of the justification process. To this end our paper proposes an orienting theory for implementing technological innovation. The key practical issue is whether people are relatively powerless (preserving hierarchy) or empowered (diminishing the importance and function of hierarchy). We trace this key issue through three perspectives. The first, based on leadership skills, preserves hierarchical arrangements. The second, a human relations approach, can preserve or diminish hierarchy depending on whether people are taken as powerless or empowered. It also suggests an approach based on psychological transactions. This exchange approach makes implementation success depend on building and maintaining adequate coalitions among interested parties.
Risk Factors for Seizures and Epilepsy in Children With Congenital Heart Disease

Objectives:To identify potential risk factors for pre- and postoperative seizures and epilepsy in children with congenital heart disease.Methods:Retrospective cohort study of neonates and infants <...
An Examination of Shaping with an African Crested Porcupine (Hystrix cristata)

Shaping through differential reinforcement of successive approximations to a target response has been a cornerstone procedure for the training of novel behavior. However, much of how it has traditi...
The Effect of Structural Affinity on the Diffusion of a Transnational Online Movement: The Case of #MeToo

Social media platforms intrinsically afford the diffusion of social movements like #MeToo across countries. However, little is known about how extrinsic, country-level factors affect the uptake of such a transnational movement. In this paper, we present a macro, comparative study of the transnational #MeToo movement on Twitter across 33 countries. Our aim is to identify how socio-economic and cultural variables might have influenced the in-country scale of participation, as well as the timings of in-country peak surges of messages related to #MeToo. Our results show that total in-country participation over a three-year timeframe is highly related to the scale of participation in peak surges; the scale of in-country participation is related to the population size and income level of the country; and the timings of peak surges are related to the country’s population size, gender equality score, and the language used in messages. We believe these findings resonate with theoretical frameworks that describe the formation of transnational social movements, and provide a quantitative perspective that complements much of the qualitative work in the literature.
A new experimental method for a fast and reliable quantification of saturates, aromatics, resins, and asphaltenes in crude oils

The complexity of the crude oil makes its compositional characterization a very challenging task. As a conventional way to characterize crude oil, SARA fractionation is based on the differences bet...
Generalizing about GC (hypoxia): Dys- & Dat-InformaticaComment on Germinal center B cells selectively oxidize fatty acids for energy while conducting minimal glycolysis

Steadily accumulating evidence supports the concept that the outputs of immune responses are influenced by local nutrient and metabolite conditions or concentrations, as well as by the molecular programming of intermediary metabolism within immune cells. Humoral immunity and germinal center reactions are one setting in which these factors are under active investigation. Hypoxia has been highlighted as one example of how a particular nutrient is distributed in primary and secondary follicles during an antibody response, and how its sensors could impact the qualities of antibody output after immunization. Based on a bio-informatic analysis of mRNA levels in germinal center and other B cells, recently published work challenges the concept that there is any hypoxia or that it has any influence. In this perspective, we perform new analyses of published genomics data to explore potential sources of disparity and elucidate aspects of what on the surface might seem to be conflicting conclusions. In particular, the replicability and variance among data sets derived from different naive as well as germinal center B cells are considered. The results of the investigation highlight several broader issues that merit consideration, especially at a time of heightened focus on scientific reports in the realm of immunity and antibody responses. From one finding of this re-analysis, it is proposed that a standard should be expected in which the relationship of new data sets compared to prior fingerprints of cell types should be reported transparently to referees and readers. In light of the strong evidence for diversity in the constituencies within germinal centers elicited by protein immunization, it also is proposed that a core practice should be to avoid overly broad conclusions about germinal centers in general when experimental systems are subject to substantial constraints imposed by technical features.
Nonreciprocal transmission based on self-induced nonlinear effects in bifacial dielectric metasurfaces

The breaking of Lorentz reciprocity law is a nontrivial task, since it usually requires bulky magnets or complicated time-modulation dynamic techniques to be accomplished. We present a simple and compact design of a nonlinear bifacial dielectric metasurface to achieve strong self-induced passive nonreciprocal transmission without the use of external biases. It is composed of two passive silicon-based metasurfaces exhibiting Fano and Lorentzian resonances embedded in an ultrathin glass substrate. Highly asymmetric field enhancement is achieved that leads to strong nonreciprocity at low excitation intensities. Moreover, a cascade design is presented to further improve the insertion loss and broaden the nonreciprocal intensity range. The proposed structure is ideal for free space optics applications, can operate under both incident polarizations, and require very low input excitation power to reach the nonreciprocal regime, which can lead to the design of new nanophotonic-based all-optical diodes, isolators, circulators, and ultrathin protective layers for sensitive optical components.
Characterizing change in students' self-assessments of understanding when engaged in instructional activities

Students’ abilities to self-assess their understanding can influence their learning and academic performance. Different factors, such as performance level, have been shown to relate to student self-assessment. In this study, hierarchical linear modeling was used to identify factors and quantify their effects on the changes observed in chemistry students’ self-assessed understanding when engaging in instructional activity. This study replicates and expands on previous findings regarding performance by showing that the worse students performed on a task, the more likely they were to lower their self-assessed understanding after that activity. Task difficulty was found to be a significant effect on change in students' self assessments with students being more likely to lower their self-assessed understanding after a more difficult task and raise it following an easier task independent of performance. Perceived comparative understanding (how students thought they compared to their surrounding peers) was also found to be a significant effect. Students who later reported their understanding to be lower than their peers, as compared to those who later reported their understanding to be about the same as their peers, were observed to have lowered their self-assessed understanding. Actual comparative performance (difference in performance of the student to their surrounding peers), gender, and feedback were not found to be significant effects on change in students’ self-assessed understanding. The results of this investigation may inform instructors on how their instructional decisions differentially impact changes in students’ judgements about their understanding.
Should rapid tests for hiv infection now be mandatory during pregnancy? Global differences in scarcity and a dilemma of technological advance

Since testing for HIV infection became possible in 1985, testing of pregnant women has been conducted primarily on a voluntary, ‘opt-in’ basis. Faden, Geller and Powers, Bayer, Wilfert, and McKenna, among others, have suggested that with the development of more reliable testing and more effective therapy to reduce maternal-fetal transmission, testing should become either routine with ‘opt-out’ provisions or mandatory. We ask, in the light of the new rapid tests for HIV, such as OraQuick, and the development of antiretroviral treatment that can reduce maternal-fetal transmission rates to <2%, whether that time is now. Illustrating our argument with cases from the United States (US), Kenya, Peru, and an undocumented Mexican worker in the US, we show that when testing is accompanied by assured multi-drug therapy for the mother, the argument for opt-out or mandatory testing for HIV in pregnancy is strong, but that it is problematic where testing is accompanied by adverse events such as spousal abuse or by inadequate intrapartum or follow-up treatment. The difference is not a ‘double standard’, but reflects the presence of conflicts between the health interests of the mother and the fetus – conflicts that would be abrogated by the assurance of adequate, continuing multi-drug therapy. In light of these conflicts, where they still occur, careful processes of informed consent are appropriate, rather than opt-out or mandatory testing.
Pains in the Lanes: Characterizing the Epidemiology of Swimmer’s Shoulder in Adolescents

Introduction: “Swimmer’s shoulder” is the colloquial phrase describing pain and injury in the anterolateral region of the shoulder, formerly referred to as supraspinatus impingement syndrome (1). The presumptive pathophysiology resembles that of other overuse injuries involving microtrauma to the local soft tissue, as the shoulder accounts for 90% of propulsive force in certain strokes (2, 3). Accordingly, population studies indicate that 40-91% of adolescent competitive swimmers report shoulder pain subjectively, with 84% and 69% exhibiting objective findings on physical exam and radiographic imaging (1, 4, 5). However, evaluation of epidemiologic risk factors that may …
Computing for Biologists: Python Programming and Principles

Computing is revolutionizing the practice of biology. This book, which assumes no prior computing experience, provides students with the tools to write their own Python programs and to understand fundamental concepts in computational biology and bioinformatics. Each major part of the book begins with a compelling biological question, followed by the algorithmic ideas and programming tools necessary to explore it: the origins of pathogenicity are examined using gene finding, the evolutionary history of sex determination systems is studied using sequence alignment, and the origin of modern humans is addressed using phylogenetic methods. In addition to providing general programming skills, this book explores the design of efficient algorithms, simulation, NP-hardness, and the maximum likelihood method, among other key concepts and methods. Easy-to-read and designed to equip students with the skills to write programs for solving a range of biological problems, the book is accompanied by numerous programming exercises, available at www.cs.hmc.edu/CFB.
Somesthetic and Vestibular Systems

The somesthetic senses convey information about touch, pressure, pain, and outside temperature. This information is essential for enabling the individual to be able to judge the position and orientation of the limbs, the existence of threats to the integrity of the body’s functioning from harmful agents in the environment, and also to be able to feel sensual enjoyment from physical expressions of affection with other adults and from a comfortable physical environment. The individual uses this knowledge about the state of the body to take actions to remedy an uncomfortable or dangerous situation, to continue in activities or remain in settings that are pleasurable, and to adjust the body as needed to carry out intentional movements. Unlike the other senses, the somesthetic system has multiple receptors and neural pathways, most of which convey fairly distinct features of bodily stimulation.
Who Speaks for the Climate?: Roots and culture

People make their own history, but they do not make it just as they please; they do not make it under circumstances chosen by themselves, but under circumstances directly encountered, given and transmitted from the past. The tradition of all the dead generations weighs like a nightmare on the brain of the living Marx, 1891, The Eighteenth Brumaire of Louis Bonaparte , 15 Today’s media representations are manifestations of past themes, resonant tropes and collective institutional as well as individual memories. By examining current media narratives, we can delve into histories of scientific and policy endeavours that have sought to understand as well as govern climate processes and effects. Through such undertakings taken up in this chapter, we can identify and ponder moments of critical discourse that have shaped ongoing climate storylines. Scientific pursuits to make sense of climate change have a long and rich history; however, a historical look at how climate has been communicated through mass media is comparably shorter and much less developed. In Annals of the Former World , writer John McPhee provided the analogy that the 4.6 billion-year history of time on Earth can be considered as distance from fingertip to fingertip with one’s arms spread wide. He wrote, ‘the Cambrian begins at the wrist … all of the Cenozoic is in a fingerprint, and in a single stroke with a medium-grained nail file you could eradicate human history’ (McPhee, 1998). Considered in this way, it would merely take a fine-grained nail file to remove the history of science communications and mass media. In fact, before the late 1980s, media portrayals of ‘climate change’ or ‘global warming’ were sporadic, compared to the amount of coverage in most regions around the world today (see Figure 2.1).
Ataxin-1 Regulators in the Spotlight

Triplet repeat diseases are characterized by expansions of the polyglutamine tracts of specific proteins, but exactly how these expansions contribute to disease pathogenesis is still under debate. In his Perspective, [Heintz][1] discusses new results (published elsewhere) showing that the polyglutamine tract of ataxin-1 (the protein mutated in spinocerebellar ataxia 1) is not sufficient to cause pathogenesis but does promote the binding of regulatory proteins that increase the stability and accumulation of the mutant ataxin-1. [1]: http://www.sciencemag.org/cgi/content/full/301/5629/59
Seasonal life history and nest architecture of a winter-active ant, Prenolepis imparis

In north Florida (USA), foraging and above-ground activity of the antPrenolepis imparis Say begins in November and ends in March or early April when the workers seal the nest until the following November. During this winter foraging period, workers' gasters become enormously corpulent through deposition of fat, doubling to tripling worker lean weight. The colony remains reproductively inactive until late August or early September when the queen's ovaries develop and she lays eggs. The single pulse of brood is probably reared on material derived from the corpulent workers. When the workers reopen the nests in November, most of the brood are callow workers or sexuals and all of the previous year's workers are again lean, their nutrient stores having been converted to new workers. The old workers become foragers while the callows become corpulent for the next year. Workers thus live between 1 and 2 (or more) years. Most nests are polygynous, and all queens contribute to the egg pool, though probably not equally.
The Business Launch Decision: An Empirical Investigation of Reasons for Not Starting a New Business

This article presents the results of a survey that examined the business launch decision. All of the individuals in the study al/ended a workshop on how to evaluate a business idea and launch a new venture. All of the individuals who all ended the workshop were interested in, but decided against, launching a new venture. The results of the study indicate that time constraints, availability of capital, and risk tolerance are perceived as significant obstacles by potential new business owners. Significant differences in the ranking of obstacles were found relative to whether the individuals believed that the obstacles to launch could be overcome, age of the respondent, and whether the individuals had previously owned a business. In addition, individuals who were more highly educated and had previous business ownership were less likely to launch a new business subsequent to the workshop. The results of the study can be used by service providers and consultants who develop training programs that assist individuals in the screening of business ideas and launching of new firms. The results of the study also can be incorporated into college curriculum to provide students with insight into obstacles impacting on business launch.
GENETIC ANALYSIS OF MATING LOCUS LINKED MUTATIONS IN CHLAMYDOMONAS REINHARDII

The mating-type (mt) locus of Chlamydomonas reinhardii has been analyzed using four mutant strains (imp-1, imp-10, imp-11 and imp-12). All have been shown, or are shown here, to carry mutations linked to either the plus (mt+) or the minus (mt-) locus, and their behavior in complementation tests has allowed us to define several distinct functions for each locus. Specifically, we propose that the mt+ locus contains the following genes or regulatory elements: a locus designated sfu, which is necessary for sexual fusion between gametes; a locus designated upp (uniparental plus), which controls aspects of chloroplast gene inheritance and perhaps also zygote maturation; and a locus designated sad, which functions in sexual adhesion. The mt- locus also contains a sad locus as well as a gene or regulatory element designated mid, which is necessary for the minus dominance in mt+/mt- diploids.
International Tax Neutrality: Revisited

Viewing the development of the standard international tax neutrality discussion as being historically fairly limited because Musgrave’s conclusions, rather than basic definitions, served as the undisputed baseline, in a previous article I reconsidered the classic international tax neutrality theories and challenged their conclusions. I argued that residence-based taxation has no advantages over source-based taxation in achieving capital export neutrality (CEN), and introduced the idea of how all international tax neutrality benchmarks can be simultaneously achieved by source-based taxation without the need for harmonized tax rates. Building on that article, Michael Knoll argued that the inconsistent meanings given to capital import neutrality (CIN) in the literature caused much confusion, that Musgrave’s view of CIN is best interpreted as ownership neutrality, and that interpreting CIN largely as I did, it is residence-based taxation that can simultaneously achieve both CEN and CIN. Agreeing with Knoll about the confusion associated with CIN, this article disagrees with viewing CIN as ownership neutrality, questions the benefits of such a view and shows that it is not necessarily true, but only under the classic analysis, that source-based taxation would always satisfy ownership neutrality. The article then replies to Knoll’s response to the arguments in my previous article, and based on three recent empirical studies on the “direct effect” of corporate taxation on capital, further develops and expands the applicability of the argument of my previous article that source-based taxation can satisfy CEN simultaneously with all other neutrality benchmarks without tax rate harmonization.[NOTE: A footnote to the first sentence of the first complete paragraph on page 146 was mistakenly struck due to the author’s typo. The footnote would cite to Wiji Arulampalam, Michael P. Devereux, and Giorgia Maffini, The Direct Incidence of Corporate Income Tax on Wages, Oxford University Center for Business (May 2008) and IZA Discussion Paper No 5293 (October 2010); Nilis aus dem Moore, Tanja Karsten and Christoph M. Schmidt, Do Wages Rise When Corporate Rates Fall? Difference-in-Differences Analyses of the German Business Tax Reform 2000 (February 2009); R. Alison Felix and James R. Hines Jr., Corporate Taxes and Union Wages in the United States, NBER Working Paper No. 16263 (August 2009).]
Integration of scheduling and dynamic optimization of batch processes under uncertainty

Integration of scheduling and dynamic optimization significantly improves the overall performance of a production process compared to the traditional sequential method. However, most integrated methods focus on solving deterministic problems without explicitly taking process uncertainty into account. We propose a novel integrated method for sequential batch processes under uncertainty. The integrated problem is formulated into a two-stage stochastic program. To solve the resulting complicated integrated problem, we develop an efficient algorithm based on the framework of generalized Benders decomposition. For a complicated case study with more than 3 million variables/equations under 100 scenarios, the direct solution approach does not find a feasible solution while the decomposition algorithm return the optimal solution in 23.9 hours. The integrated method returns a higher average profit than the sequential method by 17.6%.
Stopping power of K electrons at extreme relativistic energies

The recent work of Anholt on $K$-vacancy production by relativistic projectiles has been applied to calculate the stopping power of the $K$ electrons. The results show that for protons of energy \ensuremath{\sim}${10}^{3}$ GeV and heavy target elements, the relativistic contributions to the stopping power amount to several times the results due to the longitudinal terms obtained from Walske's work.
Feature selection for noisy variation patterns using kernel principal component analysis

Kernel Principal Component Analysis (KPCA) is a technique widely used to understand and visualize non-linear variation patterns by inverse mapping the projected data from a high-dimensional feature space back to the original input space. Variation patterns often occur in a small number of relevant features out of the overall set of features that are recorded in the data. It is, therefore, crucial to discern this set of relevant features that define the pattern. Here we propose a feature selection procedure that augments KPCA to obtain importance estimates of the features given the noisy training data. Our feature selection strategy involves projecting the data points onto sparse random vectors for calculating the kernel matrix. We then match pairs of such projections, and determine the preimages of the data with and without a feature, thereby trying to identify the importance of that feature. Thus, preimages' differences within pairs are used to identify the relevant features. An advantage of our method is it can be used with any suitable KPCA algorithm. Moreover, the computations can be parallelized easily leading to significant speedup. We demonstrate our method on several simulated and real data sets, and compare the results to alternative approaches in the literature.
TAP46 Plays a Positive Role in the ABSCISIC ACID INSENSITIVE5-Regulated Gene Expression in Arabidopsis

TAP46 is a protein phosphatase2A (PP2A)-associated protein that regulates PP2A activity in Arabidopsis (Arabidopsis thaliana). To study how PP2A is involved in abscisic acid (ABA) signaling in plants, we studied the function of TAP46 in ABA-regulated seed maturation and seedling development. Expression of TAP46 coincides with the action of ABA in developing seeds and during seed germination, and the TAP46 transcript reaches to the highest level in mature seeds. Real-time polymerase chain reaction analysis indicates that external ABA can increase TAP46 transcript level transiently during seed germination. Overexpression of TAP46 increases plant sensitivity to ABA, while tap46 knockdown mutants are less sensitive to ABA during seed germination, suggesting that TAP46 functions positively in ABA signaling. Overexpression of TAP46 also leads to lower PP2A activity, while tap46-1 knockdown mutant displays higher PP2A activity, suggesting that TAP46 negatively regulates PP2A activity in Arabidopsis. Both TAP46 and PP2A interact with the ABA-regulated transcription factor ABA INSENSITIVE5 (ABI5) in vivo, and TAP46’s binding to ABI5 can stabilize ABI5. Furthermore, TAP46’s binding to the phosphorylated ABI5 may prevent PP2A or PP2A-like protein phosphatases from removing the phosphate from ABI5, thereby maintaining ABI5 in its active form. Overexpression of TAP46 and inhibition of activities of PP2A or PP2A-like protein phosphatases can increase transcript levels of several ABI5-regulated genes, suggesting that TAP46 is a positive factor in the ABA-regulated gene expression in Arabidopsis.
The regularization of linear differential-algebraic equations

Differential-algebraic equations naturally arise in numerous important applied contexts, e.g., electrical circuits, constrained dynamical motion and fluid dynamics. The authors show how the structure of the solution space for some typical problems can be illuminated through the introduction of various regularizations whichh often can be given natural physical interpretations.
Metallophilic interactions from dispersion-corrected density-functional theory.

In this article, we present the first comprehensive study of metallophilic (aurophilic) interactions using dispersion-corrected density-functional theory. Dispersion interactions (an essential component of metallophilicity) are treated using the exchange-hole dipole moment (XDM) model. By comparing against coupled-cluster benchmark calculations on simple dimers, we show that LC-ωPBE-XDM is a viable functional to study interactions between closed-shell transition metals and that it performs uniformly better than second-order Moller-Plesset theory, the basic computational technique used in previous works. We apply LC-ωPBE-XDM to address several open questions regarding metallophilicity, such as the interplay between dispersion and relativistic effects, the interaction strength along group 11, the additivity of homo- and hetero-metallophilic effects, the stability of [E(AuPH3)4]+ cations (E = N, P, As, Sb), and the role of metallophilic effects in crystal packing. We find that relativistic effects explain the prevalence of aurophilicity not by stabilizing metal-metal contacts, but by preventing gold from forming ionic structures involving bridge anions (which are otherwise common for Ag and Cu) as a result of the increased electron affinity of the metal. Dispersion effects are less important than previously assumed and their stabilization contribution is relatively independent of the metal.