bluuebunny/crossref_metadata_2025 huggingface dataset:
The Operation Called Verstehen: Towards a Redefinition of the Problem
Authors: McCarthy Thomas
Published: January 2016

One of the more constant elements in the ‘legacy of logical positivism’ has been a rather low estimate of the importance of the concept of Verstehen for a logic of the social sciences. To be sure, it has been the accepted practice among philosophers under the influence of this movement that any extended treatment of the logic of the social sciences include an analysis of the role of Verstehen. But these analyses have almost invariably taken the form of a whittling down to size of an outsized concept with, it is often noted, rather suspicious origins in German metaphysical thought.

Apart from the philosophical arguments advanced, there are a number of historical considerations which throw some light on the sceptical attitude of the logical positivists and of their descendants towards the idea of a procedure peculiar to the social sciences.
Bressan and Suppes on Modality
Authors: Van Fraassen Bas C.
Published: January 2016

Professors Bressan and Suppes have both argued that modality is of great importance to the philosophy of science. I shall not dispute this, but I shall raise some problems of interpretation, which arise if one considers the possibility of a philosophical retrenchment with respect to the use of modal concepts.

Professor Bressan uses the discussion initiated by Mach's attempted definition of mass as a paradigm example of the use of modal concepts in foundational work in physics. He mentions the modal terms used in informal axiomatizations of mechanics which followed Mach, and explains how mass is defined in his own formalized axiomatic mechanics.

On the other hand, in his book Introduction to Logic, Professor Suppes had said unequivocally that he knew of no problem in philosophy of science to which modality is relevant.
Technology Assessment as a Critique of a Civilization
Authors: Skolimowski Henryk
Published: January 2016

My concern with Technology Assessment is born out of my larger concern with Philosophy of Technology. What is Philosophy of Technology ? It is a systematic reflection on the nature of contemporary technology, its role and function in society and civilization at large. It may be said without exaggeration that technology is the major force shaping the destiny of the present western civilization: thus shaping the destiny of Society, and therefore, to a large degree, shaping the destiny of its individuals. It is quite obvious that technology is not a collection of tools, but a vital social and cultural force determining our future. It is not an assembly of gadgets, but a part of our world view, indeed an intrinsic part of the western mentality: whenever we westerners think technology, we invariably think ‘manipulation’ and ‘control.’
Explanation and Subsumption
Authors: Cummins Robert
Published: January 2016

Quine once claimed that modal logic derived from a use-mention mistake (p. 196). In this paper, I will peddle an, equally outrageous claim: the thesis that subsumption is an essential goal of fundamental explanatory theorizing rests on a failure to distinguish explaining what made x happen from explaining why we believe what we do about what made x happen. I don't mean to suggest that the distinction wasn't noticed (except perhaps by Hume); only that it wasn't vigorously enforced. There have always been philosophers who assimilated a belief to its justification with malice aforethought.

Everyone knows that subsumption is not sufficient for explanation: the length of a pendulum is not explained by appeal to its period and the pendulum law, and emission spectra are not explained by Balmer's formula. But the spirit of the deductive-nomological account of explanation lives on in the belief that subsumption is an essential feature of an explanatory theory.
Toward a Historical Meta-Method for Assessing Normative Methodologies: Rationability, Serendipity, and the Robinson Crusoe Fallacy
Authors: Wykstra Stephen J.
Published: January 2016

During the past two decades, much philosophy of science has been focused on issues about the norms and methods by which scientific theories are rationally appraised; and increasingly, philosophers have turned to history of science as a touchstone for assessing normative methodologies purporting to elucidate scientific rationality. But even among such historical methodologists, there is much disagreement and unclarity about how historical study of science can arbitrate between rival methodological theories; and until progress is made at this meta-methodological level, the very legitimacy of this role for history will remain controversial. (Keynotes in the controversy are sounded in Kuhn (1970b , pp. 235—41; Lakatos (1971); Giere (1973); McMullin (1976); Burian (1977); and Laudan (1977, pp. 158-63).) This paper begins by arguing that the meta-method implicit in much historical methodology is different from the explicit meta-methodology most often touted.
Grades of Organization and the Units of Selection Controversy
Authors: Richardson Robert C.
Published: January 2016

R. C. Lewontin (1970) proposed three criteria as jointly sufficient for a unit of evolutionary change and immediately went on to argue that selection could operate simultaneously at a variety of levels of organization. For natural selection to operate on a unit, there must be variation in the objects in question: natural selection “chooses” between alternatives, so there must be different alternatives. This variation must affect fitness: the variation available must create different probabilities of reproductive success. Third, this variation in fitness must be heritable: there must be a correlation between parents and offspring for the traits yielding variation in fitness. In brief, for there to be evolution by natural selection, there must be heritable variation in fitness.

Among the concerns that might be raised over Lewontin's formula, one is particularly important. It was clearly brought out by Williams (1966) and is emphasized by Elliott Sober (1981).
Can Darwinian Inheritance Be Extended from Biology to Epistemology?
Authors: Kary Carla E.
Published: January 2016

Despite continuing controversy over the detailed structure of the biological theory of evolution, and the scientific credentials of some of its central principles (see Goudge (1961), Peters (1976), Smart (1963), Williams (1970)), its striking success in explaining the development of living things has frequently inspired attempts to apply it beyond the biological domain (for example, Mach (1910) and White (1949)). Recently attempts have been made to explain the historical development of human concepts and ideas in terms of a Darwinian evolutionary theory. Various theories of “evolutionary epistemology” have been proposed by Stephen Toulmin (1972), Donald Campbell (1974), and Nicholas Rescher (1977), to name a few. In order to assess these theories adequately it would be useful to know in a general fashion under what circumstances and in what form’ a Darwinian evolutionary theory should be employed within non-biological domains.
Science and Play
Authors: Goldman Michael
Published: January 2016

Many philosophers interested in problems of scientific progress—what it is and whether it is possible—have in recent years, and with good reason, focused on the challenges directed by Kuhn (1962) and Feyerabend (1975) to the traditional belief in progress by accretion. I have argued (in response to Feyerabend's proliferation theory) that the proper locus for a solution to these problems must be the social (or what I prefer to call the “material”) conditions in which proposed competing theories must exist (Goldman 1980)). Recently, Gonzalo Munévar has proposed similar criteria in his book Radical Knowledge (1981). Our approaches have much in common. Most importantly they eschew the wholly “intellectual” criteria offered by almost all philosophers; that is, criteria which focus entirely on a theory's ability to solve problems arising only in thought (whether they be called ‘conceptual’ or ‘empirical’ problems).
Models, High-Energy Theoretical Physics and Realism
Authors: Cushing James T.
Published: January 2016

Let me say at the outset that the following exercise is an attempt to make some sense out of what I have seen my colleagues (and indeed at times myself) doing in science - more particularly in theoretical high-energy physics. I do not claim that my conclusions are final or permanent. In fact, it appears to me that Professor MacKinnon's new book, Scientific Explanation and Atomic Physics, may; present a suitable framework within which to discuss the issues raised here. In any event, since most of this paper consists of a story to be told, it may be of interest to philosophers of science.

Today I shall use developments In the field of theoretical high-energy physics to examine three issues of interest to the philosophy of science. First will be the use of highly abstract, formal models, in the generation and evolution of theories.
The Philosophical Basis of Cost-Risk-Benefit Analyses
Authors: Bantz David A.
Published: January 2016

The Emperor Vespasian, presented with an invention to enable columns to be transported cheaply, praised the inventor but declined to make use of the innovation, apparently fearing the risk of upheaval from the displaced workers (Gimpel 1976, p. 9). Imbued as they are with the notions of progress and efficiency, few leaders in the modern world seem to have followed Vespasian's precedent and rejected the promise of technological innovations. Yet the sheer magnitude of the possible consequences of some technologies, and the multiplicity of choices made possible by competing technological solutions to this or that problem have fostered techniques for the appraisal of benefits and costs (including risks) in proposed courses of action. What information do these techniques give us, and what are the grounds for using them to guide decision making?
Beyond Darwinism? The Challenge of Macroevolution to the Synthetic Theory of Evolution
Authors: Ayala Francisco J.
Published: January 2016

The current theory of biological evolution (the “Synthetic Theory” or “Modern Synthesis”) may be traced to Theodosius Dobzhansky's Genetics and the Origin of Species, published in 1937: a synthesis of genetic knowledge and Darwin's theory of evolution by natural selection. The excitement provoked by Dobzhansky's book soon became reflected in many important contributions which incorporated into the Modern Synthesis relevant fields of biological knowledge. Notable landmarks are Ernst Mayr's Systematics and the Origin of Species (1942), Julian S. Huxley's Evolution: The Modern Synthesis (1942), George Gaylord Simpson's Tempo and Mode in Evolution (1944), and G. Ledyard Stebbins’ Variation and Evolution in Plants (1950). It seemed to many scientists that the theory of evolution was essentially complete and that all that was left was to fill in the details.
Stochastic Locality and the Bell Theorems
Authors: Hellman Geoffrey
Published: January 2016

As was remarked two years ago at a symposium of the PSA on locality and hidden variables (Shimony 1981), the Bell theorems together with experiments supporting the quantum correlations (violating the inequalities of the theorems) provide a rather remarkable opportunity for philosophy. Shimony summed this up in the nice phrase, “experimental metaphysics”. For, as he pointed out, arguments based on Bell-type theorems, concluding that certain experiments should exhibit correlations obeying a certain inequality, generally employ premises of a metaphysical character, e.g., that the systems in question are deterministic (in the experimental observables). If, in fact, the experimental predictions are violated, and if one has reason to believe any other premises involved, then one must give up the metaphysical hypothesis.
Realism and the Anthropocentrics
Authors: Brown James Robert
Published: January 2016

It always seems to me extreme rashness on the part of some when they want to make human abilities the measure of what nature can do. On the contrary, there is not a single effect in nature, even the least that exists, such that the most ingenious theorist can arrive at a complete understanding of it. —Galileo

Most anthropocentrics are realists. By this I simply mean that most who are anthropocentrics do not realise it, and that when they are convinced of the fact they will abandon their anthropocentric beliefs and adopt some other view. So, for instance, when we are convinced that God did not make us in his image but rather, the contrary, we become outright atheists or at least radically change our theology. The would be realist William Newton-Smith, as we shall see, is such an anthropocentric, and merely pointing this out should be adequate for undermining his view.
Methodological Issues in Contemporary Americanist Archaeology
Authors: Dunnell Robert C
Published: January 2016

The central purpose of the symposium in which this paper was originally presented was to elicit from anthropologists those problems in their discipline which, from the perspective of a practitioner, might merit philosophical attention. Setting aside the difficulties that must arise when an anthropologist, unfamiliar with the scholarly tradition of philosophy, attempts to identify philosophically interesting issues, any anthropologist is confronted with a further problem. Anthropology is not a coherent discipline in the same fashion as many other academic departments. Nor is any anthropologist really “expert” in more than one of the major disciplines (I would caution wariness of those who claim more) and most only within a particular strain of the relevant discipline.

Being an archaeologist, I feel constrained to treat that discipline.
Explaining the Success of Science
Authors: Sargent Rose-Mary
Published: January 2016

Ever since Hilary Putnam claimed that a realist philosophy is “the only philosophy that doesn’t make the success of science a miracle,” explanations for the success of science have proliferated in the philosophical literature (Putnam 1975, p. 73). Realists argue that the success of science, as exhibited by our ability to accurately predict and explain a wide range of phenomena, indicates that our theories have identified some of the underlying causal structures of the world (e.g., Boyd 1985, Ellis 1985, McMullin 1984, Salmon 1984). Nonrealists counter that success cannot provide a warrant for belief in the truth of scientific theories because there have been successful theories in the past that are now believed to be false (Laudan 1981b). Instead, they offer a naturalized account whereby our theories are designed to be successful predictors and only those which fulfill this goal survive (Laudan 1987, van Fraassen, 1980).
Herbert Feigl: 1902-1988
Authors: Savage C. Wade
Published: January 2016

Herbert Feigl was born December 14, 1902 in Reichenberg, Austria, and he died in Minneapolis, Minnesota, on June 1,1988. His wife, Maria, followed him in death on February 13,1989. He is survived by a son, Eric O. Feigl, who is professor of physiology at the University of Washington.

Feigl's parents were Jewish but not religious; indeed, his father was an outspoken atheist. His father was a weaver and later an influential textile manufacturer, who would have preferred the son to become an industrial chemist. His mother was a devotee of the arts and an amateur pianist, who would play Beethoven sonatas over and over at the young son's request. His high school interests were philosophy, science fiction, physics, and chemistry (which was his major). Moritz Schlick became his favorite philosopher after he read the latter's Allgemeine Erkenntnisslehre. His chief intellectual hero was Einstein.
Theoretical Models, Biological Complexity and the Semantic View of Theories
Authors: Horan Barbara L.
Published: January 2016

In this paper I discuss how, given the complexity of biological systems, reliance on theoretical models in the development and testing of biological theories leads to anti-realism. This is the result of the uniqueness and hence diversity of biological phenomena, in contrast with the uniformity of items in the domain of physics. I have argued elsewhere (Horan, 1986, 1989a, 1989b) that the use of theoretical models creates an unresolvable tension between the explanatory strength and predictive power of hypotheses, and I review this argument here. My discussion is in part motivated by the claims of Nancy Cartwright (1983), who has argued that the use of ceteris paribus laws in physics creates an antagonism between truth and explanation that requires theoretical models to figure centrally in scientific explanation, thereby precluding realism. I argue instead that in biology it is the use of theoretical models that creates this conflict, and conclude that adequate biological explanation cannot rely on the modelling approach alone.
Learning Simple Things: A Connectionist Learning Problem from Various Perspectives
Authors: Stabler Edward P.
Published: January 2016

The performance of a connectionist learning system on a simple problem has been described by Hinton and is briefly reviewed here: a finite function is learned, and the system generalizes correctly from partial information by finding simple “features” of the environment. For comparison, a very similar problem is formulated in the Gold paradigm of discrete learning functions. Identification in the limit from positive text of a large class of functions including Hinton's is achievable with a trivial, conservative learning strategy. Using Valiant's approach, we place an arbitrary finite bound on function complexity and then we can guarantee text and resource efficiency relative to a probabilistic criterion of success. But the connectionist system generalizes. That is, it uses a non-conservative learning strategy. We define a simple, non-conservative strategy that also generalizes like the connectionist system, finding simple “features” of the environment.
Cartwright, Capacities, and Probabilities
Authors: Irzik Gürol
Published: January 2016

Nancy Cartwright’s new book Nature’s Capacities and their Measurement (1989)2 attempts to achieve something remarkable: refute Hume’s most crucial theses concerning causation and let in capacities largely through methodological arguments. The two central theses of Hume which Cartwright challenges are:

(1)

Generic causal facts (e.g., causal laws) are reducible to regularities.

(2)

Singular causal facts are true in virtue of generic causal facts.

Cartwright’s arguments against (1) and (2) are methodological in the sense that she arrives at her conclusions by considering our best methods for studying the relationship between probability and causation. Cartwright rejects (1) on the grounds that if we look at the way in which probabilities are related to causal relations as expressed in her principle CC, or if we carefully study the methodology of causal modelling employed in the social, behavioral, and life sciences, we see that to get certain causal information from probabilities we must presuppose the truth of other generic causal facts.
Realism and Methodological Change
Authors: Leplin Jarrett
Published: January 2016

An effective way to challenge scientific realism these days is to ask whether evidence for a theory’s truth can ever outstrip evidence for its utility. Granted that we might have strong evidence of a theory’s explanatory, predictive, heuristic, and technological utility, might we have in addition evidence of its truth? A negative answer claims that all the evidence in support of a theory is, immediately, evidence of pragmatic virtues, and only indirectly, if at all, evidence of truth. Realism then reduces to a willingness to infer truth from utility. Evidently, none of the evidence by which theories are tested will pertain to this inference, so the only recourse for sustaining it is to a metalevel at which truth and utility are compared in the abstract. And there enormous problems loom.
The Super Bowl and the Ox-Phos Controversy: “Winner-take-all” Competition in Philosophy of Science
Authors: Allchin Douglas
Published: January 2016

Imagine two theories in a scientific controversy cast as competing teams in the Super Bowl, and you may get a “Scoreboard of experimental evidence” such as the following, published in a review article in 1970 (after Racker 1970, 135):

This figure compares two hypotheses in a debate in bioenergetics in the 1960s and 70s known as the Ox-Phos Controversy (Rowen 1986; Allchin 1990; Weber 1991). But its format, suggested by its title, bears a striking resemblance to the half-time recaps in televised football games: parallel assessments in several categories ask us to compare, say, how many yards rushed, number of first downs, passes completed, evidence for the role of the membrane, or evidence for ion transport, etc. (see also Sindermann 1982). Why did the review author—Efraim Racker, a research biochemist—borrow the scoreboard framework from sports to convey his assessment in science?
Ecological Explanation and the Population-Growth Thesis
Authors: Shrader-Frechette Kristin
Published: January 2016

Many ecologists have questioned the status of proposed ecological
“laws,” charging that they are devoid of empirical content and predictive
power or that they are tautological, trivial, circular, or nontestable
(Peters 1976, 1978,1991; Simberloff 1983, 1984; Simberloff and Boecklen
1981; Strong and Simberloff 1981; Strong and Levin 1979; see also Williams
1970; Ferguson 1976; Rosenberg 1978; Stebbins 1978; Caplan 1978; and
Shrader-Frechette and McCoy 1990). As a result, a number of ecologists have
urged their colleagues instead to “study … real organisms,” rather than
worry about untestable theories and laws (Van Valen and Pitelka 1974, 925;
Mclntosh 1982, 23).

In this essay we investigate the epistemological status of a prominent
“ecological law” in order to gain insights about the characteristics of
ecological explanation.
Earman on the Projectibility of Grue
Authors: Lange Marc
Published: January 2016

In Bayes or Bust?, John Earman (1992,
104-113) attempts to express in Bayesian terms a sense of “projectibility”
in which it is logically impossible for “All emeralds are green” and “All
emeralds are grue” simultaneously to be projectible. I argue that Earman
overlooks an important sense in which these two hypotheses cannot both be
projectible. This sense is important because it connects projectibility to
lawlikeness, as Goodman intended. Whether this suggests a solution to
Goodman's riddle remains unsettled, awaiting an account of lawlikeness. I
explore one avenue that might prove illuminating.

Suppose we discover that object a is G, where
our background beliefs K include that Ea. Earman notes that by Bayes's
theorem, hypothesis H (“All E's are G”) is confirmed—i.e.,
.
Experiment, Speculation and Law: Faraday's Analysis of Arago's
Wheel
Authors: Steinle Friedrich
Published: January 2016

This paper deals with the mutual relation of speculative considerations,
experimental activity, and the attempt to establish “laws of nature.” I
shall not give a general analysis, but instead study a historical example.
It is taken from the work of Michael Faraday - one of the most original and
most successful experimenters.

I shall start by giving a rough sketch of Faraday's view, thereby making
clear the particular question on which my paper concentrates. In part three,
I analyze an episode of Faraday's actual work, and conclude in part four
with a rough analysis of the type of explanation given by Faraday.

Faraday repeatedly emphasizes the necessity of distinguishing “that
knowledge which consists of assumption, by which I mean theory and
hypothesis, from that which is the knowledge of facts and laws; never
raising the former to the dignity or authority of the latter, nor confusing
the latter more than is inevitable with the former.”
Ceteris Paribus Laws and Psychological Explanations
Authors: Wallis Charles
Published: January 2016

Two important components of Fodor's philosophy of cognitive science rely
heavily upon ceteris paribus laws, thus requiring that Fodor forward an
analysis of ceteris paribus laws. First, because Fodor has long held (1975,
1990) that all of the laws of the special
sciences are ceteris paribus laws, he must demonstrate the scientific
legitimacy of ceteris paribus laws. Second, ceteris paribus laws play a
prominent role in Fodor's most recent (1990) theory of representational
content, and solution to the “disjunction problem,” a well-known problem for
his approach. Fodor recently (1991a) offered an analysis of ceteris paribus
laws for the special sciences (particularly cognitive science). I ask two
questions with regard to Fodor's analysis: Does the analysis underwrite
Fodor's theory of representation? Does the analysis provide adequate
solutions to the problems for ceteris paribus laws as articulated by Hempel
(1965, 1988) and Giere (1988)? I answer both questions negatively.
Is Cognitive Neuropsychology Possible?
Authors: Bub Jeffrey
Published: January 2016

The aim of contemporary cognitive neuropsychology is to articulate the
functional architecture underlying normal human cognitive abilities, on the
basis of patterns of performance over a variety of cognitive tasks involving
subjects with varying degrees of brain-damage. An example of a contemporary
functional architecture is the following model for the recognition and
production of spoken and written words:

The modular processing components in this ‘box-and-arrow’ functional
architecture represent functionally independent subsystems that perform
computational transformations on the representations that originate as input
along the connecting links, providing a theory of cognition at the
algorithmic and representational level (not the implementational or
‘hardware’ level).
What are Quanta, and Why Does it Matter?
Authors: Huggett Nick
Published: January 2016

There is an emerging story about many particle quantum mechanics (MPQM) and quantum field theory (QFT) based partly on views inherited from physics, and partly on new work, especially that of Paul Teller and Michael Redhead. Three important steps in the tale go like this—(a) The transition from classical mechanics (CM) to quantum mechanics (QM) involves a significant change in particle metaphysics, (b) QFT cannot be viewed as particulate even in a MPQM sense, although (c) an ontologically enlightening understanding of QFT can be obtained from the occupation representation. Though there is some truth to all of these claims, I wish to argue that, as usually understood, they are in fact false.

The ever present danger in metaphysical debates such as these is that participants will be running around on the same pitch but playing different games; some waving cricket bats at the ball, some aiming for a netball hoop and others trying for a touch-down.
Science, Probability, and the Proposition
Authors: van Fraassen Bas C.
Published: January 2016

Traditionally, philosophy of science has focused on the product of science: the scientific hypothesis, principle, law, or more grandiosely, the theory. Using logician's license I'll think of hypotheses and theories as ‘little’ and ‘big’ (or ‘weak’ and ‘strong’) propositions. The tradition spoke of the product as (scientific) knowledge; the more recent phrase “current scientific opinion” carries the same connotation of uniqueness. For this to make sense, something is required: a proposition must be capable of being true or false, capable of being fully believed or disbelieved (and if you like, known).

Probabilism requires us to look at every aspect of science in a new way. In his radical brand of probabilism, Richard Jeffrey told us to reconceptualize knowledge as 'probable knowledge’ and propositions as ‘probasitions’—and never to resolve doubt but simply to quantify it, keeping all possibilities in play.
Modelling-based experiment retrieval: a case study with gene expression clustering
Authors: Blomstedt Paul , Dutta Ritabrata , Seth Sohan , Brazma Alvis , Kaski Samuel
Published: January 2016

Motivation: Public and private repositories of experimental data are growing to sizes that require dedicated methods for finding relevant data. To improve on the state of the art of keyword searches from annotations, methods for content-based retrieval have been proposed. In the context of gene expression experiments, most methods retrieve gene expression profiles, requiring each experiment to be expressed as a single profile, typically of case versus control. A more general, recently suggested alternative is to retrieve experiments whose models are good for modelling the query dataset. However, for very noisy and high-dimensional query data, this retrieval criterion turns out to be very noisy as well.

Results: We propose doing retrieval using a denoised model of the query dataset, instead of the original noisy dataset itself. To this end, we introduce a general probabilistic framework, where each experiment is modelled separately and the retrieval is done by finding related models. For retrieval of gene expression experiments, we use a probabilistic model called product partition model, which induces a clustering of genes that show similar expression patterns across a number of samples. The suggested metric for retrieval using clusterings is the normalized information distance. Empirical results finally suggest that inference for the full probabilistic model can be approximated with good performance using computationally faster heuristic clustering approaches (e.g. k-means). The method is highly scalable and straightforward to apply to construct a general-purpose gene expression experiment retrieval method.

Availability and implementation: The method can be implemented using standard clustering algorithms and normalized information distance, available in many statistical software packages.

Contact:  paul.blomstedt@aalto.fi or samuel.kaski@aalto.fi

Supplementary information:  Supplementary data are available at Bioinformatics online.
Bayesian variable selection for binary outcomes in high-dimensional genomic studies using non-local priors
Authors: Nikooienejad Amir , Wang Wenyi , Johnson Valen E.
Published: January 2016

Motivation: The advent of new genomic technologies has resulted in the production of massive data sets. Analyses of these data require new statistical and computational methods. In this article, we propose one such method that is useful in selecting explanatory variables for prediction of a binary response. Although this problem has recently been addressed using penalized likelihood methods, we adopt a Bayesian approach that utilizes a mixture of non-local prior densities and point masses on the binary regression coefficient vectors.

Results: The resulting method, which we call iMOMLogit, provides improved performance in identifying true models and reducing estimation and prediction error in a number of simulation studies. More importantly, its application to several genomic datasets produces predictions that have high accuracy using far fewer explanatory variables than competing methods. We also describe a novel approach for setting prior hyperparameters by examining the total variation distance between the prior distributions on the regression parameters and the distribution of the maximum likelihood estimator under the null distribution. Finally, we describe a computational algorithm that can be used to implement iMOMLogit in ultrahigh-dimensional settings (p>>n) and provide diagnostics to assess the probability that this algorithm has identified the highest posterior probability model.

Availability and implementation: Software to implement this method can be downloaded at: http://www.stat.tamu.edu/∼amir/code.html.

Contact:  wwang7@mdanderson.org or vjohnson@stat.tamu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
UCSC Data Integrator and Variant Annotation Integrator
Authors: Hinrichs Angie S. , Raney Brian J. , Speir Matthew L. , Rhead Brooke , Casper Jonathan , Karolchik Donna , Kuhn Robert M. , Rosenbloom Kate R. , Zweig Ann S. , Haussler David , Kent W. James
Published: January 2016

Summary: Two new tools on the UCSC Genome Browser web site provide improved ways of combining information from multiple datasets, optionally including the user's own custom track data and/or data from track hubs. The Data Integrator combines columns from multiple data tracks, showing all items from the first track along with overlapping items from the other tracks. The Variant Annotation Integrator is tailored to adding functional annotations to variant calls; it offers a more restricted set of underlying data tracks but adds predictions of each variant's consequences for any overlapping or nearby gene transcript. When available, it optionally adds additional annotations including effect prediction scores from dbNSFP for missense mutations, ENCODE regulatory summary tracks and conservation scores.

Availability and implementation: The web tools are freely available at http://genome.ucsc.edu/ and the underlying database is available for download at http://hgdownload.cse.ucsc.edu/. The software (written in C and Javascript) is available from https://genome-store.ucsc.edu/ and is freely available for academic and non-profit usage; commercial users must obtain a license.

Contact: angie@soe.ucsc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Perceptions of Emergency Department Triage Nurses About Prehospital Emergency Rescuers in Italy: A Latent Threat to Clinical Handover
Authors: Dojmi Di Delupis Francesco , Mancini Niccolò , Ruggeri Marco , Pisanelli Paolo
Published: January 2016

Objectives

In Italy, volunteer rescuers respond to most prehospital emergency calls. These rescuers provide the majority of patient information during handover at the emergency department triage. Standardized terminology between rescuers and triage nurses is lacking in Italy, and miscommunication may cause a poor handover. Even though rescuers are professional health providers, their qualification is not legally recognized, and triage nurses have a pervasive sense of inadequacy about the rescuers' competences.

This work explored triage nurses' perceptions of rescuers and the causes of these perceptions to verify whether difficult interprofessional relationships negatively influence the clinical handover process.

Methods

We performed a survey among 402 triage nurses for 3 main areas of rescuers' competency: communication, knowledge, and decision making. For each area, we identified communications, decision making, and knowledge indicators. A scale score of 6 or higher was considered not sufficient.

Results

We found that 75.5% (n = 302/400) of triage nurses regard rescuers' ability to recognize life-threatening situations as not sufficient (communication ability indicator). Approximately 66% (n = 264/401) of triage nurses regard rescuers' ability to administer oxygen as not sufficient (decision-making indicator), and approximately 58% (n = 232/402) of nurses regard rescuers' ability to report the reason for the emergency call as not sufficient (knowledge indicator).

Conclusions

The results of this survey show that the overall perception of triage nurses about prehospital rescuers is slightly below sufficiency. This perception could cause errors during the prehospital or hospital handover at the triage and could lead to delayed decisions and incorrect treatment.
A Notch and Su(H) dependent enhancer complex coordinates expression ofnabinDrosophila
Authors: Stroebele Elizabeth , Erives Albert
Published: January 2016

ABTRACT

The transcription factor Suppressor of Hairless and its co-activator, the Notch intracellular domain, are polyglutamine (pQ)-rich factors that target enhancer elements and interact with other locally-bound pQ-rich factors. To understand the functional repertoire of such enhancers, we identify conserved regulatory belts with binding sites for the pQ-rich effectors of both Notch and BMP/Dpp signaling, and the pQ-deficient tissue selectors Apterous (Ap), Scalloped (Sd), and Vestigial (Vg). We find that the densest such binding site cluster in the genome is located in the BMP-induciblenablocus, a homolog of the vertebrate transcriptional co-factorsNAB1/NAB2. We report three major findings. First, we find that thisnabregulatory belt is a novel enhancer driving dorsal wing margin expression in regions of peak phosphorylated-Mad in wing imaginal discs. Second, we show that Ap is developmentally required to license thenabdorsal wing margin enhancer (DWME) to read-out Notch signaling in the dorsal wing compartment. Third, we find that thenabDWME is embedded in a complex of intronic enhancers, including a wing quadrant enhancer, a proximal wing disc enhancer, and a larval brain enhancer. This enhancer complex coordinates globalnabexpression via both tissue-specific activation and inter-enhancer silencing. We suggest that DWME integration of BMP signaling maintainsnabexpression in proliferating margin descendants that have divided away from Notch-Delta boundary signaling. As such, uniform expression of genes likenabandvestigialin proliferating compartments would typically require both boundary and non-boundary lineage-specific enhancers.
A research-based primer on the potential psychosocial impacts of flooding
Authors: Johal Sarb , Mounsey Zoe
Published: January 2016

Purpose

– Following recent flooding in New Zealand a brief review of research on psychosocial impacts of flooding was undertaken to identify lessons. The paper aims to discuss this issue.

Design/methodology/approach

– A pragmatic review of the literature concerning psychosocial or mental health impact following flooding incidents in locations with similarities to New Zealand identified. In total, 12 papers from between 2008 and 2015 were reviewed to identify lessons for New Zealand.

Findings

– The review findings illustrate how floods can have great impacts on people’s psychosocial needs and mental health. The extended timeframe and disruptive nature of the impacts of flooding are such that the effects of secondary stressors are highly significant as they prolong the welfare, physical and psychosocial needs of those affected.

Originality/value

– This brief review provides important insights into the psychosocial impacts of flooding by examining research from similar areas to New Zealand.
Orexin gene transfer into the amygdala suppresses both spontaneous and emotion‐induced cataplexy in orexin‐knockout mice
Authors: Liu Meng , Blanco‐Centurion Carlos , Konadhode Roda Rani , Luan Liju , Shiromani Priyattam J.
Published: January 2016

Narcolepsy is a chronic sleep disorder linked to the loss of orexin‐producing neurons in the hypothalamus. Cataplexy, a sudden loss of muscle tone during waking, is an important distinguishing symptom of narcolepsy and it is often triggered by strong emotions. The neural circuit underlying cataplexy attacks is not known, but is likely to involve the amygdala, a region implicated in regulating emotions. In mice models of narcolepsy, transfer of the orexin gene into surrogate neurons has been successful in ameliorating narcoleptic symptoms. However, it is not known whether this method also blocks cataplexy triggered by strong emotions. To examine this possibility, the gene encoding mouse prepro‐orexin was transferred into amygdala neurons of orexin‐knockout (KO) mice (rAAV‐orexin; n = 8). Orexin‐KO mice that did not receive gene transfer (no‐rAAV; n = 7) or received only the reporter gene (rAAV‐GFP; n = 7) served as controls. Three weeks later, the animal's sleep and behaviour were recorded at night (no‐odour control night), followed by another recording at night in the presence of predator odour (odour night). Orexin‐KO mice given the orexin gene transfer into surrogate amygdala neurons had significantly less spontaneous bouts of cataplexy, and predator odour did not induce cataplexy compared with control mice. Moreover, the mice with orexin gene transfer were awake more during the odour night. These results demonstrate that orexin gene transfer into amygdala neurons can suppress both spontaneous and emotion‐induced cataplexy attacks in narcoleptic mice. It suggests that manipulating amygdala pathways is a potential strategy for treating cataplexy in narcolepsy.
Origin stories
A Brief History of Creation Science and the Search for the Origin of Life
Bill Mesler and H. James Cleaves II
Norton, 2015. 332 pp.
Authors: Strick James
Published: January 2016

Looking back at our ever-evolving understanding of what it means to be alive
Chlamydia trachomatisgenotypes in a cross-sectional study of urogenital samples from remote Northern and Central Australia
Authors: Giffard Philip M , Brenner Nicole C , Tabrizi Sepehr N , Garland Suzanne M , Holt Deborah C , Andersson Patiyan , Lilliebridge Rachael A , Tong Steven Y C , Karimi Mahdad , Boylan Prudence , Ryder Nathan , Johns Tracy , Singh Gurmeet
Published: January 2016

Objectives

The objective was to determine the frequency of trachoma genotypes ofChlamydia trachomatis-positive urogenital tract (UGT) specimens from remote areas of the Australian Northern Territory (NT).

Setting

The setting was analysis of remnants ofC. trachomatispositive primarily UGT specimens obtained in the course of clinical practice. The specimens were obtained from two pathology service providers.

Participants

From 3356C. trachomatisspecimens collected during May 2012–April 2013, 439 were selected for genotyping, with a focus on specimens from postpubescent patients, in remote Aboriginal communities where ocular trachoma is potentially present.

Primary and secondary outcome measures

The primary outcome measure was the proportion of successfully genotyped UGT specimens that were trachoma genotypes. The secondary outcome measures were the distribution of genotypes, and the frequencies of different classes of specimens able to be genotyped.

Results

Zero of 217 successfully genotyped UGT specimens yielded trachoma genotypes (95% CI for frequency=0–0.017). For UGT specimens, the genotypes were E (41%), F (22%), D (21%) and K (7%), with J, H and G and mixed genotypes each at 1–4%. Four of the five genotyped eye swabs yielded trachoma genotype Ba, and the other genotype J. Two hundred twenty-two specimens (50.6%) were successfully genotyped. Urine specimens were less likely to be typable than vaginal swabs (p<0.0001).

Conclusions

Unlike in some other studies, in the remote NT, trachoma genotypes ofC. trachomatiswere not found circulating in UGT specimens from 2012 to 2013. Therefore,C. trachomatisgenotypes in UGT specimens from young children can be informative as to whether the organism has been acquired through sexual contact. We suggest inclusion ofC. trachomatisgenotyping in guidelines examining the source of sexually transmitted infections in young children in areas where trachoma genotypes may continue to circulate, and continued surveillance of UGTC. trachomatisgenotypes.
Impact of health insurance for tertiary care on postoperative outcomes and seeking care for symptoms: quasi-experimental evidence from Karnataka, India
Authors: Sood Neeraj , Wagner Zachary
Published: January 2016

Objectives

To evaluate the effects of a government insurance programme covering tertiary care for the poor in Karnataka, India—Vajpayee Arogyashree Scheme (VAS)—on treatment seeking and postoperative outcomes.

Design

Geographic regression discontinuity.

Setting

572 villages in Karnataka, India.

Participants

3478 households in 300 villages where VAS was implemented and 3486 households in 272 neighbouring matched villages ineligible for VAS.

Intervention

A government insurance programme that provided free tertiary care to households below the poverty line in half of villages in Karnataka from February 2010 to August 2012.

Main outcome measure

Seeking treatment for symptoms, posthospitalisation well-being, occurrence of infections during hospitalisation and need for rehospitalisation.

Results

The prevalence of symptoms was nearly identical for households in VAS-eligible villages compared with households in VAS-ineligible villages. However, households eligible for VAS were 4.96 percentage points (95% CI 1 to 8.9; p=0.014) more likely to seek treatment for their symptoms. The increase in treatment seeking was more pronounced for symptoms of cardiac conditions, the condition most frequently covered by VAS. Respondents from VAS-eligible villages reported greater improvements in well-being after a hospitalisation in all categories assessed and they were statistically significant in 3 of the 6 categories (walking ability, pain and anxiety). Respondents eligible for VAS were 9.4 percentage points less likely to report any infection after their hospitalisation (95% CI −20.2 to 1.4; p=0.087) and 16.5 percentage points less likely to have to be rehospitalised after the initial hospitalisation (95% CI −28.7 to −4.3; p<0.01).

Conclusions

Insurance for tertiary care increased treatment seeking among eligible households. Moreover, insured patients experienced better posthospitalisation outcomes, suggesting better quality of care received. These results suggest that there are several pathways through which tertiary care insurance could improve health, aside from increasing utilisation of the services that the programme directly subsidises.
Olympia Interstadial: vegetation, landscape history, and paleoclimatic implications of a mid-Wisconsinan (MIS3) nonglacial sequence from southwest British Columbia, Canada
Authors: Hebda Richard J. , Lian Olav B. , Hicock Stephen R.
Published: January 2016

Lithostratigraphic, 14C, and palynologic analyses of peat and silty peat at three nearby sites reveal a 25 000 year vegetation and climate history of the Olympia Interstade for the Fraser Lowland, British Columbia, 300 km within the southern limit of the Cordilleran Ice Sheet. At Lynn Valley, Polypodiaceae fern spores and nonarboreal pollen dominate >47.8 14C ka BP, reflecting unstable and cold landscapes. A Pinus–Poaceae zone follows, representing pine parkland and cool dry climate. Fluctuating values of Picea and Tsuga mertensiana pollen at Lynn and Seymour valleys and Port Moody characterize most of the Olympia Interstade during local peat deposition in Cyperaceae and Myrica wetlands until about 26.7 14C ka BP under a cool and moist climate. A brief Pinus – Tsuga heterophylla zone at Lynn Valley 44–39 14C ka BP suggests a climatic optimum. A Poaceae–Artemisia assemblage and deposition of silty sand after 26.7 14C ka BP reflect cooling and drying after which a unique Lycopodium assemblage at Lynn Valley suggests cold arid climate and Fraser Glaciation onset. These sequences have no progression to vegetation typical of warm, interglacial, Holocene-like climates, indicating an interstadial not an interglacial interval. Correlation with vegetation changes elsewhere in western North America suggests that the Olympia Interstade started about ∼52 14C ka BP (∼57 cal ka BP) and ended about 26 14C ka BP (30 cal ka BP).
Bright solitons and their interactions of the (3 + 1)-dimensional coupled nonlinear Schrödinger system for an optical fiber
Authors: Sun Ya , Tian Bo , Wang Yu-Feng , Wang Yun-Po , Huang Zhi-Ruo
Published: January 2016

Under investigation in this paper is the [Formula: see text]-dimensional coupled nonlinear Schrödinger system for an optical fiber with birefringence. With the Hirota method, bilinear forms of the system are derived via an auxiliary function, and the bright one- and two-soliton solutions are constructed. Based on those soliton solutions, soliton propagation and interaction are investigated analytically and graphically. Non-singular cases of the bright one-soliton solutions are presented, from which the single-peak and two-peak solitons can arise, respectively. Through the analysis on the bright two-soliton solutions, the elastic and inelastic interactions are investigated. Three kinds of the elastic interactions are presented, between the two one-peak solitons, a one-peak soliton and a two-peak soliton, and the two two-peak solitons.