bluuebunny/crossref_metadata_2025_split huggingface dataset:
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. —GalileoMost 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.
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.
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.
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.”
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

Abstract
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

Abstract
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&gt;&gt;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

Abstract
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

ObjectivesIn 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.MethodsWe 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.ResultsWe 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).ConclusionsThe 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

ABTRACTThe 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

AbstractNarcolepsy 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.