bluuebunny/crossref_metadata_2025 huggingface dataset:
Lorentz’s Local Time and the Theorem of Corresponding States
Authors: Rynasiewicz Robert
Published: January 2016

1.

Here is a well known theorem. Consider the homogeneous Maxwell equations

(where E and H are functions of x, y, z, and t, and ).

Use the coordinate substitutions

and the following substitutions for the field variables

Then, if terms depending on second and higher powers of (v/c) are dropped, the resulting equations have the same form as the original homogeneous Maxwell equations, i.e.,
Prediction, Accommodation, and the Logic of Discovery
Authors: Maher Patrick
Published: January 2016

It is widely believed that if a piece of evidence for a theory was known at the time the theory was proposed, then it does not confirm the theory as strongly as it would if the evidence had been discovered after the theory was proposed. I shall call this view the predictivist thesis. Those who have endorsed it include Leibniz (1678), Huygens (1690, preface), Whewell (1847 vol. 2, p. 64f.), Peirce (1883), Duhem (1914, ch. II, §5), Popper (1965, p. 241f.), Lakatos (1970, p. 123), and Kuhn (1977, p. 322). On the other hand, the thesis has been rejected by a number of philosophers, including Mill (1872 bk. III, ch. 14, §6), Keynes (1921, p. 305), Rosenkrantz (1977, p. 169f.), Horwich (1982, pp. 108-117) and Schlesinger (1987). Others, while not rejecting the predictivist thesis, nevertheless regard the justification of the thesis as problematic; these include Hempel (1966, p. 38) and Gardner (1982).
The Essence of Space-Time
Authors: Maudlin Tim
Published: January 2016

The debate over the ontological status of space has been waged over the millennia on many battlefields. In ancient times the major focus was on the possibility of a vacuum, an entity that was both something and yet, in another way, nothing. Newton shifted the scene of action to dynamics, to the question of the ontological commitments needed to give an adequate explanation of observable phenomena. But along with the dynamical effects of Newtonian absolute space came also the spectre of motions unobservable in principle, a notion attacked from Leibniz onward as conceptually absurd or meaningless. So the theater of operation was moved again, especially by verificationists, this time into theories of meaning. Now John Norton and John Earman have opened an entirely new line of assault on the question. They argue that considerations about the possibility of determinism have direct implications for the substantivalist-relationist controversy.
Philosophers of Experiment
Authors: Hacking Ian
Published: January 2016

The Neglect of Experiment:that is the title of Alan Franklin's (1986). He did not mean to imply that scientists were neglecting experiments, spinning well financed cobwebs of theories while laboratories decayed for lack of funds. He meant that historians and philosophers neglected the experimental side of science. That was true, and is no longer so. Although his title was fine when he was writing, the times have passed it by.

A decade before there had been almost no reflective philosophy of experiment. What little had been published was not seen as writing about experiment—that was not something to write about—but as discussion of the theory/observation distinction, or the impossibility of eliminating a theory by crucial experiment, etc. The even-handedDictionary of Scientific Biographydiscreetly cut articles on experimenters and expanded those on theorists. Thaddeus Trenn's (1977) on the experimental discovery of isotopes was poorly received.
Ceteris Paribus Clauses and Causality in Economics
Authors: Hausman Daniel M.
Published: January 2016

Explicit or implicit ceteris paribus clauses are pervasive in economics. People do not always buy more of x when the price of x decreases. The generalization holds only “other things being equal” or ceteris paribus. Not everybody wants more wealth, but economists have held that the generalization holds, ceteris paribus. When government imposes price controls, shortages do not always arise, but, ceteris paribus, they do. Ceteris paribus clauses are common in other sciences, but I shall confine my remarks to economics.

Many have found such ceteris paribus clauses problematic. For they are vague, and they seem to insulate theories from empirical criticism and correction. When the observed phenomena are not as the theory predicted, one can (or so it has been alleged) always claim that other things were not “equal”, that there was some “disturbance” or “interference” and thus that the ceteris paribus condition was not met.
Non-Bayesian Confirmation Theory, and the Principle of Explanatory Surplus
Authors: Gillies Donald A.
Published: January 2016

One of the most obvious features of empirical science is that scientists attempt to relate their theories to data, that is to the results of observation and experiment. In so doing, they will find it necessary to use the term ‘confirms’ or ‘confirmation’ or at least terms with more or less the same meaning. Thus scientists may think that a theory is well- confirmed by a considerable body of observational evidence. In this case they will regard it as rational to have a high degree of confidence in the theory, and, in particular, to use it in practical applications. Alternatively a theory T may be seen as badly confirmed by the evidence. In this case it would be thought undesirable to use T in practice, and the problem would become that of modifying or replacing T so as to obtain a new theory T’ which is better confirmed than T.
Finite Axiomatizability and Scientific Discovery
Authors: Osherson Daniel N. , Weinstein Scott
Published: January 2016

Imagine a scientist who examines an unending sequence of data about an unknown reality and responds to each datum by announcing a first-order theory in a fixed language L. The scientist hopes to determine the truth or falsity of every sentence of L, but he does not feel obliged to reach a stage in his investigation when all such questions will have been resolved. One way to represent the scientist's project is as follows. Let the unknown reality correspond to the L-structure S. Then the scientist hopes that for every sentence ϕ ∊ L, if S ╞ ϕ, then all but finitely many of the theories he emits, imply ϕ and do not imply - ϕ Following Kelly & Glymour (1987), we say in this case that the scientist “AE-identifies” S. The AE prefix signifies that for all ϕ ∊ L, there is a stage beginning at which the scientist's theories correctly decide ϕ.
The Many Worlds Interpretation of Set Theory
Authors: Hellman Geoffrey
Published: January 2016

As standardly presented in axiomatic form, set theory exhibits two fundamental features which together give rise to a number of foundational and philosophical problems. These features are so basic that they are seldom even isolated. The first is that the axioms are taken as categorical assertions (e.g. “There exists an empty set”, “There exists an infinite set”, “The power set of any set exists”, etc.). The second is that actualist quantifiers are employed in these axioms, so that they appear to be about actual objects; the domain of these quantifiers forms the fixed universe of sets (up to a choice of urelement basis), relata of a unique, fixed membership relation entering into the statement of the axioms.

Such presentations are associated with the philosophical positions of platonism and set-theoretic foundationalism.
How not to Russell Carnap’s Aufbau
Authors: Richardson Alan
Published: January 2016

Rudolf Carnap is principally renowned for stating with remarkable precision and rigor a rich variety of philosophical doctrines — doctrines which, thanks mainly to Carnap’s meticulous formulations, the philosophical world now holds to be clearly and fundamentally mistaken. Thus, it is Carnap who, in Meaning and Necessity (Carnap 1947), presents in detail the linguistic doctrine of logical truth and the semantic underpinnings of the analytic/synthetic distinction, providing thereby the grist for the mill of Quine’s highly influential and important attacks on precisely these doctrines. Again, it was Carnap who, more than any other, precisely delineated the program of inductive logic. This program is now, thanks largely to Goodman’s (1983) New Riddle of Induction, also considered hopeless. Carnap is now firmly associated with a bewildering variety of discredited views: reductionism and the unity of science; the verification criterion of meaning; logic as an uninterpreted calculus; Russellian logicism even in the face of Gödel’s devastating incompleteness results; etc.
On the Possibility of Directed Mutations in Bacteria: Statistical Analyses and Reductionist Strategies
Authors: Sarkar Sahotra
Published: January 2016

A recent set of experiments by Cairnset al.(1988) purport to show that some mutations in a strain ofE. colibacteria are directed in the sense that they are induced, somehow, in an environment that is suited for them. If this claim is true it would limit the validity of the neo-Darwinian assumption that evolution proceeds by “random variation and natural selection” which requires that there be no correlation between the genesis of a particular mutation and the fitness of the corresponding phenotype in the environment in which the mutation occurs. Instead, it would argue for the occurrence of some “neo-Lamarckian” processes in evolution in the sense that the genesis of some mutations would have a positive correlation with the fitness of the resultant phenotype in that environment. Thus, one of the most fundamental tenets of the neo-Darwinian interpretation of evolution would be brought into question.
Acceptance Without Belief
Authors: Maher Patrick
Published: January 2016

Bas van Fraassen (1980) maintained that acceptance of a scientific theory does not involve belief that the theory is true, though it does involve belief that the theory is empirically adequate. This provoked a large literature attempting to refute van Fraassen’s position. For the most part, the critics attempted to show that van Fraassen’s position violates principles of inductive inference, or of rationality.2 Such criticisms do not question the possibility of conforming to van Fraassen’s conception of science; they merely argue that there is good reason not to do so.

But some of van Fraassen’s critics have taken a different tack. Simon Blackburn (1984, p. 223) has remarked, and Sam Mitchell (1988) and Paul Horwich (forthcoming) have argued, that acceptance of a theory, as understood by van Fraassen, is the same as believing the theory to be true. If this is right, then what van Fraassen is advocating is a logically contradictory position, and thus one to which it is impossible to conform.
Scientific Realism, Perceptual Beliefs, and Justification
Authors: Otte Richard
Published: January 2016

If one compares various skeptical arguments about our perceptual beliefs with arguments against scientific realism one immediately notices important similarities. Skeptical arguments about perceptual beliefs are often based on the premise that all of our perceptual beliefs could be wrong. Our experience is consistent with many different states of affairs; some familiar examples are hallucination, an evil demon, and brains in a vat. Thus it is claimed we have no reason to believe that the perceptual beliefs we normally form are true and alternative beliefs are false.

One of the most powerful arguments against scientific realism is based on the claim that our data underdetermines our theory. There exist empirically equivalent theories, which means that there is no observation that could lead us to accept one and reject the other. Each member of a class of empirically equivalent theories will be equally supported by the evidence.
I. Dynamical Reduction Theories: Changing Quantum Theory so the Statevector Represents Reality
Authors: Ghirardi GianCarlo , Pearle Philip
Published: January 2016

We dedicate these papers to the memory of John Bell, whose contributions to, support for, and encouragement of the research program described here has meant more than words can say to those involved in it.

In Schrödinger’s “cat paradox” example, a nucleus which has a 50% probability of decaying within an hour is coupled to a cat by a “hellish contraption” which, if it detects the decay, will kill the cat. If we take the point of view that what we see around us is real, what occurs in reality is one of the two following evolutions :

(—> means “evolves in an hour into“).

According to Schrödinger’s equation, the evolution of the statevector describing this situation is

The right hand side of Eq. (1.2) does not correspond to either the reality on the right hand side of (1.1a) nor to the reality on the right hand side of (1.1b).
Material Models in Biology
Authors: Griesemer James R.
Published: January 2016

Propositions are no more constitutive of science than they are of any activity: a body of knowledge is not all there is to the life of science. Thus I take the premise underlying the topic of this symposium to be uncontroversial, there is a “non-propositional” side of science and of biology in particular. From time to time, however, philosophers ask whether the “non-propositional” side of science is theoretically superfluous, or as Duhem put it, logically dispensable. What they mean to ask is whether science can be fully analyzed in propositional terms; must philosophy of science, in other words, consider the non-propositional side in order to adequately account for science?

Negative answers to the question often rest on the tacit view that the most (or only) important thing about science is scientific theories.
On Values in Science: Is the Epistemic/Non-Epistemic Distinction Useful?
Authors: Rooney Phyllis
Published: January 2016

The debate about values in science in the last decade or so reflects an important shift in what many acknowledge as the “post-positivist” era in philosophy of science. It reflects the erosion of the fact-value distinction in at least one of its more simplistic forms (facts belong in science, values outside), and it marks the path to a more enhanced understanding of the roles of both facts and values in scientific inquiry. This discussion has, above all, contributed to what we might call a revaluation of value: from the point of view of the epistemologist or philosopher of science values are neither uniform nor uniformly “bad”.
Experimental Reproducibility and the Experimenters’ Regress
Authors: Radder Hans
Published: January 2016

Many philosophers of science tend to take for granted the proposition that, as a rule, scientific experiments are reproducible (or, in other words, repeatable, replicable). Very few of them, however, have examined the issue in any detail (a recent exception is Hones 1990). Yet, by now an important body of literature exists, mainly written by sociologists and historians of science, in which the above proposition is discussed and analyzed on the basis of elaborate studies of experimental practice. These studies claim to offer not only a descriptively adequate account of experimentation, but also a number of fundamental philosophical conclusions concerning (experimental) science as a whole.

In the present paper I analyze and evaluate the views of H.M. Collins, an early and influential thinker concerning the issue in question. In particular I discuss what he has called the ‘experimenters’ regress’.
Neo-classical Economics and Evolutionary Theory: Strange Bedfellows?
Authors: Rosenberg Alex
Published: January 2016

On the surface and to a first approximation, economic theory and evolutionary theory share salient features: a commitment to optimality and maximizing, a consequent similarity in mathematical formalism, an appeal to equilibrium as the preferred explanatory strategy. Moreover, both have at various times been stigmatized as empirically empty. However, the theory of natural selection has been widely accepted as the scientific cornerstone of modern biology, while microeconomics has remained open to repeated challenges as an explanation of human action and its aggregate consequences.

Because of their similarity, evolutionary theory looks like part of a powerful defense of the status quo in economic theory. I think that Darwinian theory is a remarkably inappropriate model, metaphor, inspiration, or theoretical framework for economic theory.
Theory-ladenness of Observations as a Test Case of Kuhn’s Approach to Scientific Inquiry
Authors: Hintikka Jaakko
Published: January 2016

The overall character of the ideas Thomas S. Kuhn has offered concerning the nature of scientific inquiry has been generally misunderstood, or, rather, misconstrued. (See Kuhn 1957,1970.) Kuhn’s ideas do not add up to a fully articulated analysis of the structure of the scientific process. Kuhn does not offer a theory of science which should be evaluated in the same way as, e.g., the hypothetico-deductive model of science or the inductivist one. What Kuhn does is best viewed as calling our attention to certain salient phenomena which a philosophical theorist of science must try to understand and to account for. We do injustice to Kuhn if we deal with his views as if they were finished products of philosophical theorizing. They are not. Rather, they are starting-points for such theorizing; they pose problems to be solved by a genuine theory of science.
Darwin and Disjunction: Foraging Theory and Univocal Assignments of Content
Authors: Shapiro Lawrence A.
Published: January 2016

According to Jerry Fodor, “[h]uffing and puffing and piling on the teleology just doesn’t help with the disjunction problem; it doesn’t lead to univocal assignments of intentional content” (1990, p. 72). That Fodor separates these two claims with only a semicolon is unfortunate, for each merits individual scrutiny. First, there is the claim that appeals to the theory of evolution by natural selection will not help with the disjunction problem. I will argue that the truth of this claim depends upon how we characterize the relation between a representational state and that which it is about Fodor assumes this relation must be a causal one, and this assumption leads inevitably to the disjunction problem.
Space-Time and Isomorphism
Authors: Mundy Brent
Published: January 2016

Leibniz indiscernibility argument: If the points of space or space-time are real, then shifting everything by a geometric symmetry transformation f (e.g., translation or rotation) produces a physically different situation, since the same bodies or events now occupy different points: whatever occupied point p now occupies the distinct point fp. This may violate identity of indiscernibles, or other principles of verifiability or theoretical parsimony.

Leibniz’s f was a symmetry of Euclidean space E, so the argument seems inapplicable to the inhomogeneous space-times of GTR. However, the underlying manifold M always possesses symmetries f, so one may take f also to move the geometric structure across M, along with the physical objects and events. The resulting variant models still represent physically distinct worlds, since the objects and geometric structure formerly at p are now at fp. Indeed there is more variability, since M has far more symmetries than E.
The Relativity Principle and the Isotropy of Boosts
Authors: Budden Tim
Published: January 2016

In 1905 Einstein derived the Lorentz transformations linking inertial coordinate systems. He took as his central principles the relativity principle (RP) and the light postulate (LP), and assumed along the way a symmetry that has become known as ‘spatial isotropy’ (Berzi and Gorini 1969). This symmetry will be defined below but it basically requires that boosting has the same effect whether to the right or left or to the north or south etc. Since it really is a symmetry about boosts I shall call it ‘boost isotropy'.

The purpose of this paper is to explore the relativistic kinematics (both Einsteinian and Galilean) resulting from implementing RP but breaking with the venerable tradition of implementing ‘boost isotropy’.
Spacetime and Holes
Authors: Brighouse Carolyn
Published: January 2016

Here I describe and defend a version of space-time substantivalism. My
account is meant partly as a reply to an argument against a particular
substantivalist position that can be found both in John Earman and John
Norton's “What price spacetime substantivalism? The hole story”, and
Earman's World Enough and Spacetime. Their
argument, the Hole Argument, purports to show that substantivalism leads to
a radical form of indeterminism within a class of theories that includes our
best theory of spacetime, namely, General Relativity (GTR). The hole
argument contends that the substantivalist must view diffeomorphic models of
a spacetime theory as representing genuinely distinct physical situations.
It is this contention I argue against.

The version of substantivalism I present, although not a traditional
account, incorporates the important features of traditional substantivalist
views.
Perception and Proper Explanatory Width
Authors: Rollins Mark
Published: January 2016

Marr's theory of vision (1982) is often said to exemplify wide
psychology. The claim rests primarily on Marr's appeal to a high level
theory of computational functions and secondarily on the sort of
representations he posits for computational processes (Burge 1986, 28). I
agree that Marr's theory embodies an exemplary form of wide psychology; what
is exemplary about it is his appeal to perceptual tasks. But I shall argue
that the result of invoking task considerations is that we need not adhere
to Marr's own restricted construal of proper width. Indeed, the larger
conclusion I want to draw is that there is no single conception of width
that has a special place in explanation.
Viewing Science
Authors: Giere Ronald N.
Published: January 2016

A presidential address provides a rare opportunity for public, disciplinary self-reflection. This is particularly true in the context of a joint meeting with related disciplines. Accordingly, rather than simply presenting my own view of science, I shall focus on those of us engaged in viewing science, particularly philosophers, psychologists, historians, and sociologists of science. I will, of course, be doing the viewing From the vantage point of the philosophy of science, which thus fills the foreground. The middle distance will be occupied by the sociology of science, while the history of science and cognitive studies of science occupy the background.

I begin with a historical view of the philosophy of science itself. The most common picture of the recent history of the philosophy of science in North America is that, after a long period of dominance, Logical Empiricism was superseded in the 1960s by an historical approach to the philosophy of science inspired by Kuhn's (1962) Structure of Scientific Revolutions.
Poincaré, Richard's Paradox and Indefinite Extensibility
Authors: Clark Peter
Published: January 2016

Sometimes themes exist only in the eye of the beholder and emerge from the history of mathematics only with the benefit (or otherwise) of hindsight. There is however at least one issue (no doubt there are others) which was clearly present throughout the foundational debates of the early Twentieth century. It formed the core component of one of the major traditions that grew up as responses to the paradoxes, though the intuition behind it has never been fully articulated nor has it been possible to give a fully fledged mathematical articulation to that intuition. Essentially the central idea is that of ‘indefinite extensibility’ generated by an appropriate form of diagonalisation and it has its fundamental source in Richard's paradox and in particular in Poincaré's response to that paradox.

Of the four great epistemological concerns around which much of the work in the foundations of mathematics this century has concentrated viz the notions of demonstrability, definability, set or class and computability only the latter clearly falls outside the scope of the Richard type reasoning.
Science, Technology and Experiments; the Natural Versus the Artificial
Authors: Kroes Peter
Published: January 2016

Against the traditional ‘discovery-view’ of experiments, Hacking has maintained that in experimental practice natural phenomena are created, not discovered. By intervening in the world with the help of technology, we create and at the same time come to know phenomena. This claim, together with the one that scientific entities are tools for intervening in the world, undermines the classic distinction between the natural and the artificial, more particularly, between science and technology: phenomena become artifacts just as technological products and scientific entities become tools for doing. Hacking's view raises the question whether it can still be said that science studies natural phenomena, and if so, in what sense. Are we not forced to give up the distinction between the natural and the artificial, between science and technology, altogether? Recently, for instance (Lelas 1993) has argued that science is a form of technology.
Update of the BIPM comparison BIPM.RI(II)-K1.F-18 of activity measurements of the radionuclide 18F to include the 2010 result of the LNE-LNHB (France)
Authors: Michotte C , Ratel G , Courte S , Cassette P , Moune M
Published: January 2016

Since 2001, six national metrology institutes (NMI) have submitted seven samples of known activity of 18F to the International Reference System (SIR) for activity comparison at the Bureau International des Poids et Mesures (BIPM), with comparison identifier BIPM.RI(II)-K1.F-18. The values of the activity submitted were between about 1 MBq and 18 MBq. The primary standardization result for the LNE-LNHB, France, replaces their earlier result of 2002 and the key comparison reference value (KCRV) has been recalculated. In the frame of the BIPM.RI(II)-K4.F18 comparison, the NPL updated their result in the KCDB. Consequently there are now five results in the BIPM.RI(II)-K1.F-18 comparison. The degrees of equivalence between each equivalent activity measured in the SIR and the updated KCRV have been calculated and the results are given in the form of a table. A graphical presentation is also given.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Differential regulation of translation and endocytosis of alternatively spliced forms of the type II bone morphogenetic protein (BMP) receptor
Authors: Amsalem Ayelet R. , Marom Barak , Shapira Keren E. , Hirschhorn Tal , Preisler Livia , Paarmann Pia , Knaus Petra , Henis Yoav I. , Ehrlich Marcelo
Published: January 2016

The expression and function of transforming growth factor-β superfamily receptors are regulated by multiple molecular mechanisms. The type II BMP receptor (BMPRII) is expressed as two alternatively spliced forms, a long and a short form (BMPRII-LF and –SF, respectively), which differ by an ∼500 amino acid C-terminal extension, unique among TGF-β superfamily receptors. Whereas this extension was proposed to modulate BMPRII signaling output, its contribution to the regulation of receptor expression was not addressed. To map regulatory determinants of BMPRII expression, we compared synthesis, degradation, distribution, and endocytic trafficking of BMPRII isoforms and mutants. We identified translational regulation of BMPRII expression and the contribution of a 3’ terminal coding sequence to this process. BMPRII-LF and -SF differed also in their steady-state levels, kinetics of degradation, intracellular distribution, and internalization rates. A single dileucine signal in the C-terminal extension of BMPRII-LF accounted for its faster clathrin-mediated endocytosis relative to BMPRII-SF, accompanied by mildly faster degradation. Higher expression of BMPRII-SF at the plasma membrane resulted in enhanced activation of Smad signaling, stressing the potential importance of the multilayered regulation of BMPRII expression at the plasma membrane.
PINCAGE: probabilistic integration of cancer genomics data for perturbed gene identification and sample classification
Authors: Świtnicki Michał P. , Juul Malene , Madsen Tobias , Sørensen Karina D. , Pedersen Jakob S.
Published: January 2016

Motivation: Cancer development and progression is driven by a complex pattern of genomic and epigenomic perturbations. Both types of perturbations can affect gene expression levels and disease outcome. Integrative analysis of cancer genomics data may therefore improve detection of perturbed genes and prediction of disease state. As different data types are usually dependent, analysis based on independence assumptions will make inefficient use of the data and potentially lead to false conclusions.

Model: Here, we present PINCAGE (Probabilistic INtegration of CAncer GEnomics data), a method that uses probabilistic integration of cancer genomics data for combined evaluation of RNA-seq gene expression and 450k array DNA methylation measurements of promoters as well as gene bodies. It models the dependence between expression and methylation using modular graphical models, which also allows future inclusion of additional data types.

Results: We apply our approach to a Breast Invasive Carcinoma dataset from The Cancer Genome Atlas consortium, which includes 82 adjacent normal and 730 cancer samples. We identify new biomarker candidates of breast cancer development (PTF1A, RABIF, RAG1AP1, TIMM17A, LOC148145) and progression (SERPINE3, ZNF706). PINCAGE discriminates better between normal and tumour tissue and between progressing and non-progressing tumours in comparison with established methods that assume independence between tested data types, especially when using evidence from multiple genes. Our method can be applied to any type of cancer or, more generally, to any genomic disease for which sufficient amount of molecular data is available.

Availability and implementation: R scripts available at http://moma.ki.au.dk/prj/pincage/

Contact: michal.switnicki@clin.au.dk or jakob.skou@clin.au.dk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Flexibility and control of thorax deformation during hawkmoth flight
Authors: Ando Noriyasu , Kanzaki Ryohei
Published: January 2016

The interaction between neuromuscular systems and body mechanics plays an important role in the production of coordinated movements in animals. Lepidopteran insects move their wings by distortion of the thorax structure via the indirect flight muscles (IFMs), which are activated by neural signals at every stroke. However, how the action of these muscles affects thorax deformation and wing kinematics is poorly understood. We measured the deformation of the dorsal thorax (mesonotum) of tethered flying hawkmoths,Agrius convolvuli, using a high-speed laser profilometer combined with simultaneous recordings of electromyograms and wing kinematics. We observed that locally amplified mesonotum deformation near the wing hinges ensures sufficient wing movement. Furthermore, phase asymmetry in IFM activity leads to phase asymmetry in mesonotum oscillations and wingbeats. Our results revealed the flexibility and controllability of the single structure of the mesonotum by neurogenic action of the IFMs.
Stress and the microbiome: linking glucocorticoids to bacterial community dynamics in wild red squirrels
Authors: Stothart Mason R. , Bobbie Colleen B. , Schulte-Hostedde Albrecht I. , Boonstra Rudy , Palme Rupert , Mykytczuk Nadia C. S. , Newman Amy E. M.
Published: January 2016

Bacterial diversity within animals is emerging as an essential component of health, but it is unknown how stress may influence the microbiome. We quantify a proximate link between the oral microbiome and hypothalamic–pituitary–adrenal (HPA) axis activity using faecal glucocorticoid metabolites (FGM) in wild red squirrels (
Tamiasciurus hudsonicus
). Not only was bacterial diversity lower at higher levels of FGM, but also between capture periods a change in bacterial relative abundance was related to an increase in FGM. These linkages between the HPA axis and microbiome communities represent a powerful capacity for stress to have multi-dimensional effects on health.
Adaptations to squid-style high-speed swimming in Jurassic belemnitids
Authors: Klug Christian , Schweigert Günter , Fuchs Dirk , Kruta Isabelle , Tischlinger Helmut
Published: January 2016

Although the calcitic hard parts of belemnites (extinct Coleoidea) are very abundant fossils, their soft parts are hardly known and their mode of life is debated. New fossils of the Jurassic belemnitidAcanthoteuthisprovided supplementary anatomical data on the fins, nuchal cartilage, collar complex, statoliths, hyponome and radula. These data yielded evidence of their pelagic habitat, their nektonic habit and high swimming velocities. The new morphological characters were included in a cladistic analysis, which confirms the position of the Belemnitida in the stem of Decabrachia (Decapodiformes).
Dr Jekyll and Mr Hyde: a strange case of 5-ethynyl-2′-deoxyuridine and 5-ethynyl-2′-deoxycytidine
Authors: Ligasová Anna , Liboska Radek , Friedecký David , Mičová Kateřina , Adam Tomáš , Oždian Tomáš , Rosenberg Ivan , Koberna Karel
Published: January 2016

5-Ethynyl-2′-deoxyuridine (EdU) and 5-ethynyl-2′-deoxycytidine (EdC) are mainly used as markers of cellular replicational activity. Although EdU is employed as a replicational marker more frequently than EdC, its cytotoxicity is commonly much higher than the toxicity of EdC. To reveal the reason of the lower cytotoxicity of EdC, we performed a DNA analysis of five EdC-treated human cell lines. Surprisingly, not a single one of the tested cell lines contained a detectable amount of EdC in their DNA. Instead, the DNA of all the cell lines contained EdU. The content of incorporated EdU differed in particular cells and EdC-related cytotoxicity was directly proportional to the content of EdU. The results of experiments with the targeted inhibition of the cytidine deaminase (CDD) and dCMP deaminase activities indicated that the dominant role in the conversion pathway of EdC to EdUTP is played by CDD in HeLa cells. Our results also showed that the deamination itself was not able to effectively prevent the conversion of EdC to EdCTP, the conversion of EdC to EdCTP occurs with much lesser effectivity than the conversion of EdU to EdUTP and the EdCTP is not effectively recognized by the replication complex as a substrate for the synthesis of nuclear DNA.
Markovian language model of the DNA and its information content
Authors: Srivastava S. , Baptista M. S.
Published: January 2016

This work proposes a Markovian memoryless model for the DNA that simplifies enormously the complexity of it. We encode nucleotide sequences into symbolic sequences, called words, from which we establish meaningful length of words and groups of words that share symbolic similarities. Interpreting a node to represent a group of similar words and edges to represent their functional connectivity allows us to construct a network of the grammatical rules governing the appearance of groups of words in the DNA. Our model allows us to predict the transition between groups of words in the DNA with unprecedented accuracy, and to easily calculate many informational quantities to better characterize the DNA. In addition, we reduce the DNA of known bacteria to a network of only tens of nodes, show how our model can be used to detect similar (or dissimilar) genes in different organisms, and which sequences of symbols are responsible for most of the information content of the DNA. Therefore, the DNA can indeed be treated as a language, a Markovian language, where a ‘word’ is an element of a group, and its grammar represents the rules behind the probability of transitions between any two groups.
Critical assessment of hydrogen effects on the slip transmission across grain boundaries in

α

-Fe
Authors: Adlakha I. , Solanki K. N.
Published: January 2016

Grain boundaries (GBs) play a fundamental role in the strengthening mechanism of crystalline structures by acting as an impediment to dislocation motion. However, the presence of an aggressive environment such as hydrogen increases the susceptibility to intergranular fracture. Further, there is a lack of systematic investigations exploring the role of hydrogen on the dislocation–grain-boundary (DGB) interactions. Thus, in this work, the effect of hydrogen on the interactions between a screw dislocation and 〈111〉 tilt GBs in
α
-Fe were examined. Our simulations reveal that the outcome of the DGB interaction strongly depends on the underlying GB dislocation network. Further, there exists a strong correlation between the GB energy and the energy barrier for slip transmission. In other words, GBs with lower interfacial energy demonstrate a higher barrier for slip transmission. The introduction of hydrogen along the GB causes the energy barrier for slip transmission to increase consistently for all of the GBs examined. The energy balance for a crack initiation in the presence of hydrogen was examined with the help of our observations and previous findings. It was found that the presence of hydrogen increases the strain energy stored within the GB which could lead to a transgranular-to-intergranular fracture mode transition.
Lifespan behavioural and neural resilience in a social insect
Authors: Giraldo Ysabel Milton , Kamhi J. Frances , Fourcassié Vincent , Moreau Mathieu , Robson Simon K. A. , Rusakov Adina , Wimberly Lindsey , Diloreto Alexandria , Kordek Adrianna , Traniello James F. A.
Published: January 2016

Analyses of senescence in social species are important to understanding how group living influences the evolution of ageing in society members. Social insects exhibit remarkable lifespan polyphenisms and division of labour, presenting excellent opportunities to test hypotheses concerning ageing and behaviour. Senescence patterns in other taxa suggest that behavioural performance in ageing workers would decrease in association with declining brain functions. Using the ant
Pheidole dentata
as a model, we found that 120-day-old minor workers, having completed 86% of their laboratory lifespan, showed no decrease in sensorimotor functions underscoring complex tasks such as alloparenting and foraging. Collaterally, we found no age-associated increases in apoptosis in functionally specialized brain compartments or decreases in synaptic densities in the mushroom bodies, regions associated with integrative processing. Furthermore, brain titres of serotonin and dopamine—neuromodulators that could negatively impact behaviour through age-related declines—increased in old workers. Unimpaired task performance appears to be based on the maintenance of brain functions supporting olfaction and motor coordination independent of age. Our study is the first to comprehensively assess lifespan task performance and its neurobiological correlates and identify constancy in behavioural performance and the absence of significant age-related neural declines.
fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks
Authors: Zhu C , Mahlich Y , Miller M , Bromberg Y
Published: January 2016

Microbial functional diversification is driven by environmental factors,i.e.microorganisms inhabiting the same environmental niche tend to be more functionally similar than those from different environments. In some cases, even closely phylogenetically related microbes differ more across environments than across taxa. While microbial similarities are often reported in terms of taxonomic relationships, no existing databases directly links microbial functions to the environment. We previously developed a method for comparing microbial functional similarities on the basis of proteins translated from the sequenced genomes. Here we describefusionDB, a novel database that uses our functional data to represent 1,374 taxonomically distinct bacteria annotated with available metadata: habitat/niche, preferred temperature, and oxygen use. Each microbe is encoded as a set of functions represented by its proteome and individual microbes are connected via common functions. Users can searchfusionDB via combinations of organism names and metadata. Moreover, the web interface allows mapping new microbial genomes to the functional spectrum of reference bacteria, rendering interactive similarity networks that highlight shared functionality.fusionDB provides a fast means of comparing microbes, identifying potential horizontal gene transfer events, and highlighting key environment-specific functionality.

fusionDB is publicly available athttp://services.bromberglab.org/fusiondb/.
Shared experience, shared memory: a common structure for brain activity during naturalistic recall
Authors: Chen J. , Leong Y.C. , Norman K.A. , Hasson U.
Published: January 2016

Our daily lives revolve around sharing experiences and memories with others. When different people recount the same events, how similar are their underlying neural representations? In this study, participants viewed a fifty-minute audio-visual movie, then verbally described the events while undergoing functional MRI. These descriptions were completely unguided and highly detailed, lasting for up to forty minutes. As each person spoke, event-specific spatial patterns were reinstated (movie-vs.-recall correlation) in default network, medial temporal, and high-level visual areas; moreover, individual event patterns were highly discriminable and similar between people during recollection (recall-vs.-recall similarity), suggesting the existence of spatially organized memory representations. In posterior medial cortex, medial prefrontal cortex, and angular gyrus, activity patterns during recall were more similar between people than to patterns elicited by the movie, indicating systematic reshaping of percept into memory across individuals. These results reveal striking similarity in how neural activity underlying real-life memories is organized and transformed in the brains of different people as they speak spontaneously about past events.
Mapping challenging mutations by whole-genome sequencing
Authors: Smith Harold E. , Fabritius Amy S. , Jaramillo-Lambert Aimee , Golden Andy
Published: January 2016

Whole-genome sequencing provides a rapid and powerful method for identifying mutations on a global scale, and has spurred a renewed enthusiasm for classical genetic screens in model organisms. The most commonly characterized category of mutation consists of monogenic, recessive traits, due to their genetic tractability. Therefore, most of the mapping methods for mutation identification by whole-genome sequencing are directed toward alleles that fulfill those criteria (i.e., single-gene, homozygous variants). However, such approaches are not entirely suitable for the characterization of a variety of more challenging mutations, such as dominant and semi-dominant alleles or multigenic traits. Therefore, we have developed strategies for the identification of those classes of mutations, using polymorphism mapping inCaenorhabditis elegansas our model for validation. We also report an alternative approach for mutation identification from traditional recombinant crosses, and a solution to the technical challenge of sequencing sterile or terminally arrested strains where population size is limiting. The methods described herein extend the applicability of whole-genome sequencing to a broader spectrum of mutations, including classes that are difficult to map by traditional means.
Voluntary carbon disclosure by Spanish companies: an empirical analysis
Authors: Gonzalez-Gonzalez Jose Maria , Zamora Ramírez Constancio
Published: January 2016

Purpose

– This paper aims to identify and analyze the factors contributing to the decision of organizations to disclose carbon information, as well as its transparency level.

Design/methodology/approach

– The Tobit regression is used to analyze the results of the Spanish companies that were invited in 2012 to respond to the Carbon Disclosure Project (CDP) questionnaire. The results of this study are interpreted according to the legitimacy and stakeholder theories.

Findings

– The results show that the probability of carbon disclosure and its transparency level are explained by the influence of pressures from society, markets, shareholders and international interactions. In the Spanish case, the factors that have shown a stronger influence are the size of the company, financial risk, their listing in the IBEX35 and FT500 indexes and the ownership concentration.

Originality/value

– One of the main contributions of this study to the previous literature lies in the used research method. Thus, while previous studies analyze the factors that can determine whether companies disclose carbon information, this paper has also considered the quantification and differentiation of the effect of these factors on the probability of supplying this information, as well as obtaining a higher score in the CDP questionnaire, representing a higher transparency level in the information provided. For this objective, the usefulness of the Tobit regression is to be highlighted.
Unlocking supply chain disruption risk within the Thai beverage industry
Authors: Tse Ying Kei , Matthews Rupert L. , Hua Tan Kim , Sato Yuji , Pongpanich Chaipong
Published: January 2016

Purpose

– A growing need for global sourcing of business has subjected firms to higher levels of uncertainty and increased risk of supply disruption. Differences in industry and infrastructure make it more difficult for firms to manage supply disruption risks effectively. The purpose of this paper is to extend developing research in this area by addressing gaps within existing literature related to environmental turbulence and uncertainties.

Design/methodology/approach

– The authors test the model using data collected from 253 senior managers and directors in the Thai beverage industry using advanced statistical techniques to explore the relationship between representations of supply disruption risk and uncertainty.

Findings

– The results show that both magnitude and probability of risk impact on the disruption risk, but the probability of loss is a dominant determinant. The authors also find that demand uncertainty and quality uncertainty affect the risk perception of purchasing managers, and are related to the magnitude of disruption risk, rather than the frequency of occurrence. Interestingly, the results show that quality uncertainty negatively impacts on the severity of disruption risk.

Research limitations/implications

– The construct validity of demand uncertainty was under the required threshold, intimating the need for further construct development.

Practical implications

– The framework provides managers with direction on how to formulate and target their disruption risk management strategies. The work also allows practitioners to critical reflect on implicit risk management strategies they may already employ and their effectiveness.

Originality/value

– The paper identifies key antecedents of supply disruption risk and tests them within a novel industrial context of the beverage industry and a novel national context of Thailand.