bluuebunny/crossref_metadata_2025 huggingface dataset:
Collective punishment is more effective than collective reward for promoting cooperation
Authors: Gao Lei , Wang Zhen , Pansini Riccardo , Li Yao-Tang , Wang Rui-Wu
Published: December 2015

Collective punishment and reward are usually regarded as two potential mechanisms to explain the evolution of cooperation. Both scenarios, however, seem problematic to understand cooperative behavior, because they can raise the second-order free-rider problem and many organisms are not able to discriminate less cooperating individuals. Even though they have been proved to increase cooperation, there has been a debate about which one being more effective. To address this issue, we resort to the N-player evolutionary snowdrift game (NESG), where a collective punishment/reward mechanism is added by allowing some players to display punishment/reward towards all remaining players. By means of numerous simulations and analyses, we find that collective punishment is more effective in promoting cooperation for a relatively high initial frequency of cooperation or for a relatively small group. When the intensity of punishment exceeds a certain threshold, a stable state of full cooperation emerges for both small and large groups. In contrast, such state does not appear for large groups playing a NESG with reward mechanism. In the case of mutualistic interactions, finally, our results show the new payoff with collective punishment/reward can lead to the coexistence of cooperators and defectors when discrimination between these two is not possible.
Identification and comparative analysis of complement C3-associated microRNAs in immune response of Apostichopus japonicus by high-throughput sequencing
Authors: Zhong Lei , Zhang Feng , Zhai Yu , Cao Yanhui , Zhang Si , Chang Yaqing
Published: December 2015

MicroRNAs (miRNAs) are important effectors in mediating host–pathogen interaction. In this report, coelomocytes miRNA libraries of three Japanese sea cucumbers Apostichopus japonicus were built by Illumina® Hiseq2000 from different time points after lipopolysaccharide challenge (at time 0 h, 6 h and 12 h). The clean data received from high throughput sequencing were used to sequences analysis. Referenced to the Strongylocentrotus purpuratus genome, 38 conserved miRNAs were found and three miRNA candidates were predicted by software. According to the evidence resulting from the expression of AjC3, expressing levels of spu-miR-133, spu-miR-137 and spu-miR-2004 altered along with the expression of AjC3 changing at different time points after LPS injection. Thus, we speculated that the three miRNAs may have influence on A. japonicus complement C3. The spu-miR-137 and miR-137 gene family in miRBase were analyzed by bioinformatics. There is an obvious discrepancy between invertebrates and vertebrates. The first and ninth nucleotides in invertebrate miR-137 are offset compared vertebrate miR-137. Importantly, this is the first attempt to map the stage of immune response regulome in echinoderms, which might be considered as information for elucidating the intrinsic mechanism underlying the immune system in this species.
A novel strategy for forensic age prediction by DNA methylation and support vector regression model
Authors: Xu Cheng , Qu Hongzhu , Wang Guangyu , Xie Bingbing , Shi Yi , Yang Yaran , Zhao Zhao , Hu Lan , Fang Xiangdong , Yan Jiangwei , Feng Lei
Published: December 2015

High deviations resulting from prediction model, gender and population difference have limited age estimation application of DNA methylation markers. Here we identified 2,957 novel age-associated DNA methylation sites (P < 0.01 and R2 > 0.5) in blood of eight pairs of Chinese Han female monozygotic twins. Among them, nine novel sites (false discovery rate < 0.01), along with three other reported sites, were further validated in 49 unrelated female volunteers with ages of 20–80 years by Sequenom Massarray. A total of 95 CpGs were covered in the PCR products and 11 of them were built the age prediction models. After comparing four different models including, multivariate linear regression, multivariate nonlinear regression, back propagation neural network and support vector regression, SVR was identified as the most robust model with the least mean absolute deviation from real chronological age (2.8 years) and an average accuracy of 4.7 years predicted by only six loci from the 11 loci, as well as an less cross-validated error compared with linear regression model. Our novel strategy provides an accurate measurement that is highly useful in estimating the individual age in forensic practice as well as in tracking the aging process in other related applications.
The Malat1 long non-coding RNA is upregulated by signalling through the PERK axis of unfolded protein response during flavivirus infection
Authors: Bhattacharyya Sankar , Vrati Sudhanshu
Published: December 2015

Flavivirus infection causes host cell death by initiation of an unfolded protein response (UPR). UPR is initiated following activation of three ER-membrane resident sensors, PERK, IRE1α and ATF6, which are otherwise kept inactive through association with the ER-chaperone GRP78. Activation precedes cellular and molecular changes that act to restore homeostasis but might eventually initiate apoptosis. These changes involve influencing function of multiple genes by either transcriptional or post-transcriptional or post-translational mechanisms. Transcriptional control includes expression of transcription factor cascades, which influence cognate gene expression. Malat1 is a long non-coding RNA which is over-expressed in many human oncogenic tissues and regulates cell cycle and survival. In this report, for the first time we show activation of Malat1 following infection by two flaviviruses, both of which activate the UPR in host cells. The temporal kinetics of expression was restricted to later time points. Further, Malat1 was also activated by pharmacological inducer of UPR, to a similar degree. Using drugs that specifically inhibit or activate the PERK or IRE1α sensors, we demonstrate that signalling through the PERK axis activates this expression, through a transcriptional mechanism. To our knowledge, this is the first report of an UPR pathway regulating the expression of an lncRNA.
Deep sequencing analysis of the heterogeneity of seed and commercial lots of the bacillus Calmette-Guérin (BCG) tuberculosis vaccine substrain Tokyo-172
Authors: Wada Takayuki , Maruyama Fumito , Iwamoto Tomotada , Maeda Shinji , Yamamoto Taro , Nakagawa Ichiro , Yamamoto Saburo , Ohara Naoya
Published: December 2015

BCG, only vaccine available to prevent tuberculosis, was established in the early 20th century by prolonged passaging of a virulent clinical strain ofMycobacterium bovis. BCG Tokyo-172, originally distributed within Japan in 1924, is one of the currently used reference substrains for the vaccine. Recently, this substrain was reported to contain two spontaneously arising, heterogeneous subpopulations (Types I and II). The proportions of the subpopulations changed over time in both distributed seed lots and commercial lots. To maintain the homogeneity of live vaccines, such variations and subpopulational mutations in lots should be restrained and monitored. We incorporated deep sequencing techniques to validate such heterogeneity in lots of the BCG Tokyo-172 substrain without cloning. By bioinformatics analysis, we not only detected the two subpopulations but also detected two intrinsic variations within these populations. The intrinsic variants could be isolated from respective lots as colonies cultured on plate media, suggesting analyses incorporating deep sequencing techniques are powerful, valid tools to detect mutations in live bacterial vaccine lots. Our data showed that spontaneous mutations in BCG vaccines could be easily monitored by deep sequencing without direct isolation of variants, revealing the complex heterogeneity of BCG Tokyo-172 and its daughter lots currently in use.
Design of aperture‐coupled microstrip patch antenna array fed by SIW for 60 GHz band
Authors: Mikulasek Tomas , Lacik Jaroslav , Puskely Jan , Raida Zbynek
Published: December 2015

This study deals with a design procedure and achieved parameters of a microstrip patch antenna array fed by a substrate integrated waveguide (SIW) operating at V‐band. The antenna array consists of 6 × 8 microstrip patch antennas which are aperture coupled with an SIW‐based feeding network. The antenna design is performed in a full‐wave electromagnetic solver (ANSYS HFSS) for the operation frequency 60 GHz. The design procedure of the proposed antenna array comprises the analysis of an isolated radiating element, the synthesis of a linear array, and the development of an SIW‐based power divider. At the operation frequency 60 GHz, a fabricated prototype has an impedance bandwidth of 1.8% for a reflection coefficient lower than −10 dB, a gain of 21.6 dBi, and a low sidelobe level below −23 dB in the E‐plane and H‐plane.
Analysis and implementation of a three‐level hybrid dc–dc converter with the balanced capacitor voltages
Authors: Lin Bor‐Ren , Zhang Sheng‐Zhi
Published: December 2015

In this study, a three‐level hybrid dc/dc converter by integrating the full‐bridge circuit, resonant circuit and three‐level flying capacitor circuit is presented to achieve the main advantages of low‐voltage stress of power devices, low circulating loss, low‐voltage ringing on the rectifier diodes and low‐output filter inductor for medium‐voltage dc‐based systems. Two full‐bridge circuits are connected in series to effectively reduce the voltage stress of switches. Half‐bridge resonant circuit shared the lagging‐leg switches of full‐bridge circuit is used and operated at fixed switching frequency to extend the zero‐voltage switching (ZVS) range from low load to full load. Thus, the drawback of narrow ZVS range in the conventional full‐bridge converter is improved. A flying capacitor is adopted to automatically balance input split capacitor voltages in each switching cycle without any additional active components or complexity control scheme. The circulating loss in the full‐bridge circuit is reduced to zero by parallel connection of outputs of full‐bridge circuit and half‐bridge resonant circuits. Finally, the theoretical analysis and performance of the proposed converter are verified by the experiments with a 1.92 kW prototype circuit.
Low-temperature vibration characteristics in InSe single crystals intercalated by Ni
Authors: Baran A. , Botko M. , Kajňaková M. , Feher A. , Feodosyev S. , Syrkin E. , Klochko M. , Tovstyuk N. , Grygorchak I. , Fomenko V.
Published: December 2015

The theoretical and experimental study of low-temperature heat capacity of InSe intercalated by nickel as a function of temperature has been carried out in range 0.3–30 K. The effect of intercalation by nickel on phonon heat capacity (Cph) of InSe has been investigated. Two peaks observed in relative change of phonon specific heat (ΔCph/Cph) suggested non-Debye excess in heat capacity for all intercalated NixInSe systems.
Transverse resistance of YBa2Cu3O7−δ single crystals with different oxygen deficiency
Authors: Khadzhai G. Ya. , Vovk R. V. , Nazyrov Z. F.
Published: December 2015

The resistivity of YBa2Cu3O7−δ single crystals across the layers was investigated in the temperature range Tc–300 K and in the range of δ corresponding to the change in Tc from 93 to 33 K. The temperature dependence of the resistivity is adequately described by an empirical expression, which includes “semiconductor” behavior and fluctuation conductivity in the three-dimensional Aslamazov–Larkin model near Tc. For high Tc, the charge carriers are scattered mainly by phonons. For low Tc, scattering by defects dominates; the coherence length ξab(0) and the electron–phonon interaction constant λ reach the values characteristic of conventional (low-temperature) superconductors with strong coupling. Heterogeneity of the samples causes anisotropy of Tc and variable-range hopping conductivity between different phases.
Collective oscillations of a two-chain electron system in a conducting channel over liquid helium
Authors: Syvokon V. E. , Sokolov S. S.
Published: December 2015

The simulation of a low-dimensional electron system over liquid helium was performed. It was shown that inclusion of an additional potential acting in the plane of the charge sheet leads to compression of the system in the direction of the external force. Such a potential arises in experiment when a system of surface electrons is formed over a profiled substrate where the potential is proportional to the holding electric field. It was found that in this case the system passes sequentially through the configurations consisting of several linear chains and undergoes a transition from the state of two-dimensional electron crystal to the zigzag configuration earlier predicted by Chaplik. With further increase in the holding field, the system becomes a single linear chain. The dispersion relations for the collective plasma oscillations of the zigzag configuration of electrons were calculated by the method of the equations of motion. It was found that one of the longitudinal oscillation modes is acoustic, whiles the other is optical. Both transverse oscillation modes were found to be optical. The results were compared with the dispersion relations earlier obtained for a single chain of electrons. It was shown that the dispersion relations of transverse plasma oscillations are more stable than the transverse mode of the oscillations of a single chain. The influence of magnetic field on the spectrum of plasma oscillations of the zigzag configuration of electrons was studied.
Heat capacity properties of quasi-one-dimensional magnet β-TeVO4
Authors: Savina Yu. A. , Bludov A. N. , Pashchenko V. A. , Gnatchenko S. L. , Zajarniuk T. , Gutowska M. U. , Szewczyk A. , Lemmens P. , Berger H.
Published: December 2015

We studied the temperature dependence of heat capacity CP(T) of a quasi-one-dimensional magnetic system β-TeVO4, in a zero magnetic field and a temperature region of 0.1 K ≤ T ≤ 300 K. The CP(T) dependence shows phase transitions at temperatures of 4.65, 3.28, and 2.32 K. Is it established that at a temperature of TN = 4.65 K there is a phase transition from a paramagnetic to an antiferromagnetic state. We provide a theoretical description of the heat capacity's temperature dependence.
Wave pattern in the wake of an arbitrary moving surface pressure disturbance
Authors: Miao Sha , Liu Yuming
Published: December 2015

We study the problem of wave pattern in the wake of an arbitrary surface pressure disturbance that moves forward at constant speed U in deep water. We seek the dependence of the location of the maximum amplitude of waves upon the pressure distribution and the Froude number F≡U/gL, where L is the characteristic length of the pressure disturbance and g is the gravitational acceleration. We show by theoretical analysis and direct numerical evaluation that half of the included angle (ϕmax) of the V-shape corresponding to the maximum amplitude of the waves in the wake at large Froude numbers behaves asymptotically as ϕmax=CF−a for F>Fc, with the constant a, coefficient C, and threshold value of Froude number Fc all being functions of the pressure distribution. It is found that for most pressure disturbances, a equals 1, but a can equal 2 for special non-smooth pressure disturbances. The condition in terms of the order of discontinuity and distribution shape of the pressure disturbance for the result of a = 2 is provided. These findings imply that for ship wakes, ϕmax generally decreases with increasing F at large Froude numbers, while the exact value of ϕmax is dependent on ship geometry and F.
Magnetic properties of solid oxygen under pressure (Review Article)
Authors: Freiman Yu. A.
Published: December 2015

Solid oxygen is a unique crystal combining properties of a simple molecular solid and a magnet. Unlike ordinary magnets, the exchange interaction in solid oxygen acts on a background of weak Van der Waals forces, providing a significant part of the total lattice energy. Therefore, the magnetic and lattice properties of solid oxygen are very closely related. This manifests itself in a very rich phase diagram and numerous anomalies of thermal, magnetic and optical properties. Low-temperature low-pressure α-O2 is a two-sublattice collinear Neel antiferromagnet. At a pressure of ∼6 GPa, α-O2 is transformed into δ-O2, in which three different magnetic structures are realized upon increasing temperature. At ∼8 GPa δ-O2 is transformed into ε-O2. In this transition, O2 molecules combine into four-molecule clusters (O2)4. This transformation is accompanied by a magnetic collapse. This review describes the evolution of the magnetic structure with increasing pressure, and analyzes the causes behind this behavior.
Oxygen-induced internal pressure in superconductors
Authors: Khirnyi V. F.
Published: December 2015

For the first time, analytical methods are used to define and investigate the properties of oxygen-created internal (chemical) pressure Pi in HTS YBa2Cu3O7−y and Tl2Ba2CuO6+x samples. We predict values for the critical temperature Tc, values of dTc/dPi for the main crystallographic axes, and also the possibility of synthesizing the compounds YBa2Cu3O7−y and Tl2Ba2CuO6+x in which Tc is equal to 166 and 92.3 K, respectively.
Parasitic effects in superconducting quantum interference device-based radiation comb generators
Authors: Bosisio R. , Giazotto F. , Solinas P.
Published: December 2015

We study several parasitic effects on the implementation of a Josephson radiation comb generator based on a dc superconducting quantum interference device (SQUID) driven by an external magnetic field. This system can be used as a radiation generator similarly to what is done in optics and metrology, and allows one to generate up to several hundreds of harmonics of the driving frequency. First we take into account how the assumption of a finite loop geometrical inductance and junction capacitance in each SQUID may alter the operation of the devices. Then, we estimate the effect of imperfections in the fabrication of an array of SQUIDs, which is an unavoidable source of errors in practical situations. We show that the role of the junction capacitance is, in general, negligible, whereas the geometrical inductance has a beneficial effect on the performance of the device. The errors on the areas and junction resistance asymmetries may deteriorate the performance, but their effect can be limited to a large extent by a suitable choice of fabrication parameters.
Diffuse electroreflectance of thin-film solar cells: Suppression of interference-related lineshape distortions
Authors: Krämmer Christoph , Huber Christian , Redinger Alex , Sperber David , Rey Germain , Siebentritt Susanne , Kalt Heinz , Hetterich Michael
Published: December 2015

Electroreflectance (ER) is a standard method to determine the band gap of semiconductor materials that has also been applied to thin-film solar cells (TFSCs). However, the lineshapes in typical ER spectra of TFSCs are significantly distorted compared to the model lineshapes, which are used for spectrum evaluation. These distortions are mainly due to thin-film interferences in the stratified system. In this letter, we demonstrate that these distortions are significantly suppressed in diffuse ER (D-ER) where the diffuse instead of the specular reflection of TFSCs is evaluated. The existence of an ER signal in the diffuse reflectance is shown by two-dimensional finite-difference time-domain simulations. Experimentally, the suppression of interference-related lineshape distortions is demonstrated on a series of Cu2ZnSnSe4 solar cells with different layer thicknesses and therefore different optical path lengths for interference. The same working principle is demonstrated for a Cu(In,Ga)(S,Se)2 solar cell as well. The resulting lineshapes in D-ER can then be interpreted using standard analysis methods such as Aspnes' Third-Derivative Functional Form.
Coulomb interaction potential and Bose-Einstein condensate
Authors: Bobrov V. B. , Zagorodny A. G. , Trigger S. A.
Published: December 2015

Based on the results of statistical quantum electrodynamics, it is shown that the Coulomb interaction potential of charged particles has no Fourier components at a zero wave vector. This result provides for the possibility of using the grand canonical ensemble to describe the Coulomb system, with independent descriptions of different varieties of charged particles. Based on this, we established that there could be an energy gap in the single-particle excitation spectrum at low pulses, given the presence of Bose-Einstein condensate in the Coulomb system, which does not contradict the existence of collective excitations, characterized by the phonon-roton spectrum.
Fundamental principles of energy consumption for gene expression
Authors: Huang Lifang , Yuan Zhanjiang , Yu Jianshe , Zhou Tianshou
Published: December 2015

How energy is consumed in gene expression is largely unknown mainly due to complexity of non-equilibrium mechanisms affecting expression levels. Here, by analyzing a representative gene model that considers complexity of gene expression, we show that negative feedback increases energy consumption but positive feedback has an opposite effect; promoter leakage always reduces energy consumption; generating more bursts needs to consume more energy; and the speed of promoter switching is at the cost of energy consumption. We also find that the relationship between energy consumption and expression noise is multi-mode, depending on both the type of feedback and the speed of promoter switching. Altogether, these results constitute fundamental principles of energy consumption for gene expression, which lay a foundation for designing biologically reasonable gene modules. In addition, we discuss possible biological implications of these principles by combining experimental facts.
Vector bright solitons associated with positive coherent coupling via Darboux transformation
Authors: Lü Xing , Ling Liming
Published: December 2015

Describing coherently coupled and orthogonally polarized waveguide modes in the Kerr medium, vector bright solitons associated with positive coherent coupling are studied in this paper. Some conserved quantities and infinitely many conservation laws are computed, and the existence of Lax pair indicates the integrability of the two-coupled nonlinear Schrödinger system with positive coherent coupling. Performing the iterative algorithm of Darboux transformation, we present formulas of one-, two-, and even N-soliton solutions. With appropriate choices of the phase parameters, collision mechanisms of vector bright solitons (of single-hump, double-hump, or flat-top profiles) are displayed, which show the elastic collision under the combined influences of group velocity dispersion, self-phase modulation, cross-phase modulation, and positive coherent coupling.
Interfacial roughness and proximity effects in superconductor/ferromagnet CuNi/Nb heterostructures
Authors: Khaydukov Yu. , Morari R. , Soltwedel O. , Keller T. , Christiani G. , Logvenov G. , Kupriyanov M. , Sidorenko A. , Keimer B.
Published: December 2015

We report an investigation of the structural and electronic properties of hybrid superconductor/ferromagnet (S/F) bilayers of composition Nb/Cu60Ni40 prepared by magnetron sputtering. X-ray and neutron reflectometry show that both the overall interfacial roughness and vertical correlations of the roughness of different interfaces are lower for heterostructures deposited on Al2O3(11¯02) substrates than for those deposited on Si(111). Mutual inductance experiments were then used to study the influence of the interfacial roughness on the superconducting transition temperature, TC. These measurements revealed a ∼4% higher TC in heterostructures deposited on Al2O3, compared to those on Si. We attribute this effect to a higher mean-free path of electrons in the S layer, caused by a suppression of diffusive scattering at the interfaces. However, the dependence of the TC on the thickness of the ferromagnetic layer is not significantly different in the two systems, indicating a weak influence of the interfacial roughness on the transparency for Cooper pairs.
The influence of magnetic field and temperature on spin-reorientation transitions in ε-In0.043Fe1.957O3 nanoparticles
Authors: Dmitriev A. I. , Morgunov R. B.
Published: December 2015

A first-order magnetic phase transition, accompanied by a decrease in magnetization and coercive force, occurs in nanoparticles that are diluted with superstrong magnets ε-In0.043Fe1.957O3 at a temperature of T = 150 K. The phase transition consists of a re-orientation of the easy magnetization axis due to the competition between the single-ion and dipole-dipole magnetic anisotropies. Temperature hysteresis of magnetization is observed near the temperature of the spin-reorientation transition, which is explained by the delay in the new phase growth with the change of the direction of the easy axis. The jump in magnetization, caused by the spin-reorientation transition, is suppressed with increasing magnetic field.
Impact of starting measurement voltage relative to flat-band voltage position on the capacitance-voltage hysteresis and on the defect characterization of InGaAs/high-k metal-oxide-semiconductor stacks
Authors: Vais Abhitosh , Franco Jacopo , Lin Han-Chung , Collaert Nadine , Mocuta Anda , De Meyer Kristin , Thean Aaron
Published: December 2015

In this work, we discuss how the position of the flat band voltage with respect to the starting voltage of the C-V measurement sweep can influence the estimation of the hysteresis in high-k/InGaAs MOS devices. We show that, with the support of experimental data and conceptual oxide defect band calculations, the interpretation and subsequent parameter extraction from flat-band voltage shifts observed in III-V MOS devices is more complex as compared to Si gate stacks. It is demonstrated that such complication arises due to the wider distribution of defect levels in the dielectric band gap in the case of InGaAs/high-k stack as compared to standard Si/SiO2/HfO2 MOS. In particular, for Al2O3 deposited on InGaAs, two wide, partially overlapping oxide defect bands are identified, centered ∼1.5 eV and ∼0.5 eV above and below the channel conduction band, respectively. Such defect levels are expected to affect the device operation and reliability.
Enhancement of photoluminescence from n-type tensile-strained GeSn wires on an insulator fabricated by lateral liquid-phase epitaxy
Authors: Shimura Takayoshi , Matsue Masahiro , Tominaga Kohei , Kajimura Keiko , Amamoto Takashi , Hosoi Takuji , Watanabe Heiji
Published: December 2015

We investigated the optical properties of undoped and n-type GeSn wires fabricated by a lateral liquid-phase epitaxial method. The Sn concentration was approximately 0.5% in the region from the seed to near the wire end. Moreover, the Sn concentration increased to 6% at the wire end, whereas Si diffusion from the seed was enhanced and extended to 200 μm from the seed. Tensile strain gradually decreased from 0.5% close the seed to 0.25% at the wire end. The photoluminescence (PL) peak was red-shifted by Sn incorporation into the Ge wires, and a PL peak at 0.66 eV was observed from the wire end. Upon n-type doping, the PL intensity of the GeSn layers was significantly enhanced to approximately 10 times higher than that of the undoped GeSn wires.
The conformational structure of adenosine molecules, isolated in low-temperature Ar matrices
Authors: Ivanov A. Yu. , Rubin Yu. V. , Egupov S. A. , Belous L. F. , Karachevtsev V. A.
Published: December 2015

FTIR spectra of adenosine (Ado) molecules, isolated in low-temperature matrices, are obtained in the infrared range of 3800–400 cm−1, with a resolution of 0.3. MP2 and DT/B3LYP quantum-mechanical methods are used to calculate the population of major structural Ado isomers. It is shown that Ado can withstand prolonged evaporation at a temperature of 465 K without thermal decomposition. The structure five major conformers that are fixed in Ar matrices at 6 K, are established. Ado anti-conformers with intramolecular hydrogen bonds O2′H-N3, are found. The population of these anti-conformers is more than one and a half times less than the syn-conformer population having the intramolecular hydrogen bond O5′H-N3. In low-temperature matrices, the majority of the dominant conformers are fixed with a C2′-endo ribose ring structure. Similar to 2′-deoxyadenosine (dA), Ado conformers with intramolecular hydrogen bonds O3′H-O5 or O5′H-O3 were not found.
Sublime Waste: Kant on the Destiny of the ‘Races’
Authors: Larrimore Mark
Published: December 2015

Wir dürfen aber den Untergang eines Weltgebäudes nicht als einen wahren Verlust der Natur bedauren. Sie beweiset ihren Reichthum in einer Art von Verschwendung … Der Mensch, der das Meisterstück der Schöpfung zu sein scheint, ist selbst von diesem Gesetze nicht ausgenommen.

Immanuel Kant was an early and influential theorist on race. What place a theory of race could have within his system is, however, far from clear. Empirical knowledge about human diversity seems not to be the kind of thing that may find its way into morally acceptable maxims. Kant's understanding of the a priori nature of the moral seems to prevent any account or theory of human difference from leading to prejudice or discrimination. On the other hand, Kant defends race it-self as an a priori concept, and the specific content of his anthropology seems to justify the exclusion of non-whites from moral concern in a new and dangerous way.
Subjecthood and Self-Determination: The Limitations of Postmodernism as Democratic Theory
Authors: Noonan Jeff
Published: December 2015

The history of Western liberal capitalist society, viewed from the perspective of the growth of democracy, is contradictory. Although the idea of negative liberty at the basis of democracies of the liberal type secured citizens against arbitrary encroachments from the state, at the same time, by securing the rights of property first and foremost, it exposed those same citizens to the more insidious and all-determining undemocratic forces of the capitalist market. The history of liberal democracy thus created the conditions for the flourishing of genuine individuality in a democratic polity at the same time as it undermined those conditions by subjecting all need fulfillment (through which individuality is developed) to market forces. Until the fragmentation of radical movements occasioned by the upheavals of the 1960s, radical theory and practice was minimally unified around the critique of the contradiction between democracy and market forces at the core of liberal society. The fundamental principle of this critique stated that democratic society could flourish if and only if need satisfaction was freed from its subordination to money demand.
Underwater Videography Outperforms Above-Water Videography and In-Person Surveys for Monitoring the Spawning of Devils Hole Pupfish
Authors: Chaudoin Ambre L. , Feuerbacher Olin G. , Bonar Scott A. , Barrett Paul J.
Published: December 2015

The monitoring of threatened and endangered fishes in remote environments continues to challenge fisheries biologists. The endangered Devils Hole Pupfish Cyprinodon diabolis, which is confined to a single warm spring in Death Valley National Park, California–Nevada, has recently experienced record declines, spurring renewed conservation and recovery efforts. In February–December 2010, we investigated the timing and frequency of spawning in the species' native habitat by using three survey methods: underwater videography, above-water videography, and in-person surveys. Videography methods incorporated fixed-position, solar-powered cameras to record continuous footage of a shallow rock shelf that Devils Hole Pupfish use for spawning. In-person surveys were conducted from a platform placed above the water's surface. The underwater camera recorded more overall spawning throughout the year (mean ± SE = 0.35 ± 0.06 events/sample) than the above-water camera (0.11 ± 0.03 events/sample). Underwater videography also recorded more peak-season spawning (March: 0.83 ± 0.18 events/sample; April: 2.39 ± 0.47 events/sample) than above-water videography (March: 0.21 ± 0.10 events/sample; April: 0.9 ± 0.32 events/sample). Although the overall number of spawning events per sample did not differ significantly between underwater videography and in-person surveys, underwater videography provided a larger data set with much less variability than data from in-person surveys. Fixed videography was more cost efficient than in-person surveys ($1.31 versus $605 per collected data-hour), and underwater videography provided more usable data than above-water videography. Furthermore, video data collection was possible even under adverse conditions, such as the extreme temperatures of the region, and could be maintained successfully with few study site visits. Our results suggest that self-contained underwater cameras can be efficient tools for monitoring remote and sensitive aquatic ecosystems.

Received April 17, 2015; accepted September 10, 2015
Purification and properties of 4-methyl-5-hydroxyethylthiazole kinase from Escherichia coli
Authors: Tani Yasushi , Kimura Keisuke , Mihara Hisaaki
Published: December 2015

4-Methyl-5-hydroxyethylthiazole kinase (ThiM) participates in thiamin biosynthesis as the key enzyme in its salvage pathway. We purified and characterized ThiM from Escherichia coli. It has broad substrate specificity toward various nucleotides and shows a preference for dATP as a phosphate donor over ATP. It is activated by divalent cations, and responds more strongly to Co2+ than to Mg2+.
How Explanatory Reasoning Justifies Pursuit: A Peircean View of IBE
Authors: Nyrup Rune
Published: December 2015

This article develops and defends an account of inference to the best explanation according to which it first and foremost justifies pursuing hypotheses rather than accepting them as true. This sidesteps the issue of why better explanations should be more likely to be true. I defend an account of justification for pursuit, inspired by Peirce’s mature account of abduction, and develop it as a formal decision-theoretic model. This account provides a straightforward connection between explanatoriness and justification for pursuit.
The Idealization of Causation in Mechanistic Explanation
Authors: Love Alan C. , Nathan Marco J.
Published: December 2015

Causal relations among components and activities are intentionally misrepresented in mechanistic explanations found routinely across the life sciences. Since several mechanists explicitly advocate accurately representing factors that make a difference to the outcome, these idealizations conflict with the stated rationale for mechanistic explanation. We argue that these idealizations signal an overlooked feature of reasoning in molecular and cell biology—mechanistic explanations do not occur in isolation—and suggest that explanatory practices within the mechanistic tradition share commonalities with model-based approaches prevalent in population biology.
The Completeness of Mechanistic Explanations
Authors: Baetu Tudor M.
Published: December 2015

The paper discusses methodological guidelines for evaluating mechanistic explanations. According to current accounts, a satisfactory mechanistic explanation should include all of the relevant features of the mechanism, its component entities and activities, and their properties and organization, as well as exhibit productive continuity. It is not specified, however, how this kind of mechanistic completeness can be demonstrated. I argue that parameter sufficiency inferences based on mathematical model simulations provide a way of determining whether a mechanism capable of producing the phenomenon of interest can be constructed from mechanistic components organized, acting, and having the properties described in the mechanistic explanation.
No Learning from Minimal Models
Authors: Fumagalli Roberto
Published: December 2015

This article examines the issue of whether consideration of so-called minimal models can prompt learning about real-world targets. Using a widely cited example as a test case, it argues against the increasingly popular view that consideration of minimal models can prompt learning about such targets. The article criticizes influential defenses of this view for failing to explicate by virtue of what properties or features minimal models supposedly prompt learning. It then argues that consideration of minimal models cannot prompt learning about real-world targets unless one supplements these models with additional information or presuppositions concerning such targets.
Reference Models: Using Models to Turn Data into Evidence
Authors: Miyake Teru
Published: December 2015

Reference models of the earth’s interior play an important role in the acquisition of knowledge about the earth’s interior and the earth as a whole. Such models are used as a sort of standard reference against which data are compared. I argue that the use of reference models merits more attention than it has gotten so far in the literature on models, for it is an example of a method of doing science that has a long and significant history, and a study of reference models could increase our understanding of this methodology.
Blurring Out Cosmic Puzzles
Authors: Benétreau-Dupin Yann
Published: December 2015

The Doomsday argument and anthropic reasoning are two puzzling examples of probabilistic confirmation. In both cases, a lack of knowledge apparently yields surprising conclusions. Since they are formulated within a Bayesian framework, they constitute a challenge to Bayesianism. Several attempts, some successful, have been made in a Bayesian framework that represents credal states by single credence functions to avoid these conclusions, but none of them can do so for all versions of the Doomsday argument. I show that adopting an imprecise framework of probabilistic reasoning allows for a more adequate representation of ignorance and explains away these puzzles.
Hypothesis Testing, “Dutch Book” Arguments, and Risk
Authors: Malinsky Daniel
Published: December 2015

“Dutch Book” arguments and references to gambling theorems are typical in the debate between Bayesians and scientists committed to “classical” statistical methods. These arguments have rarely convinced non-Bayesian scientists to abandon certain conventional practices (like fixed-level null hypothesis significance testing), partially because many scientists feel that gambling theorems have little relevance to their research activities. In other words, scientists “don’t bet.” This article examines one attempt, by Schervish, Seidenfeld, and Kadane, to progress beyond such apparent stalemates by connecting “Dutch Book”–type mathematical results with principles actually endorsed by practicing experimentalists.
Numerical Methods, Complexity, and Epistemic Hierarchies
Authors: Fillion Nicolas , Bangu Sorin
Published: December 2015

Modern mathematical sciences are hard to imagine without appeal to efficient computational algorithms. We address several conceptual problems arising from this interaction by outlining rival but complementary perspectives on mathematical tractability. More specifically, we articulate three alternative characterizations of the complexity hierarchy of mathematical problems that are themselves based on different understandings of computational constraints. These distinctions resolve the tension between epistemic contexts in which exact solutions can be found and the ones in which they cannot; however, contrary to a persistent myth, we conclude that having an exact solution is not generally more epistemologically beneficial than lacking one.
Mechanisms and Model-Based Functional Magnetic Resonance Imaging
Authors: Povich Mark
Published: December 2015

Mechanistic explanations satisfy widely held norms of explanation: the ability to manipulate and answer counterfactual questions about the explanandum phenomenon. A currently debated issue is whether any nonmechanistic explanations can satisfy these explanatory norms. Weiskopf argues that the models of object recognition and categorization, JIM, SUSTAIN, and ALCOVE, are not mechanistic yet satisfy these norms of explanation. In this article I argue that these models are mechanism sketches. My argument applies recent research using model-based functional magnetic resonance imaging, a novel neuroimaging method whose significance for current debates on psychological models and mechanistic explanation has yet to be explored.
Biological Individuality and Scientific Practice
Authors: Kovaka Karen
Published: December 2015

I consider the relationship between scientific practice and the philosophical debate surrounding biological individuality. I argue for the sensitivity account, on which biologists do not require a resolution to the individuality debate. This view puts me in disagreement with much of the literature on biological individuality, where it has become common to claim that there is a relationship of dependence between biologists’ conceptions of individuality and the quality of their empirical work.
Embedded Mechanisms and Phylogenetics
Authors: Matthews Lucas J.
Published: December 2015

A strong case has been made for the role and value of mechanistic explanation in neuroscience and molecular biology. A similar demonstration in other domains of scientific investigation, however, remains an important challenge of scope for the new mechanists. This article helps answer that challenge by demonstrating one valuable role mechanisms play in phylogenetics. Using the transition/transversion (ti/tv) rate parameter as a case example, this article argues that models embedded with mechanisms produce stronger phylogenetic tree hypotheses, as measured by maximum likelihood logLvalues. Two important implications for the new mechanistic account of explanation are considered.
Weak Discernibility and Relations between Quanta
Authors: Norton Joshua
Published: December 2015

Some authors (Muller and Saunders, Huggett and Norton) have attempted to defend Leibniz’s Identity of Indiscernibles through weak discernibility. The idea is that if there is a symmetric, nonreflexive physical relation that holds between two particles, then those particles cannot be identical. In this article I focus only on Muller and Saunders’s account and argue that the means by which they achieve weak discernibility is not through a quantum mechanical observable but an alternate mathematical construction that is both unorthodox and incomplete.
A Pluralist View about Information
Authors: Lombardi Olimpia , Fortin Sebastian , Vanni Leonardo
Published: December 2015

Focusing on Shannon information, this article shows that, even on the basis of the same formalism, there may be different interpretations of the concept of information, and that disagreements may be deep enough to lead to very different conclusions about the informational characterization of certain physical situations. On this basis, a pluralist view is argued for, according to which the concept of information is primarily a formal concept that can adopt different interpretations that are not mutually exclusive, but each useful in a different specific context.
Commensuration Bias in Peer Review
Authors: Lee Carole J.
Published: December 2015

To arrive at their final evaluation of a manuscript or grant proposal, reviewers must convert a submission’s strengths and weaknesses for heterogeneous peer review criteria into a single metric of quality or merit. I identify this process of commensuration as the locus for a new kind of peer review bias. Commensuration bias illuminates how the systematic prioritization of some peer review criteria over others permits and facilitates problematic patterns of publication and funding in science. Commensuration bias also foregrounds a range of structural strategies for realigning peer review practices and institutions with the aims of science.
Does Science License Metaphysics?
Authors: Robus Olin M.
Published: December 2015

Naturalized metaphysicians defend the thesis that science licenses metaphysics, such that only metaphysical results based on the best science are legitimate. This view is problematic, due to the fact that the reasons they identify for such license are apparently self-defeating. Anjan Chakravartty defends a revised approach to understanding the licensing relation. I argue that the proposed response is a step forward on behalf of naturalizing metaphysics but still does not take seriously the contention that science involves, inextricably, a contribution from the a priori. I conclude by considering what options the naturalized metaphysician is left with.
Structural Chaos
Authors: Mayo-Wilson Conor
Published: December 2015

A dynamical system is calledchaoticif small changes to its initial conditions can create large changes in its behavior. By analogy, we call a dynamical systemstructurally chaoticif small changes to the equations describing the evolution of the system produce large changes in its behavior. Although there are many definitions of “chaos,” there are few mathematically precise candidate definitions of “structural chaos.” I propose a definition, and I explain two new theorems that show that a set of models is structurally chaotic if it contains a chaotic function. I conclude by discussing the relationship between structural chaos and structural stability.
Cheap Talk, Reinforcement Learning, and the Emergence of Cooperation
Authors: Alexander J. McKenzie
Published: December 2015

Cheap talk has often been thought incapable of supporting the emergence of cooperation because costless signals, easily faked, are unlikely to be reliable. I show how, in a social network model of cheap talk with reinforcement learning, cheap talk does enable the emergence of cooperation, provided that individuals also temporally discount the past. This establishes one mechanism that suffices for moving a population of initially uncooperative individuals to a state of mutually beneficial cooperation even in the absence of formal institutions.
International Court of Justice
Authors: Thirlway Hugh , Hoss Cristina
Published: December 2015

The International Court of Justice (ICJ, the Court) is a principal organ of the United Nations, along with the Security Council, the Economic and Social Council, the Trusteeship Council, the General Assembly, and the Secretariat; it is defined as the “principal judicial organ” of the organization (UN Charter, Art. 92). Its operation is governed by its Statute, which is annexed to the Charter and “forms an integral part” of it (UN Charter, Art. 92). It is composed of fifteen judges elected by the Security Council and the General Assembly for a term of office of nine years (renewable); the required qualifications for election are laid down in the Statute, which also provides that the electors are to bear in mind that “in the body as a whole the representation of the main forms of civilization and of the principal legal systems of the world should be assured” (Art. 9). Only states may be parties to cases before it; it is open to those that are parties to its Statute (which includes all UN member states). Its jurisdiction “comprises all cases which the parties refer to it and all matters specially provided for” in treaties (including the UN Charter). The Statute provides for a system of compulsory jurisdiction as between states that accept this by means of a formal declaration (often qualified by reservations). The decisions of the Court are binding; it also has power to give nonbinding advisory opinions at the request of bodies “authorized by or in accordance with the [UN] Charter . . . to make such a request.” These include the Security Council and the General Assembly and other organs and specialized agencies so authorized by the General Assembly.