bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proof-producing translation of higher-order logic into pure and stateful ML
Authors: MYREEN MAGNUS O. , OWENS SCOTT 
Published: January 2014

AbstractThe higher-order logic found in proof assistants such as Coq and various HOL systems provides a convenient setting for the development and verification of functional programs. However, to efficiently run these programs, they must be converted (or ‘extracted’) to functional programs in a programming language such as ML or Haskell. With current techniques, this step, which must be trusted, relates similar looking objects that have very different semantic definitions, such as the set-theoretic model of a logic and the operational semantics of a programming language. In this paper, we show how to increase the trustworthiness of this step with an automated technique. Given a functional program expressed in higher-order logic, our technique provides the corresponding program for a functional language defined with an operational semantics, and it provides a mechanically checked theorem relating the two. This theorem can then be used to transfer verified properties of the logical function to the program. We have implemented our technique in the HOL4 theorem prover, translating functions to a subset of Standard ML, and have applied the implementation to examples including functional data structures, a parser generator, cryptographic algorithms, a garbage collector and the 500-line kernel of the HOL light theorem prover. This paper extends our previous conference publication with new material that shows how functions defined in terms of a state-and-exception monad can be translated, with proofs, into stateful ML code. The HOL light example is also new.
Fine-scale nutrient and carbonate system dynamics around cold-water coral reefs in the northeast Atlantic
Authors: Findlay Helen S. , Hennige Sebastian J. , Wicks Laura C. , Navas Juan Moreno , Woodward E. Malcolm S. , Roberts J. Murray 
Published: January 2014

AbstractOcean acidification has been suggested as a serious threat to the future existence of cold-water corals (CWC). However, there are few fine-scale temporal and spatial datasets of carbonate and nutrients conditions available for these reefs, which can provide a baseline definition of extant conditions. Here we provide observational data from four different sites in the northeast Atlantic that are known habitats for CWC. These habitats differ by depth and by the nature of the coral habitat. At depths where CWC are known to occur across these sites the dissolved inorganic carbon ranged from 2088 to 2186 μmol kg−1, alkalinity ranged from 2299 to 2346 μmol kg−1 and aragonite Ω ranged from 1.35 to 2.44. At two sites fine-scale hydrodynamics caused increased variability in the carbonate and nutrient conditions over daily time-scales. The observed high level of variability must be taken into account when assessing CWC sensitivities to future environmental change.
A geometrical approach explains Lake Ball (Marimo) formations in the green alga, Aegagropila linnaei
Authors: Togashi Tatsuya , Sasaki Hironobu , Yoshimura Jin 
Published: January 2014

AbstractAn extremely rare alga, Aegagropila linnaei, is known for its beautiful spherical filamentous aggregations called Lake Ball (Marimo). It has long been a mystery in biology as to why this species forms 3D ball-like aggregations. This alga also forms two-dimensional mat-like aggregations. Here we show that forming ball-like aggregations is an adaptive strategy to increase biomass in the extremely limited environments suitable for growth of this alga. We estimate the maximum biomass attained by ball colonies and compare it to that attained by mat colonies. As a result, a ball colony can become larger in areal biomass than the mat colony. In the two large ball colonies studied so far, they actually have larger biomasses than the mat colonies. The uniqueness of Lake Balls in nature seems to be due to the rarity of such environmental conditions. This implies that the conservation of this alga is difficult, but important.
Age-dependent postoperative cognitive impairment and Alzheimer-related neuropathology in mice
Authors: Xu Zhipeng , Dong Yuanlin , Wang Hui , Culley Deborah J. , Marcantonio Edward R. , Crosby Gregory , Tanzi Rudolph E. , Zhang Yiying , Xie Zhongcong 
Published: January 2014

AbstractPost-operative cognitive dysfunction (POCD) is associated with increased cost of care, morbidity and mortality. However, its pathogenesis remains largely to be determined. Specifically, it is unknown why elderly patients are more likely to develop POCD and whether POCD is dependent on general anesthesia. We therefore set out to investigate the effects of peripheral surgery on the cognition and Alzheimer-related neuropathology in mice with different ages. Abdominal surgery under local anesthesia was established in the mice. The surgery induced post-operative elevation in brain β-amyloid (Aβ) levels and cognitive impairment in the 18 month-old wild-type and 9 month-old Alzheimer's disease transgenic mice, but not the 9 month-old wild-type mice. The Aβ accumulation likely resulted from elevation of beta-site amyloid precursor protein cleaving enzyme and phosphorylated eukaryotic translation initiation factor 2α. γ-Secretase inhibitor compound E ameliorated the surgery-induced brain Aβ accumulation and cognitive impairment in the 18 month-old mice. These data suggested that the peripheral surgery was able to induce cognitive impairment independent of general anesthesia and that the combination of peripheral surgery with aging- or Alzheimer gene mutation-associated Aβ accumulation was needed for the POCD to occur. These findings would likely promote more research to investigate the pathogenesis of POCD.
Genetic Influences on Receptive Joint Attention in Chimpanzees (Pan troglodytes)
Authors: Hopkins William D. , Keebaugh Alaine C. , Reamer Lisa A. , Schaeffer Jennifer , Schapiro Steven J. , Young Larry J. 
Published: January 2014

AbstractDespite their genetic similarity to humans, our understanding of the role of genes on cognitive traits in chimpanzees remains virtually unexplored. Here, we examined the relationship between genetic variation in the arginine vasopressin V1a receptor gene (AVPR1A) and social cognition in chimpanzees. Studies have shown that chimpanzees are polymorphic for a deletion in a sequence in the 5′ flanking region of the AVPR1A, DupB, which contains the variable RS3 repetitive element, which has been associated with variation in social behavior in humans. Results revealed that performance on the social cognition task was significantly heritable. Furthermore, males with one DupB+ allele performed significantly better and were more responsive to socio-communicative cues than males homozygous for the DupB- deletion. Performance on a non-social cognition task was not associated with the AVPR1A genotype. The collective findings show that AVPR1A polymorphisms are associated with individual differences in performance on a receptive joint attention task in chimpanzees.
TALE proteins bind to both active and inactive chromatin
Authors: Scott James N. F. , Kupinski Adam P. , Kirkham Christopher M. , Tuma Roman , Boyes Joan 
Published: January 2014

TALE (transcription activator-like effector) proteins can be tailored to bind to any DNA sequence of choice and thus are of immense utility for genome editing and the specific delivery of transcription activators. However, to perform these functions, they need to occupy their sites in chromatin. In the present study, we have systematically assessed TALE binding to chromatin substrates and find that in vitro TALEs bind to their target site on nucleosomes at the more accessible entry/exit sites, but not at the nucleosome dyad. We show further that in vivo TALEs bind to transcriptionally repressed chromatin and that transcription increases binding by only 2-fold. These data therefore imply that TALEs are likely to bind to their target in vivo even at inactive loci.
Apoptosome and inflammasome: conserved machineries for caspase activation
Authors: Chai Jijie , Shi Yigong 
Published: January 2014

AbstractApoptosome and inflammasome are multimeric protein complexes that mediate the activation of specific caspases at the onset of apoptosis and inflammation. The central component of apoptosome or inflammasome is a tripartite scaffold protein, exemplified by Apaf-1 and NLRC4, which contains an amino-terminal homotypic interaction motif, a central nucleotide-binding oligomerization domain and a carboxyl-terminal ligand-sensing domain. In the absence of death cue or an inflammatory signal, Apaf-1 or NLRC4 exists in an auto-inhibited, monomeric state, which is stabilized by adenosine diphosphate (ADP). Binding to an apoptosis- or inflammation-inducing ligand, together with replacement of ADP by adenosine triphosphate (ATP), results in the formation of a multimeric apoptosome or inflammasome. The assembled apoptosome and inflammasome serve as dedicated machineries to facilitate the activation of specific caspases. In this review, we describe the structure and functional mechanisms of mammalian inflammasome and apoptosomes from three representative organisms. Emphasis is placed on the molecular mechanism of caspase activation and the shared features of apoptosomes and inflammasomes.
China's funding system and research innovation
Authors: Qiu Jane 
Published: January 2014

Abstract
In the past decade, China's total expenditure on research and development (R&D) has been increasing by about 20% per year. And the total output of scientific research from China has not failed to impress: a 2011 study by Britain's Royal Society found that, in 2004–08, the country produced 10% of the world's published scientific articles, putting it second after the United States.
But a study conducted by the World Bank and China's State Council concluded in the year 2012 that Chinese research quality falls short. It noted that the country produces relatively few high-impact articles, and that the majority of Chinese patents constitute minor novelties rather than genuine innovations.
So what has gone wrong? And what needs to be changed to spur innovation in China significantly? In a forum organized by National Science Review, its executive associate editor Mu-ming Poo asked four leading scientists in China.

Yadong Li
Chemist of Tsinghua University in Beijing (Courtesy of Yadong Li)

Yi Rao
Biologist of Peking University in Beijing (Courtesy of Yi Rao)

Dingsheng Wang
Physicist of Institute of Physics, Chinese Academy of Sciences in Beijing (Courtesy of Dingsheng Wang)

Pinxian Wang
Geologist of Tongji University in Shanghai (Courtesy of Pinxian Wang)

Mu-ming Poo (Chair)
Neuroscientist of Institute of Neuroscience, Chinese Academy of Sciences in Shanghai (Courtesy of Mu-ming Poo)
Preliminary X-ray crystallographic analysis of glutathione transferase zeta 1 (GSTZ1a-1a)
Authors: Boone Christopher D. , Zhong Guo , Smeltz Marci , James Margaret O. , McKenna Robert 
Published: January 2014

Glutathione transferase zeta 1 (GSTZ1-1) is a homodimeric enzyme found in the cytosol and mitochondrial matrix of the liver and other tissues. It catalyzes the glutathione-dependent isomerization of maleylacetoacetate to fumarylacetoacetate in the tyrosine catabolic pathway and can metabolize small halogenated carboxylic acids. GSTZ1a-1a crystals diffracted to a resolution of 3.1 Å and belonged to space group P1, with unit-cell parameters a = 42.0, b = 49.6, c = 54.6 Å, α = 82.9, β = 69.9, γ = 73.4°, with a calculated Matthews coefficient of 2.1 Å3 Da−1 assuming a dimer in the crystallographic asymmetric unit. Refinement of the structure is currently in progress.
Crystallization and preliminary X-ray diffraction analysis of human DNA primase
Authors: Baranovskiy Andrey G. , Gu Jianyou , Babayeva Nigar D. , Agarkar Vinod B. , Suwa Yoshiaki , Tahirov Tahir H. 
Published: January 2014

Human primase synthesizes RNA primers and transfers them to the active site of Pol α with subsequent extension with dNTPs. Human primase is a heterodimer of two subunits: a small catalytic subunit (p49) and a large subunit (p58). The structural details of the initiation and elongation steps of primer synthesis, as well as primer length counting, are not known. To address these questions, structural studies of human primase were initiated. Two types of crystals were obtained. The best diffracting crystals belonged to space group P1, with unit-cell parameters a = 86.2, b = 88.9, c = 94.68 Å, α = 93.82, β = 96.57, γ = 111.72°, and contained two heterodimers of full-length p49 and p59 subunits in the asymmetric unit.
Image‐ray Tomography
Authors: Dell Sergius , Gajewski Dirk , Tygel Martin 
Published: January 2014

ABSTRACTSeismic tomography is a well‐established approach to invert smooth macro‐velocity models from kinematic parameters, such as traveltimes and their derivatives, which can be directly estimated from data. Tomographic methods differ more with respect to data domains than in the specifications of inverse‐problem solving schemes. Typical examples are stereotomography, which is applied to prestack data and Normal‐Incidence‐Point‐wave tomography, which is applied to common midpoint stacked data. One of the main challenges within the tomographic approach is the reliable estimation of the kinematic attributes from the data that are used in the inversion process. Estimations in the prestack domain (weak and noisy signals), as well as in the post‐stack domain (occurrence of triplications and diffractions leading to numerous conflicting dip situations) may lead to parameter inaccuracies that will adversely impact the resulting velocity models. To overcome the above limitations, a new tomographic procedure applied in the time‐migrated domain is proposed. We call this method Image‐Incident‐Point‐wave tomography. The new scheme can be seen as an alternative to Normal‐Incidence‐Point‐wave tomography. The latter method is based on traveltime attributes associated with normal rays, whereas the Image‐Incidence‐Point‐wave technique is based on the corresponding quantities for the image rays. Compared to Normal‐Incidence‐Point‐wave tomography the proposed method eases the selection of the tomography attributes, which is shown by synthetic and field data examples. Moreover, the method provides a direct way to convert time‐migration velocities into depth‐migration velocities without the need of any Dix‐style inversion.
Fault imaging in sparsely sampled 3D seismic data using common‐reflection‐surface processing and attribute analysis – a study in the Upper Rhine Graben
Authors: Buness Hermann A. , von Hartmann Hartwig , Rumpel Hanna‐Maria , Krawczyk Charlotte M. , Schulz Rüdiger 
Published: January 2014

ABSTRACTCost reduction in seismic reconnaissance is an issue in geothermal exploration and can principally be achieved by sparse acquisition. To address the adherent decrease in signal/noise ratio, the common‐reflection‐surface method has been proposed. We reduced the data density of an existing 3D dataset and evaluated the results of common‐reflection‐surface processing using seismic attributes. The application of the common‐reflection‐surface method leads in all cases to an improvement of the signal/noise ratio. The most distinct improvement can be seen in the low fold regions. The improvement depends strongly on the midpoint aperture, and there is a tradeoff between reflector continuity and horizontal resolution. If small scale targets are to be imaged, a small aperture size is necessary, which may be far below the Fresnel zone for a specific reflector. The substantial reduction of the data density leads in our case to an irrecoverable information loss.
Anatomy of a population cycle: the role of density dependence and demographic variability on numerical instability and periodicity
Authors: Row Jeffrey R. , Wilson Paul J. , Murray Dennis L. 
Published: January 2014

Summary

Determining the causes of cyclic fluctuations in population size is a central tenet in population ecology and provides insights into population regulatory mechanisms. We have a firm understanding of how direct and delayed density dependence affects population stability and cyclic dynamics, but there remains considerable uncertainty in the specific processes contributing to demographic variability and consequent change in cyclic propensity.

Spatiotemporal variability in cyclic propensity, including recent attenuation or loss of cyclicity among several temperate populations and the implications of habitat fragmentation and climate change on this pattern, highlights the heightened need to understand processes underlying cyclic variation. Because these stressors can differentially impact survival and productivity and thereby impose variable time delays in density dependence, there is a specific need to elucidate how demographic vital rates interact with the type and action of density dependence to contribute to population stability and cyclic variation.

Here, we address this knowledge gap by comparing the stability of time series derived from general and species‐specific (Canada lynx: Lynx canadensis; small rodents: Microtus, Lemmus and Clethrionomys spp.) matrix population models, which vary in their demographic rates and the direct action of density dependence.

Our results reveal that density dependence acting exclusively on survival as opposed to productivity is destabilizing, suggesting that a shift in the action of population regulation toward reproductive output may decrease cyclic propensity and cycle amplitude. This result was the same whether delayed density dependence was pulsatile and acted on a single time period (e.g. t−1, t−2 or t−3) vs. more constant by affecting a successive range of years (e.g. t−1,…, t−3).

Consistent with our general models, reductions in reproductive potential in both the lynx and small rodent systems led to notably large drops in cyclic propensity and amplitude, suggesting that changes in this vital rate may contribute to the spatial or temporal variability observed in the cyclic dynamics of both systems.

Collectively, our results reveal that the type of density dependence and its effect on different demographic parameters can profoundly influence numeric stability and cyclic propensity and therefore may shift populations across the cyclic‐to‐noncyclic boundary.
What's Queer about Political Science?
Authors: Smith Nicola J. , Lee Donna 
Published: January 2014

Research Highlights and Abstract The study of gender, sexuality—and, in particular, queer theory—is central to the social sciences and humanities. Our analysis of citation practices shows that queer theorist Judith Butler is one of the most cited social theorists of all time. Yet political science remains distinctly untroubled by queer theory, and gender and sexuality are frequently treated as marginal (not central) concerns. We argue that queer theory has much to offer political science, not only by highlighting the importance of sexuality and the body but also in analysing ‘power’ and in politicising ‘the political’ itself. We suggest that the ‘queering’ of political science is long overdue, not least through politicising processes of knowledge-production in the discipline. There is something queer (by which we mean strange) going on in the scholarly practice of political science. Why are political science scholars continuing to disregard issues of gender and sexuality—and in particular queer theory—in their lecture theatres, seminar rooms, textbooks, and journal articles? Such everyday issues around common human experience are considered by other social scientists to be central to the practice and theory of social relations. In this article we discuss how these commonplace issues are being written out of (or, more accurately, have never been written in to) contemporary political science. First, we present and discuss our findings on citation practice in order to evidence the queerness of what does and does not get cited in political science scholarship. We then go on to critique this practice before suggesting a broader agenda for the analysis of the political based on a queer theoretical approach.
Evaluation of cheese meltability using convection and conduction melt profilers
Authors: Ko Sanghoon , Gunasekaran Sundaram 
Published: January 2014

The University of Wisconsin (UW) Melt Profiler was operated under convection and conduction heating modes for evaluating the melt/flow properties of cheese. Five processed cheeses, each with a different solid fat index (SFI = 1+, 5−, 5+, 6− and 8+), were tested. In general, the higher the SFI of the cheese, the lower the time and temperature at the softening point. Similar trends were also observed between the cheese SFI values and the time and temperature at the rapid flow point. As conduction heating is more effective than convection heating, the heating method affected the cheese melt/flow parameters remarkably. Furthermore, TSP and TRF tended to be higher when the cheeses were tested at higher temperatures.
Transcriptomic response of cowpea bruchids to N‐acetylglucosamine‐specific lectins
Authors: Wang Li‐Hua , Chi Yong Hun , Guo Feng‐Guang , Li‐Byarlay Hongmei , Balfe Susan , Fang Ji‐Chao , Pittendrigh Barry R. , Zhu‐Salzman Keyan 
Published: January 2014

AbstractGriffonia simplicifolia lectin II (GSII) and wheat germ agglutinin (WGA) are N‐acetylglucosamine‐binding lectins. Previous studies demonstrated that they have anti‐insect activity, a property potentially useful in pest control. To gain some insight into the insect response to dietary lectins, we performed transcriptomic analysis using the cowpea bruchid (Callosobruchus maculatus) midgut microarray platform we built. Compared to the nonnutritional cellulose treatment, dietary lectins induced more profound changes in gene expression. Ingestion of relatively high doses of lectins for 24 h resulted in alteration of gene expression involved in sugar and lipid metabolism, transport, development, defense, and stress tolerance. Metabolic genes were largely downregulated. Moreover, we observed disorganized microvilli resulting from ingestion of WGA. This morphological change is consistent with the lectin‐induced changes in genes related to midgut epithelial cell repair. In addition, suboptimal nutrient conditions may serve as a stress signal to trigger senescence processes, leading to growth arrest and developmental delay.
Anti‐obesity effect of Allomyrina dichotoma (Arthropoda: Insecta) larvae ethanol extract on 3T3‐L1 adipocyte differentiation
Authors: Chung Mi Yeon , Yoon Young‐Il , Hwang Jae‐Sam , Goo Tae‐Won , Yun Eun‐Young 
Published: January 2014

AbstractAlthough Korean horn beetle (Allomyrina dichotoma) larvae have been long used as an oriental medicine for the treatment of liver diseases in Korea, there is little scientific evidence of their effects. In this study, we investigated the anti‐obesity activity of A. dichotoma larvae extract (ADE) by using 3T3‐L1 cells as an in vitro model of adipogenesis. To analyze its role as an inhibitor of adipogenesis, 3T3‐L1 cells were treated with both ADE and differentiation inducer (DM) at the same time, and then the amount of lipid was quantified. We then analyzed the mRNA and protein expression level of adipogenic or lipogenic genes. The results showed that formation of lipid droplets in differentiated 3T3‐L1 cells was markedly decreased, and triglyceride content was reduced by 22.15% in response to 2000 μg/mL ADE. In addition, ADE downregulated mRNA and protein expression of transcription factors peroxisome proliferator‐activated receptor (PPAR)‐γ and CCAAT/enhancer binding protein (C/EBP)‐α implicated in adipogenesis, and significantly decreased the expression levels of adipocyte fatty acid binding protein (aP2), fatty acid synthase (FAS), stearoyl‐coenzyme desaturase‐1 (SCD1), and lipoprotein lipase (LPL) related to lipogenesis. Our results demonstrate that ADE suppressed adipogenesis and lipogenesis in 3T3‐L1 cells, suggesting that ADE has anti‐obesity activity as a food supplement.