bluuebunny/crossref_metadata_2025_split huggingface dataset:
ARITHMETICAL INTERPRETATIONS AND KRIPKE FRAMES OF PREDICATE MODAL LOGIC OF PROVABILITY
Authors: KURAHASHI TAISHI 
Published: October 2012

AbstractSolovay proved the arithmetical completeness theorem for the system GL of propositional modal logic of provability. Montagna proved that this completeness does not hold for a natural extension QGL of GL to the predicate modal logic. Let Th(QGL) be the set of all theorems of QGL, Fr(QGL) be the set of all formulas valid in all transitive and conversely well-founded Kripke frames, and let PL(T) be the set of all predicate modal formulas provable in Tfor any arithmetical interpretation. Montagna’s results are described as Th(QGL) ⊊ (Fr(QGL), PL(PA) ⊈ Fr(QGL), and Th(QGL) ⊊ PL(PA).In this paper, we prove the following three theorems: (1) Fr(QGL) ⊈ PL(T) for any Σ1-sound recursively enumerable extension T of I Σ1, (2) PL(T) ⊈ Fr(QGL) for any recursively enumerable A-theory T extending I Σ1, and (3) Th(QGL) ⊊ Fr(QGL) ∩ PL(T) for any recursively enumerable A-theory T extending I Σ2.To prove these theorems, we use iterated consistency assertions and nonstandard models of arithmetic, and we improve Artemov’s lemma which is used to prove Vardanyan’s theorem on the Π02-completeness of PL(T).
The origin of Ina: Evidence for inflated lava flows on the Moon
Authors: Garry W. B. , Robinson M. S. , Zimbelman J. R. , Bleacher J. E. , Hawke B. R. , Crumpler L. S. , Braden S. E. , Sato H. 
Published: October 2012

Ina is an enigmatic volcanic feature on the Moon known for its irregularly shaped mounds, the origin of which has been debated since the Apollo Missions. Three main units are observed on the floor of the depression (2.9 km across, ≤64 m deep) located at the summit of a low‐shield volcano: irregularly shaped mounds up to 20 m tall, a lower unit 1 to 5 m in relief that surrounds the mounds, and blocky material. Analyses of Lunar Reconnaissance Orbiter Camera images and topography show that features in Ina are morphologically similar to terrestrial inflated lava flows. Comparison of these unusual lunar mounds and possible terrestrial analogs leads us to hypothesize that features in Ina were formed through lava flow inflation processes. While the source of the lava remains unclear, this new model suggests that as the mounds inflated, breakouts along their margins served as sources for surface flows that created the lower morphologic unit. Over time, mass wasting of both morphologic units has exposed fresh surfaces observed in the blocky unit. Ina is different than the terrestrial analogs presented in this study in that the lunar features formed within a depression, no vent sources are observed, and no cracks are observed on the mounds. However, lava flow inflation processes explain many of the morphologic relationships observed in Ina and are proposed to be analogous with inflated lava flows on Earth.
Reliability of decadal predictions
Authors: Corti S. , Weisheimer A. , Palmer T. N. , Doblas‐Reyes F. J. , Magnusson L. 
Published: October 2012

The reliability of multi‐year predictions of climate is assessed using probabilistic Attributes Diagrams for near‐surface air temperature and sea surface temperature, based on 54 member ensembles of initialised decadal hindcasts using the ECMWF coupled model. It is shown that the reliability from the ensemble system is good over global land areas, Europe and Africa and for the North Atlantic, Indian Ocean and, to a lesser extent, North Pacific basins for lead times up to 6–9 years. North Atlantic SSTs are reliably predicted even when the climate trend is removed, consistent with the known predictability for this region. By contrast, reliability in the Indian Ocean, where external forcing accounts for most of the variability, deteriorates severely after detrending. More conventional measures of forecast quality, such as the anomaly correlation coefficient (ACC) of the ensemble mean, are also considered, showing that the ensemble has significant skill in predicting multi‐annual temperature averages.
The role of large‐scale atmospheric flow and Rossby wave breaking in the evolution of extreme windstorms over Europe
Authors: Hanley John , Caballero Rodrigo 
Published: October 2012

We investigate the relationship between large‐scale atmospheric flow and the evolution of the most extreme windstorms affecting Western Continental Europe. The 25 most destructive Western Continental European wind storms are selected from a 43‐year climatology. 22 of these storms are grouped as having a similar trajectory and evolution. We show that these storms typically occur during particularly strong and persistent positive NAO anomalies which peak approximately 2 days before the storms' peak intensity; the NAO pattern then shifts eastward to a position over the European continent when the storms strike Europe. A temporal composite of potential temperature on the 2‐PVU surface suggests that this NAO shift is the result of simultaneous cyclonic and anticyclonic wave breaking penetrating further to the east than during a typical high‐NAO event. This creates an extremely intense, zonally‐orientated jet over the North Atlantic whose baroclinicity favours explosive intensification of storms while steering them into Western Continental Europe.
Seismicity precursors to large earthquakes unified in a stress accumulation framework
Authors: Mignan Arnaud 
Published: October 2012

Various seismicity patterns before large earthquakes have been reported in the literature. They include foreshocks (medium‐term acceleration and short‐term activation), quiescence, doughnut patterns and event migration. The existence of these precursory patterns is however debated. Here, we develop an approach based on the concept of stress accumulation to unify and categorize all claimed seismic precursors in a same physical framework. We first extend the Non‐Critical Precursory Accelerating Seismicity Theory (N‐C PAST), which already explains most precursors, to additionally include short‐term activation. Theoretical results are then compared to the time series observed prior to the 2009Mw = 6.3 L'Aquila, Italy, earthquake. We finally show that different precursory paths are possible before large earthquakes, with possible coupling of different patterns or non‐occurrence of any. This is described by a logic tree defined from the combined probabilities of occurrence of the mainshock at a given stress state and of precursory silent slip on the fault. In the case of the L'Aquila earthquake, the observed precursory path is coupling of quiescence and accelerating seismic release, followed by activation. These results provide guidelines for future research on earthquake predictability.
Observation of the multifractal spectrum in the heliosphere and the heliosheath by Voyager 1 and 2
Authors: Macek W. M. , Wawrzaszek A. , Carbone V. 
Published: October 2012

We present first results of the multifractal scaling of the fluctuations of the interplanetary magnetic field strength as measured onboard Voyager 2 in the very distant heliosphere and even in the heliosheath. More specifically, the spectra observed by Voyager 2 in a wide range of heliospheric distances from 6 to 90 astronomical units (AU) are compared with those of Voyager 1 already analyzed between 7 and 107 AU. We focus on the singularity multifractal spectrum before and after crossing the termination heliospheric shock by Voyager 1 at 94 AU and Voyager 2 at 84 AU from the Sun. It is worth noting that the spectrum is prevalently right‐skewed inside the whole heliosphere. Moreover, we have observed a change of the asymmetry of the spectrum at the termination shock, where the spectrum changes from (left‐) right‐skewed in the very distant heliosphere to the (right‐) left‐skewed or possibly symmetric spectrum in the heliosheath. We confirm that the degree of multifractality falls steadily with the distance from the Sun. In addition, the multifractal structure is apparently modulated by the solar activity, with a time shift of several years, corresponding to a distance of about 10 AU, resulting from the evolution of the whole heliosphere. Hence this basic result also brings significant additional support to some earlier claims suggesting that the solar wind termination shock is asymmetric.
The Pathophysiology of Schizophrenia
Authors: Szegedi Armin , Egan Michael 
Published: October 2012

Schizophrenia is a clinically and neurobiologically heterogeneous disorder that affects approximately 1% of the population worldwide. In the last century it has undergone and continues to undergo substantial changes in its conceptualization, the earlier concepts being driven mainly by clinical symptom classification, while in more recent years neurobiological findings are increasingly implemented. Many individuals experience a variety of symptoms, often in the symptom domains of positive, negative or affective symptoms as well as cognitive impairment. Affected individuals typically experience initial symptoms in the later teens or early adulthood, leading in a majority of cases to a chronic course of the disorder. Functional impairment is generally substantial, resulting in substantial burden of disease and reduced quality of life for the individual. The discovery of antipsychotic drugs in the mid 1950s fundamentally changed the prognosis for the patients, as mainly positive symptoms for the first time became amenable to treatment. However, though antipsychotic drugs have been developed further, overall efficacy has not been improved substantially, but the available antipsychotics vary mainly in their safety and tolerability profile, as well as individual response rates, which still cannot be predicted reliably.
An increasing amount of neurobiological data has been accumulated in the last decades, providing evidence for the involvement of dopamine and glutamate as well as other neurotransmitters in the etiopathology of various symptoms in schizophrenia. Evidence of structural abnormalities (e.g. volumetric reductions) has been found in neuropathological and neuroimaging studies. Cognitive impairment and its association with prefrontal cortical function have been well documented. The contribution of genetic factors is well established in addition to environmental and developmental factors, though the contribution of various candidate genes still remains to be elucidated in detail. The totality of neurobiological data has prompted integrative neurobiological theories, which are likely to have implications for drug discovery and drug development efforts in the future.
Structures of trans-2-enoyl-CoA reductases from Clostridium acetobutylicum and Treponema denticola: insights into the substrate specificity and the catalytic mechanism
Authors: Hu Kuan , Zhao Meng , Zhang Tianlong , Zha Manwu , Zhong Chen , Jiang Yu , Ding Jianping 
Published: October 2012

TERs (trans-2-enoyl-CoA reductases; EC 1.3.1.44), which specifically catalyse the reduction of crotonyl-CoA to butyryl-CoA using NADH as cofactor, have recently been applied in the design of robust synthetic pathways to produce butan-1-ol as a biofuel. We report in the present paper the characterization of a CaTER (a TER homologue in Clostridium acetobutylicum), the structures of CaTER in apo form and in complexes with NADH and NAD+, and the structure of TdTER (Treponema denticola TER) in complex with NAD+. Structural and sequence comparisons show that CaTER and TdTER share approximately 45% overall sequence identity and high structural similarities with the FabV class enoyl-acyl carrier protein reductases in the bacterial fatty acid synthesis pathway, suggesting that both types of enzymes belong to the same family. CaTER and TdTER function as monomers and consist of a cofactor-binding domain and a substrate-binding domain with the catalytic active site located at the interface of the two domains. Structural analyses of CaTER together with mutagenesis and biochemical data indicate that the conserved Glu75 determines the cofactor specificity, and the conserved Tyr225, Tyr235 and Lys244 play critical roles in catalysis. Upon cofactor binding, the substrate-binding loop changes from an open conformation to a closed conformation, narrowing a hydrophobic channel to the catalytic site. A modelling study shows that the hydrophobic channel is optimal in both width and length for the binding of crotonyl-CoA. These results provide molecular bases for the high substrate specificity and the catalytic mechanism of TERs.
Sorafenib treatment improves hepatopulmonary syndrome in rats with biliary cirrhosis
Authors: Chang Ching-Chih , Chuang Chiao-Lin , Lee Fa-Yauh , Wang Sun-Sang , Lin Han-Chieh , Huang Hui-Chun , Teng Tzu-Hua , Hsu Shao-Jung , Hsieh Hsian-Guey , Lee Shou-Dong 
Published: October 2012

HPS (hepatopulmonary syndrome) is characterized by oxygen desaturation in patients with chronic liver disease. The initiation of HPS comes from abnormal pulmonary vasodilatation and/or angiogenesis. In the present study, we evaluated anti-angiogenesis therapy using sorafenib in experimental HPS animals. HPS was induced by CBDL (common bile duct ligation) in rats. A 2-week 10 mg·(kg of body weight)−1·day−1 treatment regimen of sorafenib or distilled water (control) was initiated 2 weeks after the surgical procedure. Haemodynamics, liver biochemistry, plasma VEGF (vascular endothelial growth factor) measurements and blood gas analysis of the CBDL rats were performed. The livers of the CBDL rats were dissected for histopathology examination, and the lungs were examined by immunohistochemical staining, real-time PCR and Western blot analysis. In another two parallel groups, intrapulmonary shunts were determined. The AaPO2 (alveolar–arterial O2 gradient) and plasma VEGF levels were reduced after sorafenib treatment [AaPO2, 7.2±3.4 mmHg in sorafenib-treated rats compared with 15.3±4.2 mmHg in controls (P=0.004); VEGF, 45.3±2.7 pg/ml in sorafenib-treated rats compared with 54.4±7.7 pg/ml in controls (P=0.021)]. Sorafenib attenuated pulmonary VEGF mRNA and VEGF, VEGFR-2 (VEGF receptor 2), phospho-VEGFR-2 and Akt protein expression. In addition, sorafenib significantly attenuated intrapulmonary angiogenesis and decreased the degree of intrapulmonary shunting by 33.7% (11.2±5.7% in sorafenib-treated rats compared with 16.9±5.9% in controls; P=0.003). Our findings suggest that sorafenib attenuates intrapulmonary shunting and decreases the AaPO2 in CBDL rats, implicating the improvement of HPS in this experimental animal model. The beneficial effect may be attributed to the reduction in intrapulmonary angiogenesis through inhibition of the VEGF/VEGFR-2/Akt pathway.
A comparison of two online cognitive‐behavioural interventions for symptoms of depression in a student population: The role of therapist responsiveness
Authors: Richards Derek , Timulak Ladislav , Hevey David 
Published: October 2012

AbstractObjectives: The study aimed to compare the efficacy of eight weekly sessions of a self‐administered online CBT treatment (cCBT; n=51) to a therapist‐assisted email CBT treatment (eCBT; n=50) in University students. Design: The design was a randomised parallel group trial. The study randomised participants with symptoms of depression to one of two available treatments. Method: Participants were offered eight weekly sessions of either cCBT or eCBT. Participants completed the Beck Depression Inventory‐II (BDI‐II) and the Clinical Outcomes in Routine Evaluation – Outcome Measure (CORE‐OM) at pre‐and post‐treatment, at weeks 16 and 32 follow‐up. The Working Alliance Inventory‐Short Form (WAI‐SR) was completed at weeks 2, 4, and 6. Results: For both groups, pre‐post within group effect sizes reported were large for the BDI‐II and the CORE‐OM and these were maintained at follow‐up. Perceptions of working alliance were similar in each group, but Bond was significantly stronger for the eCBT condition. WAI scores correlated more positively with the outcome on BDI‐II for those in the eCBT condition than the cCBT condition, but not significantly. Conclusion: There were no significant differences between the two online treatments, both reduced depressive symptoms and improved general functioning. Similarly, at post‐treatment and follow‐up, clinical improvement and recovery was demonstrated for both groups equally. The study demonstrates the possibility for cCBT in a university setting that may contribute to addressing the shortcomings in meeting increasing demands that mental health services presently face.
ON ABSORPTION BY CIRCUMSTELLAR DUST, WITH THE PROGENITOR OF SN 2012aw AS A CASE STUDY
Authors: Kochanek C. S. , Khan R. , Dai X. 
Published: October 2012

ABSTRACT
We use the progenitor of SN 2012aw to illustrate the consequences of modeling circumstellar dust using Galactic (interstellar) extinction laws that (1) ignore dust emission in the near-IR and beyond, (2) average over dust compositions, and (3) mischaracterize the optical/UV absorption by assuming that scattered photons are lost to the observer. The primary consequences for the progenitor of SN 2012aw are that both the luminosity and the absorption are significantly overestimated. In particular, the stellar luminosity is most likely in the range 104.8 < L
*/L
☉ < 105.0 and the star was not extremely massive for a Type IIP progenitor, with M
* < 15 M
☉. Given the properties of the circumstellar dust and the early X-ray/radio detections of SN 2012aw, the star was probably obscured by an ongoing wind with

to 10−5.0
M
☉ yr−1 at the time of the explosion, roughly consistent with the expected mass-loss rates for a star of its temperature (T
* ≃ 3600+300
− 200 K) and luminosity. In the spirit of Galactic extinction laws, we supply simple interpolation formulae for circumstellar extinction by dusty graphitic and silicate shells as a function of wavelength (λ ⩾ 0.3 μm) and total (absorption plus scattering) V-band optical depth (τ
V
⩽ 20). These do not include the contributions of dust emission, but provide a simple, physical alternative to incorrectly using interstellar extinction laws.
Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads
Authors: Li Wei , Jiang Tao 
Published: October 2012

AbstractMotivation: RNA-Seq uses the high-throughput sequencing technology to identify and quantify transcriptome at an unprecedented high resolution and low cost. However, RNA-Seq reads are usually not uniformly distributed and biases in RNA-Seq data post great challenges in many applications including transcriptome assembly and the expression level estimation of genes or isoforms. Much effort has been made in the literature to calibrate the expression level estimation from biased RNA-Seq data, but the effect of biases on transcriptome assembly remains largely unexplored.Results: Here, we propose a statistical framework for both transcriptome assembly and isoform expression level estimation from biased RNA-Seq data. Using a quasi-multinomial distribution model, our method is able to capture various types of RNA-Seq biases, including positional, sequencing and mappability biases. Our experimental results on simulated and real RNA-Seq datasets exhibit interesting effects of RNA-Seq biases on both transcriptome assembly and isoform expression level estimation. The advantage of our method is clearly shown in the experimental analysis by its high sensitivity and precision in transcriptome assembly and the high concordance of its estimated expression levels with quantitative reverse transcription–polymerase chain reaction data.Availability: CEM is freely available at http://www.cs.ucr.edu/~liw/cem.html.Contact: liw@cs.ucr.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches
Authors: Mendes Nuno D. , Heyne Steffen , Freitas Ana T. , Sagot Marie-France , Backofen Rolf 
Published: October 2012

Abstract
Motivation: The computational search for novel microRNA (miRNA) precursors often involves some sort of structural analysis with the aim of identifying which type of structures are prone to being recognized and processed by the cellular miRNA-maturation machinery. A natural way to tackle this problem is to perform clustering over the candidate structures along with known miRNA precursor structures. Mixed clusters allow then the identification of candidates that are similar to known precursors. Given the large number of pre-miRNA candidates that can be identified in single-genome approaches, even after applying several filters for precursor robustness and stability, a conventional structural clustering approach is unfeasible.
Results: We propose a method to represent candidate structures in a feature space, which summarizes key sequence/structure characteristics of each candidate. We demonstrate that proximity in this feature space is related to sequence/structure similarity, and we select candidates that have a high similarity to known precursors. Additional filtering steps are then applied to further reduce the number of candidates to those with greater transcriptional potential. Our method is compared with another single-genome method (TripletSVM) in two datasets, showing better performance in one and comparable performance in the other, for larger training sets. Additionally, we show that our approach allows for a better interpretation of the results.
Availability and Implementation: The MinDist method is implemented using Perl scripts and is freely available at http://www.cravela.org/?mindist=1.
Contact: backofen@informatik.uni-freiburg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
An ensemble correlation-based gene selection algorithm for cancer classification with gene expression data
Authors: Piao Yongjun , Piao Minghao , Park Kiejung , Ryu Keun Ho 
Published: October 2012

Abstract
Motivation: Gene selection for cancer classification is one of the most important topics in the biomedical field. However, microarray data pose a severe challenge for computational techniques. We need dimension reduction techniques that identify a small set of genes to achieve better learning performance. From the perspective of machine learning, the selection of genes can be considered to be a feature selection problem that aims to find a small subset of features that has the most discriminative information for the target.
Results: In this article, we proposed an Ensemble Correlation-Based Gene Selection algorithm based on symmetrical uncertainty and Support Vector Machine. In our method, symmetrical uncertainty was used to analyze the relevance of the genes, the different starting points of the relevant subset were used to generate the gene subsets and the Support Vector Machine was used as an evaluation criterion of the wrapper. The efficiency and effectiveness of our method were demonstrated through comparisons with other feature selection techniques, and the results show that our method outperformed other methods published in the literature.
Availability: By request from the author.
Contact: pyz@dblab.chungbuk.ac.kr; khryu@dblab.cbnu.ac.kr