bluuebunny/crossref_metadata_2025_split huggingface dataset:
A logic programming approach to predict effective compiler settings for embedded software
Authors: BLACKMORE CRAIG , RAY OLIVER , EDER KERSTIN 
Published: September 2015

AbstractThis paper introduces a new logic-based method for optimising the selection of compiler flags on embedded architectures. In particular, we use Inductive Logic Programming (ILP) to learn logical rules that relate effective compiler flags to specific program features. Unlike earlier work, we aim to infer human-readable rules and we seek to develop a relational first-order approach which automatically discovers relevant features rather than relying on a vector of predetermined attributes. To this end we generated a data set by measuring execution times of 60 benchmarks on an embedded system development board and we developed an ILP prototype which outperforms the current state-of-the-art learning approach in 34 of the 60 benchmarks. Finally, we combined the strengths of the current state of the art and our ILP method in a hybrid approach which reduced execution times by an average of 8% and up to 50% in some cases.
Planning as tabled logic programming
Authors: ZHOU NENG-FA , BARTÁK ROMAN , DOVIER AGOSTINO 
Published: September 2015

AbstractThis paper describes Picat's planner, its implementation, and planning models for several domains used in International Planning Competition (IPC) 2014. Picat's planner is implemented by use of tabling. During search, every state encountered is tabled, and tabled states are used to effectively perform resource-bounded search. In Picat, structured data can be used to avoid enumerating all possible permutations of objects, and term sharing is used to avoid duplication of common state data. This paper presents several modeling techniques through the example models, ranging from designing state representations to facilitate data sharing and symmetry breaking, encoding actions with operations for efficient precondition checking and state updating, to incorporating domain knowledge and heuristics. Broadly, this paper demonstrates the effectiveness of tabled logic programming for planning, and argues the importance of modeling despite recent significant progress in domain-independent PDDL planners.
Rewriting recursive aggregates in answer set programming: back to monotonicity
Authors: ALVIANO MARIO , FABER WOLFGANG , GEBSER MARTIN 
Published: September 2015

AbstractAggregation functions are widely used in answer set programming for representing and reasoning on knowledge involving sets of objects collectively. Current implementations simplify the structure of programs in order to optimize the overall performance. In particular, aggregates are rewritten into simpler forms known as monotone aggregates. Since the evaluation of normal programs with monotone aggregates is in general on a lower complexity level than the evaluation of normal programs with arbitrary aggregates, any faithful translation function must introduce disjunction in rule heads in some cases. However, no function of this kind is known. The paper closes this gap by introducing a polynomial, faithful, and modular translation for rewriting common aggregation functions into the simpler form accepted by current solvers. A prototype system allows for experimenting with arbitrary recursive aggregates, which are also supported in the recent version 4.5 of the groundergringo, using the methods presented in this paper.
Optimizing phylogenetic supertrees using answer set programming
Authors: KOPONEN LAURA , OIKARINEN EMILIA , JANHUNEN TOMI , SÄILÄ LAURA 
Published: September 2015

AbstractThe supertree construction problem is about combining several phylogenetic trees with possibly conflicting information into a single tree that has all the leaves of the source trees as its leaves and the relationships between the leaves are as consistent with the source trees as possible. This leads to an optimization problem that is computationally challenging and typically heuristic methods, such as matrix representation with parsimony (MRP), are used. In this paper we consider the use of answer set programming to solve the supertree construction problem in terms of two alternative encodings. The first is based on an existing encoding of trees using substructures known as quartets, while the other novel encoding captures the relationships present in trees through direct projections. We use these encodings to compute a genus-level supertree for the family of cats (Felidae). Furthermore, we compare our results to recent supertrees obtained by the MRP method.
A denotational semantics for equilibrium logic
Authors: AGUADO FELICIDAD , CABALAR PEDRO , PEARCE DAVID , PÉREZ GILBERTO , VIDAL CONCEPCIÓN 
Published: September 2015

AbstractIn this paper we provide an alternative semantics for Equilibrium Logic and its monotonic basis, the logic of Here-and-There (also known as Gödel'sG3logic) that relies on the idea ofdenotationof a formula, that is, a function that collects the set of models of that formula. Using the three-valued logicG3as a starting point and an ordering relation (for which equilibrium/stable models are minimal elements) we provide several elementary operations for sets of interpretations. By analysing structural properties of the denotation of formulas, we show some expressiveness results forG3such as, for instance, that conjunction is not expressible in terms of the other connectives. Moreover, the denotational semantics allows us to capture the set of equilibrium models of a formula with a simple and compact set expression. We also use this semantics to provide several formal definitions for entailment relations that are usual in the literature, and further introduce a new one calledstrong entailment. We say that α strongly entails β when the equilibrium models of α ∧ γ are also equilibrium models of β ∧ γ for any context γ. We also provide a characterisation of strong entailment in terms of the denotational semantics, and give an example of a sufficient condition that can be applied in some cases.
Comparison of Three Questionnaires to Screen for Borderline	Personality Disorder in Adolescents and Young Adults
Authors: van Alebeek Anne , van der Heijden Paul T. , Hessels Christel , Thong Melissa S.Y. , van Aken Marcel 
Published: September 2015

Abstract. One of the most common personality disorders among adolescents and young adults is the Borderline Personality Disorder (BPD). The objective of current study was to assess three questionnaires that can reliably screen for BPD in adolescents and young adults (N = 53): the McLean Screening Instrument for BPD (MSI-BPD; Zanarini et al., 2003 ), the Personality Diagnostic Questionnaire 4th edition – BPD scale (PDQ-4 BPD; Hyler, 1994 ), and the SCID-II Patient Questionnaire – BPD scale (SCID-II-PQ BPD). The nine criteria of BPD according to the Diagnostic and Statistical Manual of Mental Disorders-IV (DSM-IV; APA, 1994 ) were measured with the Structural Clinical Interview for DSM-IV Axis II disorders – BPD scale (SCID-II; First, Spitzer, Gibbon, Williams, & Benjamin, 1995 ). Correlations between the questionnaires and the SCID-II were calculated. In addition, the sensitivity and specificity of the questionnaires were tested. All instruments predicted the BPD diagnosis equally well.
Tumor suppressor Nf2/merlin drives Schwann cell changes following electromagnetic field exposure through Hippo-dependent mechanisms
Authors: Colciago A , Melfi S , Giannotti G , Bonalume V , Ballabio M , Caffino L , Fumagalli F , Magnaghi V 
Published: September 2015

AbstractPrevious evidence showed mutations of the neurofibromin type 2 gene (Nf2), encoding the tumor suppressor protein merlin, in sporadic and vestibular schwannomas affecting Schwann cells (SCs). Accordingly, efforts have been addressed to identify possible factors, even environmental, that may regulate neurofibromas growth. In this context, we investigated the exposure of SC to an electromagnetic field (EMF), which is an environmental issue modulating biological processes. Here, we show that SC exposed to 50 Hz EMFs changes their morphology, proliferation, migration and myelinating capability. In these cells, merlin is downregulated, leading to activation of two intracellular signaling pathways, ERK/AKT and Hippo. Interestingly, SC changes their phenotype toward a proliferative/migrating state, which in principle may be pathologically relevant for schwannoma development.
Heme-based catalytic properties of human serum albumin
Authors: Ascenzi P , di Masi A , Fanali G , Fasano M 
Published: September 2015

AbstractHuman serum albumin (HSA): (i) controls the plasma oncotic pressure, (ii) modulates fluid distribution between the body compartments, (iii) represents the depot and carrier of endogenous and exogenous compounds, (iv) increases the apparent solubility and lifetime of hydrophobic compounds, (v) affects pharmacokinetics of many drugs, (vi) inactivates toxic compounds, (vii) induces chemical modifications of some ligands, (viii) displays antioxidant properties, and (ix) shows enzymatic properties. Under physiological and pathological conditions, HSA has a pivotal role in heme scavenging transferring the metal-macrocycle from high- and low-density lipoproteins to hemopexin, thus acquiring globin-like reactivity. Here, the heme-based catalytic properties of HSA are reviewed and the structural bases of drug-dependent allosteric regulation are highlighted.
Mutations in SLC12A5 in epilepsy of infancy with migrating focal seizures
Authors: Stödberg Tommy , McTague Amy , Ruiz Arnaud J. , Hirata Hiromi , Zhen Juan , Long Philip , Farabella Irene , Meyer Esther , Kawahara Atsuo , Vassallo Grace , Stivaros Stavros M. , Bjursell Magnus K. , Stranneheim Henrik , Tigerschiöld Stephanie , Persson Bengt , Bangash Iftikhar , Das Krishna , Hughes Deborah , Lesko Nicole , Lundeberg Joakim , Scott Rod C. , Poduri Annapurna , Scheffer Ingrid E. , Smith Holly , Gissen Paul , Schorge Stephanie , Reith Maarten E. A. , Topf Maya , Kullmann Dimitri M. , Harvey Robert J. , Wedell Anna , Kurian Manju A. 
Published: September 2015

AbstractThe potassium-chloride co-transporter KCC2, encoded by SLC12A5, plays a fundamental role in fast synaptic inhibition by maintaining a hyperpolarizing gradient for chloride ions. KCC2 dysfunction has been implicated in human epilepsy, but to date, no monogenic KCC2-related epilepsy disorders have been described. Here we show recessive loss-of-function SLC12A5 mutations in patients with a severe infantile-onset pharmacoresistant epilepsy syndrome, epilepsy of infancy with migrating focal seizures (EIMFS). Decreased KCC2 surface expression, reduced protein glycosylation and impaired chloride extrusion contribute to loss of KCC2 activity, thereby impairing normal synaptic inhibition and promoting neuronal excitability in this early-onset epileptic encephalopathy.
Novel mutations in PIEZO1 cause an autosomal recessive generalized lymphatic dysplasia with non-immune hydrops fetalis
Authors: Fotiou Elisavet , Martin-Almedina Silvia , Simpson Michael A. , Lin Shin , Gordon Kristiana , Brice Glen , Atton Giles , Jeffery Iona , Rees David C. , Mignot Cyril , Vogt Julie , Homfray Tessa , Snyder Michael P. , Rockson Stanley G. , Jeffery Steve , Mortimer Peter S. , Mansour Sahar , Ostergaard Pia 
Published: September 2015

AbstractGeneralized lymphatic dysplasia (GLD) is a rare form of primary lymphoedema characterized by a uniform, widespread lymphoedema affecting all segments of the body, with systemic involvement such as intestinal and/or pulmonary lymphangiectasia, pleural effusions, chylothoraces and/or pericardial effusions. This may present prenatally as non-immune hydrops. Here we report homozygous and compound heterozygous mutations in PIEZO1, resulting in an autosomal recessive form of GLD with a high incidence of non-immune hydrops fetalis and childhood onset of facial and four limb lymphoedema. Mutations in PIEZO1, which encodes a mechanically activated ion channel, have been reported with autosomal dominant dehydrated hereditary stomatocytosis and non-immune hydrops of unknown aetiology. Besides its role in red blood cells, our findings indicate that PIEZO1 is also involved in the development of lymphatic structures.
Abscisic acid transporters cooperate to control seed germination
Authors: Kang Joohyun , Yim Sojeong , Choi Hyunju , Kim Areum , Lee Keun Pyo , Lopez-Molina Luis , Martinoia Enrico , Lee Youngsook 
Published: September 2015

AbstractSeed germination is a key developmental process that has to be tightly controlled to avoid germination under unfavourable conditions. Abscisic acid (ABA) is an essential repressor of seed germination. In Arabidopsis, it has been shown that the endosperm, a single cell layer surrounding the embryo, synthesizes and continuously releases ABA towards the embryo. The mechanism of ABA transport from the endosperm to the embryo was hitherto unknown. Here we show that four AtABCG transporters act in concert to deliver ABA from the endosperm to the embryo: AtABCG25 and AtABCG31 export ABA from the endosperm, whereas AtABCG30 and AtABCG40 import ABA into the embryo. Thus, this work establishes that radicle extension and subsequent embryonic growth are suppressed by the coordinated activity of multiple ABA transporters expressed in different tissues.
Kinase-independent role for CRAF-driving tumour radioresistance via CHK2
Authors: Advani Sunil J. , Camargo Maria Fernanda , Seguin Laetitia , Mielgo Ainhoa , Anand Sudarshan , Hicks Angel M. , Aguilera Joseph , Franovic Aleksandra , Weis Sara M. , Cheresh David A. 
Published: September 2015

AbstractAlthough oncology therapy regimens commonly include radiation and genotoxic drugs, tumour cells typically develop resistance to these interventions. Here we report that treatment of tumours with ionizing radiation or genotoxic drugs drives p21-activated kinase 1 (PAK1)-mediated phosphorylation of CRAF on Serine 338 (pS338) triggering a kinase-independent mechanism of DNA repair and therapeutic resistance. CRAF pS338 recruits CHK2, a cell cycle checkpoint kinase involved in DNA repair, and promotes CHK2 phosphorylation/activation to enhance the tumour cell DNA damage response. Accordingly, a phospho-mimetic mutant of CRAF (S338D) is sufficient to induce the CRAF/CHK2 association enhancing tumour radioresistance, while an allosteric CRAF inhibitor sensitizes tumour cells to ionizing radiation or genotoxic drugs. Our findings establish a role for CRAF in the DNA damage response that is independent from its canonical function as a kinase.
Activity-regulated trafficking of the palmitoyl-acyl transferase DHHC5
Authors: Brigidi G. Stefano , Santyr Brendan , Shimell Jordan , Jovellar Blair , Bamji Shernaz X. 
Published: September 2015

AbstractSynaptic plasticity is mediated by the dynamic localization of proteins to and from synapses. This is controlled, in part, through activity-induced palmitoylation of synaptic proteins. Here we report that the ability of the palmitoyl-acyl transferase, DHHC5, to palmitoylate substrates in an activity-dependent manner is dependent on changes in its subcellular localization. Under basal conditions, DHHC5 is bound to PSD-95 and Fyn kinase, and is stabilized at the synaptic membrane through Fyn-mediated phosphorylation of a tyrosine residue within the endocytic motif of DHHC5. In contrast, DHHC5’s substrate, δ-catenin, is highly localized to dendritic shafts, resulting in the segregation of the enzyme/substrate pair. Neuronal activity disrupts DHHC5/PSD-95/Fyn kinase complexes, enhancing DHHC5 endocytosis, its translocation to dendritic shafts and its association with δ-catenin. Following DHHC5-mediated palmitoylation of δ-catenin, DHHC5 and δ-catenin are trafficked together back into spines where δ-catenin increases cadherin stabilization and recruitment of AMPA receptors to the synaptic membrane.
Monomeric C-reactive protein-a key molecule driving development of Alzheimer’s disease associated with brain ischaemia?
Authors: Slevin M. , Matou S. , Zeinolabediny Y. , Corpas R. , Weston R. , Liu D. , Boras E. , Di Napoli M. , Petcu E. , Sarroca S. , Popa-Wagner A. , Love S. , Font M. A. , Potempa L. A. , Al-baradie R. , Sanfeliu C. , Revilla S. , Badimon L. , Krupinski J. 
Published: September 2015

AbstractAlzheimer’s disease (AD) increases dramatically in patients with ischaemic stroke. Monomeric C-reactive protein (mCRP) appears in the ECM of ischaemic tissue after stroke, associating with microvasculature, neurons and AD-plaques, Aβ, also, being able to dissociate native-CRP into inflammatory, mCRP in vivo. Here, mCRP injected into the hippocampal region of mice was retained within the retrosplenial tract of the dorsal 3rd ventrical and surrounding major vessels. Mice developed behavioural/cognitive deficits within 1 month, concomitant with mCRP staining within abnormal looking neurons expressing p-tau and in beta-amyloid 1-42-plaque positive regions. mCRP co-localised with CD105 in microvessels suggesting angiogenesis. Phospho-arrays/Western blotting identified signalling activation in endothelial cells and neurons through p-IRS-1, p-Tau and p-ERK1/2-which was blocked following pre-incubation with mCRP-antibody. mCRP increased vascular monolayer permeability and gap junctions, increased NCAM expression and produced haemorrhagic angiogenesis in mouse matrigel implants. mCRP induced tau244–372 aggregation and assembly in vitro. IHC study of human AD/stroke patients revealed co-localization of mCRP with Aβ plaques, tau-like fibrils and IRS-1/P-Tau positive neurons and high mCRP-levels spreading from infarcted core regions matched reduced expression of Aβ/Tau. mCRP may be responsible for promoting dementia after ischaemia and mCRP clearance could inform therapeutic avenues to reduce the risk of future dementia.
Boron-rich benzene and pyrene derivatives for the detection of thermal neutrons
Authors: Yemam Henok A. , Mahl Adam , Koldemir Unsal , Remedes Tyler , Parkin Sean , Greife Uwe , Sellinger Alan 
Published: September 2015

AbstractA synthetic methodology is developed to generate boron rich aromatic small molecules based on benzene and pyrene moieties for the detection of thermal neutrons. The prepared aromatic compounds have a relatively high boron content up to 7.4 wt%, which is important for application in neutron detection as 10B (20% of natural abundance boron) has a large neutron induced reaction cross-section. This is demonstrated by preparing blends of the synthesized molecules with fluorescent dopants in poly(vinyltoluene) matrices resulting in comparable scintillation light output and neutron capture as state-of-the art commercial scintillators, but with the advantage of much lower cost. The boron-rich benzene and pyrene derivatives are prepared by Suzuki conditions using both microwave and traditional heating, affording yields of 40–93%. This new procedure is simple and straightforward and has the potential to be scaled up.
Generalized Kirchhoff-Law-Johnson-Noise (KLJN) secure key exchange system using arbitrary resistors
Authors: Vadai Gergely , Mingesz Robert , Gingl Zoltan 
Published: September 2015

AbstractThe Kirchhoff-Law-Johnson-Noise (KLJN) secure key exchange system has been introduced as a simple, very low cost and efficient classical physical alternative to quantum key distribution systems. The ideal system uses only a few electronic components—identical resistor pairs, switches and interconnecting wires—in order to guarantee perfectly protected data transmission. We show that a generalized KLJN system can provide unconditional security even if it is used with significantly less limitations. The more universal conditions ease practical realizations considerably and support more robust protection against attacks. Our theoretical results are confirmed by numerical simulations.
Comparative Proteomics Analyses of Two Races of Fusarium oxysporum f. sp. conglutinans that Differ in Pathogenicity
Authors: Li Erfeng , Ling Jian , Wang Gang , Xiao Jiling , Yang Yuhong , Mao Zhenchuan , Wang Xuchu , Xie Bingyan 
Published: September 2015

AbstractFusarium oxysporum is a soil-inhabiting fungus that induces vascular wilt and root rot in a variety of plants. F. oxysporum f. sp. conglutinans (Foc), which comprises two races, can cause wilt disease in cabbage. Compared with race 1 (52557−TM, R1), race 2 (58385−TM, R2) exhibits much stronger pathogenicity. Here, we provide the first proteome reference maps for Foc mycelium and conidia and identify 145 proteins with different abundances among the two races. Of these proteins, most of the high-abundance proteins in the R2 mycelium and conidia are involved in carbohydrate, amino acid and ion metabolism, which indicates that these proteins may play important roles in isolate R2’s stronger pathogenicity. The expression levels of 20 typical genes demonstrate similarly altered patterns compared to the proteomic analysis. The protein glucanosyltransferase, which is involved in carbohydrate metabolism, was selected for research. We knocked out the corresponding gene (gas1) and found that Foc-∆gas1 significantly reduced growth rate and virulence compared with wild type isolates. These results deepened our understanding of the proteins related to F. oxysporum pathogenicity in cabbage Fusarium wilt and provided new opportunities to control this disease.
Ice-templated Self-assembly of VOPO4–Graphene Nanocomposites for Vertically Porous 3D Supercapacitor Electrodes
Authors: Lee Kwang Hoon , Lee Young-Woo , Lee Seung Woo , Ha Jeong Sook , Lee Sang-Soo , Son Jeong Gon 
Published: September 2015

AbstractA simple ice-templated self-assembly process is used to prepare a three-dimensional (3D) and vertically porous nanocomposite of layered vanadium phosphates (VOPO4) and graphene nanosheets with high surface area and high electrical conductivity. The resulting 3D VOPO4–graphene nanocomposite has a much higher capacitance of 527.9 F g−1 at a current density of 0.5 A g−1, compared with ~247 F g−1 of simple 3D VOPO4, with solid cycling stability. The enhanced pseudocapacitive behavior mainly originates from vertically porous structures from directionally grown ice crystals and simultaneously inducing radial segregation and forming inter-stacked structures of VOPO4–graphene nanosheets. This VOPO4–graphene nanocomposite electrode exhibits high surface area, vertically porous structure to the separator, structural stability from interstacked structure and high electrical conductivity, which would provide the short diffusion paths of electrolyte ions and fast transportation of charges within the conductive frameworks. In addition, an asymmetric supercapacitor (ASC) is fabricated by using vertically porous VOPO4–graphene as the positive electrode and vertically porous 3D graphene as the negative electrode; it exhibits a wide cell voltage of 1.6 V and a largely enhanced energy density of 108 Wh kg−1.
An information-theoretic model for link prediction in complex networks
Authors: Zhu Boyao , Xia Yongxiang 
Published: September 2015

AbstractVarious structural features of networks have been applied to develop link prediction methods. However, because different features highlight different aspects of network structural properties, it is very difficult to benefit from all of the features that might be available. In this paper, we investigate the role of network topology in predicting missing links from the perspective of information theory. In this way, the contributions of different structural features to link prediction are measured in terms of their values of information. Then, an information-theoretic model is proposed that is applicable to multiple structural features. Furthermore, we design a novel link prediction index, called Neighbor Set Information (NSI), based on the information-theoretic model. According to our experimental results, the NSI index performs well in real-world networks, compared with other typical proximity indices.