bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantum‐mechanical condensed matter simulations with CRYSTAL
Authors: Dovesi Roberto , Erba Alessandro , Orlando Roberto , Zicovich‐Wilson Claudio M. , Civalleri Bartolomeo , Maschio Lorenzo , Rérat Michel , Casassa Silvia , Baima Jacopo , Salustro Simone , Kirtman Bernard 
Published: March 2018

The latest release of theCrystalprogram for solid‐state quantum‐mechanical ab initio simulations is presented. The program adopts atom‐centered Gaussian‐type functions as a basis set, which makes it possible to perform all‐electron as well as pseudopotential calculations. Systems of any periodicity can be treated at the same level of accuracy (from 0D molecules, clusters and nanocrystals, to 1D polymers, helices, nanorods, and nanotubes, to 2D monolayers and slab models for surfaces, to actual 3D bulk crystals), without any artificial repetition along nonperiodic directions for 0–2D systems. Density functional theory calculations can be performed with a variety of functionals belonging to several classes: local‐density (LDA), generalized‐gradient (GGA), meta‐GGA, global hybrid, range‐separated hybrid, and self‐consistent system‐specific hybrid. In particular, hybrid functionals can be used at a modest computational cost, comparable to that of pure LDA and GGA formulations, because of the efficient implementation of exact nonlocal Fock exchange. Both translational and point‐symmetry features are fully exploited at all steps of the calculation, thus drastically reducing the corresponding computational cost. The various properties computed encompass electronic structure (including magnetic spin‐polarized open‐shell systems, electron density analysis), geometry (including full or constrained optimization, transition‐state search), vibrational properties (frequencies, infrared and Raman intensities, phonon density of states), thermal properties (quasi‐harmonic approximation), linear and nonlinear optical properties (static and dynamic [hyper]polarizabilities), strain properties (elasticity, piezoelectricity, photoelasticity), electron transport properties (Boltzmann, transport across nanojunctions), as well as X‐ray and inelastic neutron spectra. The program is distributed in serial, parallel, and massively parallel versions. In this paper, the original developments that have been devised and implemented in the last 4 years (since the distribution of the previous public version,Crystal14, occurred in December 2013) are described.This article is categorized under:Software > Quantum ChemistryStructure and Mechanism > Computational Materials ScienceElectronic Structure Theory > Density Functional Theory
Automatic synthesis of fuzzy systems: An evolutionary overview with a genetic programming perspective
Authors: Koshiyama Adriano S. , Tanscheit Ricardo , Vellasco Marley M. B. R. 
Published: March 2018

Studies in Evolutionary Fuzzy Systems (EFSs) began in the 90s and have experienced a fast development since then, with applications to areas such as pattern recognition, curve‐fitting and regression, forecasting and control. An EFS results from the combination of a Fuzzy Inference System (FIS) with an Evolutionary Algorithm (EA). This relationship can be established for multiple purposes: fine‐tuning of FIS's parameters, selection of fuzzy rules, learning a rule base or membership functions from scratch, and so forth. Each facet of this relationship creates a strand in the literature, as membership function fine‐tuning, fuzzy rule‐based learning, and so forth and the purpose here is to outline some of what has been done in each aspect. Special focus is given to Genetic Programming‐based EFSs by providing a taxonomy of the main architectures available, as well as by pointing out the gaps that still prevail in the literature. The concluding remarks address some further topics of current research and trends, such as interpretability analysis, multiobjective optimization, and synthesis of a FIS through Evolving methods.This article is categorized under:Technologies > Computational IntelligenceTechnologies > Machine Learning
The Immunome of Colon Cancer: Functional in Silico Analysis of Antigenic Proteins Deduced from IgG Microarray Profiling
Authors: Luna Coronell Johana A. , Sergelen Khulan , Hofer Philipp , Gyurján István , Brezina Stefanie , Hettegger Peter , Leeb Gernot , Mach Karl , Gsur Andrea , Weinhäusel Andreas 
Published: March 2018

Abstract
Characterization of the colon cancer immunome and its autoantibody signature from differentially-reactive antigens (DIRAGs) could provide insights into aberrant cellular mechanisms or enriched networks associated with diseases. The purpose of this study was to characterize the antibody profile of plasma samples from 32 colorectal cancer (CRC) patients and 32 controls using proteins isolated from 15,417 human cDNA expression clones on microarrays. 671 unique DIRAGs were identified and 632 were more highly reactive in CRC samples. Bioinformatics analyses reveal that compared to control samples, the immunoproteomic IgG profiling of CRC samples is mainly associated with cell death, survival, and proliferation pathways, especially proteins involved in EIF2 and mTOR signaling. Ribosomal proteins (e.g., RPL7, RPL22, and RPL27A) and CRC-related genes such as APC, AXIN1, E2F4, MSH2, PMS2, and TP53 were highly enriched. In addition, differential pathways were observed between the CRC and control samples. Furthermore, 103 DIRAGs were reported in the SEREX antigen database, demonstrating our ability to identify known and new reactive antigens. We also found an overlap of 7 antigens with 48 “CRC genes.” These data indicate that immunomics profiling on protein microarrays is able to reveal the complexity of immune responses in cancerous diseases and faithfully reflects the underlying pathology.
Coronary heart disease, heart failure, and the risk of dementia: A systematic review and meta‐analysis
Authors: Wolters Frank J. , Segufa Reffat A. , Darweesh Sirwan K.L. , Bos Daniel , Ikram Mohammad Arfan , Sabayan Behnam , Hofman Albert , Sedaghat Sanaz 
Published: March 2018

AbstractIntroductionCardiovascular risk factors are closely linked with dementia risk, but whether heart disease predisposes to dementia is uncertain.MethodsWe systematically reviewed the literature and meta‐analyzed risk estimates from longitudinal studies reporting the association of coronary heart disease (CHD) or heart failure (HF) with risk of dementia.ResultsWe identified 16 studies (1,309,483 individuals) regarding CHD, and seven studies (1,958,702 individuals) about HF. A history of CHD was associated with a 27% increased risk of dementia (pooled relative risk [RR] [95% confidence interval, CI]: 1.27 [1.07–1.50]), albeit with considerable heterogeneity across studies (I2 = 80%). HF was associated with 60% increased dementia risk (pooled RR 1.60 [1.19–2.13]) with moderate heterogeneity (I2 = 59%). Among prospective population‐based cohorts, pooled estimates were similar (for CHD, RR 1.26 [1.06–1.49], nine studies; and HF, RR 1.80 [1.41–2.31], four studies) and highly consistent (I2 = 0%).ConclusionCHD and HF are associated with an increased risk of dementia.
Bărbulescu v. Romania (Eur. Ct. H.R.)
Authors: Sterling Nichole L. , Fedeles Emily R. 
Published: March 2018

On September 5, 2017, a decision of the Grand Chamber of the European Court of Human Rights (ECHR) in Bărbulescu v. Romania (Bărbulescu) helped define the boundaries regarding employee privacy in the European workplace. The Bărbulescu decision held that a Romanian employee's legally protected right to privacy was violated when his employer monitored personal messages he sent from a company account, reversing a previous decision by the ECHR in this case that had expanded employers' rights to monitor employees.
IS FERTILITY AFTER THE DEMOGRAPHIC TRANSITION MALADAPTIVE?
Authors: Hopcroft Rosemary L. 
Published: March 2018

SummaryFitness is always relative to the fitness of others in the group or breeding population. Even in very low-fertility societies, individual fitness as measured by the share of genes in subsequent generations may still be maximized. Further, sexual selection theory from evolutionary biology suggests that the relationship between status and fertility will differ for males and females. For this reason it is important to examine the relationship between status and fertility separately for males and females–something few demographic studies of fertility do. When male fertility is measured separately, high-status men (as measured by their wealth and personal income) have higher fertility than low-status men, even in very low-fertility societies, so individual males appear to be maximizing their fitness within the constraints posed by a modern society. Thus male fertility cannot be considered maladaptive. When female fertility is measured separately, in both very high- and very low-fertility societies, there is not much variance across women of different statuses in completed fertility. Only in societies currently changing rapidly (with falling fertility rates) is somewhat high variance across women of different statuses in completed fertility found. What is seen across all phases of the demographic transition appears to be a continuation of two somewhat different evolved human reproductive strategies–one male, one female–in changing social and material contexts. Whether contemporary female fertility is maladaptive remains an open question.
Locals don't have accents: children weigh phonological proficiency over syntactic or semantic proficiency when categorizing individuals
Authors: HWANG Hyesung G. , MARKSON Lori 
Published: March 2018

AbstractChildren categorize native-accented speakers as local and non-native-accented speakers as foreign, suggesting they use accent (i.e., phonological proficiency) to determine social group membership. However, it is unclear if accent is the strongest – and only – group marker children use to determine social group membership, or whether other aspects of language, such as syntax and semantics, are also important markers. To test this, five- to eight-year-old monolingual English-speaking children were asked to judge whether individuals who varied in phonological, syntactic, and semantic proficiency were local or foreign. Children were also asked which individual they wanted as a friend. Children prioritized phonological proficiency over syntactic and semantic proficiency to determine social group membership. However, with age, children begin to shift toward prioritizing syntactic and semantic proficiency over phonological proficiency in their friendship decisions, suggesting that the capacity to integrate different aspects of a speaker's linguistic proficiency changes with development.
Genetic diversity ofJatropha curcascollections from different islands in Indonesia
Authors: Anggraeni Tantri Dyah Ayu , Satyawan Dani , Kang Yang Jae , Ha Jungmin , Kim Moon Young , Chitikineni Annapurna , Varshney Rajeev K. , Lee Suk-Ha 
Published: March 2018

AbstractJatropha curcasL. is a potential bioenergy crop but has a lack of improved cultivars with high yields and oil content. Therefore, increasing our understanding ofJ. curcasgermplasm is important for designing breeding strategies. This study was performed to investigate the genetic diversity and population structure of IndonesianJ. curcaspopulations from six different islands. To construct a reference, wede novoassembled the scaffolds (N50 = 355.5 kb) using 182 Gb Illumina HiSeq sequencing data from ThaiJ. curcasvariety Chai Nat. Genetic diversity analysis among 52 IndonesianJ. curcasaccessions was conducted based on yield traits and single nucleotide polymorphism (SNP) markers detected by mapping genotyping-by-sequencing reads from Indonesian population to Chai Nat scaffolds. Strong variation in yield traits was detected among accessions. UsingJ. integerrimaas an outgroup, 13,916 SNPs were detected. AmongJ. curcasaccessions, including accessions from other countries (Thailand, the Philippines and China), 856 SNPs were detected, but only 297 SNPs were detected among IndonesianJ. curcaspopulations, representing low genetic diversity. Through phylogenetic and structural analysis, the populations were clustered into two major groups. Group one consists of populations from Bangka and Sulawesi in the northern part of Indonesia, which are located at a distance of 1572.59 km. Group two contains populations from islands in the southern part: Java, Lombok-Sumbawa, Flores and Timor. These results indicate that introduction of diverseJ. curcasgermplasms is necessary for the improvement of the genetic variation in the Indonesian collections.
Longitudinal slotted waveguide array feed networks
Authors: Soleiman Meiguni J. , Keshavarz Haddad S. , Hosseinbeig A. 
Published: March 2018

AbstractIn this paper, two new feed network designs for single layer and double layer slotted waveguide array antennas are presented. A microstrip to substrate integrated waveguide transition is applied to the single layer antenna. The aperture coupling mechanism is used in order to find the optimum feed network for double-layer structure and to obtain stable radiation characteristics over the frequency band. The prototypes of the proposed antennas have been fabricated and tested. The measured results were compared very well with the simulation results obtained from CST microwave studio and showed low side lobe level at the center frequency of 11.5 GHz for the low-profile 4-channel slotted waveguide arrays.
Die NEP-Skala – hinter den (deutschen) Kulissen des Umweltbewusstseins
Authors: Schleyer-Lindenmann Alexandra , Ittner Heidi , Dauvier Bruno , Piolat Michel 
Published: March 2018

Zusammenfassung. Angesichts existentieller Umweltprobleme ist eine valide Messung von Umweltbewusstsein und -einstellungen nach wie vor ein zentrales Anliegen umwelt- und sozialpsychologischer Forschung. Es überrascht daher, dass für das seit Jahrzehnten international und disziplinübergreifend meistgenutzte Instrument, die New Ecological Paradigm Scale (NEP-Skala) von Dunlap, Van Liere, Mertig & Jones (2000) , bislang keine psychometrisch differenziert betrachtete deutsche Fassung vorliegt. Dabei wird die theoretische und empirische Verwendung der Originalskala durchaus kritisch diskutiert. Diese Lücke will der vorliegende Beitrag schließen: Es wird eine deutschsprachige Übersetzung der NEP-Skala vorgestellt, für die anhand einer universitären Stichprobe (N = 573) erste empirische Validitätshinweise vorgelegt werden. Dabei ergibt sich ein Faktormodell zweiter Ordnung mit 4 korrelierten Faktoren erster Ordnung, das theoretisch differenziert betrachtet wird. Eine Schmid-Leiman-Lösung weist auf die Möglichkeit einer verkürzten Skala hin, die direkt das höher angesiedelte Konstrukt „Umweltbewusstsein“ messen könnte. Die Ergebnisse unterstreichen die Notwendigkeit, stets die Dimensionalität der Skala methodisch angemessen zu überprüfen als auch, 20 Jahre nach der letzten Überarbeitung, inhaltliche Erweiterungen anzustoßen.
Brain-specific functional relationship networks inform autism spectrum disorder gene prediction
Authors: Duda Marlena , Zhang Hongjiu , Li Hong-Dong , Wall Dennis P. , Burmeister Margit , Guan Yuanfang 
Published: March 2018

AbstractAutism spectrum disorder (ASD) is a neuropsychiatric disorder with strong evidence of genetic contribution, and increased research efforts have resulted in an ever-growing list of ASD candidate genes. However, only a fraction of the hundreds of nominated ASD-related genes have identified de novo or transmitted loss of function (LOF) mutations that can be directly attributed to the disorder. For this reason, a means of prioritizing candidate genes for ASD would help filter out false-positive results and allow researchers to focus on genes that are more likely to be causative. Here we constructed a machine learning model by leveraging a brain-specific functional relationship network (FRN) of genes to produce a genome-wide ranking of ASD risk genes. We rigorously validated our gene ranking using results from two independent sequencing experiments, together representing over 5000 simplex and multiplex ASD families. Finally, through functional enrichment analysis on our highly prioritized candidate gene network, we identified a small number of pathways that are key in early neural development, providing further support for their potential role in ASD.
Intrinsic functional connectivity predicts remission on antidepressants: a randomized controlled trial to identify clinically applicable imaging biomarkers
Authors: Goldstein-Piekarski Andrea N. , Staveland Brooke R. , Ball Tali M. , Yesavage Jerome , Korgaonkar Mayuresh S. , Williams Leanne M. 
Published: March 2018

AbstractDefault mode network (DMN) dysfunction (particularly within the anterior cingulate cortex (ACC) and medial prefrontal cortex (mPFC)) has been implicated in major depressive disorder (MDD); however, its contribution to treatment outcome has not been clearly established. Here we tested the role of DMN functional connectivity as a general and differential biomarker for predicting treatment outcomes in a large, unmedicated adult sample with MDD. Seventy-five MDD outpatients completed fMRI scans before and 8 weeks after randomization to escitalopram, sertraline, or venlafaxine-XR. A whole-brain voxel-wise t-test identified profiles of pretreatment intrinsic functional connectivity that distinguished patients who were subsequently classified as remitters or non-remitters at follow-up. Connectivity was seeded in the PCC, an important node of the DMN. We further characterized differences between remitters, non-remitters, and 31 healthy controls and characterized changes pretreatment to posttreatment. Remitters were distinguished from non-remitters by relatively intact connectivity between the PCC and ACC/mPFC, not distinguishable from healthy controls, while non-remitters showed relative hypo-connectivity. In validation analyses, we demonstrate that PCC–ACC/mPFC connectivity predicts remission status with >80% cross-validated accuracy. In analyses testing whether intrinsic connectivity differentially relates to outcomes for a specific type of antidepressant, interaction models did not survive the corrected threshold. Our findings demonstrate that the overall capacity to remit on commonly used antidepressants may depend on intact organization of intrinsic functional connectivity between PCC and ACC/mPFC prior to treatment. The findings highlight the potential utility of functional scans for advancing a more precise approach to tailoring antidepressant treatment choices.
Astrocytic JWA deletion exacerbates dopaminergic neurodegeneration by decreasing glutamate transporters in mice
Authors: Wang Rihua , Zhao Xue , Xu Jin , Wen Yifan , Li Aiping , Lu Ming , Zhou Jianwei 
Published: March 2018

Abstract
Astrocytic JWA exerts neuroprotective roles by alleviating oxidative stress and inhibiting inflammation. However, the molecular mechanisms of how astrocytic JWA is involved in dopaminergic neurodegeneration in Parkinson’s disease (PD) remain largely unknown. In this study, we found that astrocyte-specific JWA knockout mice (JWA CKO) exacerbated dopamine (DA) neuronal loss and motor dysfunction, and reduced the levels of DA and its metabolites in a 1-methyl-4-phenyl-1, 2, 3, 6-tetrahydropyridine/probenecid (MPTP/p)-induced PD model. Astrocytic JWA deficiency repressed expression of excitatory amino-acid transporter 2 (GLT-1) and glutamate uptake both in vivo and in vitro. Further, the regulation of GLT-1 expression was involved in JWA-triggered activation of the MAPK and PI3K signaling pathways. JWA-increased GLT-1 expression was abolished by inhibitors of MEK and PI3K. Silencing CREB also abrogated JWA-increased GLT-1 expression and glutamate uptake. Additionally, JWA deficiency activated glial fibrillary acidic protein (GFAP), and increased the expression of STAT3. Similarly to the MPTP model, paraquat (PQ) exposure produced PD-like phenotypes in JWA CKO mice. Taken together, our findings provide novel insights into astrocytic JWA function in the pathogenesis of neurotoxin mouse models of PD.
Statistical ensembles without typicality
Authors: Boes Paul , Wilming Henrik , Eisert Jens , Gallego Rodrigo 
Published: March 2018

AbstractMaximum-entropy ensembles are key primitives in statistical mechanics. Several approaches have been developed in order to justify the use of these ensembles in statistical descriptions. However, there is still no full consensus on the precise reasoning justifying the use of such ensembles. In this work, we provide an approach to derive maximum-entropy ensembles, taking a strictly operational perspective. We investigate the set of possible transitions that a system can undergo together with an environment, when one only has partial information about the system and its environment. The set of these transitions encodes thermodynamic laws and limitations on thermodynamic tasks as particular cases. Our main result is that the possible transitions are exactly those that are possible if both system and environment are assigned the maximum-entropy state compatible with the partial information. This justifies the overwhelming success of such ensembles and provides a derivation independent of typicality or information-theoretic measures.
Insc:LGN tetramers promote asymmetric divisions of mammary stem cells
Authors: Culurgioni Simone , Mari Sara , Bonetti Paola , Gallini Sara , Bonetto Greta , Brennich Martha , Round Adam , Nicassio Francesco , Mapelli Marina 
Published: March 2018

AbstractAsymmetric cell divisions balance stem cell proliferation and differentiation to sustain tissue morphogenesis and homeostasis. During asymmetric divisions, fate determinants and niche contacts segregate unequally between daughters, but little is known on how this is achieved mechanistically. In Drosophila neuroblasts and murine mammary stem cells, the association of the spindle orientation protein LGN with the stem cell adaptor Inscuteable has been connected to asymmetry. Here we report the crystal structure of Drosophila LGN in complex with the asymmetric domain of Inscuteable, which reveals a tetrameric arrangement of intertwined molecules. We show that Insc:LGN tetramers constitute stable cores of Par3–Insc-LGN-GαiGDP complexes, which cannot be dissociated by NuMA. In mammary stem cells, the asymmetric domain of Insc bound to LGN:GαiGDP suffices to drive asymmetric fate, and reverts aberrant symmetric divisions induced by p53 loss. We suggest a novel role for the Insc-bound pool of LGN acting independently of microtubule motors to promote asymmetric fate specification.
MRN complex-dependent recruitment of ubiquitylated BLM helicase to DSBs negatively regulates DNA repair pathways
Authors: Tripathi Vivek , Agarwal Himanshi , Priya Swati , Batra Harish , Modi Priyanka , Pandey Monica , Saha Dhurjhoti , Raghavan Sathees C. , Sengupta Sagar 
Published: March 2018

AbstractMutations in BLM in Bloom Syndrome patients predispose them to multiple types of cancers. Here we report that BLM is recruited in a biphasic manner to annotated DSBs. BLM recruitment is dependent on the presence of NBS1, MRE11 and ATM. While ATM activity is essential for BLM recruitment in early phase, it is dispensable in late phase when MRE11 exonuclease activity and RNF8-mediated ubiquitylation of BLM are the key determinants. Interaction between polyubiquitylated BLM and NBS1 is essential for the helicase to be retained at the DSBs. The helicase activity of BLM is required for the recruitment of HR and c-NHEJ factors onto the chromatin in S- and G1-phase, respectively. During the repair phase, BLM inhibits HR in S-phase and c-NHEJ in G1-phase. Consequently, inhibition of helicase activity of BLM enhances the rate of DNA alterations. Thus BLM utilizes its pro- and anti-repair functions to maintain genome stability.