bluuebunny/crossref_metadata_2025 huggingface dataset:
Computational Models in Developmental Psychology
Authors: Shultz Thomas R.
Published: February 2014

Computational modeling implements developmental theory in a precise manner, allowing generation, explanation, integration, and prediction. Several modeling techniques are applied to development: symbolic rules, neural networks, dynamic systems, Bayesian processing of probability distributions, developmental robotics, and mathematical analysis. The relative strengths and weaknesses of each approach are identified and examples of each technique are described. Ways in which computational modeling contributes to developmental issues are documented. A probabilistic model of the vocabulary spurt shows that various psychological explanations for it are unnecessary. Constructive neural networks clarify the distinction between learning and development and show how it is possible to escape Fodor’s paradox. Connectionist modeling reveals different versions of innateness and how learning and evolution might interact. Agent-based models analyze the basic principles of evolution in a testable, experimental fashion that generates complete evolutionary records. Challenges posed by stimulus poverty and lack of negative examples are explored in neural-network models that learn morphology or syntax probabilistically from indirect negative evidence.
Spatial Development
Authors: Newcombe Nora S. , Uttal David H. , Sauter Megan
Published: February 2014

This chapter is a selective review of spatial development, stressing several points. First, we suggest that spatial development can be usefully considered to have two strands: (a) the development of intraobject (or intrinsic) representations along with the ability to transform them (e.g., in mental rotation) and (b) the development of interobject (or extrinsic) representations and the ability to use them to navigate. Second, we argue that both lines of development begin from strong starting points, but also undergo considerable development. They are far from innately specified, nor do they have a modular architecture. Third, we discuss the amplification of spatial skills by human symbolic capabilities, including language, use of maps and models, and gesture. Fourth, we identify areas where research is lacking, most notably the formal description of intraobject skills and the charting of their normative development, the exploration of the sources of individual differences in navigation-relevant skills, and the applications of research to education.
Imitation
Authors: Meltzoff Andrew N. , Williamson Rebecca A.
Published: February 2014

Human beings are the most imitative creatures in the animal kingdom. Imitation has both cognitive and social aspects and is a powerful mechanism for learning about and from people. Imitation raises theoretical questions about perception–action coupling, memory, representation, social cognition, and social affinities toward others “like me.” Childhood imitation is attracting attention both within and outside of developmental psychology. Modern studies of imitative development are bringing to bear the techniques of cognitive neuroscience, machine learning, education, and cognitive-developmental science. By using neuroscience tools and cognitive modeling, scientists are uncovering the mechanisms that underlie imitation. Evolutionary biologists are using imitation to investigate social learning in other species and to compare this to the abilities of human infants. Engineers are designing robots that can learn like babies—imitating the skilled actions of experts in an unsupervised manner. Educational psychologists are increasingly attending to how children learn through observation, role-modeling, and apprenticeship in informal settings and using this to revise pedagogical practices in formal educational settings. This chapter provides an analysis of the development of children’s imitative ability, the mechanisms that underlie it, and the functions it serves in social, cognitive, and cultural learning from infancy to early childhood.
Executive Function
Authors: Carlson Stephanie M. , Zelazo Philip David , Faja Susan
Published: February 2014

Executive function (EF) refers to the set of neurocognitive skills involved in goal-directed problem solving, including working memory, inhibitory control, and set shifting/flexibility. EF depends importantly upon neural networks involving prefrontal cortex, and continues to improve into early adulthood, although major advances in EF occur during the preschool period. Individual differences in EF are increasingly recognized as a key predictor of long-term cognitive and social developmental outcomes. Research suggests that EF is influenced by both distal and proximal factors in development (e.g., socioeconomic status, culture, language, caregiving, gene–environment interactions, and sleep). Importantly, EF can be trained, with corresponding changes to brain structure and function. In this chapter, we review the structure of EF, including “hot EF” (EF in motivationally significant contexts), age-related changes, atypical development, measurement issues, theories of underlying mechanisms, outcomes associated with EF, influences on EF development, and the recent emergence of training studies.
Reasoning
Authors: Kuhn Deanna
Published: February 2014

Reasoning is defined here as purposeful thinking consciously executed in the service of enhancing understanding, in contrast to inference, which may be implicit and automatic. As such, reasoning is implicated in much of human mental activity. A set of general questions about the nature of reasoning and its development are addressed: When does reasoning begin? To what extent can it be reduced to its components or processing demands? To what extent are dual processes and executive functions involved? How does reasoning in one context influence how a related context will be approached? Does reasoning skill develop, and to what extent does this development depend on specific kinds of experience? How are both the competence and the disposition to reason well best fostered?
Imagination
Authors: Taylor Marjorie
Published: February 2014

Imagination refers to the capacity to mentally transcend time, place, and/or circumstance to think about what might have been, plan and anticipate the future, create fictional worlds, and consider remote and close alternatives to actual experiences. This multifaceted capacity emerges early in life and develops substantially during the preschool years. The first section of this chapter reviews the development of social imagination in pretend play, narrative, and mental time travel, suggesting that the simulation of imagined social scenarios involving self and/or others in all three domains contributes to the development of real-world social understanding. The final sections of the chapter discuss the relation between imagination and creativity, compare imagination in typically developing children and children on the autism spectrum, and suggest directions for future research.
Moral Development
Authors: Smetana Judith
Published: February 2014

This chapter describes moral judgment development through the lens of social domain theory. Morality, or individuals’ concepts of justice, welfare, and rights, is seen as a distinct system or organized domain of social knowledge that develops separately from concepts of social conventions and personal issues; these concepts are constructed from children’s differentiated social interactions and social experiences. In this chapter, basic theoretical propositions of social domain theory and methods used to test those propositions are described, and then relevant empirical research is reviewed. The chapter highlights how children’s understanding and interpretation of their social worlds are elaborated and change from infancy through adolescence. The complexity and diversity of social life is described as entailing a consideration of moral concepts as informed by informational assumptions and knowledge of regularities in the affective consequences of different events. It is also considered in terms of the coexistence of and coordination with other social knowledge domains.
Speech Perception in Infancy
Authors: Werker Janet F. , Gervain Judit
Published: February 2014

We discuss the development of speech perception and its contribution to the acquisition of the native language(s) during the first year of life, reviewing recent empirical evidence as well as current theoretical debates. We situate the discussion in an epigenetic framework in an attempt to transcend the traditional nature/nurture controversy. As we illustrate, some perceptual and learning mechanisms are best described as experience-expectant processes, embedded in our biology and awaiting minimal environmental input, while others are experience-dependent, emerging as a function of sufficient exposure and learning. We argue for a cascading model of development, whereby the initial biases guide learning and constrain the influence of the environmental input. To illustrate this, we first review the perceptual abilities of newborn infants, then discuss how these broad-based abilities are attuned to the native language at different levels (phonology, syntax, lexicon etc.).
Developmental Psychology
Authors: Zelazo Philip David
Published: February 2014

ThisHandbooksurveys what is now known about psychological development from birth to biological maturity, and it reflects the emergence of a new synthetic approach to developmental science that is based on several theoretical and methodological commitments. According to this new view: (1) psychological phenomena are usefully studied at multiple levels of analysis; (2) psychological development depends on neural plasticity, which extends across the lifespan; (3) the effect of any particular influence on psychological development will depend on the context in which it occurs; (4) psychological phenomena, and developmental changes in psychological phenomena, typically reflect multiple, simultaneous causal influences; and (5) these causal influences are often reciprocal. Research based on this synthetic approach provides new insights into the way in which processes operating at many levels of analysis (cultural, social, cognitive, neural, and molecular) work together to yield human behavior and changes in human behavior.
The Development of Stress Reactivity
Authors: Gunnar Megan R. , Herrera Adriana M.
Published: February 2014

Stress is a normal component of life, yet individuals differ markedly in the frequency with which they experience stressful life events and their vulnerability or resilience in the face of these challenges. We approach the study of stress and development from a psychobiological perspective, emphasizing the role of the hypothalamic-pituitary-adrenocortical (HPA) system. We describe the anatomy and physiology of the HPA system and its relations with other neurobiological systems that process information about stressors and regulate behavioral and physiological responses. This review also covers psychological and evolutionary perspectives on stress, as well as the human literature on stress reactivity and regulation in typically developing children, children with behavioral and emotional problems, and children exposed to significant adversity early in life.
The Structure of Temperament and Personality Traits
Authors: Shiner Rebecca L. , DeYoung Colin G.
Published: February 2014

In this chapter, we offer a developmental perspective on temperament and personality traits from early childhood through adulthood. First, we address the relationship between temperament and personality and the methods used to ascertain the structure of traits in these two research traditions. We argue that the temperament and personality traditions provide different ways of describing the same basic traits. Second, we describe the current status of the most prominent temperament models and the Big Five personality trait model. Third, we articulate a structural model that integrates contemporary findings on temperament and personality traits from early childhood through adulthood. Fourth, we discuss current research on the psychological and biological processes that underlie individual differences in the Big Five traits in childhood and adulthood. This is an exciting time in the study of personality development, in part because of the marked progress in uncovering the basic structure of traits across the lifespan.
Temperamental Contributions to Inhibited and Uninhibited Profiles
Authors: Kagan Jerome
Published: February 2014

A temperamental bias is currently defined as a behavioral profile with a partial origin in the child’s biology that varies among individuals. These biases, which appear early in development, are sculpted by experience into a variety of personality profiles. This chapter first describes possible genetic and nongenetic bases for temperamental categories, followed by a detailed presentation of the research on high- and low-reactive infants who are biased to become inhibited or uninhibited children. The chapter concludes with a discussion of the implications of these two temperaments to psychopathology and speculations on the temperamental variation among reproductively isolated human groups. A large number of questions remain unanswered. Perhaps the most critical is discovering the genes and resulting neurochemical or neuroanatomical features that contribute to the high- and low-reactive profiles.
Attachment Theory and Research
Authors: Thompson Ross A.
Published: February 2014

Attachment theory has long been at the forefront of research efforts to understand the origins and enduring impact of early parent–child relationships. It has also expanded into a theory of lifespan implications with relevance to problems in developmental psychopathology, early intervention, and mental representation. This review of the expanding research literature on attachment is organized around eight questions: (a) To whom do attachments develop? (b) What are the biological foundations of attachment? (c) How does culture influence attachment and its consequences? (d) What contributes to attachments becoming secure or insecure? (e) How does attachment security change over time? (f) What are the later outcomes of secure or insecure attachments? (g) How does attachment influence thinking and social representations? (h) What are the clinical implications of attachment research? The answers to these questions summarize what has been learned about the importance of early parent–child relationships and identify future research priorities.
Prosocial Development
Authors: Eisenberg Nancy , Spinrad Tracy L. , Morris Amanda S.
Published: February 2014

In this chapter, we distinguish between different forms of empathy-related responding (i.e., empathy, sympathy, personal distress) and prosocial behavior. The capacity for empathy and sympathy emerges in the early years of life and generally increases with age across childhood. Individual differences in sympathy and prosocial behavior covary, and both tend to be fairly stable across time. Prosocial tendencies are related to prosocial moral reasoning, social competence, self-regulation, and low aggression/externalizing problems. Although individual differences in prosocial and empathic/sympathetic responding are partly due to heredity, environmental factors are also associated with such differences. Authoritative, supportive parenting involving modeling, reasoning, and practices that help children to understand others’ internal states has been associated with higher levels of prosocial behavior. Moreover, securely attached children tend to be prosocial. In addition, peers and siblings can encourage, reinforce, and model prosocial behavior. School interventions, as well as experience with volunteering, appear to affect the degree to which children are sympathetic and engage in prosocial behavior.
An Overview of Developmental Psychopathology
Authors: Cicchetti Dante
Published: February 2014

Historical origins of the field are reviewed and the meaning of a developmental psychopathology perspective is described. Definitional principles and conceptual issues of the field are discussed, and these parameters include (1) the mutual interplay between normality and psychopathology; (2) a multiple-levels-of-analysis and multidisciplinary approach; (3) developmental pathways to psychopathology and resilient functioning; (4) translational research; and (5) prevention and intervention. Examples are derived from research conducted with individuals at high risk for developing psychopathology and those suffering from mental disorders. Future directions and challenges for translating research into practice and policy are proffered. Advances in the knowledge base in developmental psychopathology not only have benefitted the scientific understanding of the relation between normal and abnormal development, but also have contributed to reducing the individual and societal burden of mental illness.
Risk and Resilience in Development
Authors: Masten Ann S.
Published: February 2014

Findings from five decades of research on risk and resilience in children and youth are highlighted in this chapter, with a focus on positive adaptation in the context of conditions that could pose a significant threat to function or development. The origins of developmental research on risk and resilience are briefly reviewed, followed by definitions of core concepts, and an overview with illustrations of central models that have guided this body of work. Findings on promotive and protective factors for resilience across diverse studies of children and youth show striking consistency, suggesting that fundamental adaptive systems support and protect human adaptation and development in the context of adversity. Exciting new technologies and scientific advances in molecular genetics, neuroscience, and the methods for studying dynamic, interdependent systems have opened new horizons for research on risk and resilience. The rising wave of future resilience science is focused on multiple levels of analysis and their integration, ranging from neurobiological processes of resilience to preparations for surviving large-scale disasters.
Chemical variation in molecular cloud cores in the Orion A cloud. II.
Authors: Tatematsu Ken'ichi , Ohashi Satoshi , Umemoto Tomofumi , Lee Jeong-Eun , Hirota Tomoya , Yamamoto Satoshi , Choi Minho , Kandori Ryo , Mizuno Norikazu
Published: February 2014

We have mapped six molecular cloud cores in the Orion A giant molecular cloud (GMC), whose kinetic temperatures range from 10 to 30 K, in CCS and N2H+ with the Nobeyama 45 m radio telescope to study their chemical characteristics. We identified 31 intensity peaks in the CCS and N2H+ emission in these molecular cloud cores. We found, for cores with temperatures lower than ∼ 25 K, that the column density ratio of N(N2H+)/N(CCS) is low toward starless core regions while it is high toward star-forming core regions, in cases where we detected both the CCS and N2H+ emission. This is very similar to the tendency found in dark clouds (kinetic temperature ∼ 10 K). The criterion found in the Orion A GMC is N(N2H+)/N(CCS) ∼ 2–3. In some cases, both CCS and N2H+ emission is detected toward protostars. A secondary late-stage CCS peak in the chemical evolution caused by CO depletion may be a possible explanation for this. We found that the chemical variation of CCS and N2H+ can also be used as a tracer of evolution in warm (10–25 K) GMC cores. On the other hand, some protostars do not accompany N2H+ intensity peaks but are associated with dust continuum emitting regions, suggesting that the N2H+ abundance might be decreased due to CO evaporation in warmer star-forming sites.
Adjuvant Radiotherapy for Stages II and III Resected Thymoma
Authors: Yan Jinchun , Liu Qin , Moseley Jessica N. , Baik Christina S. , Chow Laura Q. M. , Goulart Bernardo H. M. , Zlotnick David , Papanicolau-Sengos Antoni , Gallaher Ian , Knopp Joy M. , Zeng Jing , Patel Shilpen
Published: February 2014

Introduction:

The role of adjuvant radiation for Masaoka stages II and III thymoma remains controversial. The aim of this study was to evaluate the clinical benefit of radiation therapy for resected stages II and III thymoma patients.

Methods:

We retrospectively reviewed the medical records of 175 thymoma patients treated from July 1996 to January 2013 at University of Washington Medical Center; 88 patients with adequate follow-up and who met histologic criteria were included. We evaluated progression-free survival (PFS) and overall survival (OS), and compared these outcomes in patients treated by surgery (S) alone versus surgery plus radiotherapy (S+RT). Cox regression models and log-rank tests were used to compare PFS and OS for S versus S+RT, and they were further assessed by margin-positive versus margin-negative subgroups using Kaplan-Meier curves.

Results:

Among the 88 thymoma patients, 22 were stage II and 18 were stage III. For all stages II and III patients, adjuvant radiation was not identified as a significant predictor for PFS (P=0.95) or OS (P=0.63). A positive surgical margin predicted for a worse OS (hazard ratio=7.1; P=0.004). Further investigation revealed for resection margin-positive patients; S+RT had higher OS than S alone (P=0.006).

Conclusions:

For stages II and III thymoma, postoperative adjuvant radiation was not associated with statistically significant differences in PFS or OS in this study. Our results indicated a potential OS benefit of adjuvant RT in patients with positive resection margins, and therefore may be considered in this patient population.
Phase II Trial of Target-guided Personalized Chemotherapy in First-line Metastatic Colorectal Cancer
Authors: Cubillo Antonio , Rodriguez-Pascual Jesús , López-Ríos Fernando , Plaza Carlos , García Elena , Álvarez Rafael , de Vicente Emilio , Quijano Yolanda , Hernando Ovidio , Rubio Carmen , Perea Sofía , Sanchez Gema , Hidalgo Manuel
Published: February 2014

Purpose:

The aim of this study was to investigate the feasibility and efficacy of personalizing treatment of patients with advanced untreated colorectal cancer (CRC).

Patients and Methods:

Patients with untreated metastatic CRC, performance status 0-1, and candidates for systemic chemotherapy were eligible. Tumor tissues were analyzed for KRAS, BRAF, and PI3K mutations and expression of topoisomerase-1 (Topo-1), excision repair cross-complementing gene 1 (ERCC1), thymidylate synthase (TS), and thymidine phosphorylase (TP). Patients with Topo-1 expression received irinotecan, whereas patients with negative Topo-1 and ERCC1 expression received oxaliplatin. Otherwise, patients received physician’s choice of treatment. If TS was positive, no fluoropyrimidine was administered and if negative, 5-flurorouracil if TP was negative, or capecitabine if TP was positive. KRAS-mutated patients were treated with bevacizumab, whereas KRAS-native received cetuximab. The primary endpoint of the study was progression-free survival (PFS).

Results:

A total of 74 patients were enrolled and 67 received personalized treatment including irinotecan (n=27), oxaliplatin (n=16), FOLFIRI (n=12), and FOLFOX (n=12). Thirty-eight patients received cetuximab and 29 bevacizumab. With a median follow-up time of 18.3 months (95% confidence interval [CI], 4-36), the overall median PFS was 8.3 months (95% CI, 6.9-9.7), representing a 12-month PFS rate of 36.5% (95% CI, 25-48). Overall clinical benefit, including response rate and disease stabilization, was 86% (95% CI, 73%-97%). The overall median survival was 21 months (95% CI, 11-40).

Conclusions:

Real-time target-guided personalized first-line treatment of patients with advanced CRC is feasible but, with the approached used, did not result in a clear improvement in PFS to warrant phase III testing.
Aqueous solutions: state of the art in
ab initio
molecular dynamics
Authors: Hassanali Ali A. , Cuny Jérôme , Verdolino Vincenzo , Parrinello Michele
Published: February 2014

The simulation of liquids by
ab initio
molecular dynamics (AIMD) has been a subject of intense activity over the last two decades. The significant increase in computational resources as well as the development of new and efficient algorithms has elevated this method to the status of a standard quantum mechanical tool that is used by both experimentalists and theoreticians. As AIMD computes the electronic structure from first principles, it is free of
ad hoc
parametrizations and has thus been applied to a large variety of physical and chemical problems. In particular, AIMD has provided microscopic insight into the structural and dynamical properties of aqueous solutions which are often challenging to probe experimentally. In this review, after a brief theoretical description of the Born–Oppenheimer and Car–Parrinello molecular dynamics formalisms, we show how AIMD has enhanced our understanding of the properties of liquid water and its constituent ions: the proton and the hydroxide ion. Thereafter, a broad overview of the application of AIMD to other aqueous systems, such as solvated organic molecules and inorganic ions, is presented. We also briefly describe the latest theoretical developments made in AIMD, such as methods for enhanced sampling and the inclusion of nuclear quantum effects.
Density functional tight binding
Authors: Elstner Marcus , Seifert Gotthard
Published: February 2014

This paper reviews the basic principles of the density-functional tight-binding (DFTB) method, which is based on density-functional theory as formulated by Hohenberg, Kohn and Sham (KS-DFT). DFTB consists of a series of models that are derived from a Taylor series expansion of the KS-DFT total energy. In the lowest order (DFTB1), densities and potentials are written as superpositions of atomic densities and potentials. The Kohn–Sham orbitals are then expanded to a set of localized atom-centred functions, which are obtained for spherical symmetric spin-unpolarized neutral atoms self-consistently. The whole Hamilton and overlap matrices contain one- and two-centre contributions only. Therefore, they can be calculated and tabulated in advance as functions of the distance between atomic pairs. The second contributions to DFTB1, the DFT double counting terms, are summarized together with nuclear repulsion energy terms and can be rewritten as the sum of pairwise repulsive terms. The second-order (DFTB2) and third-order (DFTB3) terms in the energy expansion correspond to a self-consistent representation, where the deviation of the ground-state density from the reference density is represented by charge monopoles only. This leads to a computationally efficient representation in terms of atomic charges (Mulliken), chemical hardness (Hubbard) parameters and scaled Coulomb laws. Therefore, no additional adjustable parameters enter the DFTB2 and DFTB3 formalism. The handling of parameters, the efficiency, the performance and extensions of DFTB are briefly discussed.
Density functional theory across chemistry, physics and biology
Authors: van Mourik Tanja , Bühl Michael , Gaigeot Marie-Pierre
Published: February 2014

The past decades have seen density functional theory (DFT) evolve from a rising star in computational quantum chemistry to one of its major players. This Theme Issue, which comes half a century after the publication of the Hohenberg–Kohn theorems that laid the foundations of modern DFT, reviews progress and challenges in present-day DFT research. Rather than trying to be comprehensive, this Theme Issue attempts to give a flavour of selected aspects of DFT.
Electronic non-adiabatic states: towards a density functional theory beyond the Born–Oppenheimer approximation
Authors: Gidopoulos Nikitas I. , Gross E. K. U.
Published: February 2014

A novel treatment of non-adiabatic couplings is proposed. The derivation is based on a theorem by Hunter stating that the wave function of the complete system of electrons and nuclei can be written, without approximation, as a Born–Oppenheimer (BO)-type product of a nuclear wave function,
X
(
R
), and an electronic one,
Φ

R

(
r
), which depends parametrically on the nuclear configuration
R
. From the variational principle, we deduce formally exact equations for
Φ

R

(
r
) and
X
(
R
). The algebraic structure of the exact nuclear equation coincides with the corresponding one in the adiabatic approximation. The electronic equation, however, contains terms not appearing in the adiabatic case, which couple the electronic and the nuclear wave functions and account for the electron–nuclear correlation beyond the BO level. It is proposed that these terms can be incorporated using an optimized local effective potential.
Excited states properties of organic molecules: from density functional theory to the
GW
and Bethe–Salpeter Green's function formalisms
Authors: Faber C. , Boulanger P. , Attaccalite C. , Duchemin I. , Blase X.
Published: February 2014

Many-body Green's function perturbation theories, such as the
GW
and Bethe–Salpeter formalisms, are starting to be routinely applied to study charged and neutral electronic excitations in molecular organic systems relevant to applications in photovoltaics, photochemistry or biology. In parallel, density functional theory and its time-dependent extensions significantly progressed along the line of range-separated hybrid functionals within the generalized Kohn–Sham formalism designed to provide correct excitation energies. We give an overview and compare these approaches with examples drawn from the study of gas phase organic systems such as fullerenes, porphyrins, bacteriochlorophylls or nucleobases molecules. The perspectives and challenges that many-body perturbation theory is facing, such as the role of self-consistency, the calculation of forces and potential energy surfaces in the excited states, or the development of embedding techniques specific to the
GW
and Bethe–Salpeter equation formalisms, are outlined.
Ornithinibacillus halotolerans sp. nov., isolated from a saline soil
Authors: Lu Qin , Yang Guiqin , Ma Chen , Qin Dongxing , Li Dingqiang , Zhou Shungui
Published: February 2014

A Gram-staining-positive, aerobic, motile, endospore-forming, rod-shaped bacterium, designated GD04T, was isolated from a saline soil sample taken in southern China and was characterized by means of a polyphasic approach. Growth occurred with 0.5–12 % (w/v) NaCl (optimum 1–2 %) and at pH 7.0–9.5 (optimum pH 8.0) and 10–45 °C (optimum 30 °C). According to the results of a phylogenetic analysis, strain GD04T belonged to the genus

Ornithinibacillus

, and was related most closely to type strains of the species

Ornithinibacillus bavariensis

and

Ornithinibacillus contaminans

(96.5 and 96.5 % 16S rRNA gene sequence similarities, respectively). The peptidoglycan amino acid type was A4β, containing l-ornithine and d-aspartic acid. The major respiratory quinone was menaquinone-7 (MK-7). The polar lipid profile of strain GD04T contained predominantly diphosphatidylglycerol with moderate amounts of phosphatidylglycerol, phosphatidylinositol, an unknown phospholipid and an unknown lipid, and a minor amount of another unknown lipid. The G+C content of genomic DNA was 39.3 mol%. The dominant cellular fatty acids were iso-C16 : 0, iso-C15 : 0 and anteiso-C15 : 0. The phenotypic, chemotaxonomic, phylogenetic and genotypic data indicated that strain GD04T represents a novel species of the genus

Ornithinibacillus

, for which the name Ornithinibacillus halotolerans sp. nov. is proposed. The type strain is GD04T ( = KCTC 33116T = CGMCC 1.12408T).
Estimating the evolution of human life history traits in age-structured populations
Authors: Baldini Ryan
Published: February 2014

I propose a method that estimates the selection response of all vital rates in an age-structured population. I assume that vital rates are determined by the additive genetic contributions of many loci. The method uses all relatedness information in the sample to inform its estimates of genetic parameters, via an MCMC Bayesian framework. One can use the results to estimate the selection response of any life history trait that is a function of the vital rates, including the age at first reproduction, total lifetime fertility, survival to adulthood, and others. This method closely ties the empirical analysis of life history evolution to dynamically complete models of natural selection, and therefore enjoys some theoretical advantages over other methods. I demonstrate the method on a simulated model of evolution with two age classes. Finally I discuss how the method can be extended to more complicated cases.
ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs
Authors: Balwierz Piotr J. , Pachkov Mikhail , Arnold Phil , Gruber Andreas J. , Zavolan Mihaela , van Nimwegen Erik
Published: February 2014

Accurate reconstruction of the regulatory networks that control gene expression is one of the key current challenges in molecular biology. Although gene expression and chromatin state dynamics are ultimately encoded by constellations of binding sites recognized by regulators such as transcriptions factors (TFs) and microRNAs (miRNAs), our understanding of this regulatory code and its context-dependent read-out remains very limited. Given that there are thousands of potential regulators in mammals, it is not practical to use direct experimentation to identify which of these play a key role for a particular system of interest. We developed a methodology that models gene expression or chromatin modifications in terms of genome-wide predictions of regulatory sites and completely automated it into a web-based tool called ISMARA (IntegratedSystem forMotifActivityResponseAnalysis). Given only gene expression or chromatin state data across a set of samples as input, ISMARA identifies the key TFs and miRNAs driving expression/chromatin changes and makes detailed predictions regarding their regulatory roles. These include predicted activities of the regulators across the samples, their genome-wide targets, enriched gene categories among the targets, and direct interactions between the regulators. Applying ISMARA to data sets from well-studied systems, we show that it consistently identifies known key regulators ab initio. We also present a number of novel predictions including regulatory interactions in innate immunity, a master regulator of mucociliary differentiation, TFs consistently disregulated in cancer, and TFs that mediate specific chromatin modifications.
9-Benzyl-6-benzylsulfanyl-9H-purin-2-amine
Authors: Hariono Maywan , Wahab Habibah A. , Tan Mei Lan , Rosli Mohd Mustaqim , Razak Ibrahim Abdul
Published: February 2014

In the title compound, C19H17N5S, the dihedral angles between the purine ring system (r.m.s. deviation = 0.009 Å) and the S-bound and methylene-bound phenyl rings are 74.67 (8) and 71.28 (7)°, respectively. In the crystal, inversion dimers linked by pairs of N—H...N hydrogen bonds generateR22(8) loops. C—H...N interactions link the dimers into (100) sheets.
1-Piperonylpiperazinium 4-chlorobenzoate
Authors: Kavitha Channappa N. , Kaur Manpreet , Anderson Brian J. , Jasinski Jerry P. , Yathirajan H. S.
Published: February 2014

In the title salt {systematic name: 1-[(1,3-benzodioxol-5-yl)methyl]piperazin-1-ium 4-chlorobenzoate}, C12H17N2O2+·C7H4ClO2−, the piperazine ring adopts a slightly disordered chair conformation. The dioxole ring is in a flattened envelope conformation with the methylene C atom forming the flap. The relative orientation of the piperonyl ring system and the piperazine rings is reflected in the N—C—C...;C torsion angle of 132.3 (1)°. In the anion, the mean plane of the carboxylate group is twisted from that of the benzene ring by 14.8 (9)°. In the crystal, the components are linked by N—H...O and weak C—H...O hydrogen bonds, forming chains along [010].
Bis[5-methoxy-2-(methoxycarbonyl)phenyl] methylphosphonate
Authors: Hussain Saghir , Deli Yang , Parveen Shagufta , Hao Xin , Zhu Changjin
Published: February 2014

In the title phosphonate, C19H21O9P, the dihedral angle between the benzene rings is 63.33 (3)°, and the P atom has a distorted tetrahedral geometry, with angles in the range 101.30 (6)–120.38 (6)°. No significant intermolecular interactions are observed in the crystal structure, and π–π interactions between symmetry-related benzene rings are beyond 4 Å.
Methyl 3′-benzyl-4′-(2,4-dichlorophenyl)-1′-methyl-2-oxo-1-propylspiro[indoline-3,2′-pyrrolidine]-3′-carboxylate
Authors: Karthikeyan S. , Sethusankar K. , Devaraj Anthonisamy , Bakthadoss Manickam
Published: February 2014

In the title compound, C30H30Cl2N2O3, the indole ring system is roughly planar, with a maximum deviation of 0.1039 (18) Å for the carbonyl C atom, and makes a dihedral angle of 86.61 (9)° with the mean plane of the pyrrolidine ring. This spiro pyrrolidine ring adopts an envelope conformation with the N atom at the flap position. The pyrrole ring of the indole ring system adopts a twisted conformation on the C—C(=O) bond. The molecular structure is stabilized by an intramolecular C—H...O hydrogen bond, which generates anS(6) ring motif, and a π–π interaction [centroid–centroid distance = 3.6577 (12) Å] involving the 2,4-dichlorophenyl ring and the benzyl ring. In the crystal, molecules are linkedviaC—H...O hydrogen bonds, formingC(9) chains running parallel to [10-1].
2-(4-Fluoro-2-nitrophenyl)-4-hydroxy-9-phenylsulfonyl-9H-carbazole-3-carbaldehyde
Authors: Gopinath S. , Sethusankar K. , Saravanan Velu , Mohanakrishnan Arasambattu K.
Published: February 2014

In the title compound, C25H15FN2O6S, the carbazole ring system is essentially planar, with a maximum deviation of 0.1534 (16) Å for the C atom connected to the 4-fluoro-2-nitrophenyl ring. It is almost orthogonal to the phenylsulfonyl and nitrophenyl rings, making dihedral angles of 88.45 (8) and 79.26 (7)°, respectively. The molecular structure is stabilized by O—H...O and C—H...O hydrogen bonds, which generate threeS(6) ring motifs. In the crystal, molecules are linked by two C—H...O hydrogen bonds, which generateC(6) andC(9) chains running in the [100] and [010] directions, respectively, so forming a two-dimensional network lying parallel to (001). There are also supramolecularR43(28) graph-set ring motifs enclosed within these networks.
9-(2,4-Difluorophenyl)-3,3,6,6-tetramethyl-3,4,5,6,7,9-hexahydro-2H-xanthene-1,8-dione
Authors: Rizwana Begum S. , Hema R. , Sumathi G. , Valliappan R. , Srinivasan N.
Published: February 2014

In the title compound, C23H24F2O3, the central pyran ring has a flat-boat conformation, whereas the two fused cyclohexenone rings adopt envelope conformations, with the C atom bearing the dimethyl substituent being the flap atom in each case. The pyran ring mean plane and the difluorophenyl ring are almost normal to each other, making a dihedral angle of 87.55 (4)°. In the crystal, molecules are linked by pairs of C—H...O hydrogen bonds, forming inversion dimers with anR22(8) ring motif. The F atom at position 2 on the difluorophenyl ring is disordered over the 2- and 6-positions, and has a refined occupancy ratio of 0.932 (3):0.068 (3).
(E)-N-(4-{[1-(Prop-2-en-1-yl)-1H-1,2,3-triazol-4-yl]methoxy}benzylidene)morpholin-4-amine
Authors: Akkurt Mehmet , Jarrahpour Aliasghar , Chermahini Mehdi Mohammadi , Shiri Pezhman , Özdemir Namık
Published: February 2014

The asymmetric unit of the title compound, C17H21N5O2, contains two crystallographically independent molecules, which are linked by a C—H...N hydrogen bond. The morpholine rings of both molecules adopt distorted chair conformations. The dihedral angles between the triazole and benzene rings are 12.8 (3)° in the first independent molecule in which the –N=C– group between the morpholine and benzene rings is disordered [site-occupancy ratio = 0.576 (7):0.424 (7)] and 88.1 (2)° in the second independent molecule. In the crystal, molecules are linked by C—H...N hydrogen bonds along the [100] direction. In addition, one weak C—H...π interaction and two weak π–π stacking interactions [centroid–centroid distances = 3.840 (3) and 3.823 (2) Å] between the triazole rings of adjacent molecules are observed. The atoms of the terminal propenyl groups in both molecules are disordered over two sets of sites [site-occupancy ratios = 0.691 (10):0.309 (10) and 0.705 (15):0.295 (15)].
Effects of merohedric twinning on the diffraction pattern
Authors: Nespolo Massimo , Ferraris Giovanni , Souvignier Bernd
Published: February 2014

In merohedric twinning, the lattices of the individuals are perfectly overlapped and the presence of twinning is not easily detected from the diffraction pattern, especially in the case of inversion twinning (class I). In general, the investigator has to consider three possible structural models: a crystal with space-group typeHand point groupP, either untwinned (H model) or twinned through an operationtin vector space (t-H model), and an untwinned crystal with space groupGwhose point groupP′ is obtained as an extension ofPthrough the twin operationt(G model). In 71 cases, consideration of the reflection conditions may directly rule out theGmodel; in seven other cases the reflection conditions suggest a space group which does not correspond to the extension ofHby the twin operation and the structure solution or at least the refinement will fail. When the twin operation belongs to a different crystal family (class IIBtwinning: the crystal has a specialized metric), thepresenceof twinning can often be recognized by the peculiar effect it has on the reflection conditions.
Brillouin-zone database on theBilbao Crystallographic Server
Authors: Aroyo Mois I. , Orobengoa Danel , de la Flor Gemma , Tasci Emre S. , Perez-Mato J. Manuel , Wondratschek Hans
Published: February 2014

The Brillouin-zone database of theBilbao Crystallographic Server(http://www.cryst.ehu.es) offersk-vector tables and figures which form the background of a classification of the irreducible representations of all 230 space groups. The symmetry properties of the wavevectors are described by the so-called reciprocal-space groups and this classification scheme is compared with the classification of Cracknellet al.[Kronecker Product Tables, Vol. 1,General Introduction and Tables of Irreducible Representations of Space Groups(1979). New York: IFI/Plenum]. The compilation provides a solution to the problems of uniqueness and completeness of space-group representations by specifying the independent parameter ranges of general and specialkvectors. Guides to thek-vector tables and figures explain the content and arrangement of the data. Recent improvements and modifications of the Brillouin-zone database, including new tables and figures for the trigonal, hexagonal and monoclinic space groups, are discussed in detail and illustrated by several examples.
I worry when […] insights into dual diagnosis from those who treat mothers misusing alcohol
Authors: Marlow Sally
Published: February 2014

Purpose

– Alcohol misuse and mental health problems in parents are both known to contribute to impaired outcomes in children, although little is known about the specific parenting behaviours that might be affected. Mental health problems in parents who misuse alcohol may impact parenting in specific ways, and these may be different for mothers and for fathers. The purpose of this paper is to make a preliminary investigation of alcohol misuse and mental health problems in mothers, and explore ways in which these might affect their parenting.

Design/methodology/approach

– Semi-structured interviews were carried out with professionals involved in services for mothers who misuse alcohol, including those working in addiction psychiatry, in primary care, and in the provision of parenting services. These interviews were then examined using thematic analysis.

Findings

– Themes emerged including specific mental health problems (depression, anxiety and personality disorders), and related issues, such as self-medication. Particularly relevant for mothers were post-natal depression, the effect on maternal alcohol misuse and mental health when children are removed, the role of domestic violence, and the importance for identification of home visits by services. Different types of alcohol misuse were linked to different mental states and different parenting behaviours in parents. Findings in the general parenting and substance misuse literature were confirmed, and a new addition was that expressed emotion may play a role in families where mothers misuse alcohol.

Originality/value

– The findings increased the understanding of the relationships between maternal alcohol misuse, mental health issues and parenting, raising several new points for consideration.
Identification of PTSD in adults with intellectual disabilities in five patients in a specialised psychiatric inpatient unit
Authors: Bakken Trine Lise , Kildahl Arvid Nikolai , Gjersøe Vibeke , Matre Espen , Kristiansen Tone , Ro Arvid , Tveter Anne Louise , Høidal Siv Helene
Published: February 2014

Purpose

– The purpose of this paper is to describe and discuss assessment of post-traumatic stress disorder (PTSD) in adults with intellectual disabilities. Existing research in this area encompasses case studies, and includes, for the most part, persons with mild intellectual disabilities.

Design/methodology/approach

– The aim of this study is to investigate symptom presentation and subsequent identification of PTSD in persons with more severe intellectual disabilities; i.e. persons with moderate or severe intellectual disabilities. Five patients in a specialised psychiatric inpatient unit for patients with intellectual disabilities were included. Information about the patients was collected through case files and interviews with key informants: family, milieu therapists, and caregivers in community settings, and observations through inpatient admission. The authors of this paper followed a training programme for trauma therapists in addition to the inpatient treatment of the five patients. The five patients all met criteria for PTSD according to the Diagnostic Manual – Intellectual Disability.

Findings

– Previously, it was not suspected that the five patients suffered from PTSD, although they had experienced terrifying incidents. All patients displayed severe changes in behaviour, which may have overshadowed symptoms of PTSD. PTSD in persons with more severe intellectual disabilities may be interpreted as challenging behaviour, or other psychiatric disorders such as psychosis.

Research limitations/implications

– The limitation of the study is the small number of participants.

Practical implications

– Practical implication is linked to clinical practice related to identification of PTSD in persons with intellectual disabilities.

Originality/value

– The paper may encourage more research into how PTSD can be identified in persons with moderate and severe intellectual disabilities. The case reports may help clinicians to look for traumatic experiences in persons with intellectual disabilities who have experienced terrifying incidents.