bluuebunny/crossref_metadata_2025 huggingface dataset:
Somatic symptom and related disorders
Authors: Brüne Martin
Published: September 2016

Somatic symptom disorders are characterized by the presentation of somatic complaints (somatization), often, but not necessarily, in the absence of a medical explanation of these sensations. The level of concern is generally disproportionate in relation to the severity of the somatic illness. Behaviourally, somatic symptom disorder entails signals that call for help and attention from others. Evolutionary considerations of why people present with somatic symptoms in the absence of a medical cause suggest that this behaviour could reflect a strategy to manipulate others in order to evoke care. Signals that aim at eliciting care from others are more persuasive if the ‘real’ intention is hidden from conscious awareness. Thus, self-deception may be involved in the presentation of somatic symptoms. Within the spectrum of somatic symptom and related disorders, the degree of self-deception may vary from high, as in illness anxiety disorder, to relatively low, as in factitious disorder.
Substance-related and addictive disorders
Authors: Brüne Martin
Published: September 2016

Substance-related and addictive disorders concern the misuse or dependence of psychotropic substances. Substance misuse or dependency is often accompanied by hazardous behaviour and legal problems. Substance dependence is characterized by the development of tolerance following recurrent exposure to the substance and increment of the consumed quantities. Behaviourally, individuals with substance-related disorders show significant craving and an inability to resist efforts to reduce the dose or terminate the intake of the substance. While psychotropic substances that can cause misuse or dependence are widespread in nature, the availability of large quantities has emerged only recently, suggesting an evolutionary ‘mismatch’. Most psychotropic substances causing misuse or dependence usurp the brain’s reward system (mainly dopaminergic substances) or the attachment system (mainly opioidergic substances). Research of gene–environment interaction has shown that social status and separation from caregivers or abusive behaviour of caregivers promotes the development of misuse or dependence.
Therapeutic dialogues I
Authors: Hobson R. Peter
Published: September 2016

In this chapter the focus moves away from stories of patients who enter treatment, to the nature of interpersonal transactions within particular sessions of Brief Psychoanalytic Therapy. Patient–therapist transactions are represented through succinct segments of dialogue drawn from transcripts of audiotaped sessions. A running commentary is interpolated among these brief sequences of verbal exchange. Special attention is paid to features of the two therapists’ styles of intervention, as well as the nature of shifts in the patients’ communicative stance. All this material anchors aspects of technique in the details of what actually transpires in episodes of Brief Psychoanalytic Therapy.
Measuring and Understanding Intellectual and Other Abilities
Authors: Armour-Thomas Eleanor , Suzuki Lisa
Published: September 2016

Measuring and understanding intellectual and other abilities remain contentious issues in the psychological and educational literature when applied to diverse populations. Central to the continuing controversy are the problems posed by the standardization principles of measurement science for populations whose cognitive development and expression vary from one cultural setting to another. Critics also point to the limited usefulness of standardized intelligence and achievement tests for providing information to guide educational intervention. Yet another issue is the source of intellectual abilities. The heritability of intellectual abilities is a widely held view within the testing profession and well supported in the literature. However, numerous studies from behavioral genetic research have found that the contribution of experience to variation in IQ is substantial and real. The growing acceptance of qualitative methodologies in the mainstream of psychological science offer promising diagnostic and prescriptive leads for understanding the cognitive processes underlying intellectual and academic abilities.
Test Use in Work Settings
Authors: Steiner Dirk D. , Schmitt Neal
Published: September 2016

Chapter 14 describes the various tools used in selecting employees in the workplace, such as cognitive ability tests, personality tests, and situational judgment tests, among others. Globalization of business has resulted in the adoption of mostly Western testing procedures by the rest of the world. The research base supporting some tests, especially cognitive ability and personality tests, is extensive; however, the use of tests seems to be more a function of their cost and the availability of skilled personnel to administer and interpret the test scores. Validation research has been conducted mostly in the United States and Europe and has sometimes focused on methods (e.g., interviews, assessment centers) rather than a more important concern with the constructs represented by these methods (e.g., cognitive ability, conscientiousness). Of particular concern is the observation that some constructs or methods of measurement produce large differences between gender or racial/ethnic subgroups.
Children and Adolescents
Authors: Joyce-Beaulieu Diana , Callueng Carmelo M.
Published: September 2016

Best practices and research in the testing and assessment of children and adolescents present a number of challenges and require consideration of a wide range of developmental factors. Neonatal and preschool assessments typically are conducted for medical and cognitive rehabilitative considerations addressing physical, sensory, communication, and brain function, which often require a cross-disciplinary approach between medical and psychological professions. Special considerations for these measures include limited predictive validity given the rapid changes in development, testing formats for preschool children, and score stability. Assessments for school-age children include norm-referenced measures of achievement, intelligence, temperament, personality, and psychopathology. Limitations for some of these measures include the representation of appropriate demographic variables in the norm samples, score stability, and potentials for rater bias. Auxiliary achievement assessment methods also may include curriculum-based measures and work samples. This chapter reviews each of these categories of assessments in light of implications for children and adolescents.
Taking Diversity into Account
Authors: Kuang Meirong , Müller Felix-Nicolai , Fang Yang , Fung Helene H. , Lang Frieder R.
Published: September 2016

Psychological assessment of the older adult population must take into account the methodological issues arising from age-related diversity. This chapter begins with an overview of theoretical considerations when assessing older adults: the need to conceptualize development as a process of selective optimization and compensation over the entire life span, and the importance of containing the influences of stereotypic images of the aging process. It discusses three central issues surrounding psychological assessment of the older adult population. First, many assessment instruments currently used for older adults were originally designed and normed for younger adults. Second, statistical norms may not reflect functional norms: older adults’ performance on standardized tests may underestimate their level of everyday functioning. Third, life-span-related contextual factors can be potential conflating elements that challenge the validity of assessment instruments among older adults, whose performance may be affected by differences in goals and motivations, memory processes and strategies, and expectations.
Indigenous Approaches to Testing and Assessment
Authors: Cheung Fanny M. , Fetvadjiev Velichko H.
Published: September 2016

This chapter discusses the need for culturally relevant tools for testing and assessment in non-Western countries, where it has been a common practice to adopt and translate psychological tests originally developed in Western countries. This etic approach assumes that Western theories and tools are universally applicable. Apart from the challenges of establishing equivalence between the original Western tests and the translated tests, the etic approach has been queried on the lack of relevance of some universal constructs that may be imposed on the local population. The indigenization movement in psychology arose in response to the imposed etic approach. Several indigenization responses in cognitive and personality assessment are presented to illustrate the introduction of emic constructs and measures. Using the combined emic-etic approach, two large-scale indigenous personality measures have been developed in China and South Africa: the Cross-cultural (Chinese) Personality Assessment Inventory (CPAI) and the South African Personality Inventory (SAPI).
Multigroup Comparisons
Authors: Byrne Barbara M.
Published: September 2016

One common weakness in multigroup comparison research is the pervading assumption that both the assessment scale and the construct(s) it is designed to measure are operating equivalently across the groups of interest. Structural equation modeling (SEM) has long been recognized as the premier methodological approach to test assumptions of equivalence. The primary focus of this chapter is directed toward the use of SEM in testing for the equivalence (also termed “invariance”) of assessment scales across independent groups. The purposes are threefold: (a) to explicate the basic notions underlying the concepts of measurement and structural equivalence; (b) to outline and describe the hierarchical set of steps involved in testing for measurement and structural equivalence; and (c) to provide an annotated, yet concise illustration of this equivalence-testing process as it relates to a commonly used assessment scale designed to measure teacher burnout across elementary and secondary female teachers.
Session 4: Addressing Barriers to Treatment Success
Authors: Peris Tara S. , Piacentini John
Published: September 2016

This chapter describes how to assist families as they apply skills learned in earlier treatment sessions to work on specific problems at home. It begins with a review of their progress with the first family problem, and, if appropriate, guides the therapist in helping families pick a new issue to address. The therapist reviews treatment progress and discusses potential barriers to change, including secondary gain, low motivation, and noncompliance. It is important that the therapist monitors and reframes blame that may arise during these discussions. The therapist should make it clear that OCD symptoms/behaviors are not done on purpose, even if there are aspects that appear to work to the child’s advantage. Strategies for addressing these obstacles are discussed and additional interventions applied as necessary.
Disrupting Hetero-Gender-Normativity
Authors: Palmer Neal A. , Kosciw Joseph G. , Greytak Emily A. , Boesen Madeline J.
Published: September 2016

For lesbian, gay, bisexual, and transgender (LGBT) youth, schools are often sites of exclusion and victimization. Research has demonstrated that LGBT youth experience elevated rates of victimization and bullying at school relative to their peers, but less research has explored the contexts and characteristics of schools that enable negative attitudes and behaviors toward LGBT youth. The authors examine how US schools construct environments that are unwelcoming and unsafe for LGBT students and largely fail to provide the supports that could improve the school learning climate. They examine strategies and practices employed by educators, students, and education advocates that can disrupt hetero- and gender-normative practices in schools. Specifically, we examine the mechanisms by which LGBT-related school supports—gay–straight alliances (GSAs), comprehensive anti-bullying/harassment school policies, supportive educators, and LGBT-inclusive curricula—support students’ well-being and academic success and challenge the hetero- and gender-normativity embedded in US secondary schools.
Retracted: AKAP12 mediates PKA-induced phosphorylation of ATR to enhance nucleotide excision repair
Authors: Jarrett Stuart G. , Wolf Horrell Erin M. , D'Orazio John A.
Published: September 2016

Loss-of-function in melanocortin 1 receptor (MC1R), a GS protein-coupled receptor that regulates signal transduction through cAMP and protein kinase A (PKA) in melanocytes, is a major inherited melanoma risk factor. Herein, we report a novel cAMP-mediated response for sensing and responding to UV-induced DNA damage regulated by A-kinase-anchoring protein 12 (AKAP12). AKAP12 is identified as a necessary participant in PKA-mediated phosphorylation of ataxia telangiectasia mutated and Rad3-related (ATR) at S435, a post-translational event required for cAMP-enhanced nucleotide excision repair (NER). Moreover, UV exposure promotes ATR-directed phosphorylation of AKAP12 at S732, which promotes nuclear translocation of AKAP12–ATR-pS435. This complex subsequently recruits XPA to UV DNA damage and enhances 5΄ strand incision. Preventing AKAP12's interaction with PKA or with ATR abrogates ATR-pS435 accumulation, delays recruitment of XPA to UV-damaged DNA, impairs NER and increases UV-induced mutagenesis. Our results define a critical role for AKAP12 as an UV-inducible scaffold for PKA-mediated ATR phosphorylation, and identify a repair complex consisting of AKAP12–ATR-pS435-XPA at photodamage, which is essential for cAMP-enhanced NER.
RETRACTION: Illuminating the dark road from schizophrenia genetic associations to disease mechanisms
Authors: Li Ming , Weinberger Daniel R
Published: September 2016

Recent large-scale genome-wide association studies (GWAS) have enabled the discovery of common genetic variations contributing to risk architectures of schizophrenia in human populations; however, the majority of GWAS-identified variants are located in large genomic regions spanning multiple genes, and recognizing the precise targets and mechanisms of these clinical associations is now the major challenge. Here, we review recent progress in schizophrenia genetics, functional genomics and related neuroscience research, and propose a functional pipeline to translate schizophrenia GWAS risk loci into disease biology and information for drug discovery. The pipeline includes identification of underlying molecular mechanisms using transcriptomic data in human brain, prioritization of putative functional causative variants by the integration of genetic epidemiological and bioinformatics methods as well as molecular approaches, and in vitro and in vivo experimental characterizations of the identified targeted species and causative variants to dissect the relevant disease biology. These approaches will accelerate progress from schizophrenia genetic studies to biological mechanisms and ultimately guide the development of prognostic, preventive and therapeutic measures.
Severe Human Illness Caused by Rift Valley Fever Virus in Mauritania, 2015
Authors: Boushab Boushab Mohamed , Fall-Malick Fatima Zahra , Ould Baba Sidi El Wafi , Ould Salem Mohamed Lemine , Belizaire Marie Roseline Darnycka , Ledib Hamade , Ould Baba Ahmed Mohamed Mahmoud , Basco Leonardo Kishi , Ba Hampaté
Published: September 2016

Background

Rift Valley Fever epizootics are characterized by numerous abortions and mortality among young animals. In humans, the illness is usually characterized by a mild self-limited febrile illness, which could progress to more serious complications.Objectives. The aim of the present prospective study was to describe severe clinical signs and symptoms of Rift Valley Fever in southern Mauritania.

Patients and methods

Suspected cases were enrolled in Kiffa (Assaba) and Aleg (Brakna) Hospital Centers from September 1 to November 7, 2015, based on the presence of fever, hemorrhagic or meningoencephalitic syndromes, and probable contact with sick animals. Suspected cases were confirmed by enzyme-linked immunosorbent assay (ELISA) and reverse transcriptase-polymerase chain reaction (RT-PCR).

Results

There were thirty-one confirmed cases. The sex ratio M/F and the average age were 2.9 and 25 years old [range, 4-70 years old], respectively. Mosquito bites, direct contact with aborted or dead animals, and frequent ingestion of milk from these animals were risk factors observed in all patients. Hemorrhagic and neurological manifestations were observed in 81% and 13% of cases, respectively. The results of laboratory analysis showed high levels of transaminases, creatinine, and urea associated with thrombocytopenia, anemia, and leukopenia. All patients who died (42%) had a hemorrhagic syndrome and 3 of them had a neurological complication. Among the cured patients, none had neurologic sequelae.

Conclusion

The hemorrhagic form was the most common clinical manifestation of RVF found in southern Mauritania and was responsible for a high mortality rate. Our results justify the implementation of a continuous epidemiological surveillance.
Update on second-trimester surgical abortion
Authors: Shaw Kate A. , Lerma Klaira
Published: September 2016

Purpose of review

To review the recent literature on surgical second-trimester abortion, with specific attention to cervical preparation techniques.

Recent findings

Confirming previous studies, a recent retrospective observational cohort study, including 54 911 abortions, estimated the total abortion-related complication rate to be 0.41% for second-trimester or later procedures. Cervical preparation is known to reduce risks associated with second-trimester dilation and evacuation (D&E). When considering adjuncts to osmotic dilators for cervical preparation prior to D&E after 16 weeks, both misoprostol and mifepristone are effective alone and in combination or as adjuncts to osmotic dilators. Misoprostol consistently has been shown to cause more pain and cramping than placebo, but is an effective adjunct to osmotic dilators after 16 weeks. Although mifepristone has fewer side-effects, at its current price, it may not be as cost-effective as misoprostol.

Second-trimester abortion is safe. The use of mifepristone and misoprostol for second-trimester abortion has improved safety and efficacy of medical and surgical methods when used alone or in combination and as adjuncts to osmotic dilators. An important aspect of D&E, cervical preparation, is not a one-size-fits-all practice; the approach and methods are contingent on patient, provider and setting and should consider all the evidence-based options.
Lipedema: A Relatively Common Disease with Extremely Common Misconceptions
Authors: Buck Donald W. , Herbst Karen L.
Published: September 2016

Lipedema, or adiposis dolorosa, is a common adipose tissue disorder that is believed to affect nearly 11% of adult women worldwide. It is characterized most commonly by disproportionate adipocyte hypertrophy of the lower extremities, significant tenderness to palpation, and a failure to respond to extreme weight loss modalities. Women with lipedema report a rapid growth of the lipedema subcutaneous adipose tissue in the setting of stress, surgery, and/or hormonal changes. Women with later stages of lipedema have a classic “column leg” appearance, with masses of nodular fat, easy bruising, and pain. Despite this relatively common disease, there are few physicians who are aware of it. As a result, patients are often misdiagnosed with lifestyle-induced obesity, and/or lymphedema, and subjected to unnecessary medical interventions and fat-shaming. Diagnosis is largely clinical and based on criteria initially established in 1951. Treatment of lipedema is effective and includes lymphatic support, such as complete decongestive therapy, and specialized suction lipectomy to spare injury to lymphatic channels and remove the diseased lipedema fat. With an incidence that may affect nearly 1 in 9 adult women, it is important to generate appropriate awareness, conduct additional research, and identify better diagnostic and treatment modalities for lipedema so these women can obtain the care that they need and deserve.
Mesh Sutured Repairs of Abdominal Wall Defects
Authors: Lanier Steven T. , Dumanian Gregory A. , Jordan Sumanas W. , Miller Kyle R. , Ali Nada A. , Stock Stuart R.
Published: September 2016

Background:

A new closure technique is introduced, which uses strips of macroporous polypropylene mesh as a suture for closure of abdominal wall defects due to failures of standard sutures and difficulties with planar meshes.

Methods:

Strips of macroporous polypropylene mesh of 2 cm width were passed through the abdominal wall and tied as simple interrupted sutures. The surgical technique and surgical outcomes are presented.

Results:

One hundred and seven patients underwent a mesh sutured abdominal wall closure. Seventy-six patients had preoperative hernias, and the mean hernia width by CT scan for those with scans was 9.1 cm. Forty-nine surgical fields were clean-contaminated, contaminated, or dirty. Five patients had infections within the first 30 days. Only one knot was removed as an office procedure. Mean follow-up at 234 days revealed 4 recurrent hernias.

Conclusions:

Mesh sutured repairs reliably appose tissue under tension using concepts of force distribution and resistance to suture pull-through. The technique reduces the amount of foreign material required in comparison to sheet meshes, and avoids the shortcomings of monofilament sutures. Mesh sutured closures seem to be tolerant of bacterial contamination with low hernia recurrence rates and have replaced our routine use of mesh sheets and bioprosthetic grafts.
The Methods Behind 2015 Informatics Capacity and Needs Assessment Study
Authors: Shah Gulzar H.
Published: September 2016

The 2015 Informatics Needs and Capacity of Local Health Departments (LHDs) survey is the most recent comprehensive source of quantitative data on LHD informatics. Conducted by the National Association of County & City Health Officials (NACCHO), this is the third nationally representative quantitative study of LHD informatics since 2009. The previous 2 comprehensive quantitative assessments were conducted by NACCHO in 2009-2010 and 2011. Given that public health informatics is rapidly evolving, the 2015 Informatics survey is a much-needed country-wide assessment of the current informatics needs and capacities of LHDs. This article outlines detailed methodology used in the 2015 Informatics survey, including instrument development, pretesting, sampling design and sample size, survey administration, and sampling weights. A 9-member advisory committee representing federal, state, and local health agency representatives guided the design and implementation of this study. The survey instrument was organized into 6 topic areas: demographics, physical infrastructure, skills and capacity available, public health workforce development needs, electronic health records, and health information exchange. The instrument was pretested with a sample of 20 LHDs and subsequently pilot-tested with 30 LHDs. The survey was administered via the Qualtrics survey software to the sample of 650 LHDs, selected using stratified random sampling. The survey was fielded for approximately 8 weeks and 324 usable responses were received, constituting a response rate of 50%. Statistical weights were developed to account for 3 factors: (a) disproportionate response rate by population size (using 7 population strata), (b) oversampling of LHDs with larger population sizes, and (c) sampling rather than a census approach.
Supportive Communication to Facilitate Chinese Patients' Adaptation to a Permanent Colostomy
Authors: Tao Hui , Songwathana Praneed , Isaramalai Sang-arun , Wang Qingxi
Published: September 2016

This study, which is a part of action research, aims to explore how supportive communication can impact individuals' adaptation to a permanent colostomy in a Chinese cultural context. Two Chinese rectal cancer patients with complexity and difficulty in living with a permanent colostomy were selected using a qualitative case study approach. The researcher (H.T.) interacted with the participants along their journey from the preoperative period until the third postoperative month after discharge via face-to-face or telephone interviews. Content analysis was applied. Supportive communication was characterized by “communication as a supportive tool,” which consisted of 4 elements: respect, description, empathy, and empowerment. The nursing strategies included (1) developing a collaborative relationship with patients and families; (2) understanding patients' concerns and problems; (3) discussing potential solutions; (4) encouraging patients to take action; (5) bringing out emotional expression; (6) normalizing negative emotions; and (7) protecting hope. The findings of this study informed that supportive communication is a valuable tool for nurses to provide informational and emotional support to Chinese patients in order to enhance their adaptation to living with a permanent colostomy. Developing an operational manual to enhance supportive communication for patients with colostomy is suggested.
Thin-film electrodes for high-capacity lithium-ion batteries: influence of phase transformations on stress
Authors: Meca Esteban , Münch Andreas , Wagner Barbara
Published: September 2016

In this study, we revisit experiments by Sethuramanet al.(2010J. Power Sources,195, 5062–5066. (doi:10.1016/j.jpowsour.2010.02.013)) on the stress evolution during the lithiation/delithiation cycle of a thin film of amorphous silicon. Based on recent work that show a two-phase process of lithiation of amorphous silicon, we formulate a phase-field model coupled to elasticity in the framework of Larché-Cahn. Using an adaptive nonlinear multigrid algorithm for the finite-volume discretization of this model, our two-dimensional numerical simulations show the formation of a sharp phase boundary between the lithiated and the amorphous silicon that continues to move as a front through the thin layer. We show that our model captures the non-monotone stress loading curve and rate dependence, as observed in recent experiments and connects characteristic features of the curve with the structure formation within the layer. We take advantage of the thin film geometry and study the corresponding one-dimensional model to establish the dependence on the material parameters and obtain a comprehensive picture of the behaviour of the system.
The Green’s functions for peridynamic non-local diffusion
Authors: Wang L. J. , Xu J. F. , Wang J. X.
Published: September 2016

In this work, we develop the Green’s function method for the solution of the peridynamic non-local diffusion model in which the spatial gradient of the generalized potential in the classical theory is replaced by an integral of a generalized response function in a horizon. We first show that the general solutions of the peridynamic non-local diffusion model can be expressed as functionals of the corresponding Green’s functions for point sources, along with volume constraints for non-local diffusion. Then, we obtain the Green’s functions by the Fourier transform method for unsteady and steady diffusions in infinite domains. We also demonstrate that the peridynamic non-local solutions converge to the classical differential solutions when the non-local length approaches zero. Finally, the peridynamic analytical solutions are applied to an infinite plate heated by a Gauss source, and the predicted variations of temperature are compared with the classical local solutions. The peridynamic non-local diffusion model predicts a lower rate of variation of the field quantities than that of the classical theory, which is consistent with experimental observations. The developed method is applicable to general diffusion-type problems.
Phenotypic innovation through recombination in genome-scale metabolic networks
Authors: Hosseini Sayed-Rzgar , Martin Olivier C. , Wagner Andreas
Published: September 2016

Recombination is an important source of metabolic innovation, especially in prokaryotes, which have evolved the ability to survive on many different sources of chemical elements and energy. Metabolic systems have a well-understood genotype–phenotype relationship, which permits a quantitative and biochemically principled understanding of how recombination creates novel phenotypes. Here, we investigate the power of recombination to create genome-scale metabolic reaction networks that enable an organism to survive in new chemical environments. To this end, we use flux balance analysis, an experimentally validated computational method that can predict metabolic phenotypes from metabolic genotypes. We show that recombination is much more likely to create novel metabolic abilities than random changes in chemical reactions of a metabolic network. We also find that phenotypic innovation is more likely when recombination occurs between parents that are genetically closely related, phenotypically highly diverse, and viable on few rather than many carbon sources. Survival on a new carbon source preferentially involves reactions that are superessential, that is, essential in many metabolic networks. We validate our observations with data from 61 reconstructed prokaryotic metabolic networks. Our systematic and quantitative analysis of metabolic systems helps understand how recombination creates innovation.
Can we test the influence of prosociality on high frequency heart rate variability? A double-blind sham-controlled approach
Authors: Beffara Brice , Mermillod Martial , Vermeulen Nicolas
Published: September 2016

The polyvagal theory (Porges, 2007) proposes that physiological flexibility dependent on heart- brain interactions is associated with prosociality. So far, whether prosociality has a causal effect on physiological flexibility is unknown. Previous studies present mitigated results on this matter. In a randomized double-blind protocol, we used a generation of social closeness procedure against a standardized control condition in order to manipulate social affiliation as a prosocial interaction factor. High frequency heart rate variability (HF-HRV, indexing physiological flexibility), electromyographical activity of the corrugator supercilii (sensitive to the valence of the interaction) and self-reported measure of social closeness were monitored before, during, and after experimental manipulation. Cooperation was measured after the experimental manipulation as an index of behavioral prosociality. Data reveal no evidence toward and effect of the experimental manipulation on these measures. We discuss methodological aspects related to the experimental constraints observed in social psychophysiology. Implications for the experimental test of the polyvagal theory are approached within alternative theoretical frameworks.
Composition fluctuations in lipid bilayers
Authors: Baoukina Svetlana , Rozmanov Dmitri , Tieleman D. Peter
Published: September 2016

Lipid bilayers constitute the basis of biological membranes. Understanding lipid mixing and phase behavior can provide important insights into membrane lateral organization (the “raft” hypothesis). Here we investigate model lipid bilayers below and above their miscibility transition temperatures. Molecular dynamics simulations with the MARTINI coarse-grained force field are employed to model bilayers on a length scale approaching 100 nm and a time scale of tens of microseconds. Using a binary mixture of saturated and unsaturated lipids, and a ternary mixture of a saturated lipid, an unsaturated lipid and cholesterol we reproduce the coexistence of liquid-crystalline and gel, as well as liquid-ordered and liquid-disordered phases. By raising the temperature or adding hybrid lipids (with a saturated and an unsaturated chain), we induce a gradual transition from a two-phase to a one-phase state. We characterize the evolution of bilayer properties along this transition. Domains of coexisting phases change to dynamic heterogeneity with local ordering and compositional de-mixing. We analyze the structural and dynamic properties of domains, sizes and lifetimes of composition fluctuations, and calculate the in-plane structure factors.
Theta Oscillations in the Human Medial Temporal Lobe during Real World Ambulatory Movement
Authors: Aghajan Zahra M. , Schuette Peter , Fields Tony , Tran Michelle , Siddiqui Sameed , Hasulak Nick , Tcheng Thomas K. , Eliashiv Dawn , Stern John , Fried Itzhak , Suthana Nanthia
Published: September 2016

Theta oscillations play a critical role in learning and memory by coordinating the spiking activity of neuronal ensembles via mechanisms such as spike timing dependent plasticity1–7. This rhythm is present in rodents where it is continuously evident during movement at frequencies within 6-12Hz8,9. In humans, however, the presence of continuous theta rhythm has been elusive; indeed, a functionally similar theta is thought to occur at lower frequency ranges (3-7Hz) and in shorter bouts10–12. This lower frequency theta rhythm is observed during a variety of behaviors, including virtual navigation, but has never been tested duringreal world ambulatory movement. Here we examined the oscillatory properties of theta within the human medial temporal lobe (MTL) in freely moving human subjects chronically implanted with the clinical NeuroPace RNS®responsive neurostimulator device, capable of wireless recordings of continuous intracranial deep brain electroencephalographic (iEEG) activity. MTL iEEG recordings, together with sub-millimeter position tracking, revealed the presence of high frequency theta oscillations (6-12Hz) during ambulation. The prevalence of these oscillations was increased during fast movement compared to slow movement. These theta bouts, although occurring more frequently, were not significantly different in durations during fast versus slow movements. In a rare opportunity to study one subject with congenital blindness, we found that both the prevalence and duration of theta bouts were much greater than those in sighted subjects. Our results suggest that higher frequency theta indeed exists in humans during movement providing critical support for conserved neurobiological mechanisms for spatial navigation. The precise link between this pattern and its behavioral correlates will be an exciting area for future studies given this novel methodology for simultaneous motion capture and long term chronic recordings from deep brain targets during ambulatory human behavior.
Predicting Protein Thermostability Upon Mutation Using Molecular Dynamics Timeseries Data
Authors: Fleming Noah , Kinsella Benjamin , Ing Christopher
Published: September 2016

A large number of human diseases result from disruptions to protein structure and function caused by missense mutations. Computational methods are frequently employed to assist in the prediction of protein stability upon mutation. These methods utilize a combination of protein sequence data, protein structure data, empirical energy functions, and physicochemical properties of amino acids. In this work, we present the first use of dynamic protein structural features in order to improve stability predictions upon mutation. This is achieved through the use of a set of timeseries extracted from microsecond timescale atomistic molecular dynamics simulations of proteins. Standard machine learning algorithms using mean, variance, and histograms of these timeseries were found to be 60-70% accurate in stability classification based on experimental ΔΔGor protein-chaperone interaction measurements. A recurrent neural network with full treatment of timeseries data was found to be 80% accurate according the F1 score. The performance of our models was found to be equal or better than two recently developed machine learning methods for binary classification as well as two industry-standard stability prediction algorithms. In addition to classification, understanding the molecular basis of protein stability disruption due to disease-causing mutations is a significant challenge that impedes the development of drugs and therapies that may be used treat genetic diseases. The use of dynamic structural features allows for novel insight into the molecular basis of protein disruption by mutation in a diverse set of soluble proteins. To assist in the interpretation of machine learning results, we present a technique for determining the importance of features to a recurrent neural network using Garson’s method. We propose a novel extension of neural interpretation diagrams by implementing Garson’s method to scale each node in the neural interpretation diagram according to its relative importance to the network.
A critical examination of the decoupling approximation for small-angle scattering from hard ellipsoids of revolution
Authors: Greene Daniel G. , Ferraro Daniel V. , Lenhoff Abraham M. , Wagner Norman J.
Published: September 2016

The decoupling approximation, proposed by Kotlarchyk & Chen [J. Chem. Phys. (1983), 79, 2461–2469], is a first-order correction to the experimentally determined apparent structure factor that is necessary because of concentration effects in polydisperse and/or nonspherical systems. While the approximation is considered accurate for spheres with low polydispersity (<10%), the corresponding limitations for nonspherical particles are unknown. The validity of this approximation is studied for monodisperse dispersions of hard ellipsoids of revolution with aspect ratios ranging from 0.333 to 3 and a guide for its accuracy is provided.
Averaging the intensity of many-layered structures for accurate stacking-fault analysis using Rietveld refinement
Authors: Coelho Alan A. , Evans John S. O. , Lewis James W.
Published: September 2016

Many technologically important synthetic and natural materials display stacking faults which lead to complex peak broadenings, asymmetries and shifts in their powder diffraction patterns. The patterns can be described using an enlarged unit cell (called a supercell) containing an explicit description of the layers. Since the supercell can contain hundreds of thousands of atoms with hundreds of thousands ofhklreflections, a Rietveld approach has been too computationally demanding for all but the simplest systems. This article describes the implementation of the speed-ups necessary to allow Rietveld refinement in the computer programTOPASVersion 6 (Bruker AXS, Karlsruhe, Germany). Techniques implemented include: a peaks buffer that allows hundreds of thousands ofhkl-dependent peak shapes to be automatically approximated by a few hundred peaks; an averaging process for hundreds of large supercells with minimum impact on computational time; a smoothing technique that allows for the use of small supercells which approximate supercells ten to 20 times larger; and efficient algorithms for stacking sequence generation. The result is Rietveld refinement of supercells operating at speeds several thousand times faster than traditional Rietveld refinements. This allows quantitative and simultaneous analysis of structure and microstructure in complex stacking-faulted samples.
Evaluation of intragranular strain and average dislocation density in single grains of a polycrystal using K-map scanning
Authors: Filippelli Ernesto , Chahine Gilbert , Borbély András
Published: September 2016

Quick scanning X-ray microscopy combined with three-dimensional reciprocal space mapping was applied to characterize intragranular orientation and strain in a single grain of uniaxially deformed Al polycrystal. The strain component perpendicular to the direction of the applied tensile load was found to be very heterogeneous with high compressive and tensile values in the grain interior and near two grain boundaries, respectively. The distribution of the magnitude of diffraction vectors indicates that dislocations are the origin of the strain. The work opens new possibilities for analysing dislocation structures and intragranular residual stress/strain in single grains of polycrystalline materials.
Towards a revisitation of vesuvianite-group nomenclature: the crystal structure of Ti-rich vesuvianite from Alchuri, Shigar Valley
Authors: Aksenov Sergey M. , Chukanov Nikita V. , Rusakov Vyacheslav S. , Panikorovskii Taras L. , Rastsvetaeva Ramiza K. , Gainov Ramil R. , Vagizov Farit G. , Lyssenko Konstantin A. , Belakovskiy Dmitry I.
Published: September 2016

Vesuvianite containing 5.85 wt% TiO2from an Alpine-cleft-type assemblage outcropped near Alchuri, Shigar Valley, Northern Areas, has been investigated by means of electron microprobe analyses, gas-chromatographic analysis of H2O, X-ray powder diffraction, single-crystal X-ray structure refinement,27Al NMR,57Fe Mössbauer spectroscopy, IR spectroscopy and optical measurements. Tetragonal unit-cell parameters are:a= 15.5326 (2),c= 11.8040 (2) Å, space groupP4/nnc. The structure was refined to finalR1= 0.031,wR2= 0.057 for 11247I> 2σ(I). A general crystal-chemical formula of studied sample can be written as follows (Z= 2):[8–9](Ca17.1Na0.9)[8]Ca1.0[5](Fe2+0.44Fe3+0.34Mg0.22)[6](Al3.59Mg0.41)[6](Al4.03Ti2.20Fe3+1.37Fe2+0.40) (Si18O68) [(OH)5.84O2.83F1.33]. The octahedral siteY2 is Al-dominant and does not contain transition elements. Another octahedral siteY3 is also Al-dominant and contains Fe2+, Fe3+and Ti. The siteY1 is split intoY1aandY1bpredominantly occupied by Fe2+and Fe3+, respectively. The role of theY1 site in the diversity of vesuvianite-group minerals is discussed.
Communication between cation environments in aluminosilicate frameworks: incommensurately modulated crystal structure of ane-plagioclase
Authors: Fredrickson Rie T. , Fredrickson Daniel C.
Published: September 2016

Despite being one of the most common minerals in the earth's crust the crystal structure of intermediatee-plagioclase remains only partially understood, due in a large part to its complex diffraction patterns including satellite reflections. In this article we present a detailed analysis of the structure ofe-plagioclase (An44) using single-crystal X-ray diffraction measured at ambient and low temperature (T= 100 K), in which the full modulated structure is successfully refined. As in earlier studies, the diffraction pattern exhibits strong maina-reflections and weake-satellite reflections. The average structure could be solved in terms of an albite-like basic cell with the triclinic centrosymmetric and non-centrosymmetric space groups P \bar 1 andP1 (treated in its C \bar 1 andC1 setting, respectively, to follow conventions in the literature), while the incommensurately modulated structure was modeled in (3 + 1)D superspace, employing both the centro- and non-centrosymmetric superspace groups X \bar 1(αβγ)0 andX1(αβγ)0, whereXrefers to a special (3 + 1)D lattice centering with centering vectors (0 0 ½ ½), (½ ½ 0 ½), and (½ ½ ½ 0). Individual positional and occupational modulations for Ca/Na were refined with deeper insights being revealed in the non-centrosymmetric structure model. Through the structural details emerging from this model, the origin of the modulation can be traced to the communication between Ca/Na site positions through their bridging aluminosilicate (Si/Al)O4tetrahedra.
Structures and physicochemical properties of vortioxetine salts
Authors: Zhou Xinbo , Hu Xiurong , Wu Suxiang , Ye Jiali , Sun Mengying , Gu Jianming , Zhu Jianrong , Zhang Zhongliang
Published: September 2016

In the present work, novel salts of the multimodal antidepressant drug vortioxetine (VT) were crystallized with pharmaceutically acceptable acids, aiming to improve the solubility of VT. The acids for VT were selected based on ΔpKabeing greater than 2 or 3. Salts of hydrobromic acid (HBr), hydrochloric acid (HCl),p-hydroxybenzoic acid (PHBA), saccharin (SAC) and L-aspartic acid (ASP) were reported. All salts were characterized by single-crystal X-ray diffraction, FT–IR, powder X-ray diffraction (PXRD) and differential scanning calorimetry (DSC). The acidic proton is transferred to the secondary N atom on the piperazine ring of VT, forming the charge-assisted hydrogen bond N+—H...X−(X= Cl, Br, O). Solubility and intrinsic dissolution rate (IDR) experiments were carried out in distilled water (pH = 7.0) to compare the solubilities of the salts with that of VT. The VT–ASP–H2O (1:1:2) salt showed 414 times higher solubility and 1722 times faster IDR compared with VT. VT–ASP–H2O (1:1:2) is a high solubility salt that is stable in a slurry experiment at 298 K in 95% ethanol. The experimental data for the VT–ASP–H2O (1:1:2) salt identify it as a promising drug candidate.
Crystal chemistry of trialkylsilyl-capped (3Z)-4-(methylthio)-3-penten-1-yne: polymorphism, twinning and ambiguity of order–disorder descriptions
Authors: Lumpi Daniel , Kautny Paul , Stöger Berthold , Fröhlich Johannes
Published: September 2016

The crystallization behavior of trimethylsilyl-capped (3Z)-4-(methylthio)-3-penten-1-yne (1-TMS) and the triisopropylsilyl andtert-butyldimethylsilyl analogues (1-TIPS) and (1-TBDMS) was investigated. (1-TMS) crystallizes in the Sohncke space groupP212121withZ′ = 1. (1-TIPS) exists as two polymorphs, both crystallizing in P\overline 1 withZ′ = 2 independent molecules. Polymorph (I) is an order–disorder (OD) twin. Two interpretations in terms ofM= 1 orM= 2 kinds of OD layers are possible, with different degrees of idealization. Polymorph (II) is fully ordered (non-twinned). Its structure can be derived from polymorph (I) by inverting the orientation of every second molecule. (1-TBDMS) (P\overline1,Z′ = 2) is an OD twin, where the OD description is unambiguously inM= 1 kinds of layers.
Accurate unrestrained DDM refinement of crystal structures from highly distorted and low-resolution powder diffraction data
Authors: Solovyov Leonid A.
Published: September 2016

The structure of benzene:ethane co-crystal at 90 K is refined with anisotropic displacement parameters without geometric restraints from high-resolution synchrotron X-ray powder diffraction (XRPD) data using the derivative difference method (DDM) with properly chosen weighting schemes. The average C—C bond precision achieved is 0.005 Å and the H-atom positions in ethane are refined independently. A new DDM weighting scheme is introduced that compensates for big distortions of experimental data. The results are compared with density functional theory (DFT) calculations reported by Maynard-Caselyet al.[(2016).IUCrJ,3, 192–199] where a rigid-body Rietveld refinement was also applied to the same dataset due to severe distortions of the powder pattern attributable to experimental peculiarities. For the crystal structure of 2-aminopyridinium fumarate–fumaric acid formerly refined applying 77 geometric restraints by Donget al.[(2013).Acta Cryst.C69, 896–900], an unrestrained DDM refinement using the same XRPD pattern surprisingly gave two times narrower dispersion of interatomic distances.