bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kinetics effects and modeling of mRNA turnover
Authors: Palumbo Maria Concetta , Farina Lorenzo , Paci Paola 
Published: March 2015

Broader comprehension of gene expression regulatory mechanisms can be gained from a global analysis of how transcription and degradation are coordinated to orchestrate complex cell responses. The role of messenger RNA (mRNA) turnover modulation in gene expression levels has become increasingly recognized. From such perspective, in this review we briefly illustrate how a simple but effective mathematical model of mRNA turnover and some experimental findings, may together shed light on the molecular mechanisms underpinning the major role of mRNA decay rates in shaping the kinetics of gene activation and repression. WIREs RNA 2015, 6:327–336. doi: 10.1002/wrna.1277This article is categorized under:

RNA Turnover and Surveillance > Regulation of RNA Stability
Loss of function mutation in glutamic pyruvate transaminase 2 (GPT2) causes developmental encephalopathy
Authors: Celis Katrina , Shuldiner Scott , Haverfield Eden V. , Cappell Joshua , Yang Rongze , Gong Da‐Wei , Chung Wendy K. 
Published: March 2015

AbstractIntellectual disability is genetically heterogeneous, and it is likely that many of the responsible genes have not yet been identified. We describe three siblings with isolated, severe developmental encephalopathy. After extensive uninformative genetic and metabolic testing, whole exome sequencing identified a homozygous novel variant in glutamic pyruvate transaminase 2 (GPT2) or alanine transaminase 2 (ALT2), c.459 C > G p.Ser153Arg that segregated with developmental encephalopathy in the family. This variant was predicted to be damaging by all in silico prediction algorithms. GPT2 is the gene encoding ALT2 which is responsible for the reversible transamination of alanine and 2‐oxoglutarate to form pyruvate and glutamate. GPT2 is expressed in brain and is in the pathway to generate glutamate, an excitatory neurotransmitter. Functional assays of recombinant wild‐type and mutant ALT2 proteins demonstrated the p.Ser153Arg mutation resulted in a severe loss of enzymatic function. We suggest that recessively inherited loss of function GPT2 mutations are a novel cause of intellectual disability.
Life and death by boundary conditions
Authors: Prosperetti Andrea 
Published: March 2015

Picano et al. (J. Fluid Mech., vol. 764, 2015, pp. 463–487) have conducted fully resolved numerical simulations of many thousands of spherical particles in a turbulent channel flow with $\mathit{Re}=5600$. Their results give a tantalizing demonstration of the vastness of the vistas that this line of research is about to open.
Detection of serum cytokines before and after pharmacological and surgical treatment in patients with cystic echinococcosis
Authors: Naik M.I. , Tenguria R.K. , Haq E. 
Published: March 2015

AbstractHuman cystic echinococcosis (CE), caused byEchinococcus granulosus, is one of the most important and widespread parasitic zoonoses. One of the problems that can be encountered after treating CE patients is the risk of post-surgical relapses or treatment failure, thus a long-term clinical and serological follow-up is required to evaluate the success or failure of therapy. In the present study immunological markers have been identified to indicate the effectiveness of pharmacological and surgical treatments. The relationship between serum cytokine levels and the outcome of chemotherapy and surgery was evaluated in 50 patients with CE. Serum interleukin (IL)-4, IL-10 and interferon-gamma (IFN-γ) concentrations were determined by enzyme-linked immunosorbent assay (ELISA) before and after pharmacological and surgical treatment. Serum cytokine levels of IL-4, IL-10 and IFN-γ were elevated in a significant proportion of patients during the active stage of disease. IL-4, IL-10 and IFN-γ were measurable in 41 (82%), 37 (74%) and 25 (50%) patients before the treatment. Clinical and radiological assessment of patients 2 years after pharmacological treatment has shown that 48 of 50 patients responded to treatment. IL-4 and IL-10 levels were decreased significantly (P< 0.05) in these patients. Conversely, patients who did not respond showed high levels of IL-4 and IL-10 and undetectable levels of IFN-γ. Hence these results suggest that serum IL-4 and IL-10 detection may be useful in the follow-up of patients with CE.
A computational analysis of flanker interference in depression
Authors: Dillon D. G. , Wiecki T. , Pechtel P. , Webb C. , Goer F. , Murray L. , Trivedi M. , Fava M. , McGrath P. J. , Weissman M. , Parsey R. , Kurian B. , Adams P. , Carmody T. , Weyandt S. , Shores-Wilson K. , Toups M. , McInnis M. , Oquendo M. A. , Cusin C. , Deldin P. , Bruder G. , Pizzagalli D. A. 
Published: March 2015

BackgroundDepression is characterized by poor executive function, but – counterintuitively – in some studies, it has been associated with highly accurate performance on certain cognitively demanding tasks. The psychological mechanisms responsible for this paradoxical finding are unclear. To address this issue, we applied a drift diffusion model (DDM) to flanker task data from depressed and healthy adults participating in the multi-site Establishing Moderators and Biosignatures of Antidepressant Response for Clinical Care for Depression (EMBARC) study.MethodOne hundred unmedicated, depressed adults and 40 healthy controls completed a flanker task. We investigated the effect of flanker interference on accuracy and response time, and used the DDM to examine group differences in three cognitive processes: prepotent response bias (tendency to respond to the distracting flankers), response inhibition (necessary to resist prepotency), and executive control (required for execution of correct response on incongruent trials).ResultsConsistent with prior reports, depressed participants responded more slowly and accurately than controls on incongruent trials. The DDM indicated that although executive control was sluggish in depressed participants, this was more than offset by decreased prepotent response bias. Among the depressed participants, anhedonia was negatively correlated with a parameter indexing the speed of executive control (r = −0.28, p = 0.007).ConclusionsExecutive control was delayed in depression but this was counterbalanced by reduced prepotent response bias, demonstrating how participants with executive function deficits can nevertheless perform accurately in a cognitive control task. Drawing on data from neural network simulations, we speculate that these results may reflect tonically reduced striatal dopamine in depression.
Quantity and spatial distribution of seeds dispersed by a western lowland gorilla population in south-east Cameroon
Authors: Petre Charles-Albert , Tagg Nikki , Beudels-Jamar Roseline , Haurez Barbara , Salah Marcel , Spetschinsky Victoria , Willie Jacob , Doucet Jean-Louis 
Published: March 2015

Abstract:Understanding the ecological function of large frugivores in tropical forests is important considering their central position in seed-dispersal networks. This study illustrates the seed-dispersal effectiveness of a western lowland gorilla (Gorilla gorilla gorilla) population in Cameroon by looking at the interaction of seed quantity, species regeneration traits and the environmental characteristics of the deposition sites (sleeping sites vs. feeding trails) in order to discuss the role of gorillas within the ecosystem. The analysis of 1030 faecal samples collected over a 3-y period (September 2009–August 2012) showed that gorillas dispersed a diverse array of species (58 spp. identified), with an average of 289 intact seeds (>5 mm) d−1 per individual. Seed damage during mouth and gut processing occurred for 12 spp., generally accounting for <5% of specific seed load. Germination trials suggested that germination success of passed seeds remained unchanged (N = 6 spp.) or improved (N = 5 spp.) after gut passage compared with hand-cleaned seeds, with one exception. Indicator species identification (IndVal method) and General Discriminant Analysis suggested that sleeping sites (N = 36), as a main type of seed deposition site, correspond to regenerating microhabitats and correspondingly degree of canopy openness is one variable discriminating significantly this type of deposition site with random locations in the forest (N = 36) used as a proxy for non-directed seed deposition on feeding trails. With a mean canopy openness of 19–27%, sleeping sites offer optimal light conditions for the seedling recruitment of non-pioneer light-demanding species, the seeds of which encompass 47.4% of the total seed load dispersed over the 3-y period. From this study, it is hypothesized that the gorilla performed directed-dispersal of some light-demanding plant species at sleeping sites, and hence, by being actively implicated in gap-phase dynamics, fulfils a valuable ecological function within its ecosystem.
A local-global principle for small triangulated categories
Authors: BENSON DAVE , IYENGAR SRIKANTH B. , KRAUSE HENNING 
Published: March 2015

AbstractLocal cohomology functors are constructed for the category of cohomological functors on an essentially small triangulated category ⊺ equipped with an action of a commutative noetherian ring. This is used to establish a local-global principle and to develop a notion of stratification, for ⊺ and the cohomological functors on it, analogous to such concepts for compactly generated triangulated categories.
Perceived Cognitive Difficulties and Cognitive Test Performance as Predictors of Employment Outcomes in People with Multiple Sclerosis
Authors: Honan Cynthia A. , Brown Rhonda F. , Batchelor Jennifer 
Published: March 2015

AbstractPerceived cognitive difficulties and cognitive impairment are important determinants of employment in people with multiple sclerosis (pwMS). However, it is not clear how they are related to adverse work outcomes and whether the relationship is influenced by depressive symptoms. Thus, this study examined perceived and actual general cognitive and prospective memory function, and cognitive appraisal accuracy, in relation to adverse work outcomes. The possible mediating and/or moderating role of depression was also examined. A cross-sectional community-based sample of 111 participants (33 males, 78 females) completed the Multiple Sclerosis Work Difficulties Questionnaire (MSWDQ), Beck Depression Inventory – Fast Screen (BDI-FS), and questions related to their current or past employment. They then underwent cognitive testing using the Screening Examination for Cognitive Impairment, Auditory Consonant Trigrams test, Zoo Map Test, and Cambridge Prospective Memory Test. Perceived general cognitive and prospective memory difficulties in the workplace and performance on the respective cognitive tests were found to predict unemployment and reduced work hours since MS diagnosis due to MS. Depression was also related to reduced work hours, but it did not explain the relationship between perceived cognitive difficulties and the work outcomes. Nor was it related to cognitive test performance. The results highlight a need to address the perceptions of cognitive difficulties together with cognitive impairment and levels of depression in vocational rehabilitation programs in pwMS. (JINS, 2015,21, 156–168)
A systematic review of ovarian cancer and fear of recurrence
Authors: Ozga Melissa , Aghajanian Carol , Myers-Virtue Shannon , McDonnell Glynnis , Jhanwar Sabrina , Hichenberg Shira , Sulimanoff Isabel 
Published: March 2015

AbstractObjective:To assess demographic, medical, and psychological factors that are associated with fear of recurrence (FCR) in ovarian cancer patients.Method:We searched PubMed, EMBASE, Cochrane, CINAHL, and PsycINFO. For PubMed, a search using Medical Subject Headings (MeSH) was run, as well as a text-word search from 1990 to July of 2014. The search terms used consisted of ovarian terms, fear terms, and recurrence/progression themes. Title and abstract reviews were conducted by two independent reviewers to determine eligibility, and discrepancies were decided by a third reviewer. Full-text reviews of potentially eligible articles were conducted by the review team, which met regularly to ensure the reliability of eligibility ratings across all articles.Results:A total of 15 articles met our inclusion criteria. Nine were quantitative studies that utilized a cross-sectional design, and the other six included three qualitative studies, two small intervention studies, and one study that utilized content analysis to explore written correspondence among ovarian cancer patients. FCR was reported as a significant concern for both older and younger women at both early and advanced stages. Women were distressed about recurrence at various times during their treatment and posttreatment. FCR was noted to be prevalent around cancer follow-up examinations. Many women reported not receiving adequate support for recurrence. FCR was also shown to be linked in some way to hopelessness, faith/spirituality, and posttraumatic stress disorder (PTSD). FCR was also linked to patients' anxiety about death and dying and uncertainty about the future of their medical health.Significance of Results:This review demonstrates that FCR is prevalent in the ovarian cancer population. Moreover, cancer recurrence fears are not adequately assessed or treated. More information is needed on the factors that may be related to women's fears about recurrence of ovarian cancer. In addition, a validated measure of FCR among ovarian cancer patients as well as a treatment intervention are needed.
Development of legal highs
Authors: Wasunna Brenda , Thomas Emily , Morgan Sally 
Published: March 2015

AbstractNew psychoactive substances (NPS) or ‘legal highs’ are defined as unregulated psychoactive substances including synthetic and/or plant derived substances (marketed as research chemicals, party pills and herbal highs) that are intended to mimic the effects of controlled drugs. Psychiatric services around the country are seeing a rise in the use of NPS complicating mental health presentations. The challenge surrounding these substances is the fact that they are not under the international drug control system and are proving to have a detrimental health effect on users. This article reviews the current literature on this subject and discusses some of the most common examples of NPS and their potential effects on mental health.
The role of bureaucrats in designing policy outcomes: the case of the 2002 General Security Service (GSS) Law
Authors: Meydani Assaf 
Published: March 2015

AbstractSince the 1980s, and mainly since the 1990s, studies in politics and law have adopted an economic attitude to explaining judicial behaviour. In contrast, this paper follows the individualistic approach by focusing on the role of individuals in bureaucracies in designing policy outcomes, using political entrepreneurship and new institutionalism as its theoretical framework. In describing a specific institutional change in Israel – the passage of the General Security Service Law in 2002 – I maintain that this institutional change is an equilibrium that resulted from the actions of empowered military bureaucrats acting as political entrepreneurs who sought to maximise their own political assets in the light of certain structural and cultural conditions, both local and international. The institutional arena was characterised by the inability of the government to function effectively (non-governability), enhanced judicialisation, the dominance of security issues in Israel, and the development of a unique shared mental model of alternative political culture. However, it was still open to changes based on new liberal attitudes about human rights. Thus, politicians influence and are influenced by a wide range of institutional norms and practices in a complex process of changes in institutional design.
The end of application of international humanitarian law
Authors: Milanovic Marko 
Published: March 2015

AbstractThis article provides an overview of the rules governing the end of application of international humanitarian law (IHL), or the law of armed conflict. It articulates the general principle that, unless there is a good reason of text, principle or policy that warrants an exception, the application of IHL will cease once the conditions that triggered its application in the first place are no longer met. For IHL to apply, its distinct thresholds of application – international armed conflict, belligerent occupation and non-international armed conflict – must continue to be satisfied at any given point in time. The article also examines situations in which a departure from the general rule is warranted, as well as the factors that need to be taken into account in determining the end of each type of armed conflict. In doing so, the article analyzes terminating processes and events, which generally end the application of IHL (but not necessarily all of it), and transformative processes and events, which end the application of one IHL sub-regime but immediately engage another. Finally, the article briefly looks at the (putative) armed conflict between the United States and Al Qaeda and its seemingly imminent end.
Conflict-related sexual violence and the policy implications of recent research
Authors: Wood Elisabeth Jean 
Published: March 2015

AbstractScholars increasingly document different forms of conflict-related sexual violence, their distinct causes, and their sharply varying deployment by armed organizations. In this paper, I first summarize recent research on this variation, emphasizing findings that contradict or complicate popular beliefs. I then discuss distinct interpretations of the claim that such violence is part of a continuum of violence between peace and war. After analyzing recent research on the internal dynamics of armed organizations, I suggest that widespread rape often occurs as a practice rather than as a strategy. Finally, I advance some principles to guide policy in light of recent research.
Simultaneous observation of the quantization and the interference pattern of a plasmonic near-field
Authors: Piazza L , Lummen T.T.A. , Quiñonez E , Murooka Y , Reed B.W. , Barwick B , Carbone F 
Published: March 2015

AbstractSurface plasmon polaritons can confine electromagnetic fields in subwavelength spaces and are of interest for photonics, optical data storage devices and biosensing applications. In analogy to photons, they exhibit wave–particle duality, whose different aspects have recently been observed in separate tailored experiments. Here we demonstrate the ability of ultrafast transmission electron microscopy to simultaneously image both the spatial interference and the quantization of such confined plasmonic fields. Our experiments are accomplished by spatiotemporally overlapping electron and light pulses on a single nanowire suspended on a graphene film. The resulting energy exchange between single electrons and the quanta of the photoinduced near-field is imaged synchronously with its spatial interference pattern. This methodology enables the control and visualization of plasmonic fields at the nanoscale, providing a promising tool for understanding the fundamental properties of confined electromagnetic fields and the development of advanced photonic circuits.
The relationship between dopamine receptor D1 and cognitive performance
Authors: Tsang Jonathan , Fullard John F , Giakoumaki Stella G , Katsel Pavel , Katsel Pavel , Karagiorga Vasiliki Eirini , Greenwood Tiffany A , Braff David L , Siever Larry J , Bitsios Panos , Haroutunian Vahram , Roussos Panos 
Published: March 2015

Abstract
Background:
Cognitive impairment cuts across traditional diagnostic boundaries and is one of the most typical symptoms in various psychiatric and neurobiological disorders.

Aims:
The objective of this study was to examine the genetic association between 94 candidate genes, including receptors and enzymes that participate in neurotransmission, with measures of cognition.

Methods:
The Clinical Dementia Rating (CDR), a global measure of cognition, and genotypes derived from a custom array of 1,536 single-nucleotide polymorphisms (SNPs) in 94 genes were available for a large postmortem cohort of Caucasian cases with Alzheimer’s disease (AD), schizophrenia and controls (n=727). A cohort of healthy young males (n=1,493) originating from the LOGOS project (Learning On Genetics Of Schizophrenia Spectrum) profiled across multiple cognitive domains was available for targeted SNP genotyping. Gene expression was quantified in the superior temporal gyrus of control samples (n=109). The regulatory effect on transcriptional activity was assessed using the luciferase reporter system.

Results:
The rs5326-A allele at the promoter region of dopamine receptor D1 (DRD1) locus was associated with: (i) poorer cognition (higher CDR) in the postmortem cohort (P=9.325×10−4); (ii) worse cognitive performance relevant to strategic planning in the LOGOS cohort (P=0.008); (iii) lower DRD1 gene expression in the superior temporal gyrus of controls (P=0.038); and (iv) decreased transcriptional activity in human neuroblastoma (SH-SY5Y) cells (P=0.026).

Conclusions:
An interdisciplinary approach combining genetics with cognitive and molecular neuroscience provided a possible mechanistic link among DRD1 and alterations in cognitive performance.
Scalable quantum memory in the ultrastrong coupling regime
Authors: Kyaw T. H. , Felicetti S. , Romero G. , Solano E. , Kwek L.-C. 
Published: March 2015

AbstractCircuit quantum electrodynamics, consisting of superconducting artificial atoms coupled to on-chip resonators, represents a prime candidate to implement the scalable quantum computing architecture because of the presence of good tunability and controllability. Furthermore, recent advances have pushed the technology towards the ultrastrong coupling regime of light-matter interaction, where the qubit-resonator coupling strength reaches a considerable fraction of the resonator frequency. Here, we propose a qubit-resonator system operating in that regime, as a quantum memory device and study the storage and retrieval of quantum information in and from the Z2 parity-protected quantum memory, within experimentally feasible schemes. We are also convinced that our proposal might pave a way to realize a scalable quantum random-access memory due to its fast storage and readout performances.
Complete genome sequence of hypervirulent and outbreak-associated Acinetobacter baumannii strain LAC-4: epidemiology, resistance genetic determinants and potential virulence factors
Authors: Ou Hong-Yu , Kuang Shan N. , He Xinyi , Molgora Brenda M. , Ewing Peter J. , Deng Zixin , Osby Melanie , Chen Wangxue , Xu H. Howard 
Published: March 2015

AbstractAcinetobacter baumannii is an important human pathogen due to its multi-drug resistance. In this study, the genome of an ST10 outbreak A. baumannii isolate LAC-4 was completely sequenced to better understand its epidemiology, antibiotic resistance genetic determinants and potential virulence factors. Compared with 20 other complete genomes of A. baumannii, LAC-4 genome harbors at least 12 copies of five distinct insertion sequences. It contains 12 and 14 copies of two novel IS elements, ISAba25 and ISAba26, respectively. Additionally, three novel composite transposons were identified: Tn6250, Tn6251 and Tn6252, two of which contain resistance genes. The antibiotic resistance genetic determinants on the LAC-4 genome correlate well with observed antimicrobial susceptibility patterns. Moreover, twelve genomic islands (GI) were identified in LAC-4 genome. Among them, the 33.4-kb GI12 contains a large number of genes which constitute the K (capsule) locus. LAC-4 harbors several unique putative virulence factor loci. Furthermore, LAC-4 and all 19 other outbreak isolates were found to harbor a heme oxygenase gene (hemO)-containing gene cluster. The sequencing of the first complete genome of an ST10 A. baumannii clinical strain should accelerate our understanding of the epidemiology, mechanisms of resistance and virulence of A. baumannii.