bluuebunny/crossref_metadata_2025 huggingface dataset:
Phytophthora
effector targets a novel component of small RNA pathway in plants to promote infection
Authors: Qiao Yongli , Shi Jinxia , Zhai Yi , Hou Yingnan , Ma Wenbo
Published: April 2015

Significance

Phytophthora
is a major threat to agriculture. However, the molecular interaction of these severe pathogens with plant hosts is poorly understood. Here, we report that the
Phytophthora
Suppressor of RNA Silencing 1 (PSR1) effectively promotes infection in
Arabidopsis thaliana
by directly targeting an essential protein containing a aspartate–glutamate–alanine–histidine-box RNA helicase domain. This PSR1-Interacting Protein 1 (PINP1) is required for the accumulation of distinct classes of endogenous small RNAs and acts as a positive regulator of plant immunity. Silencing of
PINP1
impaired the assembly of microRNA-processing complexes in the nucleus, leading to defects in development and immunity. This study revealed a conserved RNA helicase as a regulator of RNA silencing and provides mechanistic insight into
Phytophthora
pathogenesis.
Uranium isotopes fingerprint biotic reduction
Authors: Stylo Malgorzata , Neubert Nadja , Wang Yuheng , Monga Nikhil , Romaniello Stephen J. , Weyer Stefan , Bernier-Latmani Rizlan
Published: April 2015

Significance

Throughout Earth’s history, redox transformations in sedimentary environments have occurred through chemical processes (abiotic pathways) or via the activity of living microorganisms (biotic pathway). Tools able to discriminate between these two mechanisms are of major interest, as they would contribute significantly to the understanding of biogeochemical events that shaped the evolution of life on our planet. Here, we show that there is a clear difference between the isotopic signature associated with abiotic and biotic transformations of uranium (U). Thus, U isotopic composition can serve as a marker for biological processes in many sedimentary rocks. Based on this result, we conclude that microbial activity has contributed to reductive sedimentary processes in many low-temperature redox-active terrestrial and marine environments.
The amplification of risk in experimental diffusion chains
Authors: Moussaïd Mehdi , Brighton Henry , Gaissmaier Wolfgang
Published: April 2015

Significance

Public risk perception of hazardous events such as contagious outbreaks, terrorist attacks, and climate change are difficult-to-anticipate social phenomena. It is unclear how risk information will spread through social networks, how laypeople influence each other, and what social dynamics generate public opinion. We examine how messages detailing risks are transmitted from one person to another in experimental diffusion chains and how people influence each other as they propagate this information. Although the content of a message is gradually lost over repeated social transmissions, subjective perceptions of risk propagate and amplify due to social influence. These results provide quantitative insights into the public response to risk and the formation of often unnecessary fears and anxieties.
Species fluctuations sustained by a cyclic succession at the edge of chaos
Authors: Benincà Elisa , Ballantine Bill , Ellner Stephen P. , Huisman Jef
Published: April 2015

Significance

The intuitive and popular idea of a balance of nature has been criticized, because species interactions may generate nonequilibrium dynamics, such as oscillations and chaos. However, field evidence of chaos in ecosystems is rare. We report on a coastal community that has displayed striking fluctuations in the abundances of barnacles, mussels, and algae for more than 20 y. Data analysis reveals that these fluctuations reflect a cyclic succession alternating between stabilizing and chaotic dynamics during the species replacement. These results are supported by a simple patch-occupancy model, which predicts very similar dynamics when exposed to seasonal variation. Our findings provide a field demonstration of nonequilibrium coexistence of competing species through a cyclic succession at the edge of chaos.
During
Drosophila
disc regeneration, JAK/STAT coordinates cell proliferation with Dilp8-mediated developmental delay
Authors: Katsuyama Tomonori , Comoglio Federico , Seimiya Makiko , Cabuy Erik , Paro Renato
Published: April 2015

Significance

The larval imaginal discs of the fruit fly are capable of fully regenerating mechanically damaged parts. Wound healing is initiated by the JNK signaling pathway. We followed the subsequent formation of the regenerating blastema by transcriptome profiling and identified the JAK/STAT pathway as a central regulatory node controlling local cellular and global physiological responses. This signaling cascade induces, together with the Wingless pathway, proliferation of cells forming the blastema. However, JAK/STAT also up-regulates
Drosophila
insulin-like peptide 8 (Dilp8), a paracrine factor involved in organismal developmental delay, thereby allowing regenerative recovery.
pH-induced molecular shedding drives the formation of amyloid fibril-derived oligomers
Authors: Tipping Kevin W. , Karamanos Theodoros K. , Jakhria Toral , Iadanza Matthew G. , Goodchild Sophia C. , Tuma Roman , Ranson Neil A. , Hewitt Eric W. , Radford Sheena E.
Published: April 2015

Significance

Oligomers formed en route to amyloid fibrils are thought to be the perpetrators of toxicity in many amyloid disorders. How amyloid fibrils contribute to disease, however, is less clear. Here, using β
2
-micoglobulin (β
2
m) as a model system, we show that the stability of amyloid fibrils is highly pH-dependent, with mild acidification enhancing the formation of fibril-derived nonnative oligomers that disrupt membranes and alter cellular function. Enhancing fibril stability by incubation with the molecular chaperone, hsp70, or by cross-linking, protects against fibril-induced membrane disruption and cellular dysfunction. The results highlight the importance of pH in determining fibril stability and suggest that uptake of fibrils into acidic cellular compartments may contribute to amyloid disease by pH-induced molecular shedding of toxic species.
Causal effects of the early caregiving environment on development of stress response systems in children
Authors: McLaughlin Katie A. , Sheridan Margaret A. , Tibu Florin , Fox Nathan A. , Zeanah Charles H. , Nelson Charles A.
Published: April 2015

Significance

Disruptions in stress response system functioning are thought to be a central mechanism by which exposure to adverse early-life environments influences human development. Although rodent models support this possibility, results from human studies have been decidedly mixed. Using data from an experimental study examining whether random assignment to a caregiving environment alters development of the autonomic nervous system and hypothalamic–pituitary–adrenal axis in humans, we provide causal evidence for persistent effects of the early caregiving environment on stress response system functioning in humans with effects that differ markedly from those observed in rodent models. We also provide evidence of a sensitive period in human development during which the environment is particularly likely to alter stress response system development.
Quantitative optical coherence tomography angiography of vascular abnormalities in the living human eye
Authors: Jia Yali , Bailey Steven T. , Hwang Thomas S. , McClintic Scott M. , Gao Simon S. , Pennesi Mark E. , Flaxel Christina J. , Lauer Andreas K. , Wilson David J. , Hornegger Joachim , Fujimoto James G. , Huang David
Published: April 2015

Significance

Retinal vascular diseases are a leading cause of blindness. Optical coherence tomography (OCT) has become the standard imaging modality for evaluating fluid accumulation in these diseases and for guiding treatment. However, fluorescein angiography (FA) is still required for initial evaluation of retinal ischemia and choroidal neovascularization, which are not visible in conventional structural OCT. The limitations of FA include poor penetration of fluorescence through blood and pigment, inability to determine the depth of the pathology due to its two-dimensional nature, and some uncommon but potentially severe complications. As a noninvasive three-dimensional alternative, OCT angiography may be used in routine screening and monitoring to provide new information for clinical diagnosis and management.
X-ray phase-contrast tomography with a compact laser-driven synchrotron source
Authors: Eggl Elena , Schleede Simone , Bech Martin , Achterhold Klaus , Loewen Roderick , Ruth Ronald D. , Pfeiffer Franz
Published: April 2015

Significance

Absorption-based X-ray tomography suffers from low contrast for soft tissue. Over the last few years, it has been shown that grating-based phase-contrast X-ray tomography can overcome this limitation. Here we present, to our knowledge, the first phase-contrast tomography acquired at a compact light source, a recently developed compact synchrotron based on inverse Compton scattering.
The prodomain of BMP4 is necessary and sufficient to generate stable BMP4/7 heterodimers with enhanced bioactivity in vivo
Authors: Neugebauer Judith M. , Kwon Sunjong , Kim Hyung-Seok , Donley Nathan , Tilak Anup , Sopory Shailaja , Christian Jan L.
Published: April 2015

Significance

Bone morphogenetic proteins (BMPs) are made as inactive precursor proteins that dimerize and are cleaved to generate a bioactive ligand along with prodomain fragments that lack signaling activity. BMP ligands signal as either homodimers, or as heterodimers that display significantly higher activity in vivo. Recombinant homodimeric BMP ligands are used clinically to stimulate bone healing, but this requires supraphysiological doses due to the short half-life of the implanted protein. The current studies demonstrate that properties intrinsic to the BMP4 prodomain contribute to the formation and activity of BMP homodimers and heterodimers in vivo. Understanding how the prodomain regulates the activity of the ligand when it is made in vivo may lead to changes in the way BMP ligands are used clinically.
Role for RNA:DNA hybrids in origin-independent replication priming in a eukaryotic system
Authors: Stuckey Ruth , García-Rodríguez Néstor , Aguilera Andrés , Wellinger Ralf Erik
Published: April 2015

Significance

R-loop formation has been related to genome instability and human disease, yet the role of R-loops in replication priming remains to be explored in the eukaryotic genome. This investigation discloses that transcription-dependent R-loops have the potential to initiate origin-independent replication events in ribosomal DNA. Taken together, our data suggest that R-loops contribute to transcription-driven endoreplication events and alterations in genome copy number.
Eliminating hepatitis B by antagonizing cellular inhibitors of apoptosis
Authors: Ebert Gregor , Allison Cody , Preston Simon , Cooney James , Toe Jesse G. , Stutz Michael D. , Ojaimi Samar , Baschuk Nikola , Nachbur Ueli , Torresi Joseph , Silke John , Begley C. Glenn , Pellegrini Marc
Published: April 2015

Significance

Current antiviral treatments for chronic hepatitis B virus (HBV) infection are effective in suppressing production of virus, but they have poor efficacy in promoting the elimination of infection. Hence, most patients with chronic HBV infection are maintained on antiviral therapies indefinitely. There is much interest in identifying treatments that promote the clearance of infected hepatocytes, thus purging the HBV DNA reservoir in the liver. Here, we show that the clinical-stage drug birinapant, which antagonizes host cell inhibitor of apoptosis proteins (cIAPs), preferentially promotes the killing of HBV-infected hepatocytes in a mouse model of HBV. Therefore, birinapant and other antagonists of cIAPs may be efficacious in the treatment of chronic HBV infection and may promote elimination of virus.
Noninvasive imaging of immune responses
Authors: Rashidian Mohammad , Keliher Edmund J. , Bilate Angelina M. , Duarte Joao N. , Wojtkiewicz Gregory R. , Jacobsen Johanne Tracey , Cragnolini Juanjo , Swee Lee Kim , Victora Gabriel D. , Weissleder Ralph , Ploegh Hidde L.
Published: April 2015

Significance

Tumors are often surrounded and invaded by bone marrow-derived cells. Imaging the infiltration of such immune cells into tumors may therefore be an attractive means of detecting tumors or of tracking the response to anticancer therapy. We show that it is possible to detect these cells noninvasively by positron emission tomography (PET) via the surface markers displayed by them. The ability to monitor the immune response in the course of therapy will enable early determination of the efficacy of treatment and will inform decisions as to whether treatment should be stopped or continued. Noninvasive monitoring could therefore change how therapies are applied and assessed, to the benefit of many patients.
Error, signal, and the placement of Ctenophora sister to all other animals
Authors: Whelan Nathan V. , Kocot Kevin M. , Moroz Leonid L. , Halanych Kenneth M.
Published: April 2015

Significance

Traditional interpretation of animal phylogeny suggests traits, such as mesoderm, muscles, and neurons, evolved only once given the assumed placement of sponges as sister to all other animals. In contrast, placement of ctenophores as the first branching animal lineage raises the possibility of multiple origins of many complex traits considered important for animal diversification and success. We consider sources of potential error and increase taxon sampling to find a single, statistically robust placement of ctenophores as our most distant animal relatives, contrary to the traditional understanding of animal phylogeny. Furthermore, ribosomal protein genes are identified as creating conflict in signal that caused some past studies to recover a sister relationship between ctenophores and cnidarians.
Low TGFβ1 expression prevents and high expression exacerbates diabetic nephropathy in mice
Authors: Hathaway Catherine K. , Gasim Adil M. H. , Grant Ruriko , Chang Albert S. , Kim Hyung-Suk , Madden Victoria J. , Bagnell C. Robert , Jennette J. Charles , Smithies Oliver , Kakoki Masao
Published: April 2015

Significance

About one third of patients with type 1 diabetes mellitus develop nephropathy, which often progresses to end-stage renal diseases. The present study demonstrates that below normal transforming growth factor (TGF) β1 expression ameliorates the nephropathy and decreased glomerular filtration rate resulting from long-standing type 1 diabetes, while above normal TGFβ1 expression makes both worse. Reducing TGFβ1 expression in the glomerulus is more important in avoiding the decrease in glomerular filtration rate than altering expression in the tubule, while expression in the tubule is more important in controlling interstitial fibrosis and albuminuria. Suppressing TGFβ1 action in the kidney as a whole, or specifically in podocytes, could be a promising option for treating/preventing the progressive deterioration of renal function in diabetes.
Two-sided block of a dual-topology F
−
channel
Authors: Turman Daniel L. , Nathanson Jacob T. , Stockbridge Randy B. , Street Timothy O. , Miller Christopher
Published: April 2015

Significance

The study's significance is in its novelty along several lines. First, the ion channel studied, a Fluc F
−
channel, is recently discovered and has been only sparsely studied yet; this work adds a piece of the puzzle to the channel's mechanistic landscape. Second, this is the first channel, to our knowledge, for which two-sided blocking has been observed; this type of blocking is a consequence of the unusual dual-topology assembly of Fluc channels. Third, the mathematical analysis of this kind of block is novel (necessarily so). Fourth, the main result—that the two ends of the pore can be simultaneously occupied by blockers but with negative cooperativity in binding—provokes future structural and mechanistic experiments.
siRNA-based spherical nucleic acids reverse impaired wound healing in diabetic mice by ganglioside GM3 synthase knockdown
Authors: Randeria Pratik S. , Seeger Mark A. , Wang Xiao-Qi , Wilson Heather , Shipp Desmond , Mirkin Chad A. , Paller Amy S.
Published: April 2015

Significance

Diabetic patients often suffer from impaired wound healing, which can develop into nonhealing diabetic ulcers, facilitate bacterial infections, and necessitate amputation. Current strategies for treatment have failed to achieve the anticipated efficacy and do not address the fundamental molecular abnormalities that prevent efficient wound closure. In this work, we introduce a previously unidentified approach to treating diabetic wound healing by using topically delivered spherical nucleic acids to effect the knockdown of ganglioside-monosialic acid 3 (GM3) synthase, a mediator of impaired wound healing, in type 2 diabetic mice. In addition to laying the groundwork for developing a therapy for a debilitating condition, this work also validates the critical role of GM3 in diabetic wound healing.
Alternative to the soft-agar assay that permits high-throughput drug and genetic screens for cellular transformation
Authors: Rotem Asaf , Janzer Andreas , Izar Benjamin , Ji Zhe , Doench John G. , Garraway Levi A. , Struhl Kevin
Published: April 2015

Significance

The paper describes an assay for cellular transformation that involves growth in low attachment (GILA). This assay is comparable to the gold-standard soft-agar assay, but it is much easier to perform and is suitable for high-throughput drug and genetic screens. We describe such screens for drugs and genes that selectively inhibit or increase transformation, but not proliferation. Such molecules are unlikely to be found through conventional drug screening. Lastly, we demonstrate the ability of Food and Drug Administration-approved noncancer drugs to selectively kill ovarian cancer cells derived from patients with chemotherapy-resistant disease, suggesting this approach may provide useful information for personalized cancer treatment.
Olfactory receptor genes expressed in distinct lineages are sequestered in different nuclear compartments
Authors: Yoon Kyoung-hye , Ragoczy Tobias , Lu Zhonghua , Kondoh Kunio , Kuang Donghui , Groudine Mark , Buck Linda B.
Published: April 2015

Significance

Odorants are detected in the mouse nose by 1,000 different odorant receptors (ORs) and 14 TAARs. Each olfactory sensory neuron (OSN) expresses one receptor allele. While ORs generate diverse odor perceptions, some TAARs appear to be involved in innate responses, raising questions about mechanisms that could segregate ORs and TAARs in functionally distinct OSN subsets. Here, we identify two OSN subsets with different epithelial expression patterns that express different subgroups of TAARs rather than ORs. Our studies show that
Taar
and
Olfr
genes localize in different nuclear compartments, suggesting a physical substrate for their differential regulation. We further find that activation of a
Taar
allele is accompanied by its escape from peripheral repressive heterochromatin to a permissive interior chromatin environment.
Unraveling functional significance of natural variations of a human galectin by glycodendrimersomes with programmable glycan surface
Authors: Zhang Shaodong , Moussodia Ralph-Olivier , Vértesy Sabine , André Sabine , Klein Michael L. , Gabius Hans-Joachim , Percec Virgil
Published: April 2015

Significance

Lectins are endogenous sugar receptors involved in diverse physiological and disease-associated processes. The functional consequences of naturally occurring single-nucleotide polymorphism and alternative splicing in lectins has been explored using glycodendrimersomes, a versatile test system with programmable glycan (complex carbohydrates) display. Importantly, glycodendrimersomes facilitate quantitative determination of lectin-mediated cross-linking, a hallmark of their activity. Threshold and kinetic effects measured for a human galectin associated with autoimmune disease document the sensitivity of the test system and highlight its potential as a new and highly versatile supramolecular sensor for biomedical applications.
Phytochemical and biological aspects of Rudraksha, the stony endocarp of Elaeocarpus ganitrus (Roxb.): a review
Authors: Singh Balbir , Ishar Mohan Paul Singh , Sharma Anupam , Arora Rohit , Arora Saroj
Published: April 2015

Rudraksha, the stony endocarp of Elaeocarpus ganitrus (Roxb.) (Elaeocarpaceae), is known for its ethnopharmacological and spiritual importance in Hindu religion. It is traditionally used to cure melancholia, mental disorders, convulsions, cephalalgia, allergies, neurological diseases, asthma, diabetes, cancer, stress and many other blood circulatory disorders. The Elaeocarpus genus contains more than 50 constituents, which are responsible for the pharmacological and biological activities of this plant. Among these constituents, alkaloids, flavonoids and phenols are considered to contribute to its pharmacological importance. The present review sums the current state of knowledge concerning the ethnopharmacology, chemical composition, pharmacology and toxicology of E. ganitrus (Roxb.).
Heterologous production of l-lysine ε-oxidase by directed evolution using a fusion reporter method
Authors: Matsui Daisuke , Asano Yasuhisa
Published: April 2015

For the heterologous production of l-lysine ε-oxidase (LodA), we constructed a new plasmid carrying LodA gene fused in-frame with an antibiotic (phleomycine) resistant gene. The new plasmid was randomly mutated and the mutated plasmids were transformed into Escherichia coli BL21 (DE3) harboring lodB, which encodes a protein (LodB) acting in posttranslational modification of LodA, and active mutants were selected by phleomycin resistance and oxidase activities. One soluble LodA variant isolated by this method contained six silent mutations and one missense mutation. At these mutation points, the codon adaptations at Lys92, Ala550, and Thr646, and the amino acid substitution at His286 to Arg contributed to the production of its functional form. The active form of LodA variant was induced by post-modification of LodB in the heterologous coexpression, and the activity increased with additional NaCl and heat treatment. This is the first report of heterologous production of LodA by random mutagenesis.
Glutamylation of Nap1 modulates histone H1 dynamics and chromosome condensation in Xenopus
Authors: Miller Kelly E. , Heald Rebecca
Published: April 2015

Linker histone H1 is required for mitotic chromosome architecture in Xenopus laevis egg extracts and, unlike core histones, exhibits rapid turnover on chromatin. Mechanisms regulating the recruitment, deposition, and dynamics of linker histones in mitosis are largely unknown. We found that the cytoplasmic histone chaperone nucleosome assembly protein 1 (Nap1) associates with the embryonic isoform of linker histone H1 (H1M) in egg extracts. Immunodepletion of Nap1 decreased H1M binding to mitotic chromosomes by nearly 50%, reduced H1M dynamics as measured by fluorescence recovery after photobleaching and caused chromosome decondensation similar to the effects of H1M depletion. Defects in H1M dynamics and chromosome condensation were rescued by adding back wild-type Nap1 but not a mutant lacking sites subject to posttranslational modification by glutamylation. Nap1 glutamylation increased the deposition of H1M on sperm nuclei and chromatin-coated beads, indicating that charge-shifting posttranslational modification of Nap1 contributes to H1M dynamics that are essential for higher order chromosome architecture.
The transcription factor lymphoid enhancer factor 1 controls invariant natural killer T cell expansion and Th2-type effector differentiation
Authors: Carr Tiffany , Krishnamoorthy Veena , Yu Shuyang , Xue Hai-Hui , Kee Barbara L. , Verykokakis Mihalis
Published: April 2015

Invariant natural killer T cells (iNKT cells) are innate-like T cells that rapidly produce cytokines that impact antimicrobial immune responses, asthma, and autoimmunity. These cells acquire multiple effector fates during their thymic development that parallel those of CD4+ T helper cells. The number of Th2-type effector iNKT cells is variable in different strains of mice, and their number impacts CD8 T, dendritic, and B cell function. Here we demonstrate a unique function for the transcription factor lymphoid enhancer factor 1 (LEF1) in the postselection expansion of iNKT cells through a direct induction of the CD127 component of the receptor for interleukin-7 (IL-7) and the transcription factor c-myc. LEF1 also directly augments expression of the effector fate–specifying transcription factor GATA3, thus promoting the development of Th2-like effector iNKT cells that produce IL-4, including those that also produce interferon-γ. Our data reveal LEF1 as a central regulator of iNKT cell number and Th2-type effector differentiation.
Otolith fluctuating asymmetry: a misconception of its biological relevance?
Authors: Díaz-Gil Carlos , Palmer Miquel , Catalán Ignacio A. , Alós Josep , Fuiman Lee A. , García Elena , Gil María del Mar , Grau Amalia , Kang Andrew , Maneja Rommel H. , Mohan John A. , Morro Bernat , Schaffler Jason J. , Buttay Lucie , Riera-Batle Inmaculada , Tolosa Borja , Morales-Nin Beatriz
Published: April 2015

For decades, disruption of the bilateral symmetry of body structures has been related to underperformance and, hence, to fitness. In fish, this concept coupled with the claimed evidence for increased fluctuating asymmetry (FA) of pairs of hard structures, such as otoliths under conditions of stress, has led to the use of otolith FA (OFA) as a proxy for individual fitness and population success. Interpreting those significant differences in OFA in relation to stress-inducing environments and using them to identify suboptimal conditions for survival is especially appealing in the context of, for example, assessing climate change using historical otolith collections. Despite several works that give evidence to support the usefulness of OFA approach, we report on a number of unpublished and published datasets from a wide range of both, wild populations and experimental designs that show no correlation between OFA and any of the usual indicators of fitness or between OFA and expected stress gradients. Our results suggest that there may be a strong bias in the published literature towards positive relationships, despite the enormous importance of negative results for understanding the significance of OFA. These results might shed light on the interpretability of OFA in both laboratory and field studies.
Associations between healthcare quality and use of electronic health record functions in ambulatory care
Authors: Ancker Jessica S , Kern Lisa M , Edwards Alison , Nosal Sarah , Stein Daniel M , Hauser Diane , Kaushal Rainu ,   with the HITEC Investigators
Published: April 2015

Objectives Contemporary electronic health records (EHRs) offer a wide variety of features, creating opportunities to influence healthcare quality in different ways. This study was designed to assess the relationship between physician use of individual EHR functions and healthcare quality.

Materials and Methods Sixty-five providers eligible for “meaningful use” were included. Data were abstracted from office visit records during the study timeframe (183 095 visits with 61 977 patients). Three EHR functions were considered potential predictors: acceptance of best practice alerts, use of order sets, and viewing panel-level reports. Eighteen clinical quality measures from the “meaningful use” program were abstracted.

Results Use of condition-specific best-practice alerts and order sets was associated with better scores on clinical quality measures capturing processes in diabetes, cancer screening, tobacco cessation, and pneumonia vaccination. For example, providers above the median in use of tobacco-related alerts had higher performance on tobacco cessation intervention metrics (median 80.6% vs. 66.7%; P < .001), and providers above the median in use of diabetes order sets had higher quality on diabetes low density lipoprotein (LDL) testing (68.2% vs. 59.5%; P == .001). Post hoc examination of the results showed that the positive associations were with measures of healthcare processes (such as rates of LDL testing), whereas there were no positive associations with measures of healthcare outcomes (such as LDL levels).

Discussion Among primary care providers in the ambulatory setting using a single EHR, intensive use of certain EHR functions was associated with increased adherence to recommended care as measured by performance on electronically reported “meaningful use” quality measures. This study is relevant to current policy as it uses quality metrics constructed by contemporary certified EHR technology, and quantitative EHR use metrics rather than self-reported use.

Conclusion In the early stages of the “meaningful use” program, use of specific EHR functions was associated with higher performance on healthcare process metrics.
Nuclear composition of magnetized gamma-ray burst jets
Authors: Shibata Sanshiro , Tominaga Nozomu
Published: April 2015

We investigate the fraction of metal nuclei in the relativistic jets of gamma-ray bursts associated with core-collapse supernovae. We simulate the fallback in jet-induced explosions with two-dimensional relativistic hydrodynamics calculations and the jet acceleration with steady, radial, relativistic magnetohydrodynamics calculations, and derive the detailed nuclear composition of the jet by post-processing calculation. We found that if the temperature at the jet launch site is above 4.7 × 109 K, quasi-statistical equilibrium is established and heavy nuclei are dissociated into light particles such as 4He during the acceleration of the jets. The criterion for the survival of metal nuclei is written in terms of the isotropic jet luminosity as $L_{\rm j}^{\rm iso} \lesssim 3.9 \times 10^{50} ( R_{\rm i}/10^{7}\ {\rm cm})^2$(1 + σi) erg s−1, where Ri and σi are the initial radius of the jets and the initial magnetization parameter, respectively. If the jet is initially dominated by radiation field (i.e., σi ≪ 1) and the isotropic luminosity is relatively high ($L_{\rm j}^{\rm iso} \gtrsim 4 \times 10^{52}$ erg s−1), the metal nuclei cannot survive in the jet. On the other hand, if the jet is mainly accelerated by magnetic field (i.e., σi ≫ 1), metal nuclei initially contained in the jet can survive without serious dissociation even in the case of a high-luminosity jet. If the jet contains metal nuclei, the dominant nuclei are 28Si, 16O, and 32S and the mean mass number can be 〈A〉 ∼ 25.
What can observations tell us about coronal heating?
Authors: Schmelz J. T. , Winebarger A. R.
Published: April 2015

The actual source of coronal heating is one of the longest standing unsolved mysteries in all of astrophysics, but it is only in recent years that observations have begun making significant contributions. Coronal loops, their structure and sub-structure, their temperature and density details, and their evolution with time, may hold the key to solving this mystery. Because spatial resolution of current observatories cannot resolve fundamental scale lengths, information about the heating of the corona must be inferred from indirect observations. Loops with unexpectedly high densities and multi-thermal cross-field temperatures were not consistent with results expected from steady uniform heating models. The hot (
T
>5 MK) plasma component of loops may also be a key observation; a new sounding rocket instrument called the Marshall Grazing Incidence X-ray Spectrometer will specifically target this observable. Finally, a loop is likely to be a tangle of magnetic strands. The High Resolution Coronal Imager observed magnetic braids untwisting and reconnecting, dispersing enough energy to heat the surrounding plasma. The existence of multi-thermal, cooling loops and hot plasma provides observational constraints that all viable coronal heating models will need to explain.
Stellar activity and coronal heating: an overview of recent results
Authors: Testa Paola , Saar Steven H. , Drake Jeremy J.
Published: April 2015

Observations of the coronae of the Sun and of solar-like stars provide complementary information to advance our understanding of stellar magnetic activity, and of the processes leading to the heating of their outer atmospheres. While solar observations allow us to study the corona at high spatial and temporal resolution, the study of stellar coronae allows us to probe stellar activity over a wide range of ages and stellar parameters. Stellar studies therefore provide us with additional tools for understanding coronal heating processes, as well as the long-term evolution of solar X-ray activity. We discuss how recent studies of stellar magnetic fields and coronae contribute to our understanding of the phenomenon of activity and coronal heating in late-type stars.
Wave heating of the solar atmosphere
Authors: Arregui Iñigo
Published: April 2015

Magnetic waves are a relevant component in the dynamics of the solar atmosphere. Their significance has increased because of their potential as a remote diagnostic tool and their presumed contribution to plasma heating processes. We discuss our current understanding of coronal heating by magnetic waves, based on recent observational evidence and theoretical advances. The discussion starts with a selection of observational discoveries that have brought magnetic waves to the forefront of the coronal heating discussion. Then, our theoretical understanding of the nature and properties of the observed waves and the physical processes that have been proposed to explain observations are described. Particular attention is given to the sequence of processes that link observed wave characteristics with concealed energy transport, dissipation and heat conversion. We conclude with a commentary on how the combination of theory and observations should help us to understand and quantify magnetic wave heating of the solar atmosphere.
Models of coronal heating, turbulence and fast reconnection
Authors: Velli M. , Pucci F. , Rappazzo F. , Tenerani A.
Published: April 2015

Coronal heating is at the origin of the EUV and X-ray emission and mass loss from the sun and many other stars. While different scenarios have been proposed to explain the heating of magnetically confined and open regions of the corona, they must all rely on the transfer, storage and dissipation of the abundant energy present in photospheric motions, which, coupled to magnetic fields, give rise to the complex phenomenology seen at the chromosphere and transition region (i.e. spicules, jets, ‘tornadoes’). Here we discuss models and numerical simulations which rely on magnetic fields and electric currents both for energy transfer and for storage in the corona. We will revisit the sources and frequency spectrum of kinetic and electromagnetic energies, the role of boundary conditions, and the routes to small scales required for effective dissipation. Because reconnection in current sheets has been, and still is, one of the most important processes for coronal heating, we will also discuss recent aspects concerning the triggering of reconnection instabilities and the transition to fast reconnection.
Shock heating in numerical simulations of kink-unstable coronal loops
Authors: Bareford M. R. , Hood A. W.
Published: April 2015

An analysis of the importance of shock heating within coronal magnetic fields has hitherto been a neglected area of study. We present new results obtained from nonlinear magnetohydrodynamic simulations of straight coronal loops. This work shows how the energy released from the magnetic field, following an ideal instability, can be converted into thermal energy, thereby heating the solar corona. Fast dissipation of magnetic energy is necessary for coronal heating and this requirement is compatible with the time scales associated with ideal instabilities. Therefore, we choose an initial loop configuration that is susceptible to the fast-growing kink, an instability that is likely to be created by convectively driven vortices, occurring where the loop field intersects the photosphere (i.e. the loop footpoints). The large-scale deformation of the field caused by the kinking creates the conditions for the formation of strong current sheets and magnetic reconnection, which have previously been considered as sites of heating, under the assumption of an enhanced resistivity. However, our simulations indicate that slow mode shocks are the primary heating mechanism, since, as well as creating current sheets, magnetic reconnection also generates plasma flows that are faster than the slow magnetoacoustic wave speed.
Recent advances in coronal heating
Authors: De Moortel Ineke , Browning Philippa
Published: April 2015

The solar corona, the tenuous outer atmosphere of the Sun, is orders of magnitude hotter than the solar surface. This ‘coronal heating problem’ requires the identification of a heat source to balance losses due to thermal conduction, radiation and (in some locations) convection. The review papers in this Theo Murphy meeting issue present an overview of recent observational findings, large- and small-scale numerical modelling of physical processes occurring in the solar atmosphere and other aspects which may affect our understanding of the proposed heating mechanisms. At the same time, they also set out the directions and challenges which must be tackled by future research. In this brief introduction, we summarize some of the issues and themes which reoccur throughout this issue.
Efficient genotype compression and analysis of large genetic variation datasets
Authors: Layer Ryan M. , Kindlon Neil , Karczewski Konrad J. , Quinlan Aaron R. ,   Exome Aggregation Consortium
Published: April 2015

The economy of human genome sequencing has catalyzed ambitious efforts to interrogate the genomes of large cohorts in search of new insight into the genetic basis of disease. This manuscript introduces Genotype Query Tools (GQT) as a new indexing strategy and toolset that addresses an analytical bottleneck by enabling interactive analyses based on genotypes, phenotypes and sample relationships. Speed improvements are achieved by operating directly on a compressed genotype index without decompression. GQT’s data compression ratios increase favorably with cohort size and relative analysis performance improves in kind. We demonstrate substantial performance improvements over state-of-the-art tools using datasets from the 1000 Genomes Project (46 fold), the Exome Aggregation Consortium (443 fold), and simulated datasets of up to 100,000 genomes (218 fold). Furthermore, we show that this indexing strategy facilitates population and statistical genetics measures such as principal component analysis and burden tests. Based on its computational efficiency and by complementing existing toolsets, GQT provides a flexible framework for current and future analyses of massive genome datasets.
Relationship between LD Score and Haseman-Elston Regression
Authors: Bulik-Sullivan Brendan
Published: April 2015

Estimating SNP-heritability from summary statistics using LD Score regression provides a convenient alternative to standard variance component models, because LD Score regression is computationally very fast and does not require individual genotype data. However, the mathematical relationship between variance component methods and LD Score regression is not clear; in particular, it is not known in general how much of an increase in standard error one incurs by working with summary data instead of individual genotypes.

In this paper, I show that in samples of unrelated individuals, LD Score regression with constrained intercept is essentially the same as Haseman-Elston (HE) regression, which is currently the state-of-the-art method for estimating SNP-heritability from ascertained case/control samples. Similar results hold for SNP-genetic correlation.
Nuclear pore proteins and the control of genome functions
Authors: Ibarra Arkaitz , Hetzer Martin W.
Published: April 2015

Nuclear pore complexes (NPCs) are composed of several copies of ∼30 different proteins called nucleoporins (Nups). NPCs penetrate the nuclear envelope (NE) and regulate the nucleocytoplasmic trafficking of macromolecules. Beyond this vital role, NPC components influence genome functions in a transport-independent manner. Nups play an evolutionarily conserved role in gene expression regulation that, in metazoans, extends into the nuclear interior. Additionally, in proliferative cells, Nups play a crucial role in genome integrity maintenance and mitotic progression. Here we discuss genome-related functions of Nups and their impact on essential DNA metabolism processes such as transcription, chromosome duplication, and segregation.
Correction of complex nonlinear signal response from a pixel array detector
Authors: van Driel Tim Brandt , Herrmann Sven , Carini Gabriella , Nielsen Martin Meedom , Lemke Henrik Till
Published: April 2015

The pulsed free-electron laser light sources represent a new challenge to photon area detectors due to the intrinsic spontaneous X-ray photon generation process that makes single-pulse detection necessary. Intensity fluctuations up to 100% between individual pulses lead to high linearity requirements in order to distinguish small signal changes. In real detectors, signal distortions as a function of the intensity distribution on the entire detector can occur. Here a robust method to correct this nonlinear response in an area detector is presented for the case of exposures to similar signals. The method is tested for the case of diffuse scattering from liquids where relevant sub-1% signal changes appear on the same order as artifacts induced by the detector electronics.
Crystal structure of 2-methyl-1H-imidazol-3-ium aquatrichlorido(oxalato-κ2O,O′)stannate(IV)
Authors: Diop Mouhamadou Birame , Diop Libasse , Plasseraud Laurent , Maris Thierry
Published: April 2015

The tin(IV) atom in the complex anion of the title salt, (C4H7N2)[Sn(C2O4)Cl3(H2O)], is in a distorted octahedral coordination environment defined by three chlorido ligands, an oxygen atom from a water molecule and two oxygen atoms from a chelating oxalate anion. The organic cation is linked through a bifurcated N—H...O hydrogen bond to the free oxygen atoms of the oxalate ligand of the complex [Sn(H2O)Cl3(C2O4)]−anion. Neighbouring stannate(IV) anions are linked through O—H...O hydrogen bonds involving the water molecule and the two non-coordinating oxalate oxygen atoms. In combination with additional N—H...Cl hydrogen bonds between cations and anions, a three-dimensional network is spanned.
Crystal structure of bis(4-methoxyphenyl) malonate
Authors: Devarajegowda H. C. , Suchetan P. A. , Sreenivasa S. , Srinivasa H. T. , Palakshamurthy B. S.
Published: April 2015

The complete molecule of the title compound, C17H16O6, is generated by crystallographic twofold symmetry, with the central methylene C atom lying on the rotation axis. The carbonyl O atom is disordered over two adjacent positions in a 0.63 (3):0.37 (3) ratio and the dihedral angle between the benzene rings in the two halves of the molecule is 79.31 (12)°. In the crystal, molecules are connected by C—H...O hydrogen bonds, generating (110) sheets. Very weak intrasheet C—H...π interactions are also observed.
Crystal structure of 2-(5-bromo-2-hydroxybenzylidene)-2,3-dihydro-1H-indene-1,3-dione
Authors: Mague Joel T. , Mohamed Shaaban K. , Akkurt Mehmet , Abdelhamid Antar A. , Albayati Mustafa R.
Published: April 2015

The title molecule, C16H9BrO3, deviates slightly from planarity. The benzene ring makes a dihedral angle of 1.02 (9)° with the plane defined by the five-membered ring of the indandione moiety. The latter exhibits a minute twist indicated by the dihedral angle of 0.47 (9)° between the planes of the five- and six-membered rings. An intramolecular C—H...O hydrogen bond between the attached benzene ring with one of the indandione carbonyl O atoms stabilizes the molecular conformation. In the crystal, the molecules form dimers across centres of inversionviapairwise O—H...O hydrogen bonds. The dimers form stacks running parallel to [010] and interact through π–π interactions between the five-membered ring of one molecule and the six-membered rings of the indandione moiety of an adjacent molecule [centroid-to-centroid distance = 3.5454 (10) Å].
Critical evaluation of the compliance of online Islamic FOREX trading with Islamic principles
Authors: Omar Rafik Fakhry , Jones Eleri
Published: April 2015

Purpose

– This study aims to evaluate the compliance of online Islamic FOREX products with Islamic jurisprudence principles and determines the degree of similarity or difference between Islamic and conventional FOREX products.

Design/methodology/approach

– This study involves the collection and analysis of secondary data from online sources (i.e. four Islamic FOREX Web sites selected on the basis that they appeared on two Islamic FOREX Web site lists) It also undertakes content analysis of the rulings of jurisprudence scholars on one of the Web sites.

Findings

– There is no evidence to suggest that the technical processes underpinning current Islamic FOREX products are any different to those underpinning conventional FOREX products. Also there are major contradiction and ambiguities in the rulings offered by the jurisprudence scholars about the permissibility of the products.

Research limitations/implications

– The study relies on the analysis of secondary data. Further research that will involve interviews with banking industry employees in both conventional and Islamic banking sectors would provide a better understanding of: how financial products are created and managed and the role of bank regulations in creating and managing different financial products.

Practical implications

– It would seem that Islamic FOREX is simply rebranding of conventional FOREX. The paper calls for a modern-day definition of usury (riba).

Social implications

– The way Islamic FOREX is marketed today to online users as synonymous with gambling, and, although branded as Islamic, the actual technical processes that underpin Islamic FOREX products are the same as conventional FOREX products and therefore not compliant with Islamic principles.

Originality/value

– This research explores the marketing of Islamic FOREX products.