Journal Articles

  • Rules for reproducibility win support
    [Nov 2014]

    Nature -

    Rules for reproducibility win support

    Nature 514, 7524 (2014). doi:10.1038/514539e

    Nearly a decade after writing a scathing critique of biomedical research, 'Why Most Published Research Findings Are False', Stanford University scientist John Ioannidis has published a follow-up. The health-policy researcher suggests a blueprint for making scientific results more reliable, including increasing the statistical certainty of

    Categories: Journal Articles
  • The top 100 papers
    [Nov 2014]

    Nature -

    The top 100 papers

    Nature 514, 7524 (2014). http://www.nature.com/doifinder/10.1038/514550a

    Authors: Richard Van Noorden, Brendan Maher & Regina Nuzzo

    Nature explores the most-cited research of all time.

    Categories: Journal Articles
  • The Ebola questions
    [Nov 2014]

    Nature -

    The Ebola questions

    Nature 514, 7524 (2014). http://www.nature.com/doifinder/10.1038/514554a

    Author: Erika Check Hayden

    Scientists know a lot about the virus that causes Ebola — but there are many puzzles that they have yet to solve.

    Categories: Journal Articles
  • Human spaceflight: Find asteroids to get to Mars
    [Nov 2014]

    Nature -

    Human spaceflight: Find asteroids to get to Mars

    Nature 514, 7524 (2014). doi:10.1038/514559a

    Author: Richard P. Binzel

    Asteroid retrieval is a distraction, says Richard P. Binzel. Better steps to interplanetary travel abound.

    Categories: Journal Articles
  • Bibliometrics: Is your most cited work your best?
    [Nov 2014]

    Nature -

    Bibliometrics: Is your most cited work your best?

    Nature 514, 7524 (2014). doi:10.1038/514561a

    Authors: John P. A. Ioannidis, Kevin W. Boyack, Henry Small, Aaron A. Sorensen & Richard Klavans

    John P. A. Ioannidis and colleagues asked the most highly cited biomedical scientists to score their top-ten papers in six ways.

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  • Role of COQ9 in coenzyme Q biosynthesis [Biochemistry]
    [Nov 2014]

    Coenzyme Q (CoQ) is an isoprenylated quinone that is essential for cellular respiration and is synthesized in mitochondria by the combined action of at least nine proteins (COQ1–9). Although most COQ proteins are known to catalyze modifications to CoQ precursors, the biochemical role of COQ9 remains unclear. Here, we report...
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  • NAADP/TPC2/Ca2+ in VEGF-induced angiogenesis [Cell Biology]
    [Nov 2014]

    Vascular endothelial growth factor (VEGF) and its receptors VEGFR1/VEGFR2 play major roles in controlling angiogenesis, including vascularization of solid tumors. Here we describe a specific Ca2+ signaling pathway linked to the VEGFR2 receptor subtype, controlling the critical angiogenic responses of endothelial cells (ECs) to VEGF. Key steps of this pathway...
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  • WWOX regulates DDR [Cell Biology]
    [Nov 2014]

    Genomic instability is a hallmark of cancer. The WW domain-containing oxidoreductase (WWOX) is a tumor suppressor spanning the common chromosomal fragile site FRA16D. Here, we report a direct role of WWOX in DNA damage response (DDR) and DNA repair. We show that Wwox deficiency results in reduced activation of the...
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  • Single-cell transcriptional heterogeneity [Cell Biology]
    [Nov 2014]

    The acute cellular response to stress generates a subpopulation of reversibly stress-tolerant cells under conditions that are lethal to the majority of the population. Stress tolerance is attributed to heterogeneity of gene expression within the population to ensure survival of a minority. We performed whole transcriptome sequencing analyses of metastatic...
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  • Parallel gene expression evolution in photophores [Evolution]
    [Nov 2014]

    Despite contingency in life’s history, the similarity of evolutionarily convergent traits may represent predictable solutions to common conditions. However, the extent to which overall gene expression levels (transcriptomes) underlying convergent traits are themselves convergent remains largely unexplored. Here, we show strong statistical support for convergent evolutionary origins and massively parallel...
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  • Genomic analyses of A. cinnamomea [Genetics]
    [Nov 2014]

    Antrodia cinnamomea, a polyporus mushroom of Taiwan, has long been used as a remedy for cancer, hypertension, and hangover, with an annual market of over $100 million (US) in Taiwan. We obtained a 32.15-Mb genome draft containing 9,254 genes. Genome ontology enrichment and pathway analyses shed light on sexual development...
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  • Novel mediators in organ protection and resolution [Immunology and Inflammation]
    [Nov 2014]

    Upon infection and inflammation, tissue repair and regeneration are essential in reestablishing function. Here we identified potent molecules present in self-limited infectious murine exudates, regenerating planaria, and human milk as well as macrophages that stimulate tissue regeneration in planaria and are proresolving. Characterization of their physical properties and isotope tracking...
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  • IRAK1 mutation defines PEL [Microbiology]
    [Nov 2014]

    Primary effusion lymphoma (PEL) is an AIDS-defining cancer. All PELs carry Kaposi sarcoma-associated herpesvirus (KSHV). X chromosome-targeted sequencing of PEL identified 34 common missense mutations in 100% of cases. This included a Phe196Ser change in the interleukin 1 receptor-associated kinase 1 (IRAK1). The mutation was verified in primary PEL exudates....
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  • FUS and synaptic homeostasis [Neuroscience]
    [Nov 2014]

    The RNA-binding protein fused-in-sarcoma (FUS) has been associated with amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD), two neurodegenerative disorders that share similar clinical and pathological features. Both missense mutations and overexpression of wild-type FUS protein can be pathogenic in human patients. To study the molecular and cellular basis...
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  • DAT variant Val559 in transgenic mice [Neuroscience]
    [Nov 2014]

    Despite the critical role of the presynaptic dopamine (DA) transporter (DAT, SLC6A3) in DA clearance and psychostimulant responses, evidence that DAT dysfunction supports risk for mental illness is indirect. Recently, we identified a rare, nonsynonymous Slc6a3 variant that produces the DAT substitution Ala559Val in two male siblings who share a...
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  • Tarantula toxins probe ion channel activity [Physiology]
    [Nov 2014]

    Electrically excitable cells, such as neurons, exhibit tremendous diversity in their firing patterns, a consequence of the complex collection of ion channels present in any specific cell. Although numerous methods are capable of measuring cellular electrical signals, understanding which types of ion channels give rise to these signals remains a...
    Categories: Journal Articles
  • Time-variant clustering for cell fate decision [Systems Biology]
    [Nov 2014]

    Both spatial characteristics and temporal features are often the subjects of concern in physical, social, and biological studies. This work tackles the clustering problems for time course data in which the cluster number and clustering structure change with respect to time, dubbed time-variant clustering. We developed a hierarchical model that...
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  • Phytochrome signaling in marine algae [Environmental Sciences]
    [Nov 2014]

    Phytochrome photosensors control a vast gene network in streptophyte plants, acting as master regulators of diverse growth and developmental processes throughout the life cycle. In contrast with their absence in known chlorophyte algal genomes and most sequenced prasinophyte algal genomes, a phytochrome is found in Micromonas pusilla, a widely distributed...
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  • Chlamydomonas repressor of cellular quiescence [Plant Biology]
    [Nov 2014]

    Microalgae are prolific photosynthetic organisms that have the potential to sustainably produce high-value chemical feedstocks. However, an industry based on microalgal biomass still is faced with challenges. For example, microalgae tend to accumulate valuable compounds, such as triacylglycerols, only under stress conditions that limit growth. To investigate the fundamental mechanisms...
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  • Protein repair in photosynthetic membranes [Plant Biology]
    [Nov 2014]

    A crucial component of protein homeostasis in cells is the repair of damaged proteins. The repair of oxygen-evolving photosystem II (PS II) supercomplexes in plant chloroplasts is a prime example of a very efficient repair process that evolved in response to the high vulnerability of PS II to photooxidative damage,...
    Categories: Journal Articles
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