Insights on the marine microbial nitrogen cycle from isotopic approaches to nitrification.

The microbial nitrogen (N) cycle involves a variety of redox processes that control the availability and speciation of N in the environment and that are involved with the production of nitrous oxide (N(2)O), a climatically important greenhouse gas. Isotopic measurements of ammonium (NH(+) (4)), nitrite (NO(-) (2)), nitrate (NO(-) (3)), and N(2)O can now be used to track the cycling of these compounds and to infer their sources and sinks, which has lead to new and exciting discoveries. For example, dual isotope measurements of NO(-) (3) and NO(-) (2) have shown that there is NO(-) (3) regeneration in the ocean's euphotic zone, as well as in and around oxygen deficient zones (ODZs), indicating that nitrification may play more roles in the ocean's N cycle than generally thought.

The theory behind the age-related positivity effect.

The "positivity effect" refers to an age-related trend that favors positive over negative stimuli in cognitive processing. Relative to their younger counterparts, older people attend to and remember more positive than negative information. Since the effect was initially identified and the conceptual basis articulated (Mather and Carstensen, 2005) scores of independent replications and related findings have appeared in the literature.

Mu killer-Mediated and Spontaneous Silencing of Zea mays Mutator Family Transposable Elements Define Distinctive Paths of Epigenetic Inactivation.

Mu killer contains a partial inverted duplication of the mudrA transposase gene and two copies of the terminal inverted repeat A (TIRA) region of the master MuDR element of maize. Mu killer can effectively silence single copy MuDR/Mu lines, and it is proposed that a ∼4 kb hairpin RNA is generated by read through transcription from a flanking gene and that this transcript serves as a substrate for siRNA production. Mu killer was sequenced, except for a recalcitrant portion in the center of the locus, and shown to be co-linear with mudrA as originally proposed.

Intensive training induces longitudinal changes in meditation state-related EEG oscillatory activity.

The capacity to focus one's attention for an extended period of time can be increased through training in contemplative practices. However, the cognitive processes engaged during meditation that support trait changes in cognition are not well characterized. We conducted a longitudinal wait-list controlled study of intensive meditation training.

Systematic underestimation of the age of selected alleles.

A common interpretation of genome-wide selection scans is that the dispersal of anatomically modern humans out of Africa and into diverse environments led to a number of genetic adaptations. If so, patterns of polymorphism from non-African individuals should show the signature of adaptations dating to 40,000-100,000 Kya, coinciding with the main exodus from Africa. However, scans of polymorphism data from a few populations have yielded conflicting results about the chronology of local, population-specific adaptations.

The power of boolean implication networks.

Human diseases have been investigated in the context of single genes as well as complex networks of genes. Though single gene approaches have been extremely successful in the past, most human diseases are complex and better characterized by multiple interacting genes commonly known as networks or pathways. With the advent of high-throughput technologies, a recent trend has been to apply network-based analysis to the huge amount of biological data.

The STAT5b Pathway Defect and Autoimmunity.

The signal transducer and activator of transcription (STAT) 5b is a universal transcription factor that plays key biological roles in allergic diseases, immunodeficiencies, autoimmunities, cancers, hematological diseases, growth disorders, and lung diseases. The identification of distinct pathological manifestations of STAT5b deficiency in humans has highlighted the critical role of the STAT5b pathway. Proper gene transcription at IL-2R α, FOXP3, Bcl-2, and growth hormone (GH) associated loci are thought to be associated with normal STAT5b transcriptional activity.

Tracking the eye non-invasively: simultaneous comparison of the scleral search coil and optical tracking techniques in the macaque monkey.

From human perception to primate neurophysiology, monitoring eye position is critical to the study of vision, attention, oculomotor control, and behavior. Two principal techniques for the precise measurement of eye position-the long-standing sclera-embedded search coil and more recent optical tracking techniques-are in use in various laboratories, but no published study compares the performance of the two methods simultaneously in the same primates. Here we compare two popular systems-a sclera-embedded search coil from C-N-C Engineering and the EyeLink 1000 optical system from SR Research-by recording simultaneously from the same eye in the macaque monkey while the animal performed a simple oculomotor task.

Global Biodiversity of Aquatic Ammonia-Oxidizing Archaea is Partitioned by Habitat.

Archaea play an important role in nitrification and are, thus, inextricably linked to the global carbon and nitrogen cycles. Since the initial discovery of an ammonia monooxygenase α-subunit (amoA) gene associated with an archaeal metagenomic fragment, archaeal amoA sequences have been detected in a wide variety of nitrifying environments. Recent sequencing efforts have revealed extensive diversity of archaeal amoA sequences within different habitats.

PowerPoint(®) Presentation Flaws and Failures: A Psychological Analysis.

Electronic slideshow presentations are often faulted anecdotally, but little empirical work has documented their faults. In Study 1 we found that eight psychological principles are often violated in PowerPoint(®) slideshows, and are violated to similar extents across different fields - for example, academic research slideshows generally were no better or worse than business slideshows. In Study 2 we found that respondents reported having noticed, and having been annoyed by, specific problems in presentations arising from violations of particular psychological principles.

Therapeutic potential of bone marrow-derived mesenchymal stem cells for cutaneous wound healing.

Despite advances in wound care, many wounds never heal and become chronic problems that result in significant morbidity and mortality to the patient. Cellular therapy for cutaneous wounds has recently come under investigation as a potential treatment modality for impaired wound healing. Bone marrow-derived mesenchymal stem cells (MSCs) are a promising source of adult progenitor cells for cytotherapy as they are easy to isolate and expand and have been shown to differentiate into various cell lineages.

The protective and therapeutic function of small heat shock proteins in neurological diseases.

Historically, small heat shock proteins (sHSPs) have been extensively studied in the context of being intracellular molecular chaperones. However, recent studies looking at the role of sHSPs in neurological diseases have demonstrated a near universal upregulation of certain sHSPs in damaged and diseased brains. Initially, it was thought that sHSPs are pathological in these disease states because they are found in the areas of damage.

Exact Covariance Thresholding into Connected Components for Large-Scale Graphical Lasso.

We consider the sparse inverse covariance regularization problem or with regularization parameter λ. Suppose the sample formed by thresholding the entries of the sample covariance matrix at λ is decomposed into connected components. We show that the induced by the connected components of the thresholded sample covariance graph (at λ) is equal to that induced by the connected components of the estimated concentration graph, obtained by solving the graphical lasso problem for the λ.

Improvement in cell capture throughput using parallel bioactivated microfluidic channels.

Optimization of targeted cell capture with microfluidic devices continues to be a challenge. On the one hand, microfluidics allow working with microliter volumes of liquids, whereas various applications in the real world require detection of target analyte in large volumes, such as capture of rare cell types in several ml of blood. This contrast of volumes (microliter vs.

Beyond natural numbers: negative number representation in parietal cortex.

Unlike natural numbers, negative numbers do not have natural physical referents. How does the brain represent such abstract mathematical concepts? Two competing hypotheses regarding representational systems for negative numbers are a rule-based model, in which symbolic rules are applied to negative numbers to translate them into positive numbers when assessing magnitudes, and an expanded magnitude model, in which negative numbers have a distinct magnitude representation. Using an event-related functional magnetic resonance imaging design, we examined brain responses in 22 adults while they performed magnitude comparisons of negative and positive numbers that were quantitatively near (difference <4) or far apart (difference >6).

Social Anxiety Modulates Risk Sensitivity through Activity in the Anterior Insula.

Decision neuroscience offers the potential for decomposing differences in behavior across individuals into components of valuation intimately tied to brain function. One application of this approach lies in novel conceptualizations of behavioral attributes that are aberrant in psychiatric disorders. We investigated the relationship between social anxiety and behavior in a novel socially determined risk task.

GRFT - Genetic Records Family Tree Web Applet.

Current software for storing and displaying records of genetic crosses does not provide an easy way to determine the lineage of an individual. The genetic records family tree (GRFT) applet processes records of genetic crosses and allows researchers to quickly visualize lineages using a family tree construct and to access other information from these records using any Internet browser. Users select from three display features: (1) a family tree view which displays a color-coded family tree for an individual, (2) a sequential list of crosses, and (3) a list of crosses matching user-defined search criteria.

Evolutionary history, immigration history, and the extent of diversification in community assembly.

During community assembly, species may accumulate not only by immigration, but also by in situ diversification. Diversification has intrigued biologists because its extent varies even among closely related lineages under similar ecological conditions. Recent research has suggested that some of this puzzling variation may be caused by stochastic differences in the history of immigration (relative timing and order of immigration by founding populations), indicating that immigration and diversification may affect community assembly interactively.

Age differences in primary prevention implantable cardioverter-defibrillator use in U.S. individuals.

Objectives: To estimate the potentially inappropriate use of implantable cardioverter-defibrillator ICDs in older U.S. adults.

Sensitivity Analysis and Bounding of Causal Effects With Alternative Identifying Assumptions.

When identification of causal effects relies on untestable assumptions regarding nonidentified parameters, sensitivity of causal effect estimates is often questioned. For proper interpretation of causal effect estimates in this situation, deriving bounds on causal parameters or exploring the sensitivity of estimates to scientifically plausible alternative assumptions can be critical. In this paper, we propose a practical way of bounding and sensitivity analysis, where multiple identifying assumptions are combined to construct tighter common bounds.

A protocol for isolation and enriched monolayer cultivation of neural precursor cells from mouse dentate gyrus.

In vitro assays are valuable tools to study the characteristics of adult neural precursor cells under controlled conditions with a defined set of parameters. We here present a detailed protocol based on our previous original publication (Babu et al., 2007) to isolate neural precursor cells from the hippocampus of adult mice and maintain and propagate them as adherent monolayer cultures.