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The Quantitative Undergraduate Biology Education and Synthesis (QUBES) platform was conceived as a "science education gateway" and designed to accelerate innovation in undergraduate science, technology, engineering, and mathematics (STEM) education. The technical infrastructure was purpose built to provide more equitable access to professional resources, support learning that reflects authentic science, and promote open educational practices. Four platform services (Open Educational Resource library access; professional learning; partner support; and customizable workspaces) support overlapping faculty user communities, provide multiple points of entry, and enable manifold use-case scenarios. The integrated nature of the platform makes it possible to collect, curate, and disseminate a diverse array of reform resources in a scalable and sustainable manner. We believe that the cyberinfrastructure provided by the QUBES platform has the capacity to broaden participation in scholarship around teaching and learning and, furthermore, that it can help to lower faculty barriers to the adoption of reform practices. Thus, we call for further exploration of the roles of cyberinfrastructure in undergraduate STEM education. [ABSTRACT FROM AUTHOR]

Summary: Scholars worldwide leverage science gateways/virtual research environments (VREs) for a wide variety of research and education endeavors spanning diverse scientific fields. Evaluating the value of a given science gateway/VRE to its constituent community is critical in obtaining the financial and human resources necessary to sustain operations and increase adoption in the user community. In this article, we feature a variety of exemplar science gateways/VREs and detail how they define impact in terms of, for example, their purpose, operation principles, and size of user base. Further, the exemplars recognize that their science gateways/VREs will continuously evolve with technological advancements and standards in cloud computing platforms, web service architectures, data management tools and cybersecurity. Correspondingly, we present a number of technology advances that could be incorporated in next‐generation science gateways/VREs to enhance their scope and scale of their operations for greater success/impact. The exemplars are selected from owners of science gateways in the Science Gateways Community Institute (SGCI) clientele in the United States, and from the owners of VREs in the International Virtual Research Environment Interest Group (VRE‐IG) of the Research Data Alliance. Thus, community‐driven best practices and technology advances are compiled from diverse expert groups with an international perspective to envisage futuristic science gateway/VRE innovations. [ABSTRACT FROM AUTHOR]

In the United States, there are multiple reports from both mathematics and biology communities that address the quantitative preparation of undergraduate life science students. Many of these reports make broad recommendations for the revision of life science curriculum to incorporate more quantitative techniques. Here, we review initiatives and progress in the United States on the state of quantitative biology education in the context of the mathematics education, biology research frontiers, and the funding system and other sources of support for systemic change to meet new demands. [ABSTRACT FROM AUTHOR]

Despite widespread calls for the incorporation of mathematical modeling into the undergraduate biology curriculum, there is lack of a common understanding around the definition of modeling, which inhibits progress. In this paper, we extend the "Rule-of-Four," initially used in calculus reform efforts, to a "Rule-of-Five" framework for models and modeling that is inclusive of varying disciplinary definitions of each. This unifying framework allows us to both build on strengths that each discipline and its students bring, but also identify gaps in modeling activities practiced by each discipline. We also discuss benefits to student learning and interdisciplinary collaboration. [ABSTRACT FROM AUTHOR]

Quantitatively linking individual variation in functional traits to demography is a necessary step to advance our understanding of trait‐based ecological processes. We constructed a population model for Asclepias syriaca to identify how functional traits affect vital rates and population growth and whether trade‐offs in chemical defence and demography alter population growth. Plants with higher foliar cardenolides had lower fibre, cellulose and lignin levels, as well as decreased sexual and clonal reproduction. Average cardenolide concentrations had the strongest effect on population growth. In both the sexual and clonal pathway, the trade‐off between reproduction and defence affected population growth. We found that both increasing the mean of the distribution of individual plant values for cardenolides and herbivory decreased population growth. However, increasing the variance in both defence and herbivory increased population growth. Functional traits can impact population growth and quantifying individual‐level variation in traits should be included in assessments of population‐level processes. [ABSTRACT FROM AUTHOR]

The article presents a series of short interviews with several contemporary artists such as the Gey Pin Ang, Massimiliano Balduzzi, Ditte Berkeley working on, through and out of song in challenging and exciting ways. Topics discussed include offers a series of glimpses into the authors’ diverse lines of research; discussions on the musical notations of the songs; and the information on the tunes and melodies of Western folk tradition.

Breathing in mammals depends on rhythms that originate from the preBötzinger complex (preBötC) of the ventral medulla and a network of brainstem and spinal premotor neurons. The rhythm-generating core of the preBötC, as well as some premotor circuits, consist of interneurons derived from Dbxl-expressing precursors (Dbxl neurons), but the structure and function of these networks remain incompletely understood. We previously developed a cell-specific detection and laser ablation system to interrogate respiratory network structure and function in a slice model of breathing that retains the preBötC, the respiratory-related hypoglossal (XII) motor nucleus and XII premotor circuits. In spontaneously rhythmic slices, cumulative ablation of Dbxl preBötC neurons decreased XII motor output by -50% after -15 cell deletions, and then decelerated and terminated rhythmic function altogether as the tally increased to -85 neurons. In contrast, cumulatively deleting Dbxl XII premotor neurons decreased motor output monotonically but did not affect frequency nor stop XII output regardless of the ablation tally. Here, we couple an existing preBötC model with a premotor population in several topological configurations to investigate which one may replicate the laser ablation experiments best. If the XII premotor population is a "small-world" network (rich in local connections with sparse long-range connections among constituent premotor neurons) and connected with the preBötC such that the total number of incoming synapses remains fixed, then the in silico system successfully replicates the in vitro laser ablation experiments. This study proposes a feasible configuration for circuits consisting of Dbxl-derived interneurons that generate inspiratory rhythm and motor pattern. [ABSTRACT FROM AUTHOR]

Objective The purpose of this study was to examine the relationship between verbal learning and memory performance and hippocampal volume in subjects with co-morbid type 2 diabetes and major depression compared with healthy control subjects and subjects with type 2 diabetes alone. Methods Twenty four subjects with type 2 diabetes and 20 subjects with type 2 diabetes and major depression were recruited from endocrinology clinics and were compared with 32 healthy control subjects recruited from the community. Subjects were scanned on a 1.5 T GE scanner, and hippocampal volumes were measured using Freesurfer. The California Verbal Learning Test assessed learning and memory. Significant predictors of verbal learning performance (e.g., age, gender, education, blood pressure, stroke risk, hemoglobin A1c, and hippocampal volume) were determined using a stepwise linear regression. Results Subjects with diabetes and depression had significantly worse performance on verbal list learning compared with healthy control subjects. Hippocampal volume was a strong predictor of performance in healthy control subjects, and age and hippocampal volume were strong predictors in subjects with type 2 diabetes alone. Age alone was a significant predictor of verbal learning performance in subjects with diabetes and depression. Conclusions The relationship between hippocampal volume and performance on the California Verbal Learning Test is decoupled in subjects with type 2 diabetes and major depression and this decoupling may contribute to poor verbal learning and memory performance in this study population. Copyright © 2014 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

This letter provides an overview of the Quantitative Undergraduate Biology Education and Synthesis (QUBES) Project funded through the National Science Foundation. The project has five distinct, but interdependent, initiatives which work together to support faculty and students in the teaching and learning of quantitative biology (QB). QUBES has adopted an integrated strategy to improving the frequency and effectiveness of QB instruction that includes coordinating a broad consortium of professional stakeholders, supporting faculty development and the implementation of new teaching practices, providing an infrastructure for collaboration and access to high quality materials, establishing new metrics for faculty teaching scholarship and documenting the project outcomes. [ABSTRACT FROM AUTHOR]

Cortical-subcortical circuits have been implicated in the pathophysiology of mood disorders. Structural and biochemical abnormalities have been identified in patients diagnosed with mood disorders using magnetic resonance imaging-related approaches. In this study, we used magnetization transfer (MT), an innovative magnetic resonance approach, to study biophysical changes in both gray and white matter regions in cortical-subcortical circuits implicated in emotional regulation and behavior. Our study samples comprised 28 patients clinically diagnosed with major depressive disorder (MDD) and 31 non-depressed subjects of comparable age and gender. MT ratio (MTR), representing the biophysical integrity of macromolecular proteins within key components of cortical-subcortical circuits-the caudate, thalamic, striatal, orbitofrontal, anterior cingulate and dorsolateral regions-was the primary outcome measure. In our study, the MTR in the head of the right caudate nucleus was significantly lower in the MDD group when compared with the comparison group. MTR values showed an inverse relationship with age in both groups, with more widespread relationships observed in the MDD group. These data indicate that focal biophysical abnormalities in the caudate nucleus may be central to the pathophysiology of depression and critical to the cortical-subcortical abnormalities that underlie mood disorders. Depression may also accentuate age-related changes in the biophysical properties of cortical and subcortical regions. These observations have broad implications for the neuronal circuitry underlying mood disorders across the lifespan. [ABSTRACT FROM AUTHOR]

BackgroundAlthough significant changes in both gray and white matter have been noted in late-life depression (LLD), the pathophysiology of implicated white-matter tracts has not been fully described. In this study we examined the integrity of specific white-matter tracts in LLD versus healthy controls (HC).MethodParticipants aged ⩾60 years were recruited from the community. The sample included 23 clinically diagnosed individuals with LLD and 23 HC. White-matter integrity metrics [fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD) and radial diffusivity (RD)] were calculated in the bilateral cingulum and uncinate fasciculus. Depression severity was measured using the Center for Epidemiological Studies Depression Scale (CESD). Composite scores for learning and memory and executive function were created using standardized neuropsychological assessments.ResultsWhite-matter integrity was lower in LLD versus HC in the bilateral cingulum and right uncinate fasciculus (p⩽0.05). In the whole sample, depression severity correlated with integrity in the bilateral cingulum and right uncinate fasciculus (p ⩽0.05). In patients, depression severity correlated with the integrity of the left uncinate fasciculus (p = 0.03); this tract also correlated with executive function (p = 0.02). Among HC, tract integrity did not correlate with depression scores; however, learning and memory correlated with integrity of the bilateral uncinate fasciculus and bilateral cingulum; executive function correlated with the right uncinate and left cingulum (p ⩽0.05).ConclusionsWhite-matter tract integrity was lower in LLD than in HC and was associated with depression severity across all participants. Tract integrity was associated with cognition in both groups but more robustly among HC. [ABSTRACT FROM PUBLISHER]

Background:The mesenchymal-epithelial transition factor (MET) receptor is dysregulated in hepatocellular carcinoma (HCC), and tivantinib (ARQ 197) is an oral, selective, MET inhibitor.Methods:This Phase-1b study assessed tivantinib safety as primary objective in patients with previously treated HCC and Child-Pugh A or B liver cirrhosis. Patients received oral tivantinib 360 mg twice daily until disease progression or unacceptable toxicity.Results:Among 21 HCC patients, common drug-related adverse events (AEs) were neutropaenia, anaemia, asthenia, leucopaenia, anorexia, diarrhoea, and fatigue. No drug-related worsening of liver function or performance status occurred, but one Child-Pugh B patient experienced drug-related bilirubin increase. Four patients had drug-related serious AEs, including one neutropaenia-related death. Haematologic toxicities were more frequent than in previous tivantinib studies but were manageable with prompt therapy. Best response was stable disease (median, 5.3 months) in 9 of 16 evaluable patients (56%). Median time to progression was 3.3 months.Conclusion:Tivantinib demonstrated a manageable safety profile and preliminary antitumour activity in patients with HCC and Child-Pugh A or B cirrhosis. [ABSTRACT FROM AUTHOR]

Vocal fold (VF) motion is a fundamental process in voice production, and is also a challenging problem for numerical computation because the VF dynamics depend on nonlinear coupling of air flow with the response of elastic channels (VF), which undergo opening and closing, and induce internal flow separation. The traditional modeling approach makes use of quasisteady flow approximation or Bernoulli's law which ignores air compressibility, and is known to be invalid during VF opening. Ahydrodynamic semicontinuum system for VF motion is presented. The airflow is modeled by a modified quasi-one-dimensional Euler system with coupling to VF velocity. The VF is modeled by a lumped two mass system with a built-in geometric condition on flow separation. The modified Euler system contains the Bernoulli's law as a special case, and is derivable from the two-dimensional compressible Navier-Stokes equations in the inviscid limit. The computational domain contains also solid walls next to VFs (flexible walls). It is shown numerically that several salient features of VFs are captured, especially transients such as the double peaks of the driving subglottal pressures at the opening and the closing stages of VF motion consistent with fully resolved two-dimensional direct simulations, and experimental data. The system is much simpler to compute than a VF model based on two-dimensional Navier-Stokes system. [ABSTRACT FROM AUTHOR]

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