Geometry as a Universal mental Construction

Geometry, etymologically the “science of measuring the Earth”, is a mathematical formalization of space. Just as formal concepts of number may be rooted in an evolutionary ancient system for perceiving numerical quantity, the fathers of geometry may have been inspired by their perception of space. Is the spatial content of formal Euclidean geometry universally present in the way humans perceive space, or is Euclidean geometry a mental construction, specific to those who have received appropriate instruction? The spatial content of the formal theories of geometry may depart from spatial perception for two reasons: first, because in geometry, only some of the features of spatial figures are theoretically relevant; and second, because some geometric concepts go beyond any possible perceptual experience. Focusing in turn on these two aspects of geometry, we will present several lines of research on US adults and children from the age of three years, and participants from an Amazonian culture, the Mundurucu. Almost all the aspects of geometry tested proved to be shared between these two cultures. Nevertheless, some aspects involve a process of mental construction where explicit instruction seem to play a role in the US, but that can still take place in the absence of instruction in geometry

Prominence, promotion and positioning of the ‘Thesis by publication’ in six countries

The international nature of doctoral education creates interesting tensions where national systems, institutional policies, disciplinary customs, individual supervisor preferences, and doctoral researcher needs meet. The Thesis by Publication (TBP), a model where published works are included within the thesis, is available to doctoral researchers in many disciplines and institutions, but it is not a universally accepted format or approached in a homogeneous way. Policy has been known to shape practice, yet we know little about how institutional policies shape TBP practices across different national contexts. This study presents a content analysis of policy documents related to the TBP in public universities across six countries: Australia, Japan, New Zealand, South Africa, Spain, and the United Kingdom. Our goal is to understand the prevalence of the TBP and related policy documentation in different contexts, and how the model is promoted and positioned within the doctoral landscape. Findings from our study challenge the often-stated notion that the TBP is a universally understood format. Our findings also show the risks in the absence of explicit policies, as well as the possible inequalities that may arise as a result of a lack of policy transparency and synergy within and across contexts.Peer reviewe

Phosphate release contributes to the rate-limiting step for unwinding by an RNA helicase

RNA helicases function in numerous aspects of RNA biology. These enzymes are RNA-stimulated ATPases that translocate on RNA and unwind or remodel structured RNA in an ATP-dependent fashion. How ATP and the ATPase cycle fuel the work performed by helicases is not completely clear. The hepatitis C virus RNA helicase, NS3, is an important model system for this class of enzymes. NS3 binding to a single-/double-strand RNA or DNA junction leads to ATP-independent melting of the duplex and formation of a complex capable of ATP-dependent unwinding by using a spring-loaded mechanism. We have established an RNA substrate for NS3 that can be unwound in a single sub-step. Our studies are consistent with a model in which a single ATP binding and/or hydrolysis event sets the unwinding spring and phosphate dissociation contributes to release of the spring, thereby driving the power stroke used for unwinding

FVCOM validation experiments : comparisons with ROMS for three idealized barotropic test problems

Author Posting. © American Geophysical Union, 2008. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 113 (2008): C07042, doi:10.1029/2007JC004557.The unstructured-grid Finite-Volume Coastal Ocean Model (FVCOM) is evaluated using three idealized benchmark test problems: the Rossby equatorial soliton, the hydraulic jump, and the three-dimensional barotropic wind-driven basin. These test cases examine the properties of numerical dispersion and damping, the performance of the nonlinear advection scheme for supercritical flow conditions, and the accuracy of the implicit vertical viscosity scheme in barotropic settings, respectively. It is demonstrated that FVCOM provides overall a second-order spatial accuracy for the vertically averaged equations (i.e., external mode), and with increasing grid resolution the model-computed solutions show a fast convergence toward the analytic solutions regardless of the particular triangulation method. Examples are provided to illustrate the ability of FVCOM to facilitate local grid refinement and speed up computation. Comparisons are also made between FVCOM and the structured-grid Regional Ocean Modeling System (ROMS) for these test cases. For the linear problem in a simple rectangular domain, i.e., the wind-driven basin case, the performance of the two models is quite similar. For the nonlinear case, such as the Rossby equatorial soliton, the second-order advection scheme used in FVCOM is almost as accurate as the fourth-order advection scheme implemented in ROMS if the horizontal resolution is relatively high. FVCOM has taken advantage of the new development in computational fluid dynamics in resolving flow problems containing discontinuities. One salient feature illustrated by the three-dimensional barotropic wind-driven basin case is that FVCOM and ROMS simulations show different responses to the refinement of grid size in the horizontal and in the vertical.For this work, H. Huang and G. Cowles were supported by the Massachusetts Marine Fisheries Institute (MFI) through NOAA grants DOC/NOAA/NA04NMF4720332 and DOC/ NOAA/NA05NMF472113; C. Chen was supported by NSF grants (OCE0234545, OCE0606928, OCE0712903, OCE0732084, and OCE0726851), NOAA grants (NA160P2323, NA06RG0029, and NA960P0113), MIT Sea grant (2006-RC-103), and Georgia Sea grant (NA26RG0373 and NA66RG0282); C. Winant was supported through NSF grant OCE-0726673; R. Beardsley was supported through NSF OCE—0227679 and the WHOI Smith Chair; K. Hedstrom was supported through NASA grant NAG13– 03021 and the Arctic Region Supercomputing Center; and D. Haidvogel was supported through grants ONR N00014- 03-1-0683 and NSF OCE 043557

Moving Beyond Too Little, Too Late: Managing Emerging Infectious Diseases in Wild Populations Requires International Policy and Partnerships

No Full Tex

Supplemental Information 6: Data S1.

Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host’s health and to provide defenses against invading pathogens. However, we have little understanding of the skin and fur bacterial microbiota on bats, or factors that influence the structure of these communities. The southwestern United States offers excellent sites for the study of external bat bacterial microbiota due to the diversity of bat species, the variety of abiotic and biotic factors that may govern bat bacterial microbiota communities, and the lack of the newly emergent fungal disease in bats, white-nose syndrome (WNS), in the southwest. To test these variables, we used 16S rRNA gene 454 pyrosequencing from swabs of external skin and fur surfaces from 163 bats from 13 species sampled from southeastern New Mexico to northwestern Arizona. Community similarity patterns, random forest models, and generalized linear mixed-effects models show that factors such as location (e.g., cave-caught versus surface-netted) and ecoregion are major contributors to the structure of bacterial communities on bats. Bats caught in caves had a distinct microbial community compared to those that were netted on the surface. Our results provide a first insight into the distribution of skin and fur bat bacteria in the WNS-free environment of New Mexico and Arizona. More importantly, it provides a baseline of bat external microbiota that can be explored for potential natural defenses against pathogens

Context-dependent conservation responses to emerging wildlife diseases

Emerging infectious diseases pose an important threat to wildlife. While established protocols exist for combating outbreaks of human and agricultural pathogens, appropriate management actions before, during, and after the invasion of wildlife pathogens have not been developed. We describe stage-specific goals and management actions that minimize disease impacts on wildlife, and the research required to implement them. Before pathogen arrival, reducing the probability of introduction through quarantine and trade restrictions is key because prevention is more cost effective than subsequent responses. On the invasion front, the main goals are limiting pathogen spread and preventing establishment. In locations experiencing an epidemic, management should focus on reducing transmission and disease, and promoting the development of resistance or tolerance. Finally, if pathogen and host populations reach a stable stage, then recovery of host populations in the face of new threats is paramount. Successful management of wildlife disease requires risk-taking, rapid implementation, and an adaptive approach."Funding was provided by the US National Science Foundation (grants EF-0914866, DGE-0741448, DEB-1115069, DEB-1336290) and the National Institutes of Health (grant 1R010AI090159)."https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/14024

Changes in PYY and gastric emptying across the phases of the menstrual cycle and the influence of the ovarian hormones

Nutrition-related studies avoid the participation of pre-menopausal women due to the potential effect of the menstrual cycle (MC) on their appetite regulation. It is generally accepted that women increase their energy intake during the luteal phase (LPh) compared to the follicular (FPh), however what happens in the menstrual phase (MPh) and how this might be regulated remains uncertain. Although some research indicates changes in the gastric emptying (GE) velocity, whether PYY is affected by the MC phase, remains unknown. The aim of this study was to assess whether eating the same breakfast in each of the three MC phases would change the GE time, the PYY response and post-prandial satiety such that they might affect subsequent food intake. Furthermore, the aim was to associate any potential differences to the fluctuations in estradiol (E2) and progesterone (P4) within a MC. Nine naturally cycling women attended to the laboratory to consume a standardised breakfast on three occasions, each of them representing one of the MC phases. Breath samples to measure GE time, plasma samples to quantify PYY levels and hunger scores were collected for a total of 4 h after which food intake was assessed by an ad-libitum buffet lunch. GE and PYY levels changed significantly across the phases of the MC (p < 0.05). GE was correlated to P4 and E2-P4 ratio (r = -0.5 and 0.4, respectively). To conclude, the appetite regulators PYY and GE time change depending upon the MC phases with GE time associated with the ovarian hormone levels which suggests the necessity of controlling the MC phase in studies looking at the appetite response

Filtration Improves the Performance of a High-Throughput Screen for Anti-Mycobacterial Compounds

The tendency for mycobacteria to aggregate poses a challenge for their use in microplate based assays. Good dispersions have been difficult to achieve in high-throughput screening (HTS) assays used in the search for novel antibacterial drugs to treat tuberculosis and other related diseases. Here we describe a method using filtration to overcome the problem of variability resulting from aggregation of mycobacteria. This method consistently yielded higher reproducibility and lower variability than conventional methods, such as settling under gravity and vortexing

Electron Cryotomography of Bacterial Secretion Systems

In biology, function arises from form. For bacterial secretion systems, which often span two membranes, avidly bind to the cell wall, and contain hundreds of individual proteins, studying form is a daunting task, made possible by electron cryotomography (ECT). ECT is the highest-resolution imaging technique currently available to visualize unique objects inside cells, providing a three-dimensional view of the shapes and locations of large macromolecular complexes in their native environment. Over the past 15 years, ECT has contributed to the study of bacterial secretion systems in two main ways: by revealing intact forms for the first time and by mapping components into these forms. Here we highlight some of these contributions, revealing structural convergence in type II secretion systems, structural divergence in type III secretion systems, unexpected structures in type IV secretion systems, and unexpected mechanisms in types V and VI secretion systems. Together, they offer a glimpse into a world of fantastic forms—nanoscale rotors, needles, pumps, and dart guns—much of which remains to be explored