A comparative study of the efficiency of chart versus computer-generated contrast sensitivity testing in glaucoma patients and controls

Purpose. The goal of this study was to assess the efficiency of chart vs. computergenerated contrast sensitivity tests in glaucoma patients and controls. Methods. A total of 64 individuals (30 young controls, 18 older controls, 16 glaucoma patients) were tested for contrast sensitivity using 4 different tests. Two tests determined contrast sensitivity (CS) for detecting large targets with sharp borders. One of these was the MARS printed chart, and the other a computerized number search test by Bailey. The second assessment determined spatial contrast sensitivity (SCS) for sinusoidal grating targets at several spatial frequencies. One of these was the printed Vistech chart, the other a computerized test by Faubert. Results. Both CS tests showed a decrease in the glaucoma group versus both the control groups (p < 0.001). The tests for SCS demonstrated a decrease in sensitivity both with age (p < 0.001) and in the presence of glaucoma (p < 0.001) across all spatial frequencies. Conclusion. The data indicated that SCS was superior in separating the three study groups. Neither of the computer-generated tests was more sensitive than its printed counterpart

Non-equilibrium phase transitions in biomolecular signal transduction

We study a mechanism for reliable switching in biomolecular signal-transduction cascades. Steady bistable states are created by system-size cooperative effects in populations of proteins, in spite of the fact that the phosphorylation-state transitions of any molecule, by means of which the switch is implemented, are highly stochastic. The emergence of switching is a nonequilibrium phase transition in an energetically driven, dissipative system described by a master equation. We use operator and functional integral methods from reaction-diffusion theory to solve for the phase structure, noise spectrum, and escape trajectories and first-passage times of a class of minimal models of switches, showing how all critical properties for switch behavior can be computed within a unified framework

Size-dependent rheology of type-I collagen networks

We investigate the system size dependent rheological response of branched type I collagen gels. When subjected to a shear strain, the highly interconnected mesh dynamically reorients, resulting in overall stiffening of the network. When a continuous shear strain is applied to a collagen network, we observe that the local apparent modulus, in the strain-stiffening regime, is strongly dependent on the gel thickness. In addition, we demonstrate that the overall network failure is determined by the ratio of the gel thickness to the mesh size. These findings have broad implications for cell-matrix interactions, the interpretation of rheological tissue data, and the engineering of biomimetic scaffolds.Comment: 3 pages, 4 figures, to appear in Biophysical Journal Letters, September 201

dictyBase, the model organism database for Dictyostelium discoideum

dictyBase () is the model organism database (MOD) for the social amoeba Dictyostelium discoideum. The unique biology and phylogenetic position of Dictyostelium offer a great opportunity to gain knowledge of processes not characterized in other organisms. The recent completion of the 34 MB genome sequence, together with the sizable scientific literature using Dictyostelium as a research organism, provided the necessary tools to create a well-annotated genome. dictyBase has leveraged software developed by the Saccharomyces Genome Database and the Generic Model Organism Database project. This has reduced the time required to develop a full-featured MOD and greatly facilitated our ability to focus on annotation and providing new functionality. We hope that manual curation of the Dictyostelium genome will facilitate the annotation of other genomes

Angle of repose and segregation in cohesive granular matter

We study the effect of fluids on the angle of repose and the segregation of granular matter poured into a silo. The experiments are conducted in two regimes where: (i) the volume fraction of the fluid is small and it forms liquid bridges between particles, and (ii) the particles are completely immersed in the fluid. The data is obtained by imaging the pile formed inside a quasi-two dimensional silo through the transparent glass side walls. In the first series of experiments, the angle of repose is observed to increase sharply with the volume fraction of the fluid and then saturates at a value that depends on the size of the particles. We systematically study the effect of viscosity by using water-glycerol mixtures to vary it over at least three orders of magnitude while keeping the surface tension almost constant. Besides surface tension, the viscosity of the fluid is observed to have an effect on the angle of repose and the extent of segregation. In case of bidisperse particles, segregation is observed to decrease and finally saturate depending on the size ratio of the particles and the viscosity of the fluid. The sharp initial change and the subsequent saturation in the extent of segregation and angle of repose occurs over similar volume fraction of the fluid. In the second series of experiments, particles are poured into a container filled with a fluid. Although the angle of repose is observed to be unchanged, segregation is observed to decrease with an increase in the viscosity of the fluid.Comment: 9 pages, 12 figure

Biocurators and Biocuration: surveying the 21st century challenges

Curated databases are an integral part of the tool set that researchers use on a daily basis for their work. For most users, however, how databases are maintained, and by whom, is rather obscure. The International Society for Biocuration (ISB) represents biocurators, software engineers, developers and researchers with an interest in biocuration. Its goals include fostering communication between biocurators, promoting and describing their work, and highlighting the added value of biocuration to the world. The ISB recently conducted a survey of biocurators to better understand their educational and scientific backgrounds, their motivations for choosing a curatorial job and their career goals. The results are reported here. From the responses received, it is evident that biocuration is performed by highly trained scientists and perceived to be a stimulating career, offering both intellectual challenges and the satisfaction of performing work essential to the modern scientific community. It is also apparent that the ISB has at least a dual role to play to facilitate biocurators’ work: (i) to promote biocuration as a career within the greater scientific community; (ii) to aid the development of resources for biomedical research through promotion of nomenclature and data-sharing standards that will allow interconnection of biological databases and better exploit the pivotal contributions that biocurators are making

Relationship Between Sexual Activity, Contraceptive Utilization and Biopsychosocial Characteristics Among Homeless Shelter Adolescents.

Objective: To determine whether biopsychosocial factors are associated with sexual activity and contraceptive utilization among homeless shelter adolescents. Methods: A retrospective study of 440 adolescents at a shelter in Pennsylvania between February 2015 and September 2019 was conducted. The cohort was evaluated to determine what relationship age, gender identity, substance use, and trauma history have with sexual activity and contraceptive utilization. Results: Sexual activity was significantly related to age (mean 15.8+1.4 years in sexually active vs. 14.7+1.6 years in abstinent youth, p\u3c0.001); remote history of self-harm behavior (relative risk ratio (RR) 1.23 [95% CI 1.03-1.46]; p=0.02), history of aggressive behavior (RR 1.21 [95% CI 1.01-1.46]; p=0.04), history of trauma (RR 1.24 [95% CI 1.04-1.48]; p=0.03), and substance use (RR 2.27 [95%CI 1.86-2.77]; p\u3c0.001). There were 55.7% sexually active females vs. 42.50% males reporting contraception use (p=0.01). After adjustment, older age and substance use remained significantly associated with sexual activity (adjusted odds ratio (AOR) 1.58 [95% CI 1.36-1.83]; p\u3c0.001 and AOR 5.18 [95% CI 3.28-8.18]; p\u3c0.001, respectively). Conclusions: Females self-reported sexual activity using contraception more than males. After adjustment, older age and substance use were associated with sexual activity. By better understanding the impact these factors can have on contraceptive utilization, informed policy and practice interventions can be developed and implemented to help increase safe sex practices in spaces where homeless adolescents access healthcare