iDNA-Prot: Identification of DNA Binding Proteins Using Random Forest with Grey Model

DNA-binding proteins play crucial roles in various cellular processes. Developing high throughput tools for rapidly and effectively identifying DNA-binding proteins is one of the major challenges in the field of genome annotation. Although many efforts have been made in this regard, further effort is needed to enhance the prediction power

Elasticity of iron at the temperature of the Earth's inner core

Seismological body-wave(1) and free-oscillation(2) studies of the Earth's solid inner core have revealed that compressional waves traverse the inner core faster along near-polar paths than in the equatorial plane. Studies have also documented local deviations from this first-order pattern of anisotropy on length scales ranging from 1 to 1,000 km (refs 3, 4). These observations, together with reports of the differential rotation(5) of the inner core, have generated considerable interest in the physical state and dynamics of the inner core, and in the structure and elasticity of its main constituent, iron, at appropriate conditions of pressure and temperature. Here we report first-principles calculations of the structure and elasticity of dense hexagonal close-packed (h.c.p.) iron at high temperatures. We find that the axial ratio c/a of h.c.p. iron increases substantially with increasing temperature, reaching a value of nearly 1.7 at a temperature of 5,700 K, where aggregate bulk and shear moduli match those of the inner core. As a consequence of the increasing c/a ratio, we have found that the single-crystal longitudinal anisotropy of h.c.p. iron at high temperature has the opposite sense from that at low temperature(6,7). By combining our results with a simple model of polycrystalline texture in the inner core, in which basal planes are partially aligned with the rotation axis, we can account for seismological observations of inner-core anisotropy.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62959/1/413057a0.pd

Operator theory and function theory in Drury-Arveson space and its quotients

The Drury-Arveson space $H^2_d$, also known as symmetric Fock space or the $d$-shift space, is a Hilbert function space that has a natural $d$-tuple of operators acting on it, which gives it the structure of a Hilbert module. This survey aims to introduce the Drury-Arveson space, to give a panoramic view of the main operator theoretic and function theoretic aspects of this space, and to describe the universal role that it plays in multivariable operator theory and in Pick interpolation theory.Comment: Final version (to appear in Handbook of Operator Theory); 42 page

Monitoring Functional Capability of Individuals with Lower Limb Amputations Using Mobile Phones

To be effective, a prescribed prosthetic device must match the functional requirements and capabilities of each patient. These capabilities are usually assessed by a clinician and reported by the Medicare K-level designation of mobility. However, it is not clear how the K-level designation objectively relates to the use of prostheses outside of a clinical environment. Here, we quantify participant activity using mobile phones and relate activity measured during real world activity to the assigned K-levels. We observe a correlation between K-level and the proportion of moderate to high activity over the course of a week. This relationship suggests that accelerometry-based technologies such as mobile phones can be used to evaluate real world activity for mobility assessment. Quantifying everyday activity promises to improve assessment of real world prosthesis use, leading to a better matching of prostheses to individuals and enabling better evaluations of future prosthetic devices.Max Nader Center for Rehabilitation Technologies and Outcome

To Fear is to Gain? The Role of Fear Recognition in Risky Decision Making in TBI Patients and Healthy Controls

Fear is an important emotional reaction that guides decision making in situations of ambiguity or uncertainty. Both recognition of facial expressions of fear and decision making ability can be impaired after traumatic brain injury (TBI), in particular when the frontal lobe is damaged. So far, it has not been investigated how recognition of fear influences risk behavior in healthy subjects and TBI patients. The ability to recognize fear is thought to be related to the ability to experience fear and to use it as a warning signal to guide decision making. We hypothesized that a better ability to recognize fear would be related to a better regulation of risk behavior, with healthy controls outperforming TBI patients. To investigate this, 59 healthy subjects and 49 TBI patients were assessed with a test for emotion recognition (Facial Expression of Emotion: Stimuli and Tests) and a gambling task (Iowa Gambling Task (IGT)). The results showed that, regardless of post traumatic amnesia duration or the presence of frontal lesions, patients were more impaired than healthy controls on both fear recognition and decision making. In both groups, a significant relationship was found between better fear recognition, the development of an advantageous strategy across the IGT and less risk behavior in the last blocks of the IGT. Educational level moderated this relationship in the final block of the IGT. This study has important clinical implications, indicating that impaired decision making and risk behavior after TBI can be preceded by deficits in the processing of fear

Antioxidant potential of bitter cumin (Centratherum anthelminticum (L.) Kuntze) seeds in in vitro models

<p>Abstract</p> <p>Background</p> <p>Bitter cumin (<it>Centratherum anthelminticum </it>(L.) Kuntze), is a medicinally important plant. Earlier, we have reported phenolic compounds, antioxidant, and anti-hyperglycemic, antimicrobial activity of bitter cumin. In this study we have further characterized the antioxidative activity of bitter cumin extracts in various in vitro models.</p> <p>Methods</p> <p>Bitter cumin seeds were extracted with a combination of acetone, methanol and water. The antioxidant activity of bitter cumin extracts were characterized in various <it>in vitro </it>model systems such as DPPH radical, ABTS radical scavenging, reducing power, oxidation of liposomes and oxidative damage to DNA.</p> <p>Results</p> <p>The phenolic extracts of bitter cumin at microgram concentration showed significant scavenging of DPPH and ABTS radicals, reduced phosphomolybdenum (Mo(VI) to Mo(V)), ferricyanide Fe(III) to Fe(II), inhibited liposomes oxidation and hydroxyl radical induced damage to prokaryotic genomic DNA. The results showed a direct correlation between phenolic acid content and antioxidant activity.</p> <p>Conclusion</p> <p>Bitter cumin is a good source of natural antioxidants.</p

Image based machine learning for identification of macrophage subsets

Macrophages play a crucial rule in orchestrating immune responses against pathogens and foreign materials. Macrophages have remarkable plasticity in response to environmental cues and are able to acquire a spectrum of activation status, best exemplified by pro-inflammatory (M1) and anti-inflammatory (M2) phenotypes at the two ends of the spectrum. Characterisation of M1 and M2 subsets is usually carried out by quantification of multiple cell surface markers, transcription factors and cytokine profiles. These approaches are time consuming, require large numbers of cells and are resource intensive. In this study, we used machine learning algorithms to develop a simple and fast imaging-based approach that enables automated identification of different macrophage functional phenotypes using their cell size and morphology. Fluorescent microscopy was used to assess cell morphology of different cell types which were stained for nucleus and actin distribution using DAPI and phalloidin respectively. By only analysing their morphology we were able to identify M1 and M2 phenotypes effectively and could distinguish them from naïve macrophages and monocytes with an average accuracy of 90%. Thus we suggest high-content and automated image analysis can be used for fast phenotyping of functionally diverse cell populations with reasonable accuracy and without the need for using multiple markers