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Summary: Molecular dynamics (MD) determines the physical motions of atoms of a biological macromolecule in a cell-like environment and is an important method in structural bioinformatics. Traditionally, measurements such as root mean square deviation, root mean square fluctuation, radius of gyration, and various energy measures have been used to analyze MD simulations. Here, we present MD-TASK, a novel software suite that employs graph theory techniques, perturbation response scanning, and dynamic cross-correlation to provide unique ways for analyzing MD trajectories. [ABSTRACT FROM AUTHOR]

The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make calculations simpler, but largely exclude users from the process. In this study, we present the PRotein Interactive MOdeling (PRIMO) pipeline for homology modeling of protein monomers. The pipeline eases the multi-step modeling process, and reduces the workload required by the user, while still allowing engagement from the user during every step. Default parameters are given for each step, which can either be modified or supplemented with additional external input. PRIMO has been designed for users of varying levels of experience with homology modeling. The pipeline incorporates a user-friendly interface that makes it easy to alter parameters used during modeling. During each stage of the modeling process, the site provides suggestions for novice users to improve the quality of their models. PRIMO provides functionality that allows users to also model ligands and ions in complex with their protein targets. Herein, we assess the accuracy of the fully automated capabilities of the server, including a comparative analysis of the available alignment programs, as well as of the refinement levels used during modeling. The tests presented here demonstrate the reliability of the PRIMO server when producing a large number of protein models. While PRIMO does focus on user involvement in the homology modeling process, the results indicate that in the presence of suitable templates, good quality models can be produced even without user intervention. This gives an idea of the base level accuracy of PRIMO, which users can improve upon by adjusting parameters in their modeling runs. The accuracy of PRIMO’s automated scripts is being continuously evaluated by the CAMEO (Continuous Automated Model EvaluatiOn) project. The PRIMO site is free for non-commercial use and can be accessed at . [ABSTRACT FROM AUTHOR]

Complex computational pipelines are becoming a staple of modern scientific research. Often these pipelines are resource intensive and require days of computing time. In such cases, it makes sense to run them over high performance computing (HPC) clusters where they can take advantage of the aggregated resources of many powerful computers. In addition to this, researchers often want to integrate their workflows into their own web servers. In these cases, software is needed to manage the submission of jobs from the web interface to the cluster and then return the results once the job has finished executing. We have developed the Job Management System (JMS), a workflow management system and web interface for high performance computing (HPC). JMS provides users with a user-friendly web interface for creating complex workflows with multiple stages. It integrates this workflow functionality with the resource manager, a tool that is used to control and manage batch jobs on HPC clusters. As such, JMS combines workflow management functionality with cluster administration functionality. In addition, JMS provides developer tools including a code editor and the ability to version tools and scripts. JMS can be used by researchers from any field to build and run complex computational pipelines and provides functionality to include these pipelines in external interfaces. JMS is currently being used to house a number of bioinformatics pipelines at the Research Unit in Bioinformatics (RUBi) at Rhodes University. JMS is an open-source project and is freely available at . [ABSTRACT FROM AUTHOR]

Background: Natural products (NPs) are important to the drug discovery process. NP research efforts are expanding world-wide and South Africa is no exception to this. While freely-accessible small molecule databases, containing compounds isolated from indigenous sources, have been established in a number of other countries, there is currently no such online database in South Africa. Description: The current research presents a South African natural compound database, named SANCDB. This is a curated and fully-referenced database containing compound information for 600 natural products extracted directly from journal articles, book chapters and theses. There is a web interface to the database, which is simple and easy to use, while allowing for compounds to be searched by a number of different criteria. Being fully referenced, each compound page contains links to the original referenced work from which the information was obtained. Further, the website provides a submission pipeline, allowing researchers to deposit compounds from their own research into the database. Conclusions: SANCDB is currently the only web-based NP database in Africa. It aims to provide a useful resource for the in silico screening of South African NPs for drug discovery purposes. The database is supported by a submission pipeline to allow growth by entries from researchers. As such, we currently present SANCDB the starting point of a platform for a community-driven, curated database tofurther natural products research in South Africa. SANCDB is freely available at https://sancdb.rubi.ru.ac.za/. [ABSTRACT FROM AUTHOR]

The article focuses on cases decided by the U.S Court of Appeals for the Eleventh Circuit under the U.S Securities Act of 1933 and U.S Securities Exchange Act of 1934 during 2012-2013. Court cases discussed include Miyahira v. Vitacost.com, Inc. that involved material misstatements along with an initial public offering, a case addressing the loss causation element of a fraud claim under U.S securities law such as the U.S Exchange Act and SEC v. Goble that addressed the issue of materiality.

Background: The Listening in Spatialized Noise-Sentences test (LiSN-S; Cameron and Dillon, 2009) was originally developed to assess auditory stream segregation skills in children aged 6 to 11 yr with suspected central auditory processing disorder. The LiSN-S creates a three-dimensional auditory environment under headphones. A simple repetition-response protocol is used to assess a listener's speech reception threshold (SRT) for target sentences presented in competing speech maskers. Performance is measured as the improvement in SRT in dB gained when either pitch, spatial, or both pitch and spatial cues are incorporated in the maskers. A North American-accented version of the LiSN-S (NA LiSN-S) is available for use in the United States and Canada. Purpose: To develop normative data for adolescents and adults on the NA LiSN-S, to compare these data with those of children aged 6 to 11 yr as documented in Cameron et al (2009), and to consolidate the child, adolescent, and adult normative and retest data to allow the software to be used with a wider population. Research Design: In a descriptive design, normative data and test-retest reliability data were collected. Study Sample: One hundred and twenty normally hearing participants took part in the normative data study (67 adolescents aged 12 yr, 1 mo, to 17 yr, 10 mo, and 53 adults aged 19 yr, 10 mo, to 30 yr, 30 mo). Forty-nine participants returned between 1 and 4 mo after the initial assessment for retesting. Participants were recruited from sites in Cincinnati, Dallas, and Calgary. Results: When combined with data collected from children aged 6 to 11 yr, a trend of improved performance as a function of increasing age was found across performance measures. ANOVA (analysis of variance) revealed a significant effect of age on performance. Planned contrasts revealed that there were no significant differences between adults and children aged 13 yr and older on the low-cue SRT; 14 yr and older on talker and spatial advantage; 15 yr and older on total advantage; and 16 yr and older on the high-cue SRT. Mean test-retest differences on the various NA LiSN-S performance measures for the combined child, adult, and adolescent data ranged from 0.05 to 0.5 dB. Paired comparisons revealed test-retest differences were not significant on any measure of the NA LiSN-S except low-cue SRT. Test-retest differences across measures did not differ as a function of age. Test and retest scores were significantly correlated for all NA LiSN-S measures. Conclusions: The ability to use either spatial or talker cues in isolation becomes adultlike by about 14 yr of age, whereas the ability to combine spatial and talker cues does not fully mature until closer to adulthood. By consolidating child, adolescent, and adult normative and retest data the NA LiSN-S can now been utilized to assess auditory processing skills in a wider population. [ABSTRACT FROM AUTHOR]

A rich literature on public policy abounds in social gerontology and related gerontology curriculum. However, much less emphasis has been placed on public policy in the geriatric education curriculum. This article discusses the need for a greater infusion of public policy into training modules and core curriculum of geriatric education. The view is presented that public policy is, by its nature, a valuable area for interdisciplinary study, cutting across the discipline-specific areas of geriatric education. This emphasis is particularly acute and timely, given rising social and political criticism of safety net programs for the elderly such as Medicare, Medicaid, and Social Security. Public policy curriculum design will be suggested as well as intervention strategies of use to public health professionals. [ABSTRACT FROM PUBLISHER]

The expansion of access to higher education and the proliferation of formal degree requirements for entry to employment have been enduring trends over the past century. This article reviews the contested development and promise of the Weberian theory of educational credentialism, which views competition for credentials as a primary determinant of modern stratification systems. The key issues that are elaborated include the relationship of educational expansion to economic growth, the relative importance of technical skills versus occupational status-group cultures in degrees and recruitment, the significance of the formalization of degrees, and the peculiar dynamics of bureaucratic and professional credential markets. The future trajectory of credentialism is assessed in light of potential policy reforms, market crises, and state interventions. [ABSTRACT FROM AUTHOR]

Presents two cases of children affected with auditory neuropathy (AN), a hearing impairment characterized by normal or near-normal hearing sensitivity but with reduced auditory perceptual or speech processing skills. Symptoms; Several ways to diagnose AN; Diversity of factors responsible for AN; Caring and rehabilitation for a patient diagnosed with AN.

The basis of social support that provides political legitimacy for age-related public policy is being called into question. Critics focus on the rapid growth of entitlement benefits for older people, both in terms of utilization and costs. Some have even suggested that if the current levels of spending are not curbed, we will sacrifice the economic legacy of our children. Programs being specifically targeted for criticism are Medicaid, Medicare, and Social Security. This article presents an issues overview of these programs in the context of current calls for reform. It suggests that aging public policy can be usefully taught and analyzed from the perspective of two conflicting schools of thought, which hold widely disparate views - the devolutionists and the safety netters. Devolutionists would tightly curtail the sustaining federal role in providing benefits to the elderly, while safety netters maintain that the federal government's role is indispensable. Relative deprivation theory, as advanced by Gurr (1970), is posited as a useful framework for explaining how aging public policy evolves and for illustrating the dynamics that underpin the process. Prescriptive recommendations are drawn out for the future of the aging network in terms of strategic positioning and advocacy. [ABSTRACT FROM AUTHOR]

Focuses on public attitudes toward the installation of a statewide regional development program in West Virginia. Public hearings held throughout the state in 1972; Gathering of public testimony on the feasibility of the preliminary boundary delineations of the regions; Regions expressing the greatest hesitancy and skepticism over the program.

A letter to the editor is presented in response to the statement in the President's Forum column published in the Winter 2006 issue of the periodical by David K. Brown.

Background: Examination of cochlear and neural potentials is necessary to assess sensory and neural status in infants, especially those cared for in neonatal intensive care units (NICU) who have high rates of hyperbilirubinemia and thus are at risk for auditory neuropathy (AN). Purpose: The purpose of this study was to determine whether recording parameters commonly used in click-evoked auditory brain stem response (ABR) are useful for recording cochlear microphonic (CM) and Wave I in infants at risk for AN. Specifically, we analyzed CM, summating potential (SP), and Waves I, Ill, and V. The overall aim was to compare latencies and amplitudes of evoked responses in infants cared for in NICUs with infants in a well-baby nursery (WBN), both of which passed newborn hearing screening. Research Design: This is a prospective study in which infants who passed ABR newborn hearing screening were grouped based on their birth history (WBN and NICU). All infants had normal hearing status when tested with diagnostic ABR at about one month of age, corrected for prematurity. Study Sample: Thirty infants (53 ears) from the WBN [mean corrected age at test = 5.0 weeks (wks.)] and thirty-two infants (59 ears) from the NICU (mean corrected age at test = 5.7 wks.) with normal hearing were included in this study. In addition, two infants were included as comparative case studies, one that was diagnosed with AN and another case that was diagnosed with bilateral sensorineural hearing loss (SNHL). Data Collection and Analysis: Diagnostic ABR, including click and tone-burst air- and bone-conduction stimuli were recorded. Peak Waves I, Ill, and V; SP; and CM latency and amplitude (peak to trough) were measured to determine if there were differences in ABR and electrocochleography (ECochG) variables between WBN and NICU infants. Results: No significant group differences were found between WBN and NICU groups for ABR waveforms, CM, or SP, including amplitude and latency values. The majority (75%) of the NICU group had hyperbilirubinemia, but overall, they did not show evidence of effects in their ECochG or ABR responses when tested at about one-month corrected age. These data may serve as a normative sample for NICU and well infant ECochG and ABR latencies at one-month corrected age. Two infant case studies, one diagnosed with AN and another with SNHL demonstrated the complexity of using ECochG and otoacoustic emissions to assess the risk of AN in individual cases. Conclusions: CM and SPs can be readily measured using standard click stimuli in both well and NICU infants. Normative ranges for latency and amplitude are useful for interpreting ECochG and ABR components. Inclusion of ECochG and ABR tests in a test battery that also includes otoacoustic emission and acoustic reflex tests may provide a more refined assessment of the risks of AN and SNHL in infants. [ABSTRACT FROM AUTHOR]

Objective: The purpose of this study was to evaluate pressurised wideband acoustic immittance (WAI) tests in children with Down syndrome (DS) and in typically developing children (TD) for prediction of conductive hearing loss (CHL) and patency of pressure equalising tubes (PETs).Design: Audiologic diagnosis was determined by audiometry in combination with distortion-product otoacoustic emissions, 0.226 kHz tympanometry and otoscopy. WAI results were compared for ears within diagnostic categories (Normal, CHL and PET) and between groups (TD and DS).Study sample: Children with DS (n = 40; mean age 6.4 years), and TD children (n = 48; mean age 5.1 years) were included.Results: Wideband absorbance was significantly lower at 1–4 kHz in ears with CHL compared to NH for both TD and DS groups. In ears with patent PETs, wideband absorbance and group delay (GD) were larger than in ears without PETs between 0.25 and 1.5 kHz. Wideband absorbance tests were performed similarly for prediction of CHL and patent PETs in TD and DS groups.Conclusions: Wideband absorbance and GD revealed specific patterns in both TD children and those with DS that can assist in detection of the presence of significant CHL, assess the patency of PETs, and provide frequency-specific information in the audiometric range. [ABSTRACT FROM PUBLISHER]

Background: Unilateral hearing loss and audiovestibular symptoms are common in the population and can be associated with retrocochlear tumours such as acoustic neuroma (AN). In order to rule out AN, many patients with asymmetric hearing loss are referred for magnetic resonance imaging (MRI). Recent work with modifications of auditory brianstem response (ASR) protocols has improved the ability of ABR to detect small acoustic tumours. This study presents our initial results using the power spectrum ABR (PSABR) as another tool in detecting patients at higher risk for AN. Methods: A prospective, observational cohort design was employed and a total of 53 subjects were recruited (19 subjects were normal controls and 34 subjects were patients with unilateral audiovestibular symptoms). All subjects underwent complete auditory testing, standard ABR, stacked ABR, and power spectrum ABR. The 34 patients also underwent gadolinium enhanced MRI. Results: Using logistic regression, our data showed that wave I-V latency was most highly predictive of tumour presence or absence. However, both stacked ABR and power spectrum ABR were predictive. Stacked ABR was also able to differentiate symptomatic patients with tumours from those without. Conclusions: This study was not designed to compare PSABR to other more established methods. Rather, our intent was to establish PSABR as a valid and practical addition to other ABR tools. More research is needed to optimize PSABR algorithms, and the method also needs to be tested and validated in larger populations of patients. Early results do indicate that PSABR could be a valid and reliable method of identifying subgroups of patients with unilateral auditory dysfunction who would best benefit from MRI. [ABSTRACT FROM AUTHOR]

This study investigates functional disability among some of the nation's most vulnerable older adults: rural Medicaid recipients. Data were provided by 221 older adults (mean age = 75.9 years; 82% women) who were receiving community-based long-term care services through Medicaid. Participants self-reported functional ability involving the completion of six basic activities of daily living (BADLs), three cognitive instrumental activities of daily living (IADLS), and four physical IADLs. Self-reports of depressed affect and the number of physical health conditions were also obtained. Path analysis was used to examine all of the associations among age, gender, number of chronic health conditions, depressed affect and functional disability. The tested model was significant [chi2 (DF = 3, n = 221) = 5.052, p = 0.168; TLI = 0.945; CFI = 0.992; RMSEA = 0.056] and explained 45.1% of the variance in BADL disability. Depressed affect significantly predicted disability in cognitive IADLs and physical IADLs, which predicted disability in BADLs. Age and gender had indirect effects on BADL, through their association with cognitive IADLs and physical IADLs. The number of chronic health conditions exerted both indirect and direct effects on BADL disability. Results are discussed within the context of the growing literature that suggests the importance of psychological variables as predictors of functional disability. Moreover, we discuss whether community-based long-term care is appropriate for older adults with high levels of functional disability. [ABSTRACT FROM AUTHOR]