Genetic region characterization (Gene RECQuest) - software to assist in identification and selection of candidate genes from genomic regions

BACKGROUND: The availability of research platforms like the web tools of the National Center for Biotechnology Information (NCBI) has transformed the time-consuming task of identifying candidate genes from genetic studies to an interactive process where data from a variety of sources are obtained to select likely genes for follow-up. This process presents its own set of challenges, as the genetic researcher has to interact with several tools in a time-intensive, manual, and cumbersome manner. We developed a method and implemented an effective software system to address these challenges by multidisciplinary efforts of professional software developers with domain experts. The method presented in this paper, Gene RECQuest, simplifies the interaction with existing research platforms through the use of advanced integration technologies. FINDINGS: Gene RECQuest is a web-based application that assists in the identification of candidate genes from linkage and association studies using information from Online Mendelian Inheritance in Man (OMIM) and PubMed. To illustrate the utility of Gene RECQuest we used it to identify genes physically located within a linkage region as potential candidate genes for a quantitative trait locus (QTL) for very low density lipoprotein (VLDL) response on chromosome 18. CONCLUSION: Gene RECQuest provides a tool which enables researchers to easily identify and organize literature supporting their own expertise and make informed decisions. It is important to note that Gene RECQuest is a data acquisition and organization software, and not a data analysis method

Raman scattering investigation of electron-phonon coupling in carbon substituted MgB<SUB>2</SUB>

Room temperature Raman scattering measurements have been carried out on well characterized samples of MgB2-xCx. The Raman line corresponding to the E2g phonon mode shows progressive hardening from 620 cm&#8722;1 in pristine MgB2 to 775 cm&#8722;1 in the sample with carbon fraction x = 0.2. The corresponding line width on the other hand increases from a value of about 220 to 286 cm&#8722;1 in samples with x = 0.1, beyond which it decreases to a value of 167 cm&#8722;1 for x = 0.2. From the average mode frequency and the line width obtained from Raman measurements and taking the values of N(0) obtained from the calculated variation in &#963;-hole density of states in MgB2-xCx, the electron-phonon coupling strength to the E2g phonon, &#955;2g, is evaluated using Allen's formula. This remains large for low C fraction, but shows a rapid decrease for x&gt;0.10. Using this value of &#955;2gappropriately weighted, TC is obtained from McMillan's equation. These values are in good agreement with the experimentally measured TC variation in MgB2-xCx

Drastic ground state changes induced by Ni substitution in NaxCoO2

We report on the effect of Ni substitution at the Co site on the physical properties of NaxCoO2 system by investigating the series NaxCo1-yNiyO2 (x=0.75, 0<y<0.15). An upturn in the resistivity is observed in all Ni substituted samples as the temperature is lowered, suggestive of the occurrence of a Metal-Insulator Transition (MIT). The temperature at which this transition occurs increases with Ni content. The temperature dependence of the resistivity in the metallic region in the Ni substituted samples shows a T2 dependence, which is qualitatively different from that observed in the pristine sample. The evolution of the Fano asymmetry parameter, extracted by analyzing the lineshape of the IR active in-plane Co-O mode, both as a function of Ni concentration and temperature corroborates the occurrence of the MIT. It is argued that the progressive substitution of the Co4+ ions with Ni increases the probability of double occupancy and therefore the on-site Coulomb interaction energy leading to a shift in the thermodynamically driven MIT to higher temperatures.Comment: 17 pages 9 figures; submitted to Journal Of Phys. Cond. Ma

Reliability and validity of an enhanced paper grip test; a simple clinical test for assessing lower limb strength

Background The paper-grip-test (PGT) involves pulling a small card from underneath the participant’s foot while asking them to grip with their hallux. The PGT is shown to be effective in detecting foot muscle-weakening but its outcome is operator-dependent. To overcome this limitation, an enhanced PGT (EPGT) is proposed that replaces the pass/fail outcome of the PGT with a continuous measurement of the pulling force that is needed to remove the card (EPGT-force). Research question Is the EPGT-force an accurate, reliable and clinically applicable measurement of strength? Methods Reliability and clinical applicability were examined in two ways. Firstly, two examiners measured EPGT-force for twenty healthy volunteers in a test/retest set-up. EPGT force was measured using a dynamometer, the hallux grip force was measured using a pressure mat. The clinical applicability of the EPGT was tested in ten people with diabetes. Postural sway was also measured. Results Interclass correlation coefficients (ICC) revealed excellent inter-rater reliability (ICC > 0.75). Intra-rater reliability was excellent for the first examiner (ICC = 0.795) and good for the second (ICC = 0.703). Linear regression analysis indicated that hallux grip force accounted (on average) for 83%±4% of the variability in EPGT force. This strong relationship between EPGT force and hallux grip force remained when the test was performed in a clinical setting with the latter accounting for 88% in EPGT force variability. Spearman rank order correlation showed that people with diabetes with a higher difference in EPGT force between limbs swayed more. Significance EPGT force is a reliable and accurate measurement of hallux grip force. Hallux grip force was previously found to be strongly correlated to the strength of all muscle groups of the foot and ankle and to the ability to maintain balance. The proposed EPGT could be used to monitor muscle weakness in clinics for better falls-risk assessment

The impact of phosphodiesterase inhibition on neurobehavioral outcomes in preclinical models of traumatic and non-traumatic spinal cord injury: a systematic review

Study designSystematic review.ObjectiveThe objective of this study was to evaluate the impact of phosphodiesterase (PDE) inhibitors on neurobehavioral outcomes in preclinical models of traumatic and non-traumatic spinal cord injury (SCI).MethodsA systematic review was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines and was registered with PROSPERO (CRD42019150639). Searches were performed in MEDLINE and Embase. Studies were included if they evaluated the impact of PDE inhibitors on neurobehavioral outcomes in preclinical models of traumatic or non-traumatic SCI. Data were extracted from relevant studies, including sample characteristics, injury model, and neurobehavioral assessment and outcomes. Risk of bias was assessed using the SYRCLE checklist.ResultsThe search yielded a total of 1,679 studies, of which 22 met inclusion criteria. Sample sizes ranged from 11 to 144 animals. PDE inhibitors used include rolipram (n = 16), cilostazol (n = 4), roflumilast (n = 1), and PDE4-I (n = 1). The injury models used were traumatic SCI (n = 18), spinal cord ischemia (n = 3), and degenerative cervical myelopathy (n = 1). The most commonly assessed outcome measures were Basso, Beattie, Bresnahan (BBB) locomotor score (n = 13), and grid walking (n = 7). Of the 22 papers that met the final inclusion criteria, 12 showed a significant improvement in neurobehavioral outcomes following the use of PDE inhibitors, four papers had mixed findings and six found PDE inhibitors to be ineffective in improving neurobehavioral recovery following an SCI. Notably, these findings were broadly consistent across different PDE inhibitors and spinal cord injury models.ConclusionIn preclinical models of traumatic and non-traumatic SCI, the administration of PDE inhibitors appeared to be associated with statistically significant improvements in neurobehavioral outcomes in a majority of included studies. However, the evidence was inconsistent with a high risk of bias. This review provides a foundation to aid the interpretation of subsequent clinical trials of PDE inhibitors in spinal cord injury.Systematic review registrationhttps://www.crd.york.ac.uk/prospero/display_record.php?RecordID=150639, identifier: CRD42019150639

Detection of component composition mismatch with axiomatic design

This paper presents a software component composition methodology based on Axiomatic Design theory and Design Structure Matrix. The methodology we propose helps overcome anomalies and functional problems such as deadlock. Our approach can be described in two steps. First, we decompose the system to detect coupled components by using the Design Structure Matrix. Secondly, we represent attribute and method dependencies of the coupled components to identify issues during software composition using Design Matrix (DM) of Axiomatic Design

Magnetic and transport behavior of Ni-substituted GdBaCo<SUB>2</SUB>O<SUB>5+δ</SUB> perovskite

Electrical resistivity, dc magnetization, ac susceptibility, thermopower, and magnetoresistance measurements have been carried out on Ni-substituted GdBaCo<SUB>2</SUB>O<SUB>5+δ</SUB>. Structural characterization of the samples was done by X-ray diffraction and results show a systematic variation in the lattice parameters with Ni substitution. Oxygen stoichiometry determined by iodometric titration suggests that oxygen content remains unaltered with Ni substitution. The metal to insulator transition (T<SUB>MIT</SUB>), the paramagnetic to ferromagnetic (FM) transition (T<SUB>C</SUB>), and ferromagnetic to antiferromagnetic (AFM) transition (T<SUB>N</SUB>) are altered strongly by Ni substitution. Magnetization and magnetoresistance studies carried out enable determination of magnetic phase diagram which suggests the stabilization of an AFM ground state for low Ni fractions, FM state for high Ni fractions, and a mixed phase at intermediate Ni fractions