Identification of new, well-populated amino-acid sidechain rotamers involving hydroxyl-hydrogen atoms and sulfhydryl-hydrogen atoms

<p>Abstract</p> <p>Background</p> <p>An important element in homology modeling is the use of rotamers to parameterize the sidechain conformation. Despite the many libraries of sidechain rotamers that have been developed, a number of rotamers have been overlooked, due to the fact that they involve hydrogen atoms.</p> <p>Results</p> <p>We identify new, well-populated rotamers that involve the hydroxyl-hydrogen atoms of Ser, Thr and Tyr, and the sulfhydryl-hydrogen atom of Cys, using high-resolution crystal structures (<1.2 Å). Although there were refinement artifacts in these structures, comparison with the electron-density maps allowed the placement of hydrogen atoms involved in hydrogen bonds. The χ2 rotamers in Ser, Thr and Cys are consistent with tetrahedral bonding, while the χ3 rotamers in Tyr are consistent with trigonal-planar bonding. Similar rotamers are found in hydrogen atoms that were computationally placed with the Reduce program from the Richardson lab.</p> <p>Conclusion</p> <p>Knowledge of these new rotamers will improve the evaluation of hydrogen-bonding networks in protein structures.</p

Brevity, Speed, and Deference: An Account from the Williams Chambers

One of the leading books on administrative law advocates judicial review for “sound governance.”Reviewing the book while sitting on the D.C. Circuit, Judge Williams posited that, even if “judges are smarter than agency heads, or have more time on their hands, or have cleverer clerks,” the proper institutional role requires more deference. Divining “sound governance” is not for courts. The Judge concluded by quoting Milton’s poem about the role of the blind: “They also serve who only stand and waite.

Inference and Optimization of Real Edges on Sparse Graphs - A Statistical Physics Perspective

Inference and optimization of real-value edge variables in sparse graphs are studied using the Bethe approximation and replica method of statistical physics. Equilibrium states of general energy functions involving a large set of real edge-variables that interact at the network nodes are obtained in various cases. When applied to the representative problem of network resource allocation, efficient distributed algorithms are also devised. Scaling properties with respect to the network connectivity and the resource availability are found, and links to probabilistic Bayesian approximation methods are established. Different cost measures are considered and algorithmic solutions in the various cases are devised and examined numerically. Simulation results are in full agreement with the theory.Comment: 21 pages, 10 figures, major changes: Sections IV to VII updated, Figs. 1 to 3 replace

Label Transfer from APOGEE to LAMOST: Precise Stellar Parameters for 450,000 LAMOST Giants

In this era of large-scale stellar spectroscopic surveys, measurements of stellar attributes ("labels," i.e. parameters and abundances) must be made precise and consistent across surveys. Here, we demonstrate that this can be achieved by a data-driven approach to spectral modeling. With The Cannon, we transfer information from the APOGEE survey to determine precise Teff, log g, [Fe/H], and [$\alpha$/M] from the spectra of 450,000 LAMOST giants. The Cannon fits a predictive model for LAMOST spectra using 9952 stars observed in common between the two surveys, taking five labels from APOGEE DR12 as ground truth: Teff, log g, [Fe/H], [\alpha/M], and K-band extinction $A_k$. The model is then used to infer Teff, log g, [Fe/H], and [$\alpha$/M] for 454,180 giants, 20% of the LAMOST DR2 stellar sample. These are the first [$\alpha$/M] values for the full set of LAMOST giants, and the largest catalog of [$\alpha$/M] for giant stars to date. Furthermore, these labels are by construction on the APOGEE label scale; for spectra with S/N > 50, cross-validation of the model yields typical uncertainties of 70K in Teff, 0.1 in log g, 0.1 in [Fe/H], and 0.04 in [$\alpha$/M], values comparable to the broadly stated, conservative APOGEE DR12 uncertainties. Thus, by using "label transfer" to tie low-resolution (LAMOST R $\sim$ 1800) spectra to the label scale of a much higher-resolution (APOGEE R $\sim$ 22,500) survey, we substantially reduce the inconsistencies between labels measured by the individual survey pipelines. This demonstrates that label transfer with The Cannon can successfully bring different surveys onto the same physical scale.Comment: 27 pages, 14 figures. Accepted by ApJ on 16 Dec 2016, implementing suggestions from the referee reports. Associated code available at https://github.com/annayqho/TheCanno

Advances in the understanding of mitochondrial DNA as a pathogenic factor in inflammatory diseases

Mitochondrial DNA (mtDNA) has many similarities with bacterial DNA because of their shared common ancestry. Increasing evidence demonstrates mtDNA to be a potent danger signal that is recognised by the innate immune system and can directly modulate the inflammatory response. In humans, elevated circulating mtDNA is found in conditions with significant tissue injury such as trauma and sepsis and increasingly in chronic organ-specific and systemic illnesses such as steatohepatitis and systemic lupus erythematosus. In this review, we examine our current understanding of mtDNA-mediated inflammation and how the mechanisms regulating mitochondrial homeostasis and mtDNA release represent exciting and previously under-recognised important factors in many human inflammatory diseases, offering many new translational opportunities

Equilibration through local information exchange in networks

We study the equilibrium states of energy functions involving a large set of real variables, defined on the links of sparsely connected networks, and interacting at the network nodes, using the cavity and replica methods. When applied to the representative problem of network resource allocation, an efficient distributed algorithm is devised, with simulations showing full agreement with theory. Scaling properties with the network connectivity and the resource availability are found.Comment: v1: 7 pages, 1 figure, v2: 4 pages, 2 figures, simplified analysis and more organized results, v3: minor change

The Effect Of Problem Based Learning On Undergraduate Oral Communication Competency

Purpose:  The aim of this study was to ascertain the effect of Problem Based Learning (PBL) on student oral communication competency gains. Methods:  Eighty students from two consecutive undergraduate Kinesiology courses (Spring semesters, 2014-15) formed into 29 small groups and were studied.  Oral communication competency was assessed using a customized rubric and digital recordings of student presentations.  Changes to oral communication competency across time were tested using a dependent t-test; a &lt; .05. Results:  Significant inter-rater agreement was found at both time points for oral communication rating, and student groups demonstrated significant oral communication gains across time.  Conclusions:  Collaborative learning was shown to improve students’ oral communication competency. Future study is required to determine the influence of student motivation and goal orientation on oral communication competency, in relation to the various phases of knowledge creation occurring within student groups.

An overview of the rare parotid gland cancer

Cancer of the parotid gland is relatively rare, but carries poor prognosis owing to its prevailing distant metastases. In addition to the disease's basic epidemiology and pathology, we review some current discoveries of its tumorigenesis molecular mechanism. Based on published salivary gland cancer clinical trial data, non-surgical antitumor efficacies amongst a range of chemotherapy, radiation, and concurrent therapy regimens are compared. We also present the current development status of novel radiation therapy and targeted therapeutics, focusing on intensity-modulated radiation therapy (IMRT), and epidermal growth factor receptor (EGFR) and vascular endothelial growth factor (VEGF) blockages, which are showing promise for improving parotid gland cancer management