A Helix Propensity Scale Based on Experimental Studies of Peptides and Proteins

AbstractThe average globular protein contains 30% α-helix, the most common type of secondary structure. Some amino acids occur more frequently in α-helices than others; this tendency is known as helix propensity. Here we derive a helix propensity scale for solvent-exposed residues in the middle positions of α-helices. The scale is based on measurements of helix propensity in 11 systems, including both proteins and peptides. Alanine has the highest helix propensity, and, excluding proline, glycine has the lowest, ∼1kcal/mol less favorable than alanine. Based on our analysis, the helix propensities of the amino acids are as follows (kcal/mol): Ala=0, Leu=0.21, Arg=0.21, Met=0.24, Lys=0.26, Gln=0.39, Glu=0.40, Ile=0.41, Trp=0.49, Ser=0.50, Tyr=0.53, Phe=0.54, Val=0.61, His=0.61, Asn=0.65, Thr=0.66, Cys=0.68, Asp=0.69, and Gly=1

The roles of phonological short-term memory and working memory in L2 grammar and vocabulary learning

This study analyzed phonological short-term memory (PSTM) and working memory (WM) and their relationship with vocabulary and grammar learning in an artificial foreign language. Nonword repetition, nonword recognition, and listening span were used as memory measures. Participants learned the singular forms of vocabulary for an artificial foreign language before being exposed to plural forms in sentence contexts. Participants were tested on their ability to induce the grammatical forms and to generalize the forms to novel utterances. Individual differences in final abilities in vocabulary and grammar correlated between 0.44 and 0.76, depending on the measure. Despite these strong associations, the results demonstrated significant independent effects of PSTM and WM on L2 vocabulary learning and on L2 grammar learning, some of which were mediated by vocabulary and some of which were direct effects

Bryophytes of Uganda : 2., new and interesting records

51 hepatics and 46 mosses are reported new to Uganda, including one moss new to Africa, one hepatic and two mosses new to mainland Africa, and 2 hepatics that are otherwise known only from their type collection

A New Shear Estimator for Weak Lensing Observations

We present a new shear estimator for weak lensing observations which properly accounts for the effects of a realistic point spread function (PSF). Images of faint galaxies are subject to gravitational shearing followed by smearing with the instrumental and/or atmospheric PSF. We construct a `finite resolution shear operator' which when applied to an observed image has the same effect as a gravitational shear applied prior to smearing. This operator allows one to calibrate essentially any shear estimator. We then specialize to the case of weighted second moment shear estimators. We compute the shear polarizability which gives the response of an individual galaxy's polarization to a gravitational shear. We then compute the response of the population of galaxies, and thereby construct an optimal weighting scheme for combining shear estimates from galaxies of various shapes, luminosities and sizes. We define a figure of merit --- an inverse shear variance per unit solid angle --- which characterizes the quality of image data for shear measurement. The new method is tested with simulated image data. We discuss the correction for anisotropy of the PSF and propose a new technique involving measuring shapes from images which have been convolved with a re-circularizing PSF. We draw attention to a hitherto ignored noise related bias and show how this can be analyzed and corrected for. The analysis here draws heavily on the properties of real PSF's and we include as an appendix a brief review, highlighting those aspects which are relevant for weak lensing.Comment: 39 pages, 9 figure

Designing with and for people living with visual impairments: audio-tactile mock-ups, audio diaries and participatory prototyping

© 2015 Taylor & Francis. Methods used to engage users in the design process often rely on visual techniques, such as paper prototypes, to facilitate the expression and communication of design ideas. The visual nature of these tools makes them inaccessible to people living with visual impairments. In addition, while using visual means to express ideas for designing graphical interfaces is appropriate, it is harder to use them to articulate the design of non-visual displays. In this article, we present an approach to conducting participatory design with people living with visual impairments incorporating various techniques to help make the design process accessible. We reflect on the benefits and challenges that we encountered when employing these techniques in the context of designing cross-modal interactive tools

Dose de-escalation of intrapleural tissue plasminogen activator therapy for pleural infection. The alteplase dose assessment for Pleural infection Therapy project

Rationale: Intrapleural therapy with a combination of tissue plasminogen activator (tPA) 10 mg and DNase 5 mg administered twice daily has been shown in randomized and open-label studies to successfully manage over 90% of patients with pleural infection without surgery. Potential bleeding risks associated with intrapleural tPA and its costs remain important concerns. The aim of the ongoing Alteplase Dose Assessment for Pleural infection Therapy (ADAPT) project is to investigate the efficacy and safety of dose de-escalation for intrapleural tPA. The first of several planned studies is presented here. Objectives: To evaluate the efficacy and safety of a reduced starting dose regimen of 5 mg of tPA with 5 mg of DNase administered intrapleurally for pleural infection. Methods: Consecutive patients with pleural infection at four participating centers in Australia, the United Kingdom, and New Zealand were included in this observational, open-label study. Treatment was initiated with tPA 5 mg and DNase 5 mg twice daily. Subsequent dose escalation was permitted at the discretion of the attending physician. Data relating to treatment success, radiological and systemic inflammatory changes (blood C-reactive protein), volume of fluid drained, length of hospital stay, and treatment complications were extracted retrospectively from the medical records. Results: We evaluated 61 patients (41 males; age, 57 ± 16 yr). Most patients (n = 58 [93.4%]) were successfully treated without requiring surgery for pleural infection. Treatment success was corroborated by clearance of pleural opacities visualized by chest radiography (from 42% [interquartile range, 22–58] to 16% [8–31] of hemithorax; P < 0.001), increase in pleural fluid drainage (from 175 ml in the 24 h preceding treatment to 2,025 ml [interquartile range, 1,247–2,984] over 72 h of therapy; P <  0.05) and a reduction in blood C-reactive protein (P < 0.05). Seven patients (11.5%) had dose escalation of tPA to 10 mg. Three patients underwent surgery. Three patients (4.9%) received blood transfusions for gradual pleural blood loss; none were hemodynamically compromised. Pain requiring escalation of analgesia affected 36% of patients; none required cessation of therapy. Conclusions: These pilot data suggest that a starting dose of 5 mg of tPA administered intrapleurally twice daily in combination with 5 mg of DNase for the treatment of pl

Structural neuroanatomy of tinnitus and hyperacusis in semantic dementia

Introduction Tinnitus and hyperacusis are common symptoms of excessive auditory perception in the general population; however, their anatomical substrates and disease associations continue to be defined. Patients with semantic dementia (SemD) frequently repor

Dietary Crude Lecithin Increases Systemic Availability of Dietary Docosahexaenoic Acid with Combined Intake in Rats

Crude lecithin, a mixture of mainly phospholipids, potentially helps to increase the systemic availability of dietary omega-3 polyunsaturated fatty acids (n-3 PUFA), such as docosahexaenoic acid (DHA). Nevertheless, no clear data exist on the effects of prolonged combined dietary supplementation of DHA and lecithin on RBC and plasma PUFA levels. In the current experiments, levels of DHA and choline, two dietary ingredients that enhance neuronal membrane formation and function, were determined in plasma and red blood cells (RBC) from rats after dietary supplementation of DHA-containing oils with and without concomitant dietary supplementation of crude lecithin for 2–3 weeks. The aim was to provide experimental evidence for the hypothesized additive effects of dietary lecithin (not containing any DHA) on top of dietary DHA on PUFA levels in plasma and RBC. Dietary supplementation of DHA-containing oils, either as vegetable algae oil or as fish oil, increased DHA, eicosapentaenoic acid (EPA), and total n-3 PUFA, and decreased total omega-6 PUFA levels in plasma and RBC, while dietary lecithin supplementation alone did not affect these levels. However, combined dietary supplementation of DHA and lecithin increased the changes induced by DHA supplementation alone. Animals receiving a lecithin-containing diet also had a higher plasma free choline concentration as compared to controls. In conclusion, dietary DHA-containing oils and crude lecithin have synergistic effects on increasing plasma and RBC n-3 PUFA levels, including DHA and EPA. By increasing the systemic availability of dietary DHA, dietary lecithin may increase the efficacy of DHA supplementation when their intake is combined.Nutricia Researc