Differential lipid dependence of function of bacterial sodium channel homologues

The lipid bilayer is important for maintaining the integrity of cellular compartments and plays a vital role in maintaining the hydrophobic/charged interactions necessary for structure, conformational flexibility and function. Despite the intimate relationship between ion channels and the membranes in which they are embedded, challenges resulting from the dynamic and complex nature of cellular membranes have limited our ability to address the functional role of these interactions. To directly assess lipid dependence of activity, we examined channel function ofthree purified bacterial sodium channel orthologues (NaChBac, NavMs, and NavSp) by cumulative 22Na+ uptake into proteoliposomes containing a 3:1 ratio of POPE and another glycerophospholipid (POPC, POPG, POPS, Cardiolipin (CL), POPA, or PI). We observed a unique lipid dependence for each homologue tested. Common to each was a low level of activity above background (uptake into protein free liposomes) when the second lipid was a zwitterionic lipid such as POPE and POPC. Maximal activity for full-length NaChBac and NavMs proteins was observed in POPE + POPG liposomes. On the other hand, full-length NavSp channels possessed a different lipid dependence, with maximal activity in liposomes containing POPE + PI. No strong lipid dependence was observed for pore-only constructs of NavMs or NavSp, that lacked the S1-S4 segments, suggesting that the lipid dependence of sodium channels may arise from their abilities to affect the voltage-sensing domains. The effect may be maximized by specific lipid-protein interactions that are uniquely favourable in each homologue, giving rise to differing lipid dependences

Making Study Populations Visible through Knowledge Graphs

Treatment recommendations within Clinical Practice Guidelines (CPGs) are largely based on findings from clinical trials and case studies, referred to here as research studies, that are often based on highly selective clinical populations, referred to here as study cohorts. When medical practitioners apply CPG recommendations, they need to understand how well their patient population matches the characteristics of those in the study cohort, and thus are confronted with the challenges of locating the study cohort information and making an analytic comparison. To address these challenges, we develop an ontology-enabled prototype system, which exposes the population descriptions in research studies in a declarative manner, with the ultimate goal of allowing medical practitioners to better understand the applicability and generalizability of treatment recommendations. We build a Study Cohort Ontology (SCO) to encode the vocabulary of study population descriptions, that are often reported in the first table in the published work, thus they are often referred to as Table 1. We leverage the well-used Semanticscience Integrated Ontology (SIO) for defining property associations between classes. Further, we model the key components of Table 1s, i.e., collections of study subjects, subject characteristics, and statistical measures in RDF knowledge graphs. We design scenarios for medical practitioners to perform population analysis, and generate cohort similarity visualizations to determine the applicability of a study population to the clinical population of interest. Our semantic approach to make study populations visible, by standardized representations of Table 1s, allows users to quickly derive clinically relevant inferences about study populations.Comment: 16 pages, 4 figures, 1 table, accepted to the ISWC 2019 Resources Track (https://iswc2019.semanticweb.org/call-for-resources-track-papers/

The Category of Node-and-Choice Forms, with Subcategories for Choice-Sequence Forms and Choice-Set Forms

The literature specifies extensive-form games in many styles, and eventually I hope to formally translate games across those styles. Toward that end, this paper defines $\mathbf{NCF}$, the category of node-and-choice forms. The category's objects are extensive forms in essentially any style, and the category's isomorphisms are made to accord with the literature's small handful of ad hoc style equivalences. Further, this paper develops two full subcategories: $\mathbf{CsqF}$ for forms whose nodes are choice-sequences, and $\mathbf{CsetF}$ for forms whose nodes are choice-sets. I show that $\mathbf{NCF}$ is "isomorphically enclosed" in $\mathbf{CsqF}$ in the sense that each $\mathbf{NCF}$ form is isomorphic to a $\mathbf{CsqF}$ form. Similarly, I show that $\mathbf{CsqF_{\tilde a}}$ is isomorphically enclosed in $\mathbf{CsetF}$ in the sense that each $\mathbf{CsqF}$ form with no-absentmindedness is isomorphic to a $\mathbf{CsetF}$ form. The converses are found to be almost immediate, and the resulting equivalences unify and simplify two ad hoc style equivalences in Kline and Luckraz 2016 and Streufert 2019. Aside from the larger agenda, this paper already makes three practical contributions. Style equivalences are made easier to derive by [1] a natural concept of isomorphic invariance and [2] the composability of isomorphic enclosures. In addition, [3] some new consequences of equivalence are systematically deduced.Comment: 43 pages, 9 figure

Gaps in detailed knowledge of human papillomavirus (HPV) and the HPV vaccine among medical students in Scotland

<p>Background: A vaccination programme targeted against human papillomavirus (HPV) types16 and 18 was introduced in the UK in 2008, with the aim of decreasing incidence of cervical disease. Vaccine roll out to 12–13 year old girls with a catch-up programme for girls aged up to 17 years and 364 days was accompanied by a very comprehensive public health information (PHI) campaign which described the role of HPV in the development of cervical cancer.</p> <p>Methods: A brief questionnaire, designed to assess acquisition of knowledge of HPV infection and its association to cervical cancer, was administered to two different cohorts of male and female 1st year medical students (school leavers: 83% in age range 17–20) at a UK university. The study was timed so that the first survey in 2008 immediately followed a summer's intensive PHI campaign and very shortly after vaccine roll-out (150 students). The second survey was exactly one year later over which time there was a sustained PHI campaign (213 students).</p> <p>Results: We addressed three research questions: knowledge about three specific details of HPV infection that could be acquired from PHI, whether length of the PHI campaign and/or vaccination of females had any bearing on HPV knowledge, and knowledge differences between men and women regarding HPV. No female student in the 2008 cohort had completed the three-dose vaccine schedule compared to 58.4% of female students in 2009. Overall, participants’ knowledge regarding the sexually transmitted nature of HPV and its association with cervical cancer was high in both year groups. However, in both years, less than 50% of students correctly identified that HPV causes over 90% of cases of cervical cancer. Males gave fewer correct answers for these two details in 2009. In 2008 only around 50% of students recognised that the current vaccine protects against a limited subset of cervical cancer-causing HPV sub-types, although there was a significant increase in correct response among female students in the 2009 cohort compared to the 2008 cohort.</p> <p>onclusions: This study highlights a lack of understanding regarding the extent of protection against cervical cancer conferred by the HPV vaccine, even among an educated population in the UK who could have a vested interest in acquiring such knowledge. The intensive PHI campaign accompanying the first year of HPV vaccination seemed to have little effect on knowledge over time. This is one of the first studies to assess detailed knowledge of HPV in both males and females. There is scope for continued improvements to PHI regarding the link between HPV infection and cervical cancer.</p&gt

Primary immunodeficiency

Primary immunodeficiency disorder (PID) refers to a heterogeneous group of over 130 disorders that result from defects in immune system development and/or function. PIDs are broadly classified as disorders of adaptive immunity (i.e., T-cell, B-cell or combined immunodeficiencies) or of innate immunity (e.g., phagocyte and complement disorders). Although the clinical manifestations of PIDs are highly variable, most disorders involve at least an increased susceptibility to infection. Early diagnosis and treatment are imperative for preventing significant disease-associated morbidity and, therefore, consultation with a clinical immunologist is essential. PIDs should be suspected in patients with: recurrent sinus or ear infections or pneumonias within a 1 year period; failure to thrive; poor response to prolonged use of antibiotics; persistent thrush or skin abscesses; or a family history of PID. Patients with multiple autoimmune diseases should also be evaluated. Diagnostic testing often involves lymphocyte proliferation assays, flow cytometry, measurement of serum immunoglobulin (Ig) levels, assessment of serum specific antibody titers in response to vaccine antigens, neutrophil function assays, stimulation assays for cytokine responses, and complement studies. The treatment of PIDs is complex and generally requires both supportive and definitive strategies. Ig replacement therapy is the mainstay of therapy for B-cell disorders, and is also an important supportive treatment for many patients with combined immunodeficiency disorders. The heterogeneous group of disorders involving the T-cell arm of the adaptive system, such as severe combined immunodeficiency (SCID), require immune reconstitution as soon as possible. The treatment of innate immunodeficiency disorders varies depending on the type of defect, but may involve antifungal and antibiotic prophylaxis, cytokine replacement, vaccinations and bone marrow transplantation. This article provides a detailed overview of the major categories of PIDs and strategies for the appropriate diagnosis and management of these rare disorders

A tetragonal-to-monoclinic phase transition in a ferroelectric perovskite: the structure of PbZr(0.52)Ti(0.48)O3

The perovskite-like ferroelectric system PbZr(1-x)Ti(x)O3 (PZT) has a nearly vertical morphotropic phase boundary (MPB) around x=0.45-0.50. Recent synchrotron x-ray powder diffraction measurements by Noheda et al. [Appl. Phys. Lett. 74, 2059 (1999)] have revealed a new monoclinic phase between the previously-established tetragonal and rhombohedral regions. In the present work we describe a Rietveld analysis of the detailed structure of the tetragonal and monoclinic PZT phases on a sample with x= 0.48 for which the lattice parameters are respectively: at= 4.044 A, ct= 4.138 A, at 325 K, and am= 5.721 A, bm= 5.708 A, cm= 4.138 A, beta= 90.496 deg., at 20K. In the tetragonal phase the shifts of the atoms along the polar [001] direction are similar to those in PbTiO3 but the refinement indicates that there are, in addition, local disordered shifts of the Pb atoms of ~0.2 A perpendicular to the polar axis.. The monoclinic structure can be viewed as a condensation along one of the directions of the local displacements present in the tetragonal phase. It equally well corresponds to a freezing-out of the local displacements along one of the directions recently reported by Corker et al.[J. Phys. Condens. Matter 10, 6251 (1998)] for rhombohedral PZT. The monoclinic structure therefore provides a microscopic picture of the MPB region in which one of the "locally" monoclinic phases in the "average" rhombohedral or tetragonal structures freezes out, and thus represents a bridge between these two phases.Comment: REVTeX, 7 figures. Modifications after referee's suggestion: new figure (figure 5), comments in 2nd para. (Sect.III) and in 2nd & 3rd para. (Sect. IV-a), in the abstract: "...of ~0.2 A perpendicular to the polar axis.

Differential lipid dependence of the function of bacterial sodium channels

The lipid bilayer is important for maintaining the integrity of cellular compartments and plays a vital role in providing the hydrophobic and charged interactions necessary for membrane protein structure, conformational flexibility and function. To directly assess the lipid dependence of activity for voltage-gated sodium channels, we compared the activity of three bacterial sodium channel homologues (NaChBac, NavMs, and NavSp) by cumulative 22Na+ uptake into proteoliposomes containing a 3:1 ratio of 1-palmitoyl 2-oleoyl phosphatidylethanolamine and different “guest” glycerophospholipids. We observed a unique lipid profile for each channel tested. NavMs and NavSp showed strong preference for different negatively-charged lipids (phosphatidylinositol and phosphatidylglycerol, respectively), whilst NaChBac exhibited a more modest variation with lipid type. To investigate the molecular bases of these differences we used synchrotron radiation circular dichroism spectroscopy to compare structures in liposomes of different composition, and molecular modeling and electrostatics calculations to rationalize the functional differences seen. We then examined pore-only constructs (with voltage sensor subdomains removed) and found that in these channels the lipid specificity was drastically reduced, suggesting that the specific lipid influences on voltage-gated sodium channels arise primarily from their abilities to interact with the voltage-sensing subdomains

Recognition of Depression in Older Medical Inpatients

BACKGROUND: Studies of recognition of depression in older (aged 65 or more) medical inpatients show low rates of recognition of depression by attending physicians. However, few studies have compared different measures of recognition of depression. OBJECTIVES: (1) To compare the validity of four indicators of recognition of depression and a global measure of recognition against a diagnosis of depression and (2) to explore the effect of patient characteristics on recognition of depression. METHODS: In a cohort of 264 medical inpatients 65 years and older (115 with major or minor depression, 78 with no depression), sensitivities, specificities, and diagnostic odds ratios (DOR) of 4 indicators of recognition (symptoms, diagnosis, treatment, and referral) and a global measure of recognition (any of the 4 indicators) were calculated. The associations between patient characteristics (age, sex, history of depression, antidepressant use before admission, severity of depression, comorbidity, duration of hospitalization, disability, and hospital of admission) and recognition were explored using multiple logistic regression. RESULTS: Less than half of the depressed patients were recognized. The indicator with the highest sensitivity was treatment (27.8%, 95% confidence interval [CI] 20.0–37.0), whereas the indicator with the best specificity was diagnosis (96.6%, 95% CI 91.9–98.7). The unadjusted DOR of global recognition was 2.6 (95% CI 1.5, 4.4). Less comorbidity, more severe depression symptoms, a history of depression, longer hospital stay, and antidepressant use before admission were significantly associated with better global recognition. CONCLUSION: Recognition of depression in elderly medical inpatients depends upon the indicator of recognition used