Development of a sequence-based in silico OspA typing method for Borrelia burgdorferi sensu lato.

Lyme disease (LD), caused by spirochete bacteria of the genus Borrelia burgdorferi sensu lato, remains the most common vector-borne disease in the northern hemisphere. Borrelia outer surface protein A (OspA) is an integral surface protein expressed during the tick cycle, and a validated vaccine target. There are at least 20 recognized Borrelia genospecies, that vary in OspA serotype. This study presents a new in silico sequence-based method for OspA typing using next-generation sequence data. Using a compiled database of over 400 Borrelia genomes encompassing the 4 most common disease-causing genospecies, we characterized OspA diversity in a manner that can accommodate existing and new OspA types and then defined boundaries for classification and assignment of OspA types based on the sequence similarity. To accommodate potential novel OspA types, we have developed a new nomenclature: OspA in silico type (IST). Beyond the ISTs that corresponded to existing OspA serotypes 1-8, we identified nine additional ISTs that cover new OspA variants in B. bavariensis (IST9-10), B. garinii (IST11-12), and other Borrelia genospecies (IST13-17). The IST typing scheme and associated OspA variants are available as part of the PubMLST Borrelia spp. database. Compared to traditional OspA serotyping methods, this new computational pipeline provides a more comprehensive and broadly applicable approach for characterization of OspA type and Borrelia genospecies to support vaccine development.

Experimental dataset of the impact assessment of vegetable intercropping on agroeconomic performances, pests and beneficials, and soil resources.

The data presented in this article were collected in the field at an experimental station in southern France under a Mediterranean climate. Experiments were conducted under three plastic walk-in tunnels used as blocks with organic farming practices over two successive years in a completely randomized design. The aim was to compare the intercropping of sweet pepper with basil, onion, lettuce, parsley or French bean to a sole crop of sweet pepper used as a control. The dataset provides information on cultural practices with details on inputs and working times used to estimate economic costs. The data also describe the climatic conditions under tunnels as well as the dynamics of soil nitrate concentration and water tension over time through treatments. Yields, economic benefits and the rates of products with visual defects are presented. In addition, some variables applied exclusively to sweet pepper crops, namely nitrate concentration in petiole sap, growth parameters, abundance of aerial pests and beneficials, incidence of root necrosis, arbuscular mycorrhizal fungi colonization rates and diversity in roots. The field dataset is made publicly available to allow free and easy access for the scientific and professional community to enable analysis and reuse. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

Probing gigahertz coherent acoustic phonons in TiO2 mesoporous thin films.

Ultrahigh-frequency acoustic-phonon resonators usually require atomically flat interfaces to avoid phonon scattering and dephasing, leading to expensive fabrication processes, such as molecular beam epitaxy. Mesoporous thin films are based on inexpensive wet chemical fabrication techniques that lead to relatively flat interfaces regardless the presence of nanopores. Here, we report mesoporous titanium dioxide-based acoustic resonators with resonances up to 90 GHz, and quality factors from 3 to 7. Numerical simulations show a good agreement with the picosecond ultrasonics experiments. We also numerically study the effect of changes in the speed of sound on the performance of the resonator. This change could be induced by liquid infiltration into the mesopores. Our findings constitute the first step towards the engineering of building blocks based on mesoporous thin films for reconfigurable optoacoustic sensors.

A Randomized Trial to Identify Accurate Measurement Methods for Adherence to Cognitive-Behavioral Therapy.

Clinician fidelity to cognitive behavioral therapy (CBT) is an important mechanism by which desired clinical outcomes are achieved and is an indicator of care quality. Despite its importance, there are few fidelity measurement methods that are efficient and have demonstrated reliability and validity. Using a randomized trial design, we compared three methods of assessing CBT adherence-a core component of fidelity-to direct observation, the gold standard. Clinicians recruited from 27 community mental health agencies (n = 126; M age = 37.69 years, SD = 12.84; 75.7% female) were randomized 1:1:1 to one of three fidelity conditions: self-report (n = 41), chart-stimulated recall (semistructured interviews with the chart available; n = 42), or behavioral rehearsal (simulated role-plays; n = 43). All participating clinicians completed fidelity assessments for up to three sessions with three different clients that were recruited from clinicians' caseloads (n = 288; M age = 13.39 years SD = 3.89; 41.7% female); sessions were also audio-recorded and coded for comparison to determine the most accurate method. All fidelity measures had parallel scales that yielded an adherence maximum score (i.e., the highest-rated intervention in a session), a mean of techniques observed, and a count total of observed techniques. Results of three-level mixed effects regression models indicated that behavioral rehearsal produced comparable scores to observation for all adherence scores (all ps > .01), indicating no difference between behavioral rehearsal and observation. Self-report and chart-stimulated recall overestimated adherence compared to observation (ps < .01). Overall, findings suggested that behavioral rehearsal indexed CBT adherence comparably to direct observation, the gold-standard, in pediatric populations. Behavioral rehearsal may at times be able to replace the need for resource-intensive direct observation in implementation research and practice.

Genetic Surveillance of SARS-CoV-2 Mpro Reveals High Sequence and Structural Conservation Prior to the Introduction of Protease Inhibitor Paxlovid.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to represent a global health emergency as a highly transmissible, airborne virus. An important coronaviral drug target for treatment of COVID-19 is the conserved main protease (Mpro). Nirmatrelvir is a potent Mpro inhibitor and the antiviral component of Paxlovid. The significant viral sequencing effort during the ongoing COVID-19 pandemic represented a unique opportunity to assess potential nirmatrelvir escape mutations from emerging variants of SARS-CoV-2. To establish the baseline mutational landscape of Mpro prior to the introduction of Mpro inhibitors, Mpro sequences and its cleavage junction regions were retrieved from ~4,892,000 high-quality SARS-CoV-2 genomes in the open-access Global Initiative on Sharing Avian Influenza Data (GISAID) database. Any mutations identified from comparison to the reference sequence (Wuhan-Hu-1) were catalogued and analyzed. Mutations at sites key to nirmatrelvir binding and protease functionality (e.g., dimerization sites) were still rare. Structural comparison of Mpro also showed conservation of key nirmatrelvir contact residues across the extended Coronaviridae family (α-, ß-, and γ-coronaviruses). Additionally, we showed that over time, the SARS-CoV-2 Mpro enzyme remained under purifying selection and was highly conserved relative to the spike protein. Now, with the emergency use authorization (EUA) of Paxlovid and its expected widespread use across the globe, it is essential to continue large-scale genomic surveillance of SARS-CoV-2 Mpro evolution. This study establishes a robust analysis framework for monitoring emergent mutations in millions of virus isolates, with the goal of identifying potential resistance to present and future SARS-CoV-2 antivirals. IMPORTANCE The recent authorization of oral severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antivirals, such as Paxlovid, has ushered in a new era of the COVID-19 pandemic. The emergence of new variants, as well as the selective pressure imposed by antiviral drugs themselves, raises concern for potential escape mutations in key drug binding motifs. To determine the potential emergence of antiviral resistance in globally circulating isolates and its implications for the clinical response to the COVID-19 pandemic, sequencing of SARS-CoV-2 viral isolates before, during, and after the introduction of new antiviral treatments is critical. The infrastructure built herein for active genetic surveillance of Mpro evolution and emergent mutations will play an important role in assessing potential antiviral resistance as the pandemic progresses and Mpro inhibitors are introduced. We anticipate our framework to be the starting point in a larger effort for global monitoring of the SARS-CoV-2 Mpro mutational landscape.

Screening Adolescents for Sensitive Health Topics in Primary Care: A Scoping Review.

We sought to aggregate common barriers and facilitators to screening adolescents for sensitive health topics (e.g., depression, chlamydia) in primary care, as well as those that are unique to a given health topic. We conducted a literature search of three databases (PsycInfo, MEDLINE, and CINAHL) and reference lists of included articles. Studies focused on barriers and facilitators to screening adolescents (ages 12-17 years) for sensitive health topics in primary care that are recommended by national guidelines. Articles were peer-reviewed, presented empirical data, and were published in English in 2006-2021. We coded barriers and facilitators using the Consolidated Framework for Implementation Research, a well-established framework within implementation science. In total, 39 studies met inclusion criteria and spanned several health topics: depression, suicide, substance use, HIV, and chlamydia. We found common barriers and facilitators to screening across health topics, with most relating to characteristics of the primary care clinics (e.g., time constraints). Other factors relevant to screening implementation ranged from confidentiality concerns to clinician knowledge. Barriers and facilitators specific to certain health topics, such as the availability of on-site laboratories for HIV screening, were also noted. Findings can guide refinements to screening implementation.

Stakeholder intention to engage in fidelity measurement methods in community mental health settings: A mixed methods study.

Background: The current gold standard for measuring fidelity (specifically, adherence) to cognitive behavioral therapy (CBT) is direct observation, a costly, resource-intensive practice that is not feasible for many community organizations to implement regularly. Recent research indicates that behavioral rehearsal (i.e., role-play between clinician and individual with regard to session delivery) and chart-stimulated recall (i.e., brief structured interview between clinician and individual about what they did in session; clinicians use the client chart to prompt memory) may provide accurate and affordable alternatives for measuring adherence to CBT in such settings, with behavioral rehearsal yielding greater correspondence with direct observation. Methods: Drawing on established causal theories from social psychology and leading implementation science frameworks, this study evaluates stakeholders' intention to use behavioral rehearsal and chart-stimulated recall. Specifically, we measured attitudes, self-efficacy, and subjective norms toward using each, and compared these factors across the two methods. We also examined the relationship between attitudes, self-efficacy, subjective norms, and intention to use each method. Finally, using an integrated approach we asked stakeholders to discuss their perception of contextual factors that may influence beliefs about using each method. These data were collected from community-based supervisors (n = 17) and clinicians (n = 66). Results: Quantitative analyses suggest moderately strong intention to use both methods across stakeholders. There were no differences in supervisors' or clinicians' attitudes, self-efficacy, subjective norms, or intention across methods. More positive attitudes and greater reported subjective norms were associated with greater reported intention to use either measure. Qualitative analyses identified participants' specific beliefs about using each fidelity measure in their organization, and results were organized using the Consolidated Framework for Implementation Research. Conclusions: Strategies are warranted to overcome or minimize potential barriers to using fidelity measurement methods and to further increase the strength of intention to use them.Plain Language Summary: The best way to measure fidelity, or how closely a clinician follows the protocol, to Cognitive Behavioral Therapy (CBT) is watching the session. This is an expensive practice that is not feasible for many community organizations to do regularly. Recent research indicates that behavioral rehearsal, or a role-play between the clinician and individual with regard to session delivery, and chart-stimulated recall, or a brief discussion between an individual and the clinician about what they did in session with the clinician having access to the chart to help them remember, may provide accurate and affordable alternatives for measuring fidelity to CBT. We just completed a study demonstrating that both methods are promising, with behavioral rehearsal offering scores that are the most similar to watching the session. Drawing on established theories from social psychology and leading implementation science frameworks, this study evaluates future supervisor and clinician motivation to use these fidelity measurement methods. Specifically, we measured supervisor (n = 17) and clinician (n = 66) attitudes, norms, self-efficacy, intentions, and anticipated barriers and facilitators to using each of these fidelity measurement tools. Quantitative and qualitative analyses suggest similar intention to use both methods, and concerns about barriers to using each method. Further research is warranted to minimize the burden associated with implementing fidelity measurement methods and deploying strategies to increase use.

Elastic and magnetoelastic properties of TbMnO3single crystal by nanosecond time resolved acoustics and first-principles calculations.

Time resolved pump and probe acoustics and first-principles calculations were employed to assess elastic properties of the TbMnO3perovskite manganite having orthorhombic symmetry. Measuring sound velocities of bulk longitudinal and shear acoustic waves propagating along at least two different directions in the high symmetry planes (100), (010) and (001), provided a powerful mean to selectively determine the six diagonal elastic constantsC11= 227 GPa,C22= 349 GPa,C33= 274 GPa,C44= 71 GPa,C55= 57 GPa,C66= 62 GPa. Among the three remaining off-diagonal ones,C23= 103 GPa was determined with a bissectrice direction. Density functional theory calculations with colinear spin-polarized provided complementary insights on their optical, elastic and magnetoelastic properties.

Factors impacting the evidence-based assessment, diagnosis and management of Acute Charcot Neuroarthropathy: a systematic review.

BACKGROUND: Acute Charcot Neuroarthropathy (CN) is a destructive condition that is characterised by acute fractures, dislocations and joint destruction in the weight-bearing foot. The acute phase is often misdiagnosed and can rapidly lead to devastating health outcomes. Early diagnosis and management of CN is imperative to attenuate progression of this condition. Consequently, timely evidence-based assessment, diagnosis and management of acute CN is imperative. OBJECTIVE: To identify the factors that impact the delivery of evidence-based care in assessment, diagnosis and management of people with acute CN. METHOD: Systematic searches were conducted in four databases to identify studies in English that included factors that impact the delivery of evidence-based care in the assessment, diagnosis and management of people with acute CN. Articles and consensus/guideline documents were assessed for inclusion by the researchers and disagreements were resolved through consensus. Additionally backward citation searching was used to source other potentially relevant documents. Information relevant to the research question was extracted and thematic analyses were performed using qualitative synthesis. RESULTS: Thirty-two articles and four additional consensus/guideline documents were included for data extraction and analyses. Information related to the research question was of expert opinion using the National Health and Medical Research Council (NHMRC) Levels of Evidence guidelines. Themes explaining practices that deviated from evidence-based care in assessment, diagnosis and management of acute CN centred around patient, health professional and health organisation/environmental. Delay to diagnosis is particularly influenced by the patient's knowledge of when to seek help, practitioner knowledge in knowing how to recognise and refer for appropriate immediate care, confusion in imaging and offloading and geographical and local health service resources to appropriately manage the condition. CONCLUSION: Individual and health professional awareness and geographical barriers are key challenges to the effective delivery of evidence-based assessment, diagnosis and management of people with acute CN. Acute CN represents a medical emergency warranting the need for expedited assessment, diagnosis and management by appropriately trained health professionals in the appropriate.

The TPOCS-self-reported Therapist Intervention Fidelity for Youth (TPOCS-SeRTIFY): A case study of pragmatic measure development.

Background: Developing pragmatic assessment tools to measure clinician use of evidence-based practices is critical to advancing implementation of evidence-based practices in mental health. This case study details our community-partnered process of developing the Therapy Process Observation Coding Scale-Self-Reported Therapist Intervention Fidelity for Youth (TPOCS-SeRTIFY), a pragmatic, clinician-report instrument to measure cognitive behavioral therapy (CBT) delivery. Approach: We describe a five-step community-partnered development process. Initial goals were to create a self-report instrument that paralleled an existing direct observation measure of clinician delivery of CBT use to facilitate later assessment of measure performance. Cognitive interviews with community clinicians (n = 6) and consultation with CBT experts (n = 6) were used to enhance interpretability and usability as part of an iterative refinement process. The instrument was administered to 247 community clinicians along with an established self-reported measure of clinician delivery of CBT and other treatments to assess preliminary psychometric performance. Preliminary psychometrics were promising. Conclusion: Our community-partnered development process showed promising success and can guide future development of pragmatic implementation measures both to facilitate measurement of ongoing implementation efforts and future research aimed at building learning mental health systems. Plain language summary: Developing brief, user-friendly, and accurate tools to measure how therapists deliver cognitive behavioral therapy (CBT) in routine practice is important for advancing the reach of CBT into community settings. To date, developing such "pragmatic" measures has been difficult. There is little known about how researchers can best develop these types of assessment tools so that they (1) are easy for clinicians in practice to use and (2) provide valid and useful information about implementation outcomes. As a result, there are few well-validated measures in existence that measure therapist use of CBT that are feasible for use in community practice. This paper contributes to the literature by describing our community-partnered process for developing a measure of therapist use of CBT (Therapy Process Observation Coding Scale -Self-Reported Therapist Intervention Fidelity for Youth; TPOCS-SeRTIFY). This descriptive case study outlines the community-partnered approach we took to develop this measure. This case study will contribute to future research by serving as a guide to others aiming to develop pragmatic implementation measures. In addition, the TPOCS-SeRTIFY is a pragmatic measure of clinician use of CBT that holds promise for its use by both researchers and clinicians to measure the success of CBT implementation efforts.

Promoting parent-infant responsiveness in families experiencing homelessness.

My Baby's First Teacher is an intervention designed specifically for parents with infants staying in emergency homeless shelters. Infants are overrepresented in shelter populations and face considerable risk to their development, including mental health. We utilized a randomized controlled design across three family shelters to evaluate the program's effectiveness with 24 dyads assigned to the intervention compared to 21 dyads in care-as-usual. Dyads were randomized by round at each site to account for shelter effects. We used path analysis to illustrate change over time and in relation to intervention assignment.

El Primer Maestro de mi Bebé es una intervención diseñada específicamente para progenitores con infantes que se alojan en refugios de emergencia para personas sin casa. En la población de los refugios, los infantes están sobrerrepresentados y enfrentan un considerable riesgo en cuanto a su desarrollo, incluyendo la salud mental. Utilizamos un diseño de control al azar a través de tres refugios de familias para evaluar la eficacia del programa con 24 díadas asignadas al grupo de intervención que fueron comparadas con 21 díadas bajo el cuidado usual. A las díadas se les colocó al azar por etapas en cada lugar para tener en cuenta los efectos del refugio. Usamos un análisis de trayectoria para ilustrar el cambio a través del tiempo y en relación con la asignación de intervención. Resultados claves: los resultados indicaron mejoras en la observada sensibilidad de progenitor-infante relacionada con la intervención en el lugar, con un control en cuanto a los niveles iniciales de sensibilidad. Los resultados fueron consistentes entre un modelo de intención de tratar y un modelo para probar la participación cierta en la intervención. No encontramos ningún efecto significativo para el estrés de crianza o la ansiedad del progenitor, aunque las tendencias sugirieron más altos puntajes para las familias de la intervención. Implicaciones para la práctica y las políticas: presentamos los resultados considerando retos específicos en contextos de casos sin casa para la salud mental infantil. Este trabajo puede servir de base para los esfuerzos de quienes proveen servicios y encuentran familias que experimentan el estar sin casa, así como también las políticas sobre los recursos para programaciones en albergues de emergencia.

Le Premier Enseignant de Mon Bébé est une intervention conçue spécialement pour les parents dont les bébés restent dans des foyers d'urgence pour sans-abris. Les bébés sont sur-représentés dans les populations de ces foyers et ils font face à un risque considérable pour leur développement, y compris pour ce qui concerne leur santé mentale. Nous avons utilisé un schéma expérimental contrôlé pour 3 trois foyers familiaux afin d'évaluer l'efficacité du programme avec 24 dyades désignées pour l'intervention comparé à 21 dyades dans le groupe de soins habituels. Les dyades ont été randomisées par ronde sur chaque site afin de contrôler les effets du foyer. Nous avons utilisé une analyse causale pour illustrer le changement au fil du temps et en relation au groupe d'intervention. Constatations Clés: Résultats a indiqué des améliorations dans la réaction observée parent-bébé liée à l'intervention en fin d'étude, contrôlant les niveaux initiaux de réaction. Les résultats sont cohérents entre un modèle intention-de-traiter et un modèle testant la véritable participation à l'intervention. Nous n'avons trouvé aucun effet important pour le stress de parentage ou la détresse du parent, bien que des tendances suggèrent des scores plus élevés pour les familles d'intervention. Nous présentons des résultats en considérant les défis uniques aux contextes de la vie des sans-abris pour la santé mentale du nourrisson. Ce travail peut orienter les efforts des prestataires de services qui rencontrent des familles faisant l'expérience d'une vie sans abri ainsi que les lois et pratiques concernant les ressources pour des programmes dans des foyers d'accueil d'urgence.

Structure and Function in Antimicrobial Piscidins: Histidine Position, Directionality of Membrane Insertion, and pH-Dependent Permeabilization.

Piscidins are histidine-enriched antimicrobial peptides that interact with lipid bilayers as amphipathic α-helices. Their activity at acidic and basic pH in vivo makes them promising templates for biomedical applications. This study focuses on p1 and p3, both 22-residue-long piscidins with 68% sequence identity. They share three histidines (H3, H4, and H11), but p1, which is significantly more permeabilizing, has a fourth histidine (H17). This study investigates how variations in amphipathic character associated with histidines affect the permeabilization properties of p1 and p3. First, we show that the permeabilization ability of p3, but not p1, is strongly inhibited at pH 6.0 when the conserved histidines are partially charged and H17 is predominantly neutral. Second, our neutron diffraction measurements performed at low water content and neutral pH indicate that the average conformation of p1 is highly tilted, with its C-terminus extending into the opposite leaflet. In contrast, p3 is surface bound with its N-terminal end tilted toward the bilayer interior. The deeper membrane insertion of p1 correlates with its behavior at full hydration: an enhanced ability to tilt, bury its histidines and C-terminus, induce membrane thinning and defects, and alter membrane conductance and viscoelastic properties. Furthermore, its pH-resiliency relates to the neutral state favored by H17. Overall, these results provide mechanistic insights into how differences in the histidine content and amphipathicity of peptides can elicit different directionality of membrane insertion and pH-dependent permeabilization. This work features complementary methods, including dye leakage assays, NMR-monitored titrations, X-ray and neutron diffraction, oriented CD, molecular dynamics, electrochemical impedance spectroscopy, surface plasmon resonance, and quartz crystal microbalance with dissipation.

Structural properties of apolipoprotein A-I mimetic peptides that promote ABCA1-dependent cholesterol efflux.

Peptides mimicking the major protein of highdensity lipoprotein (HDL), apolipoprotein A-I (apoA-I), are promising therapeutics for cardiovascular diseases. Similar to apoA-I, their atheroprotective property is attributed to their ability to form discoidal HDL-like particles by extracting cellular cholesterol and phospholipids from lipid microdomains created by the ABCA1 transporter in a process called cholesterol efflux. The structural features of peptides that enable cholesterol efflux are not well understood. Herein, four synthetic amphipathic peptides denoted ELK, which only contain Glu, Leu, Lys, and sometimes Ala, and which have a wide range of net charges and hydrophobicities, were examined for cholesterol efflux. Experiments show that ELKs with a net neutral charge and a hydrophobic face that subtends an angle of at least 140° are optimal for cholesterol efflux. All-atom molecular dynamics simulations show that peptides that are effective in promoting cholesterol efflux stabilize HDL nanodiscs formed by these peptides by the orderly covering of the hydrophobic acyl chains on the edge of the disc. In contrast to apoA-I, which forms an anti-parallel double belt around the HDL, active peptides assemble in a mostly anti-parallel "picket fence" arrangement. These results shed light on the efflux ability of apoA-I mimetics and inform the future design of such therapeutics.

Identification of a novel lipid binding motif in apolipoprotein B by the analysis of hydrophobic cluster domains.

Apolipoprotein B (apoB) is a large amphipathic protein that is the structural scaffold for the formation of several classes of lipoproteins involved in lipid transport throughout the body. The goal of the present study was to identify specific domains in the apoB sequence that contribute to its lipid binding properties. A sequence analysis algorithm was developed to identify stretches of hydrophobic amino acids devoid of charged amino acids, which are referred to as hydrophobic cluster domains (HCDs). This analysis identified 78 HCDs in apoB with hydrophobic stretches ranging from 6 to 26 residues. Each HCD was analyzed in silico for secondary structure and lipid binding properties, and a subset was synthesized for experimental evaluation. One HCD peptide, B38, showed high affinity binding to both isolated HDL and LDL, and could exchange between lipoproteins. All-atom molecular dynamics simulations indicate that B38 inserts 3.7Å below the phosphate plane of the bilayer. B38 forms an unusual α-helix with a broad hydrophobic face and polar serine and threonine residues on the opposite face. Based on this structure, we hypothesized that B38 could efflux cholesterol from cells. B38 showed a 12-fold greater activity than the 5A peptide, a bihelical Class A amphipathic helix (EC50 of 0.2658 vs. 3.188µM; p<0.0001), in promoting cholesterol efflux from ABCA1 expressing BHK-1 cells. In conclusion, we have identified novel domains within apoB that contribute to its lipid biding properties. Additionally, we have discovered a unique amphipathic helix design for efficient ABCA1-specific cholesterol efflux.

Lipid and Peptide Diffusion in Bilayers: The Saffman-Delbrück Model and Periodic Boundary Conditions.

The periodic Saffman-Delbrück (PSD) model, an extension of the Saffman-Delbrück model developed to describe the effects of periodic boundary conditions on the diffusion constants of lipids and proteins obtained from simulation, is tested using the coarse-grained Martini and all-atom CHARMM36 (C36) force fields. Simulations of pure Martini dipalmitoylphosphatidylcholine (DPPC) bilayers and those with one embedded gramicidin A (gA) dimer or one gA monomer with sizes ranging from 512 to 2048 lipids support the PSD model. Underestimates of D∞ (the value of the diffusion constant for an infinite system) from the 512-lipid system are 35% for DPPC, 45% for the gA monomer, and 70% for the gA dimer. Simulations of all-atom DPPC and dioleoylphosphatidylcholine (DOPC) bilayers yield diffusion constants not far from experiment. However, the PSD model predicts that diffusion constants at the sizes of the simulation should underestimate experiment by approximately a factor of 3 for DPPC and 2 for DOPC. This likely implies a deficiency in the C36 force field. A Bayesian method for extrapolating diffusion constants of lipids and proteins in membranes obtained from simulation to infinite system size is provided.

Simulations of Membrane-Disrupting Peptides I: Alamethicin Pore Stability and Spontaneous Insertion.

An all-atom molecular dynamics simulation of the archetype barrel-stave alamethicin (alm) pore in a 1,2-dioleoyl-sn-glycero-3-phosphocholine bilayer at 313 K indicates that ∼7 µs is required for equilibration of a preformed 6-peptide pore; the pore remains stable for the duration of the remaining 7 µs of the trajectory, and the structure factors agree well with experiment. A 5 µs simulation of 10 surface-bound alm peptides shows significant peptide unfolding and some unbinding, but no insertion. Simulations at 363 and 413 K with a -0.2 V electric field yield peptide insertion in 1 µs. Insertion is initiated by the folding of residues 3-11 into an α-helix, and mediated by membrane water or by previously inserted peptides. The stability of five alm pore peptides at 413 K with a -0.2 V electric field demonstrates a significant preference for a transmembrane orientation. Hence, and in contrast to the cationic antimicrobial peptide described in the following article, alm shows a strong preference for the inserted over the surface-bound state.

Simulations of Membrane-Disrupting Peptides II: AMP Piscidin 1 Favors Surface Defects over Pores.

Antimicrobial peptides (AMPs) that disrupt bacterial membranes are promising therapeutics against the growing number of antibiotic-resistant bacteria. The mechanism of membrane disruption by the AMP piscidin 1 was examined with multimicrosecond all-atom molecular dynamics simulations and solid-state NMR spectroscopy. The primary simulation was initialized with 20 peptides in four barrel-stave pores in a fully hydrated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol bilayer. The four pores relaxed to toroidal by 200 ns, only one porelike structure containing two transmembrane helices remained at 26 µs, and none of the 18 peptides released to the surface reinserted to form pores. The simulation was repeated at 413 K with an applied electric field and all peptides were surface-bound by 200 ns. Trajectories of surface-bound piscidin with and without applied fields at 313 and 413 K and totaling 6 µs show transient distortions of the bilayer/water interface (consistent with (31)P NMR), but no insertion to transmembrane or pore states. (15)N chemical shifts confirm a fully surface-bound conformation. Taken together, the simulation and experimental results imply that transient defects rather than stable pores are responsible for membrane disruption by piscidin 1, and likely other AMPs.

[Quality and safety management for radiotherapy]. / Démarches d'amélioration de la qualité et gestion des risques en radiothérapie.

Quality and safety management have been implemented for many years in healthcare structures (hospitals treating cancer, private radiotherapy centres). Their structure and formalization have improved progressively over time. These recommendations aim at describing the link between quality and safety management through its organization scheme based on quality-safety policy, process approach, document management and quality measurement. Dedicated tools, such as experience feedback, a priori risk mapping, to-do-lists and check-lists are shown as examples and recommended as routine practice.

Protein dynamics and the all-ferrous [Fe4 S4 ] cluster in the nitrogenase iron protein.

In nitrogen fixation by Azotobacter vinelandii nitrogenase, the iron protein (FeP) binds to and subsequently transfers electrons to the molybdenum-FeP, which contains the nitrogen fixation site, along with hydrolysis of two ATPs. However, the nature of the reduced state cluster is not completely clear. While reduced FeP is generally thought to contain an [Fe4 S4 ](1+) cluster, evidence also exists for an all-ferrous [Fe4 S4 ](0) cluster. Since the former indicates a single electron is transferred per two ATPs hydrolyzed while the latter indicates two electrons could be transferred per two ATPs hydrolyzed, an all-ferrous [Fe4 S4 ](0) cluster in FeP is potenially two times more efficient. However, the 1+/0 reduction potential has been measured in the protein at both 460 and 790 mV, causing the biological significance to be questioned. Here, "density functional theory plus Poisson Boltzmann" calculations show that cluster movement relative to the protein surface observed in the crystal structures could account for both measured values. In addition, elastic network mode analysis indicates that such movement occurs in low frequency vibrations of the protein, implying protein dynamics might lead to variations in reduction potential. Furthermore, the different reductants used in the conflicting measurements of the reduction potential could be differentially affecting the protein dynamics. Moreover, even if the all-ferrous cluster is not the biologically relevant cluster, mutagenesis to stabilize the conformation with the more exposed cluster may be useful for bioengineering more efficient enzymes.

Verbal fluency tests: Normative data for the Latin American Spanish speaking adult population.

OBJECTIVE: To generate normative data for the Verbal Fluency Tests across 11 countries in Latin America, with country-specific adjustments for gender, age, and education, where appropriate. METHOD: The sample consisted of 3,977 healthy adults who were recruited from Argentina, Bolivia, Chile, Cuba, El Salvador, Guatemala, Honduras, Mexico, Paraguay, Peru, and, Puerto Rico. Each subject was administered the Verbal Fluency Test as part of a larger neuropsychological battery. A standardized five-step statistical procedure was used to generate the norms. RESULTS: The final multiple linear regression models for the letter F explained 8-30% of the variance, 7-32% for letter A, 8-32% for the letter S, and 16-43% for the animal category in Verbal Fluency Test scores. Although t-tests showed significant differences between men and women on the Verbal Fluency Test, they did not have an effect size larger than 0.3. As a result, gender-adjusted norms were not generated. CONCLUSIONS: This is the first normative multicenter study conducted in Latin America aiming to create norms for the Verbal Fluency Test; this study will have important outcomes for the future of neuropsychology in the region.