A mixed methods study to inform and evaluate a longitudinal nurse practitioner/community health worker intervention to address social determinants of health and chronic obstructive pulmonary disease self-management.

BACKGROUND: Individuals with low socioeconomic status experience higher prevalence and worse outcomes of chronic obstructive pulmonary disease (COPD). We undertook a quality improvement initiative at our safety net hospital in which a nurse practitioner (NP)/community health worker (CHW) team followed patients with COPD, frequent admissions, and unmet SDOH needs from hospitalization through one month post-discharge. We report our mixed methods approach to inform development and preliminary evaluation of this intervention. METHODS: We first assessed characteristics of patients admitted with COPD in 2018 (n = 1811), performing multivariable logistic regression to identify factors associated with ≥ 2 admissions per year. We then tested a standardized tool to screen for unmet SDOH needs in a convenience sample of 51 frequently hospitalized patients with COPD. From January-July 2019, we pilot tested the NP/CHW intervention with 57 patients, reviewed NP/CHW logs, and conducted qualitative interviews with 16 patient participants to explore impressions of the intervention. RESULTS: Patients with Medicaid insurance, mental health disorders, cardiac disease, and substance use disorder had increased odds of having ≥ 2 admissions. COPD severity, comorbidities, and unmet SDOH needs made COPD self-management challenging. Seventy-four percent of frequently admitted patients with COPD completing SDOH screening had unmet SDOH needs. Patients perceived that the NP/CHW intervention addressed these barriers by connecting them to resources and providing emotional support. CONCLUSIONS: Many patients with COPD admitted at our safety-net hospital experience unmet SDOH needs that impede COPD self-management. A longitudinal NP/CHW intervention to address unmet SDOH needs following discharge appears feasible and acceptable.

Opposing effects of glutamine and asparagine govern prion formation by intrinsically disordered proteins.

Sequences rich in glutamine (Q) and asparagine (N) residues often fail to fold at the monomer level. This, coupled to their unusual hydrogen-bonding abilities, provides the driving force to switch between disordered monomers and amyloids. Such transitions govern processes as diverse as human protein-folding diseases, bacterial biofilm assembly, and the inheritance of yeast prions (protein-based genetic elements). A systematic survey of prion-forming domains suggested that Q and N residues have distinct effects on amyloid formation. Here, we use cell biological, biochemical, and computational techniques to compare Q/N-rich protein variants, replacing Ns with Qs and Qs with Ns. We find that the two residues have strong and opposing effects: N richness promotes assembly of benign self-templating amyloids; Q richness promotes formation of toxic nonamyloid conformers. Molecular simulations focusing on intrinsic folding differences between Qs and Ns suggest that their different behaviors are due to the enhanced turn-forming propensity of Ns over Qs.

A distant trophoblast-specific enhancer controls HLA-G expression at the maternal-fetal interface.

HLA-G, a nonclassical HLA molecule uniquely expressed in the placenta, is a central component of fetus-induced immune tolerance during pregnancy. The tissue-specific expression of HLA-G, however, remains poorly understood. Here, systematic interrogation of the HLA-G locus using massively parallel reporter assay (MPRA) uncovered a previously unidentified cis-regulatory element 12 kb upstream of HLA-G with enhancer activity, Enhancer L Strikingly, clustered regularly-interspaced short palindromic repeats (CRISPR)/Cas9-mediated deletion of this enhancer resulted in ablation of HLA-G expression in JEG3 cells and in primary human trophoblasts isolated from placenta. RNA-seq analysis demonstrated that Enhancer L specifically controls HLA-G expression. Moreover, DNase-seq and chromatin conformation capture (3C) defined Enhancer L as a cell type-specific enhancer that loops into the HLA-G promoter. Interestingly, MPRA-based saturation mutagenesis of Enhancer L identified motifs for transcription factors of the CEBP and GATA families essential for placentation. These factors associate with Enhancer L and regulate HLA-G expression. Our findings identify long-range chromatin looping mediated by core trophoblast transcription factors as the mechanism controlling tissue-specific HLA-G expression at the maternal-fetal interface. More broadly, these results establish the combination of MPRA and CRISPR/Cas9 deletion as a powerful strategy to investigate human immune gene regulation.

Differentiated human stem cells resemble fetal, not adult, ß cells.

Human pluripotent stem cells (hPSCs) have the potential to generate any human cell type, and one widely recognized goal is to make pancreatic ß cells. To this end, comparisons between differentiated cell types produced in vitro and their in vivo counterparts are essential to validate hPSC-derived cells. Genome-wide transcriptional analysis of sorted insulin-expressing (INS(+)) cells derived from three independent hPSC lines, human fetal pancreata, and adult human islets points to two major conclusions: (i) Different hPSC lines produce highly similar INS(+) cells and (ii) hPSC-derived INS(+) (hPSC-INS(+)) cells more closely resemble human fetal ß cells than adult ß cells. This study provides a direct comparison of transcriptional programs between pure hPSC-INS(+) cells and true ß cells and provides a catalog of genes whose manipulation may convert hPSC-INS(+) cells into functional ß cells.

Experimental and mathematical analysis of in vitro Pitavastatin hepatic uptake across species.

1. To investigate the non-linear kinetics of in vitro hepatocyte uptake across species, the OATP substrate Pitavastatin was used as a probe. 2. Experiments were conducted at AstraZeneca (Alderley Park, Macclesfield) using freshly isolated rat, dog and human hepatocytes, utilising the "oil spin" methodology described by Hassen et al. (1996). Very few mechanistic models have previously been used to characterise the uptake process. 3. Here two candidate pharmacokinetic non-linear compartmental models are proposed. Both models have been shown to be structurally identifiable and distinghishable previously, which establishes that all unknown parameters could be identified from the experimental observations available and that input/output relationships for both the candidate models were structurally different. 4. A kinetic modelling software package, FACSIMILE (MCPA Software, Faringdon, UK), was used to obtain numerical solutions for the system equations and for parameter estimation. Model fits gave good agreement with the in vitro data and suggest the current widely accepted assumption that the rate of diffusion across the hepatocyte cell membrane is the same at both 4 °C and 37 °C is not valid, at least for Pitavastatin. Although this finding has already been proposed, this is the first time it is comprehensively debunked using statistical testing.

A global sampling approach to designing and reengineering RNA secondary structures.

The development of algorithms for designing artificial RNA sequences that fold into specific secondary structures has many potential biomedical and synthetic biology applications. To date, this problem remains computationally difficult, and current strategies to address it resort to heuristics and stochastic search techniques. The most popular methods consist of two steps: First a random seed sequence is generated; next, this seed is progressively modified (i.e. mutated) to adopt the desired folding properties. Although computationally inexpensive, this approach raises several questions such as (i) the influence of the seed; and (ii) the efficiency of single-path directed searches that may be affected by energy barriers in the mutational landscape. In this article, we present RNA-ensign, a novel paradigm for RNA design. Instead of taking a progressive adaptive walk driven by local search criteria, we use an efficient global sampling algorithm to examine large regions of the mutational landscape under structural and thermodynamical constraints until a solution is found. When considering the influence of the seeds and the target secondary structures, our results show that, compared to single-path directed searches, our approach is more robust, succeeds more often and generates more thermodynamically stable sequences. An ensemble approach to RNA design is thus well worth pursuing as a complement to existing approaches. RNA-ensign is available at http://csb.cs.mcgill.ca/RNAensign.

Drugging the epigenome in the age of precision medicine.

BACKGROUND: Modulating the epigenome has long been considered a potential opportunity for therapeutic intervention in numerous disease areas with several approved therapies marketed, primarily for cancer. Despite the overall promise of early approaches, however, these drugs have been plagued by poor pharmacokinetic and safety/tolerability profiles due in large part to off-target effects and a lack of specificity. RESULTS: Recently, there has been marked progress in the field on a new generation of epigenomic therapies which address these challenges directly by targeting defined loci with highly precise, durable, and tunable approaches. Here, we review the promise and pitfalls of epigenetic drug development to date and provide an outlook on recent advances and their promise for future therapeutic applications. CONCLUSIONS: Novel therapeutic modalities leveraging epigenetics and epigenomics with increased precision are well positioned to advance the field and treat patients across disease areas in the coming years.

A Financial Incentives Program to Promote Smoking Cessation Among Recently Hospitalized Individuals: Feasibility and Acceptability Study.

BACKGROUND: Hospitalization is an opportunity to engage underserved individuals in tobacco treatment who may not otherwise have access to it. Tobacco treatment interventions that begin during hospitalization and continue for at least 1 postdischarge month are effective in promoting smoking cessation. However, there is low usage of postdischarge tobacco treatment services. Financial incentives for smoking cessation are an intervention in which participants receive incentives, such as cash payments or vouchers for goods, to encourage individuals to stop smoking or to reward individuals for maintaining abstinence. OBJECTIVE: We sought to determine the feasibility and acceptability of a novel postdischarge financial incentive intervention that uses a smartphone application paired to measurements of exhaled carbon monoxide (CO) concentration levels to promote smoking cessation in individuals who smoke cigarettes. METHODS: We collaborated with Vincere Health, Inc. to tailor their mobile application that uses facial recognition features, a portable breath test CO monitor, and smartphone technology to deliver financial incentives to a participant's digital wallet after the completion of each CO test. The program includes 3 racks. Track 1: Noncontingent incentives for conducting CO tests. Track 2: Combination of noncontingent and contingent incentives for CO levels <10 parts per million (ppm). Track 3: Contingent incentives only for CO levels <10 ppm. After obtaining informed consent, we pilot-tested the program from September to November 2020 with a convenience sample of 33 hospitalized individuals at Boston Medical Center, a large safety-net hospital in New England. Participants received text reminders to conduct CO tests twice daily for 30 days postdischarge. We collected data on engagement, CO levels, and incentives earned. We measured feasibility and acceptability quantitatively and qualitatively at 2 and 4 weeks. RESULTS: Seventy-six percent (25/33) completed the program and 61% (20/33) conducted at least 1 breath test each week. Seven patients had consecutive CO levels <10 ppm during the last 7 days of the program. Engagement with the financial incentive intervention as well as in-treatment abstinence was highest in Track 3 that delivered financial incentives contingent on CO levels <10 ppm. Participants reported high program satisfaction and that the intervention helped motivate smoking cessation. Participants suggested increasing program duration to at least 3 months and adding supplemental text messaging to increase motivation to stop smoking. CONCLUSIONS: Financial incentives paired to measurements of exhaled CO concentration levels is a novel smartphone-based tobacco cessation approach that is feasible and acceptable. Future studies should examine the efficacy of the intervention after it is refined to add a counseling or text-messaging component.

STITCHER: Dynamic assembly of likely amyloid and prion ß-structures from secondary structure predictions.

The supersecondary structure of amyloids and prions, proteins of intense clinical and biological interest, are difficult to determine by standard experimental or computational means. In addition, significant conformational heterogeneity is known or suspected to exist in many amyloid fibrils. Previous work has demonstrated that probability-based prediction of discrete ß-strand pairs can offer insight into these structures. Here, we devise a system of energetic rules that can be used to dynamically assemble these discrete ß-strand pairs into complete amyloid ß-structures. The STITCHER algorithm progressively 'stitches' strand-pairs into full ß-sheets based on a novel free-energy model, incorporating experimentally observed amino-acid side-chain stacking contributions, entropic estimates, and steric restrictions for amyloidal parallel ß-sheet construction. A dynamic program computes the top 50 structures and returns both the highest scoring structure and a consensus structure taken by polling this list for common discrete elements. Putative structural heterogeneity can be inferred from sequence regions that compose poorly. Predictions show agreement with experimental models of Alzheimer's amyloid beta peptide and the Podospora anserina Het-s prion. Predictions of the HET-s homolog HET-S also reflect experimental observations of poor amyloid formation. We put forward predicted structures for the yeast prion Sup35, suggesting N-terminal structural stability enabled by tyrosine ladders, and C-terminal heterogeneity. Predictions for the Rnq1 prion and alpha-synuclein are also given, identifying a similar mix of homogenous and heterogeneous secondary structure elements. STITCHER provides novel insight into the energetic basis of amyloid structure, provides accurate structure predictions, and can help guide future experimental studies.

A method for probing the mutational landscape of amyloid structure.

MOTIVATION: Proteins of all kinds can self-assemble into highly ordered ß-sheet aggregates known as amyloid fibrils, important both biologically and clinically. However, the specific molecular structure of a fibril can vary dramatically depending on sequence and environmental conditions, and mutations can drastically alter amyloid function and pathogenicity. Experimental structure determination has proven extremely difficult with only a handful of NMR-based models proposed, suggesting a need for computational methods. RESULTS: We present AmyloidMutants, a statistical mechanics approach for de novo prediction and analysis of wild-type and mutant amyloid structures. Based on the premise of protein mutational landscapes, AmyloidMutants energetically quantifies the effects of sequence mutation on fibril conformation and stability. Tested on non-mutant, full-length amyloid structures with known chemical shift data, AmyloidMutants offers roughly 2-fold improvement in prediction accuracy over existing tools. Moreover, AmyloidMutants is the only method to predict complete super-secondary structures, enabling accurate discrimination of topologically dissimilar amyloid conformations that correspond to the same sequence locations. Applied to mutant prediction, AmyloidMutants identifies a global conformational switch between Aß and its highly-toxic 'Iowa' mutant in agreement with a recent experimental model based on partial chemical shift data. Predictions on mutant, yeast-toxic strains of HET-s suggest similar alternate folds. When applied to HET-s and a HET-s mutant with core asparagines replaced by glutamines (both highly amyloidogenic chemically similar residues abundant in many amyloids), AmyloidMutants surprisingly predicts a greatly reduced capacity of the glutamine mutant to form amyloid. We confirm this finding by conducting mutagenesis experiments. AVAILABILITY: Our tool is publically available on the web at http://amyloid.csail.mit.edu/. CONTACT: lindquist_admin@wi.mit.edu; bab@csail.mit.edu.

Discovery, optimisation and in vivo evaluation of novel GPR119 agonists.

GPR119 is increasingly seen as an attractive target for the treatment of type II diabetes and other elements of the metabolic syndrome. During a programme aimed at developing agonists of the GPR119 receptor, we identified compounds that were potent with reduced hERG liabilities, that had good pharmacokinetic properties and that displayed excellent glucose-lowering effects in vivo. However, further profiling in a GPR119 knock-out (KO) mouse model revealed that the biological effects were not exclusively due to GPR119 agonism, highlighting the value of transgenic animals in drug discovery programs.

Rapid Cycle Evaluation and Adaptation of an Inpatient Tobacco Treatment Service at a U.S. Safety-Net Hospital.

Background: To address disparities in smoking rates, our safety-net hospital implemented an inpatient tobacco treatment intervention: an "opt-out" electronic health record (EHR)-based Best Practice Alert + order-set, which triggers consultation to a Tobacco Treatment Consult (TTC) service for all hospitalized patients who smoke cigarettes. We report on development, implementation, and adaptation of the intervention, informed by a pre-implementation needs assessment and two rapid-cycle evaluations guided by the Consolidated Framework for Implementation Research (CFIR) and Expert Recommendations for Implementing Change (ERIC) compilation. Methods: We identified stakeholders affected by implementation and conducted a local needs assessment starting 6 months-pre-launch. We then conducted two rapid-cycle evaluations during the first 6 months post-implementation. The CFIR informed survey and interview guide development, data collection, assessment of barriers and facilitators, and selection of ERIC strategies to implement and adapt the intervention. Results: Key themes were: (1) Understanding the hospital's priority to improving tobacco performance metrics was critical in gaining leadership buy-in (CFIR Domain: Outer setting; Construct: External Policy and Incentives). (2) CFIR-based rapid-cycle evaluations allowed us to recognize implementation challenges early and select ERIC strategies clustering into 3 broad categories (conducting needs assessment; developing stakeholder relationships; training and educating stakeholders) to make real-time adaptations, creating an acceptable clinical workflow. (3) Minimizing clinician burden allowed the successful implementation of the TTC service. (4) Demonstrating improved 6-month quit rates and tobacco performance metrics were key to sustaining the program. Conclusions: Rapid-cycle evaluations to gather pre-implementation and early-implementation data, focusing on modifiable barriers and facilitators, allowed us to develop and refine the intervention to improve acceptability, adoption, and sustainability, enabling us to improve tobacco performance metrics in a short timeline. Future directions include spreading rapid-cycle evaluations to promote implementation of inpatient tobacco treatment programs to other settings and assessing long-term sustainability and return on investment of these programs.

The accuracy of the central venous blood gas for acid-base monitoring.

BACKGROUND: Routine use of central venous blood gases (VBGs) may reduce complications from prolonged arterial cannulation. We investigated the reliability of the VBG as a substitute for arterial blood gas (ABG) in multiple care settings. METHODS: We developed a VBG adjustment rule of ABG pH = VBG pH + 0.05, ABG CO(2) = VBG PCO(2) -5 mm Hg from prior studies and validated this relationship with simultaneous venous and arterial blood obtained from 187 medical/surgical intensive care, cardiac catheterization laboratory, and coronary care unit patients with central venous access. RESULTS: The overall accuracy of a normal adjusted VBG (aVBG) to predict a normal ABG was 90%. After adjustment, the mean systematic difference (bias) between ABG and VBG pH decreased from 0.035 +/- 0.02 to -0.015 +/- 0.02 and PCO(2) bias decreased from -4.5 +/- 3.5 to 0.5 +/- 3.5. Intraclass correlation coefficients for agreement improved after applying the adjustment rule to venous pH (from 0.84 to 0.93, P < .001) and PCO(2) (from 0.66 to 0.84, P < .001). Overall diagnostic accuracy of VBG improved from 45% to 74% after adjustment. Multiple logistic regression demonstrated that the factor independently associated with discrepancy between VBG and ABG diagnoses was an abnormal aVBG (OR 6.8, 95% CI 2.8-16.5). CONCLUSIONS: Because of the high agreement between a normal aVBG with a normal ABG and the small bias between these tests, we recommend use of the adjusted central VBG.

3-Chlorotyrosine in sputum of COPD patients: relationship with airway inflammation.

The airways of patients with chronic obstructive pulmonary disease (COPD) are associated with increased numbers of inflammatory cells, in particular neutrophils and macrophages. Contained within the primary granules of neutrophils is the heme enzyme called myeloperoxidase (MPO) that has been used as a biomarker of neutrophilic inflammation in COPD and other inflammatory diseases. MPO is the only enzyme in the body that produces hypochlorous acid (HOCl), which effectively chlorinates tyrosine residues in proteins. The presence of 3-chlorotyrosine (3Cl-Tyr) in sputum of COPD patients has yet to be established. Spontaneously produced sputum was collected from 14 stable COPD patients, and ultra-centrifuged to prepare sol phase samples for analysis. Sputum 3Cl-Tyr levels were measured using Mass Spectrometry (LC-MSMS). Sputum MPO activity was measured using a standard chromogenic substrate assay. The Spearman rank correlation was used to analyse the data. We report for the first time the measurement of 3Cl-Tyr in sputum from stable COPD patients. The sputum levels of 3Cl-Tyr correlated well with sputum MPO activity (r = 0.88; p < 0.0001). The presence of 3Cl-Tyr in the sputum of stable COPD patients suggests an active process related to MPO that may play a role in the pathophysiology of this disease.

Effectiveness of an Opt-Out Electronic Heath Record-Based Tobacco Treatment Consult Service at an Urban Safety Net Hospital.

BACKGROUND: To address the burden of tobacco use in underserved populations, our safety net hospital developed a tobacco treatment intervention consisting of an "opt-out" electronic health record-based best practice alert + order set, which triggers consultation to an inpatient tobacco treatment consult (TTC) service for all hospitalized smokers. RESEARCH QUESTION: We sought to understand if the intervention would increase patient-level outcomes (receipt of tobacco treatment during hospitalization and at discharge; 6-month smoking abstinence) and improve hospital-wide performance on tobacco treatment metrics. DESIGN AND METHODS: We conducted two retrospective quasi-experimental analyses to examine effectiveness of the TTC service. Using a pragmatic design and multivariable logistic regression, we compared patient-level outcomes of receipt of nicotine replacement therapy and 6-month quit rates between smokers seen by the service (n = 505) and eligible smokers not seen because of time constraints (n = 680) between July 2016 and December 2016. In addition, we conducted an interrupted time series analysis to examine the effect of the TTC service on hospital-level performance measures, comparing reported Joint Commission measure rates for inpatient (Tob-2) and postdischarge (Tob-3) tobacco treatment preimplementation (January 2015-June 2016) vs postimplementation (July 2016-December 2017) of the intervention. RESULTS: Compared with inpatient smokers not seen by the TTC service, smokers seen by the TTC service had higher odds of receiving nicotine replacement during hospitalization (260 of 505 [51.5%] vs 244 of 680 [35.9%]; adjusted ORs [AOR], 1.93 [95% CI, 1.5-2.45]) and at discharge (164 of 505 [32.5%] vs 84 of 680 [12.4%]; AOR, 3.41 [95% CI, 2.54-4.61]), as well as higher odds of 6-month smoking abstinence (75 of 505 [14.9%] vs 68 of 680 [10%]; AOR, 1.48 [95% CI, 1.03-2.12]). Hospital-wide, the intervention was associated with a change in slope trends for Tob-3 (P < .01), but not for Tob-2. INTERPRETATION: The "opt-out" electronic health record-based TTC service at our large safety net hospital was effective at improving both patient-level outcomes and hospital-level performance metrics, and could be implemented at other safety net hospitals that care for hard-to-reach smokers.

Feasibility, Acceptability, and Adoption of an Inpatient Tobacco Treatment Service at a Safety-Net Hospital: A Mixed-Methods Study.

Rationale: Hospitalization is an opportunity to engage smokers who may not seek tobacco treatment. Our safety-net hospital developed and implemented an inpatient intervention consisting of an "opt-out" electronic health record-based Best Practice Alert (BPA)+order-set, designed to trigger referral to the Tobacco Treatment Consult (TTC) service (a team staffed by tobacco treatment specialists) for all hospitalized smokers, regardless of motivation to quit.Objectives: We performed a sequential explanatory mixed-methods study to evaluate the feasibility, acceptability, and adoption of the TTC service.Methods: Among all admissions of adult "current smokers" between July 2016 and June 2017, we calculated the percentage of patients whose clinicians accepted the order-set (through a simple "order" click), thus generating the TTC referral. We then determined the extent of clinician follow-through of TTC recommendations for prescribing nicotine replacement therapy among 1,651 consecutive smokers seen by the TTC service. Finally, we conducted qualitative interviews with inpatient clinicians (n = 25) to understand their rationale for adoption or nonuse of the TTC intervention, including perceived usefulness, barriers to adoption, and strategies to improve the utility of the service.Results: Clinicians accepted the TTC order-set for 4,100 out of 6,598 "current smokers" (62.1%) for whom the BPA fired, typically after initially deferring the BPA. Rates of acceptance significantly differed across clinical services (range: 8% [obstetrics-gynecology] to 82.2% [cardiology]; P < 0.00001). A chart review showed that 43.5% (719/1,651) of the patients seen by the TTC service desired outpatient nicotine replacement therapy, but only half of these patients (48.8%; 351/719) received a discharge prescription from the inpatient team. Clinicians expressed that they valued the TTC service, but that BPA fatigue, time constraints, competing priorities, and poor communication with the TTC service were barriers to using the service and following recommendations. Clinicians suggested strategies to address barriers to the use of tobacco treatment interventions during hospitalization and after discharge.Conclusions: Implementing a large-scale "opt-out" tobacco treatment service for hospitalized smokers at a safety-net hospital is feasible and acceptable, but suffers from inconsistent adoption due to a variety of clinician barriers. System-level changes are needed to increase uptake and sustain inpatient tobacco treatment interventions to promote smoking cessation.

Modeling ensembles of transmembrane beta-barrel proteins.

Transmembrane beta-barrel (TMB) proteins are embedded in the outer membrane of gram-negative bacteria, mitochondria, and chloroplasts. Despite their importance, very few nonhomologous TMB structures have been determined by X-ray diffraction because of the experimental difficulty encountered in crystallizing transmembrane proteins. We introduce the program partiFold to investigate the folding landscape of TMBs. By computing the Boltzmann partition function, partiFold estimates inter-beta-strand residue interaction probabilities, predicts contacts and per-residue X-ray crystal structure B-values, and samples conformations from the Boltzmann low energy ensemble. This broad range of predictive capabilities is achieved using a single, parameterizable grammatical model to describe potential beta-barrel supersecondary structures, combined with a novel energy function of stacked amino acid pair statistical potentials. PartiFold outperforms existing programs for inter-beta-strand residue contact prediction on TMB proteins, offering both higher average predictive accuracy as well as more consistent results. Moreover, the integration of these contact probabilities inside a stochastic contact map can be used to infer a more meaningful picture of the TMB folding landscape, which cannot be achieved with other methods. Partifold's predictions of B-values are competitive with recent methods specifically designed for this problem. Finally, we show that sampling TMBs from the Boltzmann ensemble matches the X-ray crystal structure better than single structure prediction methods. A webserver running partiFold is available at http://partiFold.csail.mit.edu/.

Learning biophysically-motivated parameters for alpha helix prediction.

BACKGROUND: Our goal is to develop a state-of-the-art protein secondary structure predictor, with an intuitive and biophysically-motivated energy model. We treat structure prediction as an optimization problem, using parameterizable cost functions representing biological "pseudo-energies". Machine learning methods are applied to estimate the values of the parameters to correctly predict known protein structures. RESULTS: Focusing on the prediction of alpha helices in proteins, we show that a model with 302 parameters can achieve a Qalpha value of 77.6% and an SOValpha value of 73.4%. Such performance numbers are among the best for techniques that do not rely on external databases (such as multiple sequence alignments). Further, it is easier to extract biological significance from a model with so few parameters. CONCLUSION: The method presented shows promise for the prediction of protein secondary structure. Biophysically-motivated elementary free-energies can be learned using SVM techniques to construct an energy cost function whose predictive performance rivals state-of-the-art. This method is general and can be extended beyond the all-alpha case described here.

Standardizing adult tracheostomy tube styles: what is the clinical and cost-effective impact?

Tracheostomy tubes are made of a variety of materials, components, and styles. In a recent merger of our hospitals, we noted a large assortment of tubes available for clinicians. The different tubes resulted in complaints from staff, which included confusion, delays in obtaining preferred tubes, and inconsistent shelf stock. A multidisciplinary task force was formed to recommend standardizing the styles of tracheostomy tubes. A comparison of tracheotomy procedures, tracheostomy tube usage, and tube costs were done 6 months before and 6 months after the standardization. The number of tube styles decreased from 9 to 4; specialty extra-long tubes decreased from 3 to 2. There were no cost savings in standardizing the tracheostomy tubes.

MARIS: method for analyzing RNA following intracellular sorting.

Transcriptional profiling is a key technique in the study of cell biology that is limited by the availability of reagents to uniquely identify specific cell types and isolate high quality RNA from them. We report a Method for Analyzing RNA following Intracellular Sorting (MARIS) that generates high quality RNA for transcriptome profiling following cellular fixation, intracellular immunofluorescent staining and FACS. MARIS can therefore be used to isolate high quality RNA from many otherwise inaccessible cell types simply based on immunofluorescent tagging of unique intracellular proteins. As proof of principle, we isolate RNA from sorted human embryonic stem cell-derived insulin-expressing cells as well as adult human ß cells. MARIS is a basic molecular biology technique that could be used across several biological disciplines.