A Structural Model of the Endogenous Human BAF Complex Informs Disease Mechanisms.

Mammalian SWI/SNF complexes are ATP-dependent chromatin remodeling complexes that regulate genomic architecture. Here, we present a structural model of the endogenously purified human canonical BAF complex bound to the nucleosome, generated using cryoelectron microscopy (cryo-EM), cross-linking mass spectrometry, and homology modeling. BAF complexes bilaterally engage the nucleosome H2A/H2B acidic patch regions through the SMARCB1 C-terminal α-helix and the SMARCA4/2 C-terminal SnAc/post-SnAc regions, with disease-associated mutations in either causing attenuated chromatin remodeling activities. Further, we define changes in BAF complex architecture upon nucleosome engagement and compare the structural model of endogenous BAF to those of related SWI/SNF-family complexes. Finally, we assign and experimentally interrogate cancer-associated hot-spot mutations localizing within the endogenous human BAF complex, identifying those that disrupt BAF subunit-subunit and subunit-nucleosome interfaces in the nucleosome-bound conformation. Taken together, this integrative structural approach provides important biophysical foundations for understanding the mechanisms of BAF complex function in normal and disease states.

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge.

This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived by 13 participating teams from four benchmark maps, including three forming a resolution series (1.8 to 3.1 Å). The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual experiments and structure data archives such as the Protein Data Bank. We recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed cryo-EM map density.

Structural basis for autophagy inhibition by the human Rubicon-Rab7 complex.

Rubicon is a potent negative regulator of autophagy and a potential target for autophagy-inducing therapeutics. Rubicon-mediated inhibition of autophagy requires the interaction of the C-terminal Rubicon homology (RH) domain of Rubicon with Rab7-GTP. Here we report the 2.8-Å crystal structure of the Rubicon RH domain in complex with Rab7-GTP. Our structure reveals a fold for the RH domain built around four zinc clusters. The switch regions of Rab7 insert into pockets on the surface of the RH domain in a mode that is distinct from those of other Rab-effector complexes. Rubicon residues at the dimer interface are required for Rubicon and Rab7 to colocalize in living cells. Mutation of Rubicon RH residues in the Rab7-binding site restores efficient autophagic flux in the presence of overexpressed Rubicon, validating the Rubicon RH domain as a promising therapeutic target.

Cryo-electron Microscopy Imaging of Alzheimer's Amyloid-beta 42 Oligomer Displayed on a Functionally and Structurally Relevant Scaffold.

Amyloid-ß peptide (Aß) oligomers are pathogenic species of amyloid aggregates in Alzheimer's disease. Like certain protein toxins, Aß oligomers permeabilize cellular membranes, presumably through a pore formation mechanism. Owing to their structural and stoichiometric heterogeneity, the structure of these pores remains to be characterized. We studied a functional Aß42-pore equivalent, created by fusing Aß42 to the oligomerizing, soluble domain of the α-hemolysin (αHL) toxin. Our data reveal Aß42-αHL oligomers to share major structural, functional, and biological properties with wild-type Aß42-pores. Single-particle cryo-EM analysis of Aß42-αHL oligomers (with an overall 3.3 Šresolution) reveals the Aß42-pore region to be intrinsically flexible. The Aß42-αHL oligomers will allow many of the features of the wild-type amyloid oligomers to be studied that cannot be otherwise, and may be a highly specific antigen for the development of immuno-base diagnostics and therapies.

Bacterial proteostasis balances energy and chaperone utilization efficiently.

Chaperones are protein complexes that help to fold and disaggregate a cell's proteins. It is not understood how four major chaperone systems of Escherichia coli work together in proteostasis: the recognition, sorting, folding, and disaggregating of the cell's many different proteins. Here, we model this machine. We combine extensive data on chaperoning, folding, and aggregation rates with expression levels of proteins and chaperones measured at different growth rates. We find that the proteostasis machine recognizes and sorts a client protein based on two biophysical properties of the client's misfolded state (M state): its stability and its kinetic accessibility from its unfolded state (U state). The machine is energy-efficient (the sickest proteins use the most ATP-expensive chaperones), comprehensive (it can handle any type of protein), and economical (the chaperone concentrations are just high enough to keep the whole proteome folded and disaggregated but no higher). The cell needs higher chaperone levels in two situations: fast growth (when protein production rates are high) and very slow growth (to mitigate the effects of protein degradation). This type of model complements experimental knowledge by showing how the various chaperones work together to achieve the broad folding and disaggregation needs of the cell.

A Data Visualization and Dissemination Resource to Support HIV Prevention and Care at the Local Level: Analysis and Uses of the AIDSVu Public Data Resource.

BACKGROUND: AIDSVu is a public resource for visualizing HIV surveillance data and other population-based information relevant to HIV prevention, care, policy, and impact assessment. OBJECTIVE: The site, AIDSVu.org, aims to make data about the US HIV epidemic widely available, easily accessible, and locally relevant to inform public health decision making. METHODS: AIDSVu develops visualizations, maps, and downloadable datasets using results from HIV surveillance systems, other population-based sources of information (eg, US Census and national probability surveys), and other data developed specifically for display and dissemination through the website (eg, pre-exposure prophylaxis [PrEP] prescriptions). Other types of content are developed to translate surveillance data into summarized content for diverse audiences using infographic panels, interactive maps, local and state fact sheets, and narrative blog posts. RESULTS: Over 10 years, AIDSVu.org has used an expanded number of data sources and has progressively provided HIV surveillance and related data at finer geographic levels, with current data resources providing HIV prevalence data down to the census tract level in many of the largest US cities. Data are available at the county level in 48 US states and at the ZIP Code level in more than 50 US cities. In 2019, over 500,000 unique users consumed AIDSVu data and resources, and HIV-related data and insights were disseminated through nearly 4,000,000 social media posts. Since AIDSVu's inception, at least 249 peer-reviewed publications have used AIDSVu data for analyses or referenced AIDSVu resources. Data uses have included targeting of HIV testing programs, identifying areas with inequitable PrEP uptake, including maps and data in academic and community grant applications, and strategically selecting locations for new HIV treatment and care facilities to serve high-need areas. CONCLUSIONS: Surveillance data should be actively used to guide and evaluate public health programs; AIDSVu translates high-quality, population-based data about the US HIV epidemic and makes that information available in formats that are not consistently available in surveillance reports. Bringing public health surveillance data to an online resource is a democratization of data, and presenting information about the HIV epidemic in more visual formats allows diverse stakeholders to engage with, understand, and use these important public health data to inform public health decision making.

Effects of Political Instability in Venezuela on Malaria Resurgence at Ecuador-Peru Border, 2018.

Mass migration from Venezuela has increased malaria resurgence risk across South America. During 2018, migrants from Venezuela constituted 96% of imported malaria cases along the Ecuador-Peru border. Plasmodium vivax predominated (96%). Autochthonous malaria cases emerged in areas previously malaria-free. Heightened malaria control and a response to this humanitarian crisis are imperative.

Quality of health economic evaluations for the ACC/AHA stable ischemic heart disease practice guideline: A systematic review.

BACKGROUND: The American College of Cardiology/American Heart Association (ACC/AHA) recently published a rigorous framework to guide integration of economic data into clinical guidelines. We assessed the quality of economic evaluations in a major ACC/AHA clinical guidance report. METHODS: We systematically identified cost-effectiveness analyses (CEAs) of RCTs cited in the ACC/AHA 2012 Guideline for the Diagnosis and Management of Patients with Stable Ischemic Heart Disease. We extracted: (1) study identifiers; (2) parent RCT information; (3) economic analysis characteristics; and (4) study quality using the Quality of Health Economic Studies instrument (QHES). RESULTS: Quality scores were categorized as high (≥75 points) or low (<75 points). Of 1,266 citations in the guideline, 219 were RCTs associated with 77 CEAs. Mean quality score was 81 (out of 100) and improved over time, though 29.9% of studies were low-quality. Cost-per-QALY was the most commonly reported primary outcome (39.0%). Low-quality studies were less likely to report study perspective, use appropriate time horizons, or address statistical and clinical uncertainty. Funding was overwhelmingly private (83%). A detailed methodological assessment of high-quality studies revealed domains of additional methodological issues not identified by the QHES. CONCLUSIONS: Economic evaluations of RCTs in the 2012 ACC/AHA ischemic heart disease guideline largely had high QHES scores but methodological issues existed among "high-quality" studies. Because the ACC/AHA has generally been more systematic in its integration of scientific evidence compared to other professional societies, it is likely that most societies will need to proceed more cautiously in their integration of economic evidence.

A Cross-Sectional Study Evaluating the Use of Free Clinics in Syracuse, NY: Patient Demographics and Barriers to Accessing Healthcare in Traditional Settings.

Free clinics provide healthcare to underserved patient populations, playing a critical role in the medical safety-net. Syracuse, New York has notable racial, socioeconomic, and educational disparities and is home to four free clinics. Little is known about these clinics' patient population. This study attempts to better define this population and the barriers they face accessing traditional care. We developed a 27-question survey investigating patient demographics, barriers to traditional healthcare, and experience at local free clinics. Our analysis included descriptive statistics, t-tests, one-way ANOVA and Chi square testing. Of 287 patients surveyed, 55% of patients were employed, 78% were uninsured, and 43% cited cost as their primary barrier to insurance. 29% rated their health as fair or poor. 21% had been to the Emergency Room (ER) in the past six months. 38% stated they would go to the ER if free clinics did not exist. Insurance coverage was unrelated to education or employment status (p = .52 and .81, respectively), but differed significantly between racial and ethnic groups (p < .007). Insured patients were more likely to have visited an ER in the past 6 months (p = .01), received preventive health services (p = .02), and seen a provider outside of the free clinic as compared to patients without insurance (p < .001). Free clinic patients represent a heterogeneous population with poor health indicators and several barriers to traditional care, especially cost. This information may aid public health agencies in developing policies to increase access to medical care and decrease morbidity and mortality among this population.

Brønsted acid catalyzed intramolecular benzylic cyclizations of alkylpyridines.

Aldehyde and ketone electrophiles incorporated into the side chains of 2- and 4-alkylpyridines participate in intramolecular aldol-like condensations with pyridine benzylic carbons in the presence of Brønsted acid catalysts. Pyridines featuring ß-ketoamide side chains undergo cyclization in the presence of 10 mol% TfOH to afford pyridyl-substituted hydroxy lactams in good yield. These products were found to be resistant to further dehydration under a variety of conditions, however treatment with thionyl chloride elicited an unusual dehydration/oxidation reaction sequence. In contrast, acid-catalyzed cyclization of pyridines tethered to aliphatic aldehydes with amine linkers gives pyridyl-substituted dehydro-piperidine products. Similarly, intramolecular condensation of salicylaldehyde- and salicylketone-substituted pyridines affords pyridyl-substituted benzofurans.

Vascular adaptations following an eight-week sprint interval training intervention in healthy men.

BACKGROUND: Sprint interval training (SIT) has been shown to improve many indices of cardiovascular risk. The effect of SIT on emerging indicators of cardiovascular health, including arterial stiffness and carotid intima media thickness, remains unclear. Thus, the purpose of this study was to assess changes in augmentation index at 75 beats per minute (AIx@75), pulse wave velocity (cfPWV), and carotid intima media thickness (CIMT) at three time points of an 8-week SIT intervention. METHODS: Eighteen sedentary men (age: 24.7±5.1 years, BMI: 26.7±5.8 kg/m2) participated in the study. Subjects trained 3 times a week for 8 weeks. Training consisted of 3-6 consecutive 30-second bouts of maximal intensity cycling, with 4.5 minutes of active recovery between bouts. Baseline, 4-week, and 8-week vascular assessments were performed. Training effects were analyzed using repeated measures ANOVA. Pearson correlations were used to determine the relationship between baseline values and the change scores (baseline to 8 weeks) of each vascular measure. RESULTS: AIx@75 (BL: -3.6±10.9%, 4W: -5.6±8.3%, 8W: -3.2±9.5%), cfPWV (BL: 5.6±1.0 m/s, 4W: 5.8±0.9 m/s, 8W: 5.6±0.7 m/s), and CIMT (BL: 0.51±0.08 mm, 4W: 0.52±0.08 mm, 8W: 0.51±0.08 mm) did not significantly change (all P>0.05). Baseline cfPWV and AIx@75 were negatively correlated to their change from baseline to 8 weeks (P<0.05). CONCLUSIONS: These findings demonstrate that 8 weeks of SIT is an insufficient stimulus to reduce cfPWV, AIx@75, or CIMT in a group of young, healthy men. Baseline arterial stiffness may modulate vascular adaptations to SIT.

Anaplastic Multiple Myeloma With a Novel Proliferation of Pleomorphic Binuclear Plasma Cells.

This study describes an unusual case of multiple myeloma that progressed to anaplastic multiple myeloma in the pleural fluid. The Wright-stained cytospin of the pleural fluid showed a predominant population of mononuclear plasma cells with pleomorphic nuclei, characterized by both small and large nuclei, which is typical of anaplastic multiple myeloma. However, there were also more binuclear plasma cells with pleomorphic nuclei. Morphometric analysis showed that the mean nuclear length was 1.9-fold and 2.3-fold higher in the large nuclei compared to the small nuclei for the mononuclear plasma cells and binuclear plasma cells, respectively (p<0.001). The patient received B cell maturation antigen chimeric antigen receptor T cell (CAR-T) therapy for relapsed disease, with a significant reduction of the serum monoclonal paraprotein level at day 51 post-therapy. Pathologists should be aware that pleomorphic binuclear plasma cells can be part of the morphologic spectrum in anaplastic multiple myeloma.

Burkitt Lymphoma With Aberrant Expression of Cytoplasmic Terminal Deoxynucleotidyl Transferase: A Case Report.

This study describes a rare case of Burkitt lymphoma with aberrant expression of cytoplasmic terminal deoxynucleotidyl transferase (TdT). Flow cytometry demonstrated a predominantly mature B cell immunophenotype as expected for Burkitt lymphoma, however, the immature marker TdT was also expressed. Immunohistochemistry showed that TdT was localized to the cytoplasm, with absent nuclear localization. The patient received standard intensive chemotherapy for Burkitt lymphoma and has remained in remission for nine years. Pathologists should be aware of this unusual phenomenon of aberrant cytoplasmic TdT expression to avoid confusing Burkitt lymphoma with B cell lymphoblastic leukemia/lymphoma.

EBV Positive Diffuse Large B Cell Lymphoma with Negative Pan-B Cell Markers, Case Report, and Literature Review.

Most B cell lymphomas are positive for one or more B cell markers including CD19, CD20, CD79a, or PAX5. However, rare cases of mature B cell lymphoma not expressing any B cell markers have been characterized and recognized as distinct diagnostic entities by current classification guidelines, including plasmablastic lymphoma, primary effusion lymphoma, and ALK-positive large B cell lymphoma. We present a case of pan-B cell marker negative, EBV positive diffuse large B cell lymphoma that is positive for OCT2, BOB1, and clonal immunoglobulin gene rearrangement that does not meet diagnostic criteria for any B cell lymphoma by current 4th and 5th Ed beta version WHO Hematolymphoid Tumors classification. In challenging cases like the one presented, utilizing OCT2 and BOB1 immunohistochemical stains can assist in determining B cell lineage. The WHO tumor classification system should consider adding OCT2 and BOB1 as alternative B cell lineage markers into their corresponding categories.

De novo design of pH-responsive self-assembling helical protein filaments.

Biological evolution has led to precise and dynamic nanostructures that reconfigure in response to pH and other environmental conditions. However, designing micrometre-scale protein nanostructures that are environmentally responsive remains a challenge. Here we describe the de novo design of pH-responsive protein filaments built from subunits containing six or nine buried histidine residues that assemble into micrometre-scale, well-ordered fibres at neutral pH. The cryogenic electron microscopy structure of an optimized design is nearly identical to the computational design model for both the subunit internal geometry and the subunit packing into the fibre. Electron, fluorescent and atomic force microscopy characterization reveal a sharp and reversible transition from assembled to disassembled fibres over 0.3 pH units, and rapid fibre disassembly in less than 1 s following a drop in pH. The midpoint of the transition can be tuned by modulating buried histidine-containing hydrogen bond networks. Computational protein design thus provides a route to creating unbound nanomaterials that rapidly respond to small pH changes.

Claims-Based Algorithm to Identify Pre-Exposure Prophylaxis Indications for Tenofovir Disoproxil Fumarate and Emtricitabine Prescriptions (2012-2014): Validation Study.

BACKGROUND: To monitor the use of tenofovir disoproxil fumarate and emtricitabine (TDF/FTC) and related medicines for pre-exposure prophylaxis (PrEP) as HIV prevention using commercial pharmacy data, it is necessary to determine whether TDF/FTC prescriptions are used for PrEP or for some other clinical indication. OBJECTIVE: This study aimed to validate an algorithm to distinguish the use of TDF/FTC for HIV prevention or infectious disease treatment. METHODS: An algorithm was developed to identify whether TDF/FTC prescriptions were for PrEP or for other indications from large-scale administrative databases. The algorithm identifies TDF/FTC prescriptions and then excludes patients with International Classification of Diseases (ICD)-9 diagnostic codes, medications, or procedures that suggest indications other than for PrEP (eg, documentation of HIV infection, chronic hepatitis B, or use of TDF/FTC for postexposure prophylaxis). For evaluation, we collected data by clinician assessment of medical records for patients with TDF/FTC prescriptions and compared the assessed indication identified by the clinician review with the assessed indication identified by the algorithm. The algorithm was then applied and evaluated in a large, urban, community-based sexual health clinic. RESULTS: The PrEP algorithm demonstrated high sensitivity and moderate specificity (99.6% and 49.6%) in the electronic medical record database and high sensitivity and specificity (99% and 87%) in data from the urban community health clinic. CONCLUSIONS: The PrEP algorithm classified the indication for PrEP in most patients treated with TDF/FTC with sufficient accuracy to be useful for surveillance purposes. The methods described can serve as a basis for developing a robust and evolving case definition for antiretroviral prescriptions for HIV prevention purposes.

Data and Process Harmonisation of Multi-National, Multi-Site Research Data.

To achieve a single fully harmonised research data set suitable for analysis from data collected at multiple sites requires not only semantic integration of collection concepts and convergence onto single collection units, but harmonisation of data collection processes. We describe our experience of identifying harmonisation challenges in the Precision ALS project, with particular focus on process alignment challenges in a multi-site multi-national research data collection project.

Collective dynamics differentiates functional divergence in protein evolution.

Protein evolution is most commonly studied by analyzing related protein sequences and generating ancestral sequences through Bayesian and Maximum Likelihood methods, and/or by resurrecting ancestral proteins in the lab and performing ligand binding studies to determine function. Structural and dynamic evolution have largely been left out of molecular evolution studies. Here we incorporate both structure and dynamics to elucidate the molecular principles behind the divergence in the evolutionary path of the steroid receptor proteins. We determine the likely structure of three evolutionarily diverged ancestral steroid receptor proteins using the Zipping and Assembly Method with FRODA (ZAMF). Our predictions are within ~2.7 Å all-atom RMSD of the respective crystal structures of the ancestral steroid receptors. Beyond static structure prediction, a particular feature of ZAMF is that it generates protein dynamics information. We investigate the differences in conformational dynamics of diverged proteins by obtaining the most collective motion through essential dynamics. Strikingly, our analysis shows that evolutionarily diverged proteins of the same family do not share the same dynamic subspace, while those sharing the same function are simultaneously clustered together and distant from those, that have functionally diverged. Dynamic analysis also enables those mutations that most affect dynamics to be identified. It correctly predicts all mutations (functional and permissive) necessary to evolve new function and ~60% of permissive mutations necessary to recover ancestral function.

Ray-Trace Modeling to Characterize Efficiency of Unconventional Luminescent Solar Concentrator Geometries.

Luminescent solar concentrators (LSCs) are a promising technology to help integrate solar cells into the built environment, as they are colorful, semitransparent, and can collect diffuse light. While LSCs have traditionally been cuboidal, in recent years, a variety of unconventional geometries have arisen, for example, circular, curved, polygonal, wedged, and leaf-shaped designs. These new designs can help reduce optical losses, facilitate incorporation into the built environment, or unlock new applications. However, as fabrication of complex geometries can be time- and resource-intensive, the ability to simulate the expected LSC performance prior to production would be highly advantageous. While a variety of software exists to model LSCs, it either cannot be applied to unconventional geometries, is not open-source, or is not tractable for most users. Therefore, here we introduce a significant upgrade of the widely used Monte Carlo ray-trace software pvtrace to include: (i) the capability to characterize unconventional geometries and improved relevance to standard measurement configurations; (ii) increased computational efficiency; and (iii) a graphical user interface (GUI) for ease-of-use. We first test these new features against data from the literature as well as experimental results from in-house fabricated LSCs, with agreement within 1% obtained for the simulated versus measured external photon efficiency. We then demonstrate the broad applicability of pvtrace by simulating 20 different unconventional geometries, including a variety of different shapes and manufacturing techniques. We show that pvtrace can be used to predict the optical efficiency of 3D-printed devices. The more versatile and accessible computational workflow afforded by our new features, coupled with 3D-printed prototypes, will enable rapid screening of more intricate LSC architectures, while reducing experimental waste. Our goal is that this accelerates sustainability-driven design in the LSC field, leading to higher optical efficiency or increased utility.

Getting PrEP to the patients who need it.

A fraction of those eligible for PrEP to prevent HIV infection receive a prescription. Newer drug regimens and updated recommendations can help you reduce that gap.