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Recent documents in eScholarship@UMMS
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A deep sequencing tool for partitioning clearance rates following antimalarial treatment in polyclonal infections

Fri, 08/05/2016 - 1:56pm

BACKGROUND AND OBJECTIVES: Current tools struggle to detect drug-resistant malaria parasites when infections contain multiple parasite clones, which is the norm in high transmission settings in Africa. Our aim was to develop and apply an approach for detecting resistance that overcomes the challenges of polyclonal infections without requiring a genetic marker for resistance.

METHODOLOGY: Clinical samples from patients treated with artemisinin combination therapy were collected from Tanzania and Cambodia. By deeply sequencing a hypervariable locus, we quantified the relative abundance of parasite subpopulations (defined by haplotypes of that locus) within infections and revealed evolutionary dynamics during treatment. Slow clearance is a phenotypic, clinical marker of artemisinin resistance; we analyzed variation in clearance rates within infections by fitting parasite clearance curves to subpopulation data.

RESULTS: In Tanzania, we found substantial variation in clearance rates within individual patients. Some parasite subpopulations cleared as slowly as resistant parasites observed in Cambodia. We evaluated possible explanations for these data, including resistance to drugs. Assuming slow clearance was a stable phenotype of subpopulations, simulations predicted that modest increases in their frequency could substantially increase time to cure.

CONCLUSIONS AND IMPLICATIONS: By characterizing parasite subpopulations within patients, our method can detect rare, slow clearing parasites in vivo whose phenotypic effects would otherwise be masked. Since our approach can be applied to polyclonal infections even when the genetics underlying resistance are unknown, it could aid in monitoring the emergence of artemisinin resistance. Our application to Tanzanian samples uncovers rare subpopulations with worrying phenotypes for closer examination.

How structural adaptability exists alongside HLA-A2 bias in the human alphabeta TCR repertoire

Fri, 08/05/2016 - 1:56pm

How T-cell receptors (TCRs) can be intrinsically biased toward MHC proteins while simultaneously display the structural adaptability required to engage diverse ligands remains a controversial puzzle. We addressed this by examining alphabeta TCR sequences and structures for evidence of physicochemical compatibility with MHC proteins. We found that human TCRs are enriched in the capacity to engage a polymorphic, positively charged "hot-spot" region that is almost exclusive to the alpha1-helix of the common human class I MHC protein, HLA-A*0201 (HLA-A2). TCR binding necessitates hot-spot burial, yielding high energetic penalties that must be offset via complementary electrostatic interactions. Enrichment of negative charges in TCR binding loops, particularly the germ-line loops encoded by the TCR Valpha and Vbeta genes, provides this capacity and is correlated with restricted positioning of TCRs over HLA-A2. Notably, this enrichment is absent from antibody genes. The data suggest a built-in TCR compatibility with HLA-A2 that biases receptors toward, but does not compel, particular binding modes. Our findings provide an instructional example for how structurally pliant MHC biases can be encoded within TCRs.

Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment

Fri, 08/05/2016 - 1:56pm

We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein-protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy.

A benchmark testing ground for integrating homology modeling and protein docking

Fri, 08/05/2016 - 1:56pm

Protein docking procedures carry out the task of predicting the structure of a protein-protein complex starting from the known structures of the individual protein components. More often than not, however, the structure of one or both components is not known, but can be derived by homology modeling on the basis of known structures of related proteins deposited in the Protein Data Bank (PDB). Thus, the problem is to develop methods that optimally integrate homology modeling and docking with the goal of predicting the structure of a complex directly from the amino acid sequences of its component proteins. One possibility is to use the best available homology modeling and docking methods. However, the models built for the individual subunits often differ to a significant degree from the bound conformation in the complex, often much more so than the differences observed between free and bound structures of the same protein, and therefore additional conformational adjustments, both at the backbone and side chain levels need to be modeled to achieve an accurate docking prediction. In particular, even homology models of overall good accuracy frequently include localized errors that unfavorably impact docking results. The predicted reliability of the different regions in the model can also serve as a useful input for the docking calculations. Here we present a benchmark dataset that should help to explore and solve combined modeling and docking problems. This dataset comprises a subset of the experimentally solved 'target' complexes from the widely used Docking Benchmark from the Weng Lab (excluding antibody-antigen complexes). This subset is extended to include the structures from the PDB related to those of the individual components of each complex, and hence represent potential templates for investigating and benchmarking integrated homology modeling and docking approaches. Template sets can be dynamically customized by specifying ranges in sequence similarity and in PDB release dates, or using other filtering options, such as excluding sets of specific structures from the template list. Multiple sequence alignments, as well as structural alignments of the templates to their corresponding subunits in the target are also provided. The resource is accessible online or can be downloaded at, and is updated on a weekly basis in synchrony with new PDB releases.

Association of common mental disorder symptoms with health and healthcare factors among women in rural western India: results of a cross-sectional survey

Thu, 08/04/2016 - 9:11am

OBJECTIVES: Information about common mental disorders (CMD) is needed to guide policy and clinical interventions in low-income and middle-income countries. This study's purpose was to characterise the association of CMD symptoms with 3 inter-related health and healthcare factors among women from rural western India based on a representative, cross-sectional survey.

SETTING: Surveys were conducted in the waiting area of various outpatient clinics at a tertiary care hospital and in 16 rural villages in the Anand district of Gujarat, India.

PARTICIPANTS: 700 Gujarati-speaking women between the ages of 18-45 years who resided in the Anand district of Gujarat, India, were recruited in a quasi-randomised manner.

PRIMARY AND SECONDARY OUTCOMES MEASURES: CMD symptoms, ascertained using WHO's Self-Reporting Questionnaire-20 (SRQ-20), were associated with self-reported (1) number of healthcare visits in the prior year; (2) health status and (3) portion of yearly income expended on healthcare.

RESULTS: Data from 658 participants were used in this analysis; 19 surveys were excluded due to incompleteness, 18 surveys were excluded because the participants were visiting hospitalised patients and 5 surveys were classified as outliers. Overall, 155 (22·8%) participants screened positive for CMD symptoms (SRQ-20 score ≥8) with most (81.9%) not previously diagnosed despite contact with healthcare provider in the prior year. On adjusted analyses, screening positive for CMD symptoms was associated with worse category in self-reported health status (cumulative OR=9.39; 95% CI 5·97 to 14·76), higher portion of household income expended on healthcare (cumulative OR=2·31; 95% CL 1·52 to 3.52) and increased healthcare visits in the prior year (incidence rate ratio=1·24; 95% CI 1·07 to 1·44).

CONCLUSIONS: The high prevalence of potential CMD among women in rural India that is unrecognised and associated with adverse health and financial indicators highlights the individual and public health burden of CMD.

Mindfulness-Based Interventions for Weight Loss and CVD Risk Management

Tue, 08/02/2016 - 3:12pm

Obesity affects more than one third of US adults and is a major cause of preventable morbidity and mortality, primarily from cardiovascular disease. Traditional behavioral interventions for weight loss typically focus on diet and exercise habits and often give little attention to the role of stress and emotions in the initiation and maintenance of unhealthy behaviors, which may account for their modest results and considerable variability in outcomes. Stress eating and emotional eating are increasingly recognized as important targets of weight loss interventions. Mindfulness-based interventions were specifically developed to promote greater self-efficacy in coping with stress and negative emotions and appear to be effective for a variety of conditions. In recent years, researchers have begun to study mindfulness interventions for weight loss and CVD risk management. This review describes the rationale for the use of mindfulness in interventions for weight loss and CVD risk management, summarizes the research to date, and suggests priorities for future research.

NEK1 variants confer susceptibility to amyotrophic lateral sclerosis

Tue, 08/02/2016 - 11:29am

To identify genetic factors contributing to amyotrophic lateral sclerosis (ALS), we conducted whole-exome analyses of 1,022 index familial ALS (FALS) cases and 7,315 controls. In a new screening strategy, we performed gene-burden analyses trained with established ALS genes and identified a significant association between loss-of-function (LOF) NEK1 variants and FALS risk. Independently, autozygosity mapping for an isolated community in the Netherlands identified a NEK1 p.Arg261His variant as a candidate risk factor. Replication analyses of sporadic ALS (SALS) cases and independent control cohorts confirmed significant disease association for both p.Arg261His (10,589 samples analyzed) and NEK1 LOF variants (3,362 samples analyzed). In total, we observed NEK1 risk variants in nearly 3% of ALS cases. NEK1 has been linked to several cellular functions, including cilia formation, DNA-damage response, microtubule stability, neuronal morphology and axonal polarity. Our results provide new and important insights into ALS etiopathogenesis and genetic etiology.

A New MI-Based Visualization Aided Validation Index for Mining Big Longitudinal Web Trial Data

Mon, 08/01/2016 - 4:34pm

Web-delivered clinical trials generate big complex data. To help untangle the heterogeneity of treatment effects, unsupervised learning methods have been widely applied. However, identifying valid patterns is a priority but challenging issue for these methods. This paper, built upon our previous research on multiple imputation (MI)-based fuzzy clustering and validation, proposes a new MI-based Visualization-aided validation index (MIVOOS) to determine the optimal number of clusters for big incomplete longitudinal Web-trial data with inflated zeros. Different from a recently developed fuzzy clustering validation index, MIVOOS uses a more suitable overlap and separation measures for Web-trial data but does not depend on the choice of fuzzifiers as the widely used Xie and Beni (XB) index. Through optimizing the view angles of 3-D projections using Sammon mapping, the optimal 2-D projection-guided MIVOOS is obtained to better visualize and verify the patterns in conjunction with trajectory patterns. Compared with XB and VOS, our newly proposed MIVOOS shows its robustness in validating big Web-trial data under different missing data mechanisms using real and simulated Web-trial data.

Structural organization of the inactive X chromosome in the mouse

Mon, 08/01/2016 - 8:39am

X-chromosome inactivation (XCI) involves major reorganization of the X chromosome as it becomes silent and heterochromatic. During female mammalian development, XCI is triggered by upregulation of the non-coding Xist RNA from one of the two X chromosomes. Xist coats the chromosome in cis and induces silencing of almost all genes via its A-repeat region, although some genes (constitutive escapees) avoid silencing in most cell types, and others (facultative escapees) escape XCI only in specific contexts. A role for Xist in organizing the inactive X (Xi) chromosome has been proposed. Recent chromosome conformation capture approaches have revealed global loss of local structure on the Xi chromosome and formation of large mega-domains, separated by a region containing the DXZ4 macrosatellite. However, the molecular architecture of the Xi chromosome, in both the silent and expressed regions, remains unclear. Here we investigate the structure, chromatin accessibility and expression status of the mouse Xi chromosome in highly polymorphic clonal neural progenitors (NPCs) and embryonic stem cells. We demonstrate a crucial role for Xist and the DXZ4-containing boundary in shaping Xi chromosome structure using allele-specific genome-wide chromosome conformation capture (Hi-C) analysis, an assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) and RNA sequencing. Deletion of the boundary disrupts mega-domain formation, and induction of Xist RNA initiates formation of the boundary and the loss of DNA accessibility. We also show that in NPCs, the Xi chromosome lacks active/inactive compartments and topologically associating domains (TADs), except around genes that escape XCI. Escapee gene clusters display TAD-like structures and retain DNA accessibility at promoter-proximal and CTCF-binding sites. Furthermore, altered patterns of facultative escape genes in different neural progenitor clones are associated with the presence of different TAD-like structures after XCI. These findings suggest a key role for transcription and CTCF in the formation of TADs in the context of the Xi chromosome in neural progenitors.

Paternal Postpartum Depression

Fri, 07/29/2016 - 5:50pm

While postpartum depression (PPD) has historically been associated primarily with mothers, recently there has been increased awareness of the experience of fathers and strategies to address postpartum depression in men. For fathers willing to seek help, the lack of recognition of paternal PPD results in limited supports and treatments. Given the potential implications of paternal PPD, it is essential for new fathers and their healthcare providers to recognize the prevalence of paternal PPD, the symptoms, and the challenges surrounding this issue for men.

Childhood Maltreatment, Emotional Dysregulation, and Psychiatric Comorbidities (poster)

Mon, 07/25/2016 - 12:32pm

There is a complex and bi-directional relationship between childhood trauma and emotional dysregulation. Childhood trauma is associated with: reduced ability to understand and regulate emotions; mediated by relational/attachment difficulties with caregivers and peers; heightened levels of internalizing and externalizing psychopathology; impaired social functioning beginning in childhood and continuing into adulthood.

Therapeutic Assignments: Structured Framework for Interaction Between Medical Students and Patients on Psychiatry Clerkships

Mon, 07/25/2016 - 12:31pm

Medical students enjoy high level of patient contact on psychiatric clerkships. They have felt that forming a relationship with a patient can have therapeutic effects by imparting hope, decreasing their isolation and providing individualized attention. However students have encountered difficulties forming alliance with their patients, either due to acuity of illness such as psychosis or due to character pathology, addiction etc. They need to feel comfortable dealing with more difficult situations such as extremes of emotion or breaks with reality. Interviewing skills must be continually developed. We hope that Therapeutic Assignments (TA) will: provide a medium for students to improve their interviewing skills; enhance their comfort around communicating with patients about sensitive topics; form a therapeutic alliance with their patients, which will support the growth of empathy and be an important aspect in the patient’s treatment.

Enhancing the Social Networks of People with Mental Illnesses: A Qualitative Study on the Role of Peer-Operated Recovery Learning Communities

Fri, 07/22/2016 - 2:08pm

In 2014, researchers from the UMass Systems and Psychosocial Advances Research Center (SPARC) partnered with the Central Massachusetts Recovery Learning Communities (RLC) to complete a pilot study exploring the relationship between RLC participation and experiences of social integration. Utilizing participatory action research (PAR) principles, investigators from both SPARC and the RLC worked collaboratively to design an exploratory qualitative study, analyze data, and present findings.

Synthesis and Testing of Modular Dual-Modality Nanoparticles for Magnetic Resonance and Multispectral Photoacoustic Imaging

Fri, 07/22/2016 - 1:58pm

Magnetic resonance (MR) and photoacoustic (PA) imaging are currently being investigated as complementing strategies for applications requiring sensitive detection of cells in vivo. While combined MR/PAI detection of cells requires biocompatible cell labeling probes, water-based synthesis of dual-modality MR/PAI probes presents significant technical challenges. Here we describe facile synthesis and characterization of hybrid modular dextran-stabilized gold/iron oxide (Au-IO) multimetallic nanoparticles (NP) enabling multimodal imaging of cells. The stable association between the IO and gold NP was achieved by priming the surface of dextran-coated IO with silver NP resulting from silver(I) reduction by aldehyde groups, which are naturally present within the dextran coating of IO at the level of 19-23 groups/particle. The Au-IO NP formed in the presence of silver-primed Au-IO were stabilized by using partially thiolated MPEG5-gPLL graft copolymer carrying residual amino groups. This stabilizer served as a carrier of near-infrared fluorophores (e.g., IRDye 800RS) for multispectral PA imaging. Dual modality imaging experiments performed in capillary phantoms of purified Au-IO-800RS NPs showed that these NPs were detectible using 3T MRI at a concentration of 25 μM iron. PA imaging achieved approximately 2.5-times higher detection sensitivity due to strong PA signal emissions at 530 and 770 nm, corresponding to gold plasmons and IRDye integrated into the coating of the hybrid NPs, respectively, with no "bleaching" of PA signal. MDA-MB-231 cells prelabeled with Au-IO-800RS retained plasma membrane integrity and were detectable by using both MR and dual-wavelength PA at 49 ± 3 cells/imaging voxel. We believe that modular assembly of multimetallic NPs shows promise for imaging analysis of engineered cells and tissues with high resolution and sensitivity.

Gold nanoparticles stabilized with MPEG-grafted poly(l-lysine): in vitro and in vivo evaluation of a potential theranostic agent

Fri, 07/22/2016 - 1:58pm

As the number of diagnostic and therapeutic applications utilizing gold nanoparticles (AuNPs) increases, so does the need for AuNPs that are stable in vivo, biocompatible, and suitable for bioconjugation. We investigated a strategy for AuNP stabilization that uses methoxypolyethylene glycol-graft-poly(l-lysine) copolymer (MPEG-gPLL) bearing free amino groups as a stabilizing molecule. MPEG-gPLL injected into water solutions of HAuCl4 with or without trisodium citrate resulted in spherical (Zav = 36 nm), monodisperse (PDI = 0.27), weakly positively charged nanoparticles (AuNP3) with electron-dense cores (diameter: 10.4 ± 2.5 nm) and surface amino groups that were amenable to covalent modification. The AuNP3 were stable against aggregation in the presence of phosphate and serum proteins and remained dispersed after their uptake into endosomes. MPEG-gPLL-stabilized AuNP3 exhibited high uptake and very low toxicity in human endothelial cells, but showed a high dose-dependent toxicity in epithelioid cancer cells. Highly stable radioactive labeling of AuNP3 with (99m)Tc allowed imaging of AuNP3 biodistribution and revealed dose-dependent long circulation in the blood. The minor fraction of AuGNP3 was found in major organs and at sites of experimentally induced inflammation. Gold analysis showed evidence of a partial degradation of the MPEG-gPLL layer in AuNP3 particles accumulated in major organs. Radiofrequency-mediated heating of AuNP3 solutions showed that AuNP3 exhibited heating behavior consistent with 10 nm core nanoparticles. We conclude that PEG-pPLL coating of AuNPs confers "stealth" properties that enable these particles to exist in vivo in a nonaggregating, biocompatible state making them suitable for potential use in biomedical applications such as noninvasive radiofrequency cancer therapy.

Substrate-Based Near-Infrared Imaging Sensors Enable Fluorescence Lifetime Contrast via Built-in Dynamic Fluorescence Quenching Elements

Fri, 07/22/2016 - 1:57pm

Enzymatic activity sensing in fluorescence lifetime (FLT) mode with “self-quenched” macromolecular near-infrared (NIR) sensors is a highly promising strategy for in vivo imaging of proteolysis. However, the mechanisms of FLT changes in such substrate-based NIR sensors have not yet been studied. We synthesized two types of sensors by linking the near-infrared fluorophore IRDye 800CW to macromolecular graft copolymers of methoxy polyethylene glycol and polylysine (MPEG-gPLL) with varying degrees of MPEGylation and studied their fragmentation induced by trypsin, elastase, plasmin, and cathepsins (B,S,L,K). We determined that the efficiency of such NIR sensors in FLT mode depends on sensor composition. While MPEG-gPLL with a high degree of MPEGylation showed rapid (τ1/2 = 0.1–0.2 min) FLT increase (Δτ = 0.25 ns) upon model proteinase-mediated hydrolysis in vivo, lower MPEGylation density resulted in no such FLT increase. Temperature-dependence of fluorescence dequenching of NIR sensors pointed to a mixed dynamic/static-quenching mode of MPEG-gPLL-linked fluorophores. We further demonstrated that although the bulk of sensor-linked fluorophores were dequenched due to the elimination of static quenching, proteolysis-mediated deletion of a fraction of short (8–10 kD) negatively charged fragments of highly MPEGylated NIR sensor is the most likely event leading to a rapid FLT increase phenomenon in quenched NIR sensors. Therefore, the optimization of “built-in” dynamic quenching elements of macromolecular NIR sensors is a potential avenue for improving their response in FLT mode.

Tweet, Like, Share: Using Social Media to Connect with the Evaluation World

Fri, 07/22/2016 - 12:23pm

Blog post to AEA365, a blog sponsored by the American Evaluation Association (AEA) dedicated to highlighting Hot Tips, Cool Tricks, Rad Resources, and Lessons Learned for evaluators. The American Evaluation Association is an international professional association of evaluators devoted to the application and exploration of program evaluation, personnel evaluation, technology, and many other forms of evaluation. Evaluation involves assessing the strengths and weaknesses of programs, policies, personnel, products, and organizations to improve their effectiveness.

Searching for Literature Using Google Scholar

Thu, 07/21/2016 - 8:53pm

Blog post to AEA365, a blog sponsored by the American Evaluation Association (AEA) dedicated to highlighting Hot Tips, Cool Tricks, Rad Resources, and Lessons Learned for evaluators. The American Evaluation Association is an international professional association of evaluators devoted to the application and exploration of program evaluation, personnel evaluation, technology, and many other forms of evaluation. Evaluation involves assessing the strengths and weaknesses of programs, policies, personnel, products, and organizations to improve their effectiveness.

Driving Change: Tips for Helping Stakeholders Stay Motivated

Thu, 07/21/2016 - 8:53pm

Blog post to AEA365, a blog sponsored by the American Evaluation Association (AEA) dedicated to highlighting Hot Tips, Cool Tricks, Rad Resources, and Lessons Learned for evaluators. The American Evaluation Association is an international professional association of evaluators devoted to the application and exploration of program evaluation, personnel evaluation, technology, and many other forms of evaluation. Evaluation involves assessing the strengths and weaknesses of programs, policies, personnel, products, and organizations to improve their effectiveness.

The Beauty of Banner Tables

Thu, 07/21/2016 - 8:53pm

Blog post to AEA365, a blog sponsored by the American Evaluation Association (AEA) dedicated to highlighting Hot Tips, Cool Tricks, Rad Resources, and Lessons Learned for evaluators. The American Evaluation Association is an international professional association of evaluators devoted to the application and exploration of program evaluation, personnel evaluation, technology, and many other forms of evaluation. Evaluation involves assessing the strengths and weaknesses of programs, policies, personnel, products, and organizations to improve their effectiveness.