Improved Triplex-Forming Isoorotamide PNA Nucleobases for A-U Recognition of RNA Duplexes.

Four new isoorotamide (Io)-containing PNA nucleobases have been designed for A-U recognition of double helical RNA. New PNA monomers were prepared efficiently and incorporated into PNA nonamers for binding A-U in a PNA:RNA2 triplex. Isothermal titration calorimetry and UV thermal melting experiments revealed slightly improved binding affinity for singly modified PNA compared to known A-binding nucleobases. Molecular dynamics simulations provided further insights into binding of Io bases in the triple helix. Together, the data revealed interesting insights into binding modes including the notion that three Hoogsteen hydrogen bonds are unnecessary for strong selective binding of an extended nucleobase. Cationic monomer Io8 additionally gave the highest affinity observed for an A-binding nucleobase to date. These results will help inform future nucleobase design toward the goal of recognizing any sequence of double helical RNA.

Failure of mecA/mecC PCR Testing to Accurately Predict Oxacillin Resistance in a Patient with Staphylococcus aureus Infective Endocarditis.

Genotypic testing for mecA/mecC is heavily relied upon for rapid optimization of antimicrobial therapy in infections due to Staphylococcus aureus. Little is known regarding optimal reporting and/or therapy for patients demonstrating lack of genotypic evidence of mecA or mecC but phenotypic oxacillin resistance. We report a case of a 77-year-old patient with S. aureus bloodstream infection and infective endocarditis with discordance between mecA/mecC genotypic results and phenotypic susceptibility testing.

Retrospective Evaluation of the Association of Oxacillin MIC on Acute Treatment Outcomes with Cefazolin and Antistaphylococcal Penicillins in Methicillin-Susceptible Staphylococcus aureus Bacteremia.

Antistaphylococcal penicillins (ASP) and cefazolin are first-line treatment of methicillin-susceptible Staphylococcus aureus (MSSA) bacteremia. Borderline oxacillin resistance (i.e., oxacillin MICs 1-8 µg/mL) is observed in strains hyperproducing beta-lactamases. This mechanism is also behind the proposed inoculum effect. Minimal data exists on the comparative efficacy of cefazolin or ASP in qualitatively susceptible strains that demonstrate MICs of oxacillin of 1 to 2 µg/mL compared to strains with MIC of oxacillin < 1 µg/mL. We performed a retrospective cohort study of acute treatment outcomes in adult patients with community-acquired MSSA bacteremia treated with cefazolin or ASP, stratified by oxacillin MIC. The primary outcome was a composite of all-cause mortality during the index inpatient admission, failure to clear blood cultures within 72 h after initiating definitive therapy, and change in therapy due to perceived lack of efficacy. A total of 402 patients were included in this study, including 226 isolates with an oxacillin MIC ≥ 1 µg/mL and 176 isolates with an MIC < 1 µg/mL. There were no differences in the rate of the primary outcome occurrence between patients with an oxacillin MIC ≥ 1 µg/mL and an MIC < 1 µg/mL (16.4% versus 15.9%, P = 0.90). There was no difference in the primary outcome between high versus low oxacillin MIC groups among those who received ASP (22.9% versus 24.1%, P = 0.86) or cefazolin (10.3% versus 11.9%, P = 0.86). In our cohort of patients with MSSA bacteremia, oxacillin MIC (i.e., ≥ 1 versus < 1 µg/mL) was not associated with acute treatment outcomes, regardless of the beta-lactam selected as definitive therapy.

IsobaricQuant enables cross-platform quantification, visualization, and filtering of isobarically-labeled peptides.

In mass spectrometry (MS)-based quantitative proteomics, labeling with isobaric mass tags such as iTRAQ and TMT can substantially improve sample throughput and reduce peptide missing values. Nonetheless, the quantification of labeled peptides tends to suffer from reduced accuracy due to the co-isolation of co-eluting precursors of similar mass-to-charge. Acquisition approaches such as multistage MS3 or ion mobility separation address this problem, yet are difficult to audit and limited to expensive instrumentation. Here we introduce IsobaricQuant, an open-source software tool for quantification, visualization, and filtering of peptides labeled with isobaric mass tags, with specific focus on precursor interference. IsobaricQuant is compatible with MS2 and MS3 acquisition strategies, has a viewer that allows assessing interference, and provides several scores to aid the filtering of scans with compression. We demonstrate that IsobaricQuant quantifications are accurate by comparing it with commonly used software. We further show that its QC scores can successfully filter out scans with reduced quantitative accuracy at MS2 and MS3 levels, removing inaccurate peptide quantifications and decreasing protein CVs. Finally, we apply IsobaricQuant to a PISA dataset and show that QC scores improve the sensitivity of the identification of protein targets of a kinase inhibitor. IsobaricQuant is available at https://github.com/Villen-Lab/isobaricquant.

Origin and Evolution of the Human Bcl2-Associated Athanogene-1 (BAG-1).

Molecular chaperones, particularly the 70-kDa heat shock proteins (Hsp70s), are key orchestrators of the cellular stress response. To perform their critical functions, Hsp70s require the presence of specific co-chaperones, which include nucleotide exchange factors containing the BCL2-associated athanogene (BAG) domain. BAG-1 is one of these proteins that function in a wide range of cellular processes, including apoptosis, protein refolding, and degradation, as well as tumorigenesis. However, the origin of BAG-1 proteins and their evolution between and within species are mostly uncharacterized. This report investigated the macro- and micro-evolution of BAG-1 using orthologous sequences and single nucleotide polymorphisms (SNPs) to elucidate the evolution and understand how natural variation affects the cellular stress response. We first collected and analyzed several BAG-1 sequences across animals, plants, and fungi; mapped intron positions and phases; reconstructed phylogeny; and analyzed protein characteristics. These data indicated that BAG-1 originated before the animals, plants, and fungi split, yet most extant fungal species have lost BAG-1. Furthermore, although BAG-1's structure has remained relatively conserved, kingdom-specific conserved differences exist at sites of known function, suggesting functional specialization within each kingdom. We then analyzed SNPs from the 1000 genomes database to determine the evolutionary patterns within humans. These analyses revealed that the SNP density is unequally distributed within the BAG1 gene, and the ratio of non-synonymous/synonymous SNPs is significantly higher than 1 in the BAG domain region, which is an indication of positive selection. To further explore this notion, we performed several biochemical assays and found that only one out of five mutations tested altered the major co-chaperone properties of BAG-1. These data collectively suggest that although the co-chaperone functions of BAG-1 are highly conserved and can probably tolerate several radical mutations, BAG-1 might have acquired specialized and potentially unexplored functions during the evolutionary process.

Concurrent action of purifying selection and gene conversion results in extreme conservation of the major stress-inducible Hsp70 genes in mammals.

Several evolutionary mechanisms alter the fate of mutations and genes within populations based on their exhibited functional effects. To understand the underlying mechanisms involved in the evolution of the cellular stress response, a very conserved mechanism in the course of organismal evolution, we studied the patterns of natural genetic variation and functional consequences of polymorphisms of two stress-inducible Hsp70 genes. These genes, HSPA1A and HSPA1B, are major orchestrators of the cellular stress response and are associated with several human diseases. Our phylogenetic analyses revealed that the duplication of HSPA1A and HSPA1B originated in a lineage proceeding to placental mammals, and henceforth they remained in conserved synteny. Additionally, analyses of synonymous and non-synonymous changes suggest that purifying selection shaped the HSPA1 gene diversification, while gene conversion resulted in high sequence conservation within species. In the human HSPA1-cluster, the vast majority of mutations are synonymous and specific genic regions are devoid of mutations. Furthermore, functional characterization of several human polymorphisms revealed subtle differences in HSPA1A stability and intracellular localization. Collectively, the observable patterns of HSPA1A-1B variation describe an evolutionary pattern, in which purifying selection and gene conversion act simultaneously and conserve a major orchestrator of the cellular stress response.

Adherence to Glaucoma Medications Over 12 Months in Two US Community Pharmacy Chains.

UNLABELLED: This study determined the degree of adherence to medications for glaucoma among patients refilling prescriptions in community pharmacies. METHODS: Data abstracted from the dispensing records for 3615 adult patients (18 years or older, predominantly over 45) receiving glaucoma medications from two retail pharmacy chains (64 stores in total) were analyzed. From a 24-month historic data capture period, the 12-month levels of adherence were determined using standard metrics, the proportion of days covered (PDC) and the medication possession ratio (MPR). The overall 12-month mean PDC was only 57%, and the mean MPR was 71%. Using a criterion by which 80% coverage was considered satisfactory adherence, only 30% had satisfactory overall 12-month PDC coverage, and only 37% had satisfactory overall 12-month MPR coverage. Refill adherence increased with age and was highest in the 65-and-older age group (p < 0.001). Differential adherence was found across medication classes, with the highest satisfactory coverage seen for those taking alpha2-adrenergic agonists (PDC = 36.0%; MPR = 47.6%) down to those taking direct cholinergic agonists (PDC = 25.0%; MPR = 31.2%) and combination products (PDC = 22.7%; MPR = 31.0%). Adherence to glaucoma medications in the community setting, as measured by pharmacy refill data, is very poor and represents a critical target for intervention. Community pharmacists are well positioned to monitor and reinforce adherence in this population.

Physician adherence to ACR gout treatment guidelines: perception versus practice.

BACKGROUND: In October 2012, the American College of Rheumatology (ACR) published recommendations for chronic gout treatment goals and pharmacotherapy. OBJECTIVES: Identify potential gaps between real-world chronic gout treatment, ACR guideline recommendations, and physicians' perceived guideline adherence by evaluating records of patients classified as having "higher" and "lower" guideline adherence as defined by the investigators. METHODS: A comprehensive quantitative survey was administered between February 11 and February 22, 2013, to physicians treating patients with gout; the survey included a patient record chart review informed by prior qualitative interviews. Eight criteria from the ACR gout management guidelines were used to compose the survey. To assess ACR guideline adherence, information from records of patients with chronic gout treated by primary care physicians (PCPs) and rheumatologists was scored from 0 (no adherence) to 8 (total adherence), in accordance with ACR guideline recommendations. Physicians also indicated how closely they believed patient treatment followed current guidelines on a 10-point scale. RESULTS: Of the 350 records of patients with chronic gout, all but 3 PCP patients were adherent on ≥ 1 guideline recommendation, but nearly all patients could be considered nonadherent, considering all potential recommendations. Patients with chronic gout treated by rheumatologists tended to be managed more closely to ACR guidelines than patients treated by PCPs (mean scores: rheumatologists 5.8/8 ± 1.7 vs 4.3/8 ± 1.7 for PCPs). Among patients classified as having "higher adherence" based on adherence scores, there was low adherence on first-line urate lowering therapy dose, acute prophylaxis dosing, and length of prophylaxis treatment. Among PCPs and rheumatologists, there was a disparity between how closely physicians believed patient treatment followed guidelines and actual adherence with ACR guidelines based on adherence scores. For 16.4% of patients treated by PCPs and 18.4% of patients seen by rheumatologists, physicians believed they closely followed ACR guidelines (score of 8-10/10) for each patient; but in actuality, adherence was lower. CONCLUSION: Although adherence with ACR guidelines is higher among rheumatologists than PCPs in treating patients with gout, overall adherence could be improved by both specialties.

Vascular risk factors and neuropsychiatric symptoms in Alzheimer's disease: the Cache County Study.

OBJECTIVE: Knowledge of potentially modifiable risk factors for neuropsychiatric symptoms (NPS) in Alzheimer's disease (AD) is important. This study longitudinally explores modifiable vascular risk factors for NPS in AD. METHODS: Participants enrolled in the Cache County Study on Memory in Aging with no dementia at baseline were subsequently assessed over three additional waves, and those with incident (new onset) dementia were invited to join the Dementia Progression Study for longitudinal follow-up. A total of 327 participants with incident AD were identified and assessed for the following vascular factors: atrial fibrillation, hypertension, diabetes mellitus, angina, coronary artery bypass surgery, myocardial infarction, cerebrovascular accident, and use of antihypertensive or diabetes medicines. A vascular index (VI) was also calculated. NPS were assessed over time using the Neuropsychiatric Inventory (NPI). Affective and Psychotic symptom clusters were assessed separately. The association between vascular factors and change in NPI total score was analyzed using linear mixed model and in symptom clusters using a random effects model. RESULTS: No individual vascular risk factors or the VI significantly predicted change in any individual NPS. The use of antihypertensive medications more than four times per week was associated with higher total NPI and Affective cluster scores. CONCLUSIONS: Use of antihypertensive medication was associated with higher total NPI and Affective cluster scores. The results of this study do not otherwise support vascular risk factors as modifiers of longitudinal change in NPS in AD.

Caregivers' relationship closeness with the person with dementia predicts both positive and negative outcomes for caregivers' physical health and psychological well-being.

Closer relationships between caregivers and care recipients with dementia are associated with positive outcomes for care recipients, but it is unclear if closeness is a risk or protective factor for the health and psychological wellbeing of caregivers. We examined 234 care dyads from the population-based Cache County Dementia Progression Study. Caregivers included spouses (49%) and adult offspring (51%). Care recipients mostly had dementia of the Alzheimer's type (62%). Linear mixed models tested associations between relationship closeness at baseline or changes in closeness prior to versus after dementia onset, with baseline levels and changes over time in caregiver affect (Affect Balance Scale, ABS), depression (Beck Depression Inventory, BDI), and mental and physical health (components of the Short-Form Health Survey, SF-12). After controlling for demographic characteristics of the caregiver, number of caregiver health conditions, and characteristics of the care recipient (type of dementia, functional ability, and behavioral disturbances), we found that higher baseline closeness predicted higher baseline SF-12 mental health scores (better mental health) and lower depression. Higher baseline closeness also predicted greater worsening over time in ABS and SF-12 mental health. In addition, caregivers who reported a loss of closeness in their relationship with the care recipient from pre- to post-dementia displayed improved scores on ABS and SF-12 mental health, but worse SF-12 physical health over the course of the study. These results suggest that closeness and loss of closeness in the care dyad may be associated with both positive and adverse outcomes for caregivers, both cross-sectionally and over time.

Random forests for classification in ecology.

Classification procedures are some of the most widely used statistical methods in ecology. Random forests (RF) is a new and powerful statistical classifier that is well established in other disciplines but is relatively unknown in ecology. Advantages of RF compared to other statistical classifiers include (1) very high classification accuracy; (2) a novel method of determining variable importance; (3) ability to model complex interactions among predictor variables; (4) flexibility to perform several types of statistical data analysis, including regression, classification, survival analysis, and unsupervised learning; and (5) an algorithm for imputing missing values. We compared the accuracies of RF and four other commonly used statistical classifiers using data on invasive plant species presence in Lava Beds National Monument, California, USA, rare lichen species presence in the Pacific Northwest, USA, and nest sites for cavity nesting birds in the Uinta Mountains, Utah, USA. We observed high classification accuracy in all applications as measured by cross-validation and, in the case of the lichen data, by independent test data, when comparing RF to other common classification methods. We also observed that the variables that RF identified as most important for classifying invasive plant species coincided with expectations based on the literature.