Abstract
We report the large effort that is producing comprehensive high-level young star cluster (YSC) catalogs for a significant fraction of galaxies observed with the Legacy ExtraGalactic UV ...Survey (LEGUS)
Hubble
treasury program. We present the methodology developed to extract cluster positions, verify their genuine nature, produce multiband photometry (from NUV to NIR), and derive their physical properties via spectral energy distribution fitting analyses. We use the nearby spiral galaxy NGC 628 as a test case for demonstrating the impact that LEGUS will have on our understanding of the formation and evolution of YSCs and compact stellar associations within their host galaxy. Our analysis of the cluster luminosity function from the UV to the NIR finds a steepening at the bright end and at all wavelengths suggesting a dearth of luminous clusters. The cluster mass function of NGC 628 is consistent with a power-law distribution of slopes
and a truncation of a few times 10
5
. After their formation, YSCs and compact associations follow different evolutionary paths. YSCs survive for a longer time frame, confirming their being potentially bound systems. Associations disappear on timescales comparable to hierarchically organized star-forming regions, suggesting that they are expanding systems. We find mass-independent cluster disruption in the inner region of NGC 628, while in the outer part of the galaxy there is little or no disruption. We observe faster disruption rates for low mass (≤10
4
) clusters, suggesting that a mass-dependent component is necessary to fully describe the YSC disruption process in NGC 628.
INTRODUCTION
Cerebrovascular dysfunction is a pathological hallmark of Alzheimer's disease (AD). Nevertheless, detecting cerebrovascular changes within bulk tissues has limited our ability to ...characterize proteomic alterations from less abundant cell types.
METHODS
We conducted quantitative proteomics on bulk brain tissues and isolated cerebrovasculature from the same individuals, encompassing control (N = 28), progressive supranuclear palsy (PSP) (N = 18), and AD (N = 21) cases.
RESULTS
Protein co‐expression network analysis identified unique cerebrovascular modules significantly correlated with amyloid plaques, cerebrovascular amyloid angiopathy (CAA), and/or tau pathology. The protein products within AD genetic risk loci were concentrated within cerebrovascular modules. The overlap between differentially abundant proteins in AD cerebrospinal fluid (CSF) and plasma with cerebrovascular network highlighted a significant increase of matrisome proteins, SMOC1 and SMOC2, in CSF, plasma, and brain.
DISCUSSION
These findings enhance our understanding of cerebrovascular deficits in AD, shedding light on potential biomarkers associated with CAA and vascular dysfunction in neurodegenerative diseases.
Large scale -omics datasets can provide new insights into normal and disease-related biology when analyzed through a systems biology framework. However, technical artefacts present in most -omics ...datasets due to variations in sample preparation, batching, platform settings, personnel, and other experimental procedures prevent useful analyses of such data without prior adjustment for these technical factors. Here, we demonstrate a tunable median polish of ratio (TAMPOR) approach for batch effect correction and agglomeration of multiple, multi-batch, site-specific cohorts into a single analyte abundance data matrix that is suitable for systems biology analyses. We illustrate the utility and versatility of TAMPOR through four distinct use cases where the method has been applied to different proteomic datasets, some of which contain a specific defect that must be addressed prior to analysis. We compare quality control metrics and sources of variance before and after application of TAMPOR to show that TAMPOR is effective at removing batch effects and other unwanted sources of variance in -omics data. We also show how TAMPOR can be used to harmonize -omics datasets even when the data are acquired using different analytical approaches. TAMPOR is a powerful and flexible approach for cleaning and harmonization of -omics data prior to downstream systems biology analysis.
As part of our ongoing studies of the human immunodeficiency virus type 1 (HIV-1) protease enzyme, we set out to develop a modular chemical synthesis of the protein from multiple peptide segments. ...Our initial attempts were frustrated by the insolubility of intermediate peptide products. To overcome this problem, we designed a synthetic strategy combining the solubility-enhancing properties of C-terminal (Arg) n tags and the biological phenomenon of autoprocessing of the Gag−Pol polyprotein that occurs during maturation of the HIV-1 virus in vivo. Synthesis of a 119-residue peptide chain containing 10 residues of the reverse transcriptase (RT) open reading frame plus an (Arg)10 tag at the C-terminus was straightforward by native chemical ligation followed by conversion of the Cys residues to Ala by Raney nickel desulfurization. The product polypeptide itself completed the final synthetic step by removing the C-terminal modification under folding conditions, to give the mature 99-residue polypeptide. High-purity homodimeric HIV-1 protease protein was obtained in excellent yield and had full enzymatic activity; the structure of the synthetic enzyme was confirmed by X-ray crystallography to a resolution of 1.07 Å. This efficient modular synthesis by a biomimetic autoprocessing strategy will enable the facile synthesis of unique chemical analogues of the HIV-1 protease to further elucidate the molecular basis of enzyme catalysis.
We have undertaken fundamental studies on the solubility properties of a peptide derived from the fourth transmembrane (TM) domain of signal peptide peptidase, a 7-TM intramembrane-cleaving protease. ...We have found that by disfavoring secondary structure formation we are able to greatly improve the solubility, handling, and purification properties of this peptide. Our findings suggest that preventing secondary structure formation by reversible modification of the polypeptide backbone of hydrophobic transmembrane peptides may be a useful strategy for the total chemical protein synthesis of integral membrane proteins.
Abstract
Objective
Patients with sickle cell disease (SCD) face inconsistent effective analgesic management, leading to high inpatient healthcare utilization and significant financial burden for ...healthcare institutions. Current evidence does not provide guidance for inpatient management of acute pain in adults with sickle cell disease. We conducted a retrospective analysis of a longitudinal cohort quality improvement project to characterize the role of individualized care plans on improving patient care and reducing financial burden in high healthcare-utilizing patients with SCD-related pain.
Methods
Individualized care plans were developed for patients with hospital admissions resulting from pain associated with sickle cell disease. A 2-year prospective longitudinal cohort quality improvement project was performed and retrospectively analyzed. Primary outcome measure was duration of hospitalization. Secondary outcome measures included: pain intensity; 7, 30, and 90-day readmission rates; cost per day; total admissions; total cost per year; analgesic regimen at index admission; and discharge disposition.
Results
Duration of hospitalization, the primary outcome, significantly decreased by 1.23 days with no worsening of pain intensity scores. Seven-day readmission decreased by 34%. Use of intravenous hydromorphone significantly decreased by 25%. The potential cost saving was $1,398,827 as a result of this quality initiative.
Conclusions
Implementation of individualized care plans reduced both admission rate and financial burden of high utilizing patients. Importantly, pain outcomes were not diminished. Results suggest that individualized care plans are a promising strategy for managing acute pain crisis in adult sickle cell patients from both care-focused and utilization outcomes.
Development of disease-modifying therapies against Alzheimer's disease (AD) requires biomarkers reflecting the diverse pathological pathways specific for AD. We measured 665 proteins in 797 ...cerebrospinal fluid (CSF) samples from patients with mild cognitive impairment with abnormal amyloid (MCI(Aβ+): n = 50), AD-dementia (n = 230), non-AD dementias (n = 322) and cognitively unimpaired controls (n = 195) using proximity ligation-based immunoassays. Here we identified >100 CSF proteins dysregulated in MCI(Aβ+) or AD compared to controls or non-AD dementias. Proteins dysregulated in MCI(Aβ+) were primarily related to protein catabolism, energy metabolism and oxidative stress, whereas those specifically dysregulated in AD dementia were related to cell remodeling, vascular function and immune system. Classification modeling unveiled biomarker panels discriminating clinical groups with high accuracies (area under the curve (AUC): 0.85-0.99), which were translated into custom multiplex assays and validated in external and independent cohorts (AUC: 0.8-0.99). Overall, this study provides novel pathophysiological leads delineating the multifactorial nature of AD and potential biomarker tools for diagnostic settings or clinical trials.
Modification of a peptide-(α)thioester with a sequence of six arginines on the thioester leaving group can render soluble all peptides derived from a polytopic integral membrane protein. This ...strategy greatly simplifies the synthesis of peptide-(α)thioester building blocks for the total chemical synthesis of integral membrane proteins by native chemical ligation.
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