Utility of routine screening for alpha-1 antitrypsin deficiency in patients with bronchiectasis

Alpha-1 antitrypsin deficiency (AATD) is a cause of bronchiectasis. Guidelines for bronchiectasis from the British Thoracic Society do not recommend to routinely test patients for AATD. In contrast, guidelines for AATD recommend routine screening. This contradiction, in part, results from the lack of data from large studies performing comprehensive screening. We screened 1600 patients with bronchiectasis at two centres in the UK from 2012 to 2016. In total, only eight individuals with AATD were identified representing 0.5% of the overall population. We conclude that routine screening for AATD in bronchiectasis in the UK has a low rate of detection. Further studies are required in different geographical regions, which may have a higher prevalence of AATD.info:eu-repo/semantics/publishedVersio

Minimizing the overlap problem in protein NMR: a computational framework for precision amino acid labeling

Motivation: Recent advances in cell-free protein expression systems allow specific labeling of proteins with amino acids containing stable isotopes (¹⁵N, ¹³C and ²H), an important feature for protein structure determination by nuclear magnetic resonance (NMR) spectroscopy. Given this labeling ability, we present a mathematical optimization framework for designing a set of protein isotopomers, or labeling schedules, to reduce the congestion in the NMR spectra. The labeling schedules, which are derived by the optimization of a cost function, are tailored to a specific protein and NMR experiment. Results: For 2D ¹⁵N-¹H HSQC experiments, we can produce an exact solution using a dynamic programming algorithm in under 2 h on a standard desktop machine. Applying the method to a standard benchmark protein, calmodulin, we are able to reduce the number of overlaps in the 500 MHZ HSQC spectrum from 10 to 1 using four samples with a true cost function, and 10 to 4 if the cost function is derived from statistical estimates. On a set of 448 curated proteins from the BMRB database, we are able to reduce the relative percent congestion by 84.9% in their HSQC spectra using only four samples. Our method can be applied in a high-throughput manner on a proteomic scale using the server we developed. On a 100-node cluster, optimal schedules can be computed for every protein coded for in the human genome in less than a month. Availability: A server for creating labeling schedules for ¹⁵N-¹H HSQC experiments as well as results for each of the individual 448 proteins used in the test set is available at http://nmr.proteomics.ics.uci.edu

Hydrologic indicators of hot spots and hot moments of mercury methylation potential along river corridors

The authors acknowledge financial support from the National Science Foundation: EAR-1226741 (to M.B.S.) and EAR-1225630 (to J.D.B.), and from the REG Trust (to M.B.S.).The biogeochemical cycling of metals and other contaminants in river-floodplain corridors is controlled by microbial activity responding to dynamic redox conditions. Riverine flooding thus has the potential to affect speciation of redox-sensitive metals such as mercury (Hg). Therefore, inundation history over a period of decades potentially holds information on past production of bioavailable Hg. We investigate this within a Northern California river system with a legacy of landscape-scale 19th century hydraulic gold mining. We combine hydraulic modeling, Hg measurements in sediment and biota, and first-order calculations of mercury transformation to assess the potential role of river floodplains in producing monomethylmercury (MMHg), a neurotoxin which accumulates in local and migratory food webs. We identify frequently inundated floodplain areas, as well as floodplain areas inundated for long periods. We quantify the probability of MMHg production potential (MPP) associated with hydrology in each sector of the river system as a function of the spatial patterns of overbank inundation and drainage, which affect long-term redox history of contaminated sediments. Our findings identify river floodplains as periodic, temporary, yet potentially important, loci of biogeochemical transformation in which contaminants may undergo change during limited periods of the hydrologic record. We suggest that inundation is an important driver of MPP in river corridors and that the entire flow history must be analyzed retrospectively in terms of inundation magnitude and frequency in order to accurately assess biogeochemical risks, rather than merely highlighting the largest floods or low-flow periods. MMHg bioaccumulation within the aquatic food web in this system may pose a major risk to humans and waterfowl that eat migratory salmonids, which are being encouraged to come up these rivers to spawn. There is a long-term pattern of MPP under the current flow regime that is likely to be accentuated by increasingly common large floods with extended duration.PostprintPeer reviewe

Common elective orthopaedic procedures and their clinical effectiveness:umbrella review of level 1 evidence

OBJECTIVE: To determine the clinical effectiveness of common elective orthopaedic procedures compared with no treatment, placebo, or non-operative care and assess the impact on clinical guidelines. DESIGN: Umbrella review of meta-analyses of randomised controlled trials or other study designs in the absence of meta-analyses of randomised controlled trials. DATA SOURCES: Ten of the most common elective orthopaedic procedures—arthroscopic anterior cruciate ligament reconstruction, arthroscopic meniscal repair of the knee, arthroscopic partial meniscectomy of the knee, arthroscopic rotator cuff repair, arthroscopic subacromial decompression, carpal tunnel decompression, lumbar spine decompression, lumbar spine fusion, total hip replacement, and total knee replacement—were studied. Medline, Embase, Cochrane Library, and bibliographies were searched until September 2020. ELIGIBILITY CRITERIA FOR SELECTING STUDIES: Meta-analyses of randomised controlled trials (or in the absence of meta-analysis other study designs) that compared the clinical effectiveness of any of the 10 orthopaedic procedures with no treatment, placebo, or non-operative care. DATA EXTRACTION AND SYNTHESIS: Summary data were extracted by two independent investigators, and a consensus was reached with the involvement of a third. The methodological quality of each meta-analysis was assessed using the Assessment of Multiple Systematic Reviews instrument. The Jadad decision algorithm was used to ascertain which meta-analysis represented the best evidence. The National Institute for Health and Care Excellence Evidence search was used to check whether recommendations for each procedure reflected the body of evidence. MAIN OUTCOME MEASURES: Quality and quantity of evidence behind common elective orthopaedic interventions and comparisons with the strength of recommendations in relevant national clinical guidelines. RESULTS: Randomised controlled trial evidence supports the superiority of carpal tunnel decompression and total knee replacement over non-operative care. No randomised controlled trials specifically compared total hip replacement or meniscal repair with non-operative care. Trial evidence for the other six procedures showed no benefit over non-operative care. CONCLUSIONS: Although they may be effective overall or in certain subgroups, no strong, high quality evidence base shows that many commonly performed elective orthopaedic procedures are more effective than non-operative alternatives. Despite the lack of strong evidence, some of these procedures are still recommended by national guidelines in certain situations. SYSTEMATIC REVIEW REGISTRATION: PROSPERO CRD42018115917

Evidence for Multiple Manipulation Processes in Prefrontal Cortex

The prefrontal cortex (PFC) is known to subserve working memory (WM) processes. Brain imaging studies of WM using delayed response tasks (DRTs) have shown memory-load-dependent activation increases in dorsal prefrontal cortex (PFC) regions. These activation increases are believed to reflect manipulation of to-be-remembered information in the service of memory-consolidation. This speculation has been based on observations of similar activation increases in tasks that overtly require manipulation by instructing participants to reorder to-be-remembered list items. In this study, we tested the assumption of functional equivalence between these two types of WM tasks. Participants performed a DRT under two conditions with memory loads ranging from 3 to 6 letters. In an “item-order” condition, participants were required to remember letters in the order in which they were presented. In a “reordering” condition, participants were required to remember the letters in alphabetical order. Load-related activation increases were observed during the encoding and maintenance periods of the order maintenance condition, whereas load-related activation decreases were observed in the same periods of the reordering condition. These results suggest that (1) the neural substrates associated with long-list retention and those associated with reordering are not equivalent, (2) cognitive processes associated with long-list retention may be more closely approximated by item-order maintenance than by reordering, and (3) multiple forms of WM manipulation are dissociable on the basis of fMRI data

Lactation and neonatal nutrition: defining and refining the critical questions.

This paper resulted from a conference entitled "Lactation and Milk: Defining and refining the critical questions" held at the University of Colorado School of Medicine from January 18-20, 2012. The mission of the conference was to identify unresolved questions and set future goals for research into human milk composition, mammary development and lactation. We first outline the unanswered questions regarding the composition of human milk (Section I) and the mechanisms by which milk components affect neonatal development, growth and health and recommend models for future research. Emerging questions about how milk components affect cognitive development and behavioral phenotype of the offspring are presented in Section II. In Section III we outline the important unanswered questions about regulation of mammary gland development, the heritability of defects, the effects of maternal nutrition, disease, metabolic status, and therapeutic drugs upon the subsequent lactation. Questions surrounding breastfeeding practice are also highlighted. In Section IV we describe the specific nutritional challenges faced by three different populations, namely preterm infants, infants born to obese mothers who may or may not have gestational diabetes, and infants born to undernourished mothers. The recognition that multidisciplinary training is critical to advancing the field led us to formulate specific training recommendations in Section V. Our recommendations for research emphasis are summarized in Section VI. In sum, we present a roadmap for multidisciplinary research into all aspects of human lactation, milk and its role in infant nutrition for the next decade and beyond