Publications by authors named "Richard Smith"

2,841 Publications

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Nitrogen mineralization from organic fertilizers and composts: Literature survey and model fitting.

J Environ Qual 2021 Oct 19. Epub 2021 Oct 19.

University of California, Department of Environmental Studies.

Organic fertilizers and composts are valuable sources of nutrients. However, their nutrient availability is often not known and can be variable. The objective of the present study was to collect net nitrogen (N) turnover data from peer-reviewed articles and fit a model that simulates gross N mineralization and gross N immobilization to determine pool sizes and their rate constants of different common organic amendments. A total of 113 datasets were included in the study. The model predicted that 61% and 72.5% of total N in feather meal and guano, respectively, would be in the mineral form after 100 days under optimal conditions. Nitrogen availability from poultry manure and poultry manure compost was lower. On average, 16-17% of total N was present as mineral N in the materials, while at the end of the 100-day simulation, 39.6% and 32.7% of total N from an average poultry manure and its compost, respectively, were in the mineral form. Yard waste compost and vermicompost are stable materials, with less than 10% of the total N in an average material being in the mineral form at the end of the 100-day simulation. Model simulations revealed that changes in the assumed temperature sensitivity of N mineralization have a strong effect on N availability of readily available organic amendments during the first weeks after incorporation. The model performed well for guano and feather meal, but was unsatisfactory for the other amendment groups. Model performance may have been hampered by different incubation protocols used in the studies included and variability in amendment properties not considered by the model. The results of this study allow estimating the release of N from a variety of organic fertilizers and composts and can be a valuable tool to improve N management of organic amendments in crop production. This article is protected by copyright. All rights reserved.
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http://dx.doi.org/10.1002/jeq2.20295DOI Listing
October 2021

Response of Amazonian forests to mid-Holocene drought: A model-data comparison.

Glob Chang Biol 2021 Oct 15. Epub 2021 Oct 15.

Department of Geography and Environmental Science, School of Archaeology, Geography and Environmental Science (SAGES), University of Reading, Whiteknights, Reading, UK.

There is a major concern for the fate of Amazonia over the coming century in the face of anthropogenic climate change. A key area of uncertainty is the scale of rainforest dieback to be expected under a future, drier climate. In this study, we use the middle Holocene (ca. 6000 years before present) as an approximate analogue for a drier future, given that palaeoclimate data show much of Amazonia was significantly drier than present at this time. Here, we use an ensemble of climate and vegetation models to explore the sensitivity of Amazonian biomes to mid-Holocene climate change. For this, we employ three dynamic vegetation models (JULES, IBIS, and SDGVM) forced by the bias-corrected mid-Holocene climate simulations from seven models that participated in the Palaeoclimate Modelling Intercomparison Project 3 (PMIP3). These model outputs are compared with a multi-proxy palaeoecological dataset to gain a better understanding of where in Amazonia we have most confidence in the mid-Holocene vegetation simulations. A robust feature of all simulations and palaeodata is that the central Amazonian rainforest biome is unaffected by mid-Holocene drought. Greater divergence in mid-Holocene simulations exists in ecotonal eastern and southern Amazonia. Vegetation models driven with climate models that simulate a drier mid-Holocene (100-150 mm per year decrease) better capture the observed (palaeodata) tropical forest dieback in these areas. Based on the relationship between simulated rainfall decrease and vegetation change, we find indications that in southern Amazonia the rate of tropical forest dieback was ~125,000 km per 100 mm rainfall decrease in the mid-Holocene. This provides a baseline sensitivity of tropical forests to drought for this region (without human-driven changes to greenhouse gases, fire, and deforestation). We highlight the need for more palaeoecological and palaeoclimate data across lowland Amazonia to constrain model responses.
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http://dx.doi.org/10.1111/gcb.15929DOI Listing
October 2021

Found Down Extremity Compartment Syndrome Secondary to Substance Use: An Observational Multicenter Study.

JB JS Open Access 2021 Oct-Dec;6(4). Epub 2021 Oct 6.

Harvard Orthopaedic Trauma Initiative, Harvard Medical School, Boston, Massachusetts.

With the worsening opioid epidemic in America, more patients are developing found down extremity compartment syndrome (FDECS). The purpose of this study was to describe this patient population, including their presenting symptoms, laboratory test results, and clinical outcomes.

Methods: We performed a 2-center retrospective review of adult patients who developed FDECS secondary to substance use from January 2006 to December 2019. Patients were managed operatively or nonoperatively at the surgeon's discretion. Data on patient demographic characteristics, laboratory values, hospital course, and clinical outcomes were collected from electronic medical records.

Results: In this study, 91 patients were included: 85 patients were managed operatively, and 6 patients were managed nonoperatively. Most patients were male, and the mean patient age (and standard deviation) was 37 ± 11 years. Opioids were the most common substance used. Patients managed operatively underwent a mean of 4 ± 3 surgical procedures, 44% received a skin graft, 25% developed a wound infection, and 11% underwent limb amputation. Patients managed nonoperatively did not undergo a subsequent fasciotomy or amputation. At a mean follow-up of 2.3 years, persistent weakness (66%), pain (78%), persistent sensory deficits (53%), and contractures (18%) were common.

Conclusions: Patients who develop FDECS secondary to substance use have high surgical complication rates and poor clinical outcomes. We found high rates of wound infection, revision surgical procedures, and amputation, often leaving young adults with lifelong disability.

Level Of Evidence: Prognostic Level IV. See Instructions for Authors for a complete description of levels of evidence.
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http://dx.doi.org/10.2106/JBJS.OA.21.00038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8500555PMC
October 2021

Sequential genetic testing of living related donors for inherited renal disease to promote informed choice and enhance safety of living donation.

Transpl Int 2021 Oct 10. Epub 2021 Oct 10.

Departments of Internal Medicine, University of Iowa, Iowa City, IA, USA.

Living kidney donors (LKDs) with a family history of renal disease are at risk of kidney disease as compared to LKDs without such history suggesting that some LKDs may be pre-symptomatic for monogenic kidney disease. LKDs with related transplant candidates whose kidney disease was considered genetic in origin were selected for genetic testing. In each case, the transplant candidate was first tested to verify the genetic diagnosis. A genetic diagnosis was confirmed in 12 of 24 transplant candidates (ADPKD-PKD1: 6, ALPORT-COL4A3: 2, ALPORT-COL4A5: 1: nephronophthisis-SDCCAG8: 1; CAKUT-HNF1B and ADTKD-MUC1: 1 each) and 2 had variants of unknown significance (VUS) in phenotype-relevant genes. Focused genetic testing was then done in 20 of 34 LKDs. 12 LKDs screened negative for the familial variant and were permitted to donate; 7 screened positive and were counseled against donation. One, the heterozygous carrier of a recessive disorder was also cleared. 6 of 7 LKDs with a family history of ADPKD were under 30 yr and in 5, by excluding ADPKD, allowed donation to safely proceed. The inclusion of genetic testing clarified the diagnosis in recipient candidates, improving safety or informed decision making in LKDs.
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http://dx.doi.org/10.1111/tri.14133DOI Listing
October 2021

Cell biology of the leaf epidermis: Fate specification, morphogenesis and coordination.

Plant Cell 2021 Oct 8. Epub 2021 Oct 8.

Howard Hughes Medical Institute and Department of Molecular Biosciences, The University of Texas at Austin, Austin TX 78712 USA.

As the outermost layer of plants, the epidermis serves as a critical interface between plants and the environment. During leaf development, the differentiation of specialized epidermal cell types, including stomatal guard cells, pavement cells and trichomes, occurs simultaneously, each providing unique and pivotal functions for plant growth and survival. Decades of molecular-genetic and physiological studies have unraveled key players and hormone signaling specifying epidermal differentiation. However, most studies focus on only one cell type at a time, and how these distinct cell types coordinate as a unit is far from well-comprehended. Here we provide a review on the current knowledge of regulatory mechanisms underpinning the fate specification, differentiation, morphogenesis, and positioning of these specialized cell types. Emphasis is given to their shared developmental origins, fate flexibility, as well as cell cycle and hormonal controls. Furthermore, we discuss computational modeling approaches to integrate how mechanical properties of individual epidermal cell types and entire tissue/organ properties mutually influence each other. We hope to illuminate the underlying mechanisms coordinating the cell differentiation that ultimately generate a functional leaf epidermis.
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http://dx.doi.org/10.1093/plcell/koab250DOI Listing
October 2021

Auxin-dependent control of cytoskeleton and cell shape regulates division orientation in the Arabidopsis embryo.

Curr Biol 2021 Sep 29. Epub 2021 Sep 29.

Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 Wageningen, the Netherlands. Electronic address:

Premitotic control of cell division orientation is critical for plant development, as cell walls prevent extensive cell remodeling or migration. While many divisions are proliferative and add cells to existing tissues, some divisions are formative and generate new tissue layers or growth axes. Such formative divisions are often asymmetric in nature, producing daughters with different fates. We have previously shown that, in the Arabidopsis thaliana embryo, developmental asymmetry is correlated with geometric asymmetry, creating daughter cells of unequal volume. Such divisions are generated by division planes that deviate from a default "minimal surface area" rule. Inhibition of auxin response leads to reversal to this default, yet the mechanisms underlying division plane choice in the embryo have been unclear. Here, we show that auxin-dependent division plane control involves alterations in cell geometry, but not in cell polarity axis or nuclear position. Through transcriptome profiling, we find that auxin regulates genes controlling cell wall and cytoskeleton properties. We confirm the involvement of microtubule (MT)-binding proteins in embryo division control. Organization of both MT and actin cytoskeleton depends on auxin response, and genetically controlled MT or actin depolymerization in embryos leads to disruption of asymmetric divisions, including reversion to the default. Our work shows how auxin-dependent control of MT and actin cytoskeleton properties interacts with cell geometry to generate asymmetric divisions during the earliest steps in plant development.
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http://dx.doi.org/10.1016/j.cub.2021.09.019DOI Listing
September 2021

Improving Signal to Noise Ratios in Ion Mobility Spectrometry and Structures for Lossless Ion Manipulations (SLIM) using a High Dynamic Range Analog-to-Digital Converter.

J Am Soc Mass Spectrom 2021 Sep 30. Epub 2021 Sep 30.

Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States.

Signal digitization is a commonly overlooked part of ion mobility-mass spectrometry (IMS-MS) workflows, yet it greatly affects signal-to-noise ratio and MS resolution measurements. Here, we report on the integration of a 2 GS/s, 14-bit ADC with structures for lossless ion manipulations (SLIM-IMS-MS) and compare the performance to a commonly used 8-bit ADC. The 14-bit ADC provided a reduction in the digitized noise by a factor of ∼6, owing largely to the use of smaller bit sizes. The low baseline allowed threshold voltage levels to be set very close to the MCP baseline voltage, allowing for as much signal to be acquired as possible without overloading or excessive digitization of MCP baseline noise. Analyses of Agilent tuning mixture ions and a mixture of heavy labeled phosphopeptides showed that the 14-bit ADC provided a ∼1.5-2× signal-to-noise (S/N) increase for high intensity ions, such as the Agilent tuning mixture ions and the 2+ and 3+ charge states of many phosphopeptide constituents. However, signal enhancements were as much as 10-fold for low intensity ions, and the 14-bit ADC enabled discernible signal intensities otherwise lost using an 8-bit digitizer. Additionally, the 14-bit ADC required ∼14-fold fewer mass spectra to be averaged to produce a mass spectrum with a similar S/N as the 8-bit ADC, demonstrating ∼10× higher measurement throughput. The high resolution, low baseline, and fast speed of the new 14-bit ADC enables high performance digitization of MS, IMS-MS, and SLIM-IMS-MS spectra and provides a much better picture of analyte profiles in complex mixtures.
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http://dx.doi.org/10.1021/jasms.1c00226DOI Listing
September 2021

Why skyscrapers after Covid-19?

Authors:
Richard G Smith

Futures 2021 Dec 20;134:102839. Epub 2021 Sep 20.

Department of Geography, Swansea University, Singleton Park, Sketty, SA2 8PP, UK.

Globalization's for global cities with highly concentrated financial districts is discussed to explain how the Covid-19 pandemic will paradoxically only serve to make the world's leading global cities more essential, valuable, and demanding of skyscrapers than ever before. Financial and corporate service firms cannot only be digitally based because they also require face-to-face interaction, collaboration, and joint-production within themselves, and between one another, in the most connected global cities to effectively function as competitive businesses. However, after Covid-19 advanced service firms will only practice remote working where and when they must; so that in-place face-to-face interactions with colleagues and clients will be overwhelmingly only concentrated in the skyscraper-laden financial districts of the world's leading global cities. The future of commercial and luxury residential skyscrapers in the world's leading global cities can be said to be secure because the impact of Covid-19 on enhancing the centrality of these few highly connected and super-wealthy cities in globalization is both understandable and predictable; skyscrapers elsewhere in the Global North or South will struggle to remain viable as firms increasingly decentralise the work of their staff away from city centre offices.
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http://dx.doi.org/10.1016/j.futures.2021.102839DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8451974PMC
December 2021

Improving Clinical Trials for Anticomplement Therapies in Complement-Mediated Glomerulopathies: Report of a Scientific Workshop Sponsored by the National Kidney Foundation.

Am J Kidney Dis 2021 Sep 24. Epub 2021 Sep 24.

University of Toronto, Toronto, Canada.

Blocking the complement system as a therapeutic strategy has been proposed for numerous glomerular diseases but presents a myriad of questions and challenges, not the least of which is demonstrating efficacy and safety. In light of these potential issues and because there are an increasing number of anti-complement therapy trials either planned or underway, the National Kidney Foundation (NKF) facilitated an all-virtual format scientific workshop entitled, "Improving Clinical Trials for Anti-complement Therapies in Complement-mediated Glomerulopathies." Attended by patient representatives and experts in glomerular diseases, complement physiology, and clinical trial design, the aim of this workshop was to develop standards applicable for designing and conducting clinical trials for anti-complement therapies across a wide spectrum of complement-mediated glomerulopathies. Discussions focused on study design, subject risk assessment and mitigation, laboratory measurements and biomarkers to support these studies, and identification of optimal outcome measures to detect benefit, specifically for trials in complement-mediated diseases. This report summarizes the discussions from this workshop and outlines consensus recommendations.
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http://dx.doi.org/10.1053/j.ajkd.2021.07.025DOI Listing
September 2021

Risk factor analysis for Salmonella contamination of broiler chicken (Gallus gallus) hatcheries in Great Britain.

Prev Vet Med 2021 Sep 13;196:105492. Epub 2021 Sep 13.

Department of Bacteriology, Animal and Plant Health Agency (APHA - Weybridge), Woodham Lane, New Haw, Addlestone, KT15 3NB, UK.

Salmonellosis is the second most commonly reported zoonosis in the European Union and contaminated meat from broiler chickens (Gallus gallus) is an important source of human infection. In Great Britain (GB), prevalence of Salmonella enterica in broiler flocks is low, having declined considerably since the introduction of the Salmonella National Control Programme in 2010. However, this decreasing trend has stabilised in recent years and serovars with known ability to persistently colonise hatcheries have been isolated from broiler flocks with increasing frequency, indicating that further controls on hatchery contamination are required. The broiler industry in GB has changed dramatically over the last 15 years, with greater intensification and dominance by a small number of very large companies which rely on relatively few hatcheries. An investigation of risk factors for Salmonella contamination in GB broiler hatcheries was therefore carried out so that relevant up-to-date advice on Salmonella control can be provided. Twenty-two hatcheries, representing most commercial scale GB broiler hatcheries, were visited between 2015 and 2018. Salmonella contamination was comprehensively investigated at each hatchery by collecting between 108 and 421 environmental swab samples per hatchery (6990 samples in total from all hatcheries). An in-depth questionnaire on hatchery operations was completed for each hatchery, and results were incorporated into a risk factor analysis (univariable followed by multivariable mixed effects logistic regression) to identify factors associated with Salmonella occurrence. Overall, 6.0 % (416/6990) of environmental samples were Salmonella-positive and Salmonella was isolated from 17/22 hatcheries. Ten different serovars were isolated, the most common being S. Senftenberg and S. Mbandaka which are known hatchery colonisers. Sixty-four risk factor variables were investigated. Twenty-two of these were initially retained based on univariable analyses (p ≤ 0.25) and six were ultimately left in the final multivariable model (p ≤ 0.05). Salmonella detection was positively associated with having ≥30 hatchers in regular use compared to fewer (Odds ratio [OR] 23.7, 95 % confidence interval [CI] 6.7-84.2), storing trays in process rooms (OR 28.8, CI 7.8-106.3), drying set-up trolleys in corridors (OR 15.6, CI 5.9-41.4) and having skips located in enclosed areas (OR 8.99, CI 5.89-41.35). Using a closed waste disposal system was negatively associated with Salmonella detection (OR 0.08, CI 0.04-0.18) and the odds of detecting Salmonella in hatcheries with 31-60 total workers was lower compared to hatcheries with ≤30 staff (OR 0.16, CI 0.06-0.40). Despite the complexities of hatchery enterprises, changes to a relatively small number of features may significantly reduce the occurrence of hatchery contamination.
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http://dx.doi.org/10.1016/j.prevetmed.2021.105492DOI Listing
September 2021

Impact of Nonadherence to NCCN Adjuvant Radiotherapy Initiation Guidelines in Head and Neck Squamous Cell Carcinoma in an Underserved Urban Population.

J Natl Compr Canc Netw 2021 Sep 22:1-7. Epub 2021 Sep 22.

6Department of Otorhinolaryngology-Head and Neck Surgery, Montefiore Medical Center, Bronx, New York.

Background: Nonadherence to NCCN Guidelines during time from surgery to postoperative radiotherapy (S-PORT) can alter survival outcomes in head and neck squamous cell carcinomna (HNSCC). There is a need to validate this impact in an underserved urban population and to understand risk factors and reasons for delay. We sought to investigate the impact of delayed PORT with outcomes of overall survival (OS) in HNSCC, to analyze predictive factors of delayed PORT, and to identify reasons for delay.

Methods: We conducted a retrospective cohort study in an urban, community-based academic center. A total of 184 patients with primary HNSCC were identified through the Montefiore Medical Center cancer registry who had been treated between March 1, 2005, and March 8, 2017, and met the inclusion and exclusion criteria. The primary exposure was S-PORT. OS, recurrence, and risk factors and reasons for treatment delay were the main outcomes and measures.

Results: Among 184 patients with HNSCC treated with PORT, the median S-PORT was 48.5 days (interquartile range, 41-67 days). The S-PORT threshold that optimally differentiated worse OS outcomes was >50 days (46.7% of our cohort; n=86). Independent of other relevant factors, patients with HNSCC and S-PORT >50 days had worse OS (hazard ratio, 2.30; 95% CI, 1.34-3.95) and greater recurrence (odds ratio, 3.51; 95% CI, 1.31-9.39). Predictors of delayed S-PORT included being underweight or obese, prolonged postoperative length of stay, and age >70 years. The most frequent reasons for PORT delay were complications related to surgery (22.09%), unrelated medical comorbidities (18.60%), and nonadherence/missed appointments (6.98%).

Conclusions: Delayed PORT beyond 50 days after surgery was associated with decreased OS and greater recurrence. Identification of predictive factors and reasons for treatment delay helps to target at-risk patients and facilitates interventions in underserved populations.
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http://dx.doi.org/10.6004/jnccn.2021.7007DOI Listing
September 2021

Advances in subcutaneous injections: PRECISE II: a study of safety and subject preference for an innovative needle-free injection system.

Drug Deliv 2021 Dec;28(1):1915-1922

Portal Instruments, Cambridge, MA, USA.

Needle-free injection is a desirable goal for many reasons, including reducing pain, anxiety, and eliminating safety risks associated with needle-stick injuries. However, development of a safe, reliable needle-free device optimized for at-home use has been met with many challenges. Portal Instruments Inc. has been developing needle-free medication delivery using a well-designed hand-held device, PRIME, that is safe, intuitive to use, and utilizes advanced electronic control of a focused, high velocity, pressurized liquid injection stream. The PRECISE II human study demonstrated that the PRIME needle-free injection system was safe, well tolerated, and strongly preferred by participants for self-injections over a standard needle and syringe. In addition, the study was able to be completed early for superiority following the success of the pre-defined interim analysis.
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http://dx.doi.org/10.1080/10717544.2021.1976309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8462839PMC
December 2021
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