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  • 1
    In: Environmental DNA, Wiley, Vol. 2, No. 3 ( 2020-07), p. 271-282
    Abstract: Environmental DNA (eDNA) analysis is increasingly being used to detect the presence and relative abundance of rare species, especially invasive or imperiled aquatic species. The rapid progress in the eDNA field has resulted in numerous studies impacting conservation and management actions. However, standardization of eDNA methods and reporting across the field is yet to be fully established, with one area being the calculation and interpretation of assay limit of detection (LOD) and limit of quantification (LOQ). Aims Here, we propose establishing consistent methods for determining and reporting of LOD and LOQ for single‐species quantitative PCR (qPCR) eDNA studies. Materials & Methods/ Results We utilize datasets from multiple cooperating laboratories to demonstrate both a discrete threshold approach and a curve‐fitting modeling approach for determining LODs and LOQs for eDNA qPCR assays. We also provide details of an R script developed and applied for the modeling method. Discussion/Conclusions Ultimately, standardization of how LOD and LOQ are determined, interpreted, and reported for eDNA assays will allow for more informed interpretation of assay results, more meaningful interlaboratory comparisons of experiments, and enhanced capacity for assessing the relative technical quality and performance of different eDNA qPCR assays.
    Type of Medium: Online Resource
    ISSN: 2637-4943 , 2637-4943
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 3001165-6
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  • 2
    In: Agriculture, Ecosystems & Environment, Elsevier BV, Vol. 137, No. 1-2 ( 2010-04-15), p. 3-12
    Type of Medium: Online Resource
    ISSN: 0167-8809
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2010
    detail.hit.zdb_id: 2013743-6
    SSG: 12
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  • 3
    In: Agronomy Journal, Wiley, Vol. 107, No. 5 ( 2015-09), p. 1627-1640
    Abstract: Biomass yield is an important factor when recommending native perennial plants and mixtures for bioenergy production. Our objective was to determine long‐term biomass yields in fertilized and unfertilized native plant monocultures and mixtures that show promise for bioenergy across diverse environments in the Upper Midwest. We measured biomass yields, species composition, and diversity annually in monocultures and mixtures ranging from 4 to 24 planted species including grasses, legumes, and other forbs; each managed with and without 67 kg N ha −1 fertilizer applied annually at nine locations for 7 yr. Without N fertilization, switchgrass ( Panicum virgatum L.) monocultures and an eight‐species mixture of grasses and legumes produced the most biomass over locations and years (5.1 Mg ha −1 ). With N fertilizer, switchgrass monocultures and a four‐species mixture of grasses produced the highest yields (6.8 and 6.4 Mg ha −1 ). Over time, biomass yields increased for switchgrass, decreased for Canada wild rye ( Elymus canadensis L.), and remained stable for the high diversity mixtures. Other mixtures had nonlinear changes in yield, likely related to changes in species composition. Although the relative abundance of individual species changed over time, Shannon diversity was constant except for the four‐species legume mixture where it decreased. Contrary to other studies, N fertilization did not decrease species diversity through time. Diversity was positively related to biomass yield following establishment, but the strength of the relationship diminished with stand age. Native plant mixtures managed with and without N fertilizer can yield similar biomass compared with highly productive monocultures in the Upper Midwest.
    Type of Medium: Online Resource
    ISSN: 0002-1962 , 1435-0645
    Language: English
    Publisher: Wiley
    Publication Date: 2015
    detail.hit.zdb_id: 1471598-3
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  • 4
    In: GCB Bioenergy, Wiley, Vol. 9, No. 2 ( 2017-02), p. 326-338
    Abstract: Native perennial bioenergy crops can mitigate greenhouse gases ( GHG ) by displacing fossil fuels with renewable energy and sequestering atmospheric carbon (C) in soil and roots. The relative contribution of root C to net GHG mitigation potential has not been compared in perennial bioenergy crops ranging in species diversity and N fertility. We measured root biomass, C, nitrogen (N), and soil organic carbon ( SOC ) in the upper 90 cm of soil for five native perennial bioenergy crops managed with and without N fertilizer. Bioenergy crops ranged in species composition and were annually harvested for 6 (one location) and 7 years (three locations) following the seeding year. Total root biomass was 84% greater in switchgrass ( Panicum virgatum L.) and a four‐species grass polyculture compared to high‐diversity polycultures; the difference was driven by more biomass at shallow soil depth (0–30 cm). Total root C (0–90 cm) ranged from 3.7 Mg C ha −1 for a 12‐species mixture to 7.6 Mg C ha −1 for switchgrass. On average, standing root C accounted for 41% of net GHG mitigation potential. After accounting for farm and ethanol production emissions, net GHG mitigation potential from fossil fuel offsets and root C was greatest for switchgrass (−8.4 Mg CO 2e ha −1  yr −1 ) and lowest for high‐diversity mixtures (−4.5 Mg CO 2e ha −1  yr −1 ). Nitrogen fertilizer did not affect net GHG mitigation potential or the contribution of roots to GHG mitigation for any bioenergy crop. SOC did not change and therefore did not contribute to GHG mitigation potential. However, associations among SOC , root biomass, and root C : N ratio suggest greater long‐term C storage in diverse polycultures vs. switchgrass. Carbon pools in roots have a greater effect on net GHG mitigation than SOC in the short‐term, yet variation in root characteristics may alter patterns in long‐term C storage among bioenergy crops.
    Type of Medium: Online Resource
    ISSN: 1757-1693 , 1757-1707
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2017
    detail.hit.zdb_id: 2495051-8
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    Wiley ; 2011
    In:  Agronomy Journal Vol. 103, No. 2 ( 2011-03), p. 509-519
    In: Agronomy Journal, Wiley, Vol. 103, No. 2 ( 2011-03), p. 509-519
    Abstract: Proposed perennial bioenergy cropping systems include both native grass monocultures and polycultures of grasses and forbs. We determined the effect of species richness and composition on establishment and initial biomass production of native plant polycultures. Twelve treatments with varying levels of species richness (1–24 species) were established. Establishment success and yield varied over eight locations. The number of species established in polyculture increased linearly as the number of species seeded increased. Average biomass yield ranged from 1.2 to 6.0 Mg ha −1 with the highest yielding treatments being grass monocultures or an eight species grass–legume mixture. An increase in species richness from one to eight species increased yield an average of 28%, but increasing species richness from 8 to 12 or 24 species had no yield advantage at most locations. Early successional species, Canada milkvetch ( Astragalus canadensis L.) and Maximilian sunflower ( Helianthus maximilian Schrad.), were dominant in mixtures and contributed a majority of the biomass to the yield. Even in high diversity plots, biomass was from only a few plant species with a single species dominating the mixture. Our results suggest that selected low diversity mixtures (one to five species) likely offer the best combination of species establishment and high yield during stand establishment. However, we expect that early successional species that were dominant during the establishment phase of our experiment will contribute less biomass as stands mature and later successional species will become dominant and provide greater biomass.
    Type of Medium: Online Resource
    ISSN: 0002-1962 , 1435-0645
    Language: English
    Publisher: Wiley
    Publication Date: 2011
    detail.hit.zdb_id: 1471598-3
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  • 6
    In: British Journal of Surgery, Oxford University Press (OUP), Vol. 106, No. 2 ( 2019-01-08), p. e103-e112
    Abstract: The World Health Organization (WHO) Surgical Safety Checklist has fostered safe practice for 10 years, yet its place in emergency surgery has not been assessed on a global scale. The aim of this study was to evaluate reported checklist use in emergency settings and examine the relationship with perioperative mortality in patients who had emergency laparotomy. Methods In two multinational cohort studies, adults undergoing emergency laparotomy were compared with those having elective gastrointestinal surgery. Relationships between reported checklist use and mortality were determined using multivariable logistic regression and bootstrapped simulation. Results Of 12 296 patients included from 76 countries, 4843 underwent emergency laparotomy. After adjusting for patient and disease factors, checklist use before emergency laparotomy was more common in countries with a high Human Development Index (HDI) (2455 of 2741, 89·6 per cent) compared with that in countries with a middle (753 of 1242, 60·6 per cent; odds ratio (OR) 0·17, 95 per cent c.i. 0·14 to 0·21, P & lt; 0·001) or low (363 of 860, 42·2 per cent; OR 0·08, 0·07 to 0·10, P & lt; 0·001) HDI. Checklist use was less common in elective surgery than for emergency laparotomy in high-HDI countries (risk difference −9·4 (95 per cent c.i. −11·9 to −6·9) per cent; P & lt; 0·001), but the relationship was reversed in low-HDI countries (+12·1 (+7·0 to +17·3) per cent; P & lt; 0·001). In multivariable models, checklist use was associated with a lower 30-day perioperative mortality (OR 0·60, 0·50 to 0·73; P & lt; 0·001). The greatest absolute benefit was seen for emergency surgery in low- and middle-HDI countries. Conclusion Checklist use in emergency laparotomy was associated with a significantly lower perioperative mortality rate. Checklist use in low-HDI countries was half that in high-HDI countries.
    Type of Medium: Online Resource
    ISSN: 0007-1323 , 1365-2168
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 2006309-X
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  • 7
    In: BJS Open, Oxford University Press (OUP), Vol. 3, No. 3 ( 2019-06), p. 403-414
    Type of Medium: Online Resource
    ISSN: 2474-9842 , 2474-9842
    URL: Issue
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 2902033-5
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  • 8
    In: Annals of the American Thoracic Society, American Thoracic Society, Vol. 15, No. 6 ( 2018-06), p. 683-692
    Type of Medium: Online Resource
    ISSN: 2329-6933 , 2325-6621
    Language: English
    Publisher: American Thoracic Society
    Publication Date: 2018
    detail.hit.zdb_id: 2702474-X
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  • 9
    In: British Journal of Surgery, Oxford University Press (OUP), Vol. 109, No. 10 ( 2022-09-09), p. 995-1003
    Abstract: There is a substantial gap in provision of adequate surgical care in many low- and middle-income countries. This study aimed to identify the economic burden of unmet surgical need for the common condition of appendicitis. Methods Data on the incidence of appendicitis from 170 countries and two different approaches were used to estimate numbers of patients who do not receive surgery: as a fixed proportion of the total unmet surgical need per country (approach 1); and based on country income status (approach 2). Indirect costs with current levels of access and local quality, and those if quality were at the standards of high-income countries, were estimated. A human capital approach was applied, focusing on the economic burden resulting from premature death and absenteeism. Results Excess mortality was 4185 per 100 000 cases of appendicitis using approach 1 and 3448 per 100 000 using approach 2. The economic burden of continuing current levels of access and local quality was US $92 492 million using approach 1 and $73 141 million using approach 2. The economic burden of not providing surgical care to the standards of high-income countries was $95 004 million using approach 1 and $75 666 million using approach 2. The largest share of these costs resulted from premature death (97.7 per cent) and lack of access (97.0 per cent) in contrast to lack of quality. Conclusion For a comparatively non-complex emergency condition such as appendicitis, increasing access to care should be prioritized. Although improving quality of care should not be neglected, increasing provision of care at current standards could reduce societal costs substantially.
    Type of Medium: Online Resource
    ISSN: 0007-1323 , 1365-2168
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2006309-X
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  • 10
    In: Blood, American Society of Hematology, Vol. 120, No. 21 ( 2012-11-16), p. 143-143
    Abstract: Abstract 143 Background: Mammalian target of rapamycin (mTOR) inhibitors enhance cytotoxic chemotherapy effects in primary acute leukemia cells in preclinical assays. This prompted a multi-center evaluation of a combination of mTOR inhibitor plus induction chemotherapy in AML. As mTOR is frequently but not uniformly activated in primary AML samples, it is unclear which patients benefit from this targeted approach. Thus, we sought to monitor mTOR kinase activity during therapy to determine whether target activation and/or inhibition predicted clinical response. We previously reported our preliminary experience monitoring pS6 in AML blasts by flow during clinical trials combining sirolimus and AML induction chemotherapy (Kasner et al, ASH 2011, #230). Here we provide the final clinical and pharmacodynamic results from this cohort of subjects. Methods: Subjects had relapsed/refractory AML or untreated AML with unfavorable risk factors (e.g. therapy-related, prior MDS or MPN, or age 〉 60 without favorable karyotype) with a median age of 60.5 years (range 32–77). Subjects received oral sirolimus (12 mg on day 1, then 4 mg daily on days 2–9) plus MEC (mitoxantrone 8 mg/m2/day, etoposide 100 mg/m2/day, cytarabine 1 gm/m2/d on days 4–8) on one of two successive clinical trials. Clinical response was assessed at hematologic recovery or day 42 using IWG criteria (CR, CRp, PR vs. non-response). Pharmacodynamic samples were collected from blood or marrow at baseline, 2 hours post-sirolimus dose on days 1 and 4, and at trough on day 4 (prior to chemotherapy administration). Concurrent blood rapamycin concentration was measured by immunoassay or HPLC. Whole blood/marrow fixation was performed using published methods (Perl, et al. Clin. Cancer Res. 2012). Positive gates for pS6 were created by comparing blasts in ex vivo stimulated (phorbol ester/PMA) and inhibited (rapamycin) conditions and/or autofluorescence (FMO) controls. Results: We enrolled 52 subjects in 2 consecutive trials; 51 were evaluable for clinical response. Toxicity was similar to published MEC data. 3 infectious deaths occurred (6%). Prolonged aplasia was not observed. 24/51 (47%) subjects responded, with 18 CR (35%), 1 CRp, and 5 PR's observed. Mean peak and trough rapamycin concentrations on day 4 were 22.0 and 8.9 ng/ml, respectively, and did not differ among clinically responding or non-responding subjects. Median survival time for the whole group was 243 days (longest follow up 1584 days). Among the 24 subjects achieving CR or PR, median duration of time to the first event (relapse or death) was 261 days. 20 subjects were able to proceed to a stem cell transplant following therapy. Serial flow cytometric analysis was performed in 46 subjects, of which 37 provided paired day 1 and day 4 flow samples and were evaluable for clinical response at count recovery. The overall response rate (ORR) among subjects with baseline constitutive pS6 was 14/27 (52%, 9 CR, 1 CRp, 4 PR). The ORR for subjects without constitutive pS6 was 4/10 (40%, 3 CR, 1 PR). Subjects with 〉 50% reduction in pS6 positive blasts on day 4 were considered to be biochemically sensitive to rapamycin, while subjects with 〈 50% reduction or increased pS6 were considered rapamycin-resistant. Categorizing subjects based upon the achievement of CR/CRp/PR vs. NR, the reduction in blasts' pS6 percent on day 4 was 72% among clinically responding subjects and 43% among those without clinical response. The ORR in rapamycin sensitive patients was 10/15 (67%, 6 CR, 4 PR, 5 NR), while in resistant subjects was 4/12 (33%, 3 CR, 1 CRp, 8 NR). Combining rapamycin resistant subjects and those with no basal pS6, the ORR was 8/22 (36%, 6 CR, 1 CRp, 1 PR, 14 NR). Conclusions: Sirolimus plus MEC is a tolerable and active regimen for patients with high risk AML. The addition of an mTOR inhibitor augmented chemotherapy response particularly among those with demonstrable baseline mTOR activation and target inhibition during therapy. These results demonstrate the diversity of AML with reference to the activation of ribosomal S6 and suggest that phospho-flow monitoring may be an effective tool for patient selection for use of signaling inhibitors in AML. Future trials of this regimen may benefit from enrichment for subjects with mTOR activation and/or rapamycin sensitivity assessment. Disclosures: Off Label Use: Rapamycin. FDA approved for solid organ transplant. Investigational use for treatment of leukemia. Weiss:Celgene: Consultancy.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2012
    detail.hit.zdb_id: 1468538-3
    detail.hit.zdb_id: 80069-7
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