A new heuristic method for solving spatially constrained forest planning problems based on mitigation of infeasibilities radiating outward from a forced choice

[Abstract]

Method for evaluation of root hairs of common bean genotypes

The objective of this work was to test a simple method for root hair evaluation of 21 common bean (Phaseolus vulgaris) genotypes, most of them used in breeding programs in Brazil. Hairs of basal and primary roots of 5-day old seedlings, produced on germination paper with no phosphorus addition, were visually evaluated by a rating scale after staining with 0.05% trypan blue. The method reveals variability among the genotypes, and the standard error of the mean is relatively low.

Low immunoglobulin levels in patients with cystic fibrosis: reduced inflammation or sign of common variable immunodeficiency syndrome?

Introduction: In children with cystic fibrosis (CF), low immunoglobulin (IgG) levels have been reported to be associated with significantly less severe lung disease. However, decreased IgG can be a sign for common variable immunodeficiency (CVID) and affect clinical outcome. The aim of this study was to analyze clinical and serological data of patients having low IgG levels in routine blood tests at annual assessment, particularly their antibody response to polysaccharide antigens. Method: Retrospective chart review of demographic data of CF patients followed at the pediatric CF clinic throughout 2009. Clinical parameters (genotype, pancreas sufficiency, FEV1), presence of Pseudomonas aeruginosa (PA) and number of exacerbations per year were correlated with immunoglobulin and vaccination antibodies levels (antibodies to pneumococcal serotypes 14, 19, 23, 1, 5 and 7F measured by enzyme-linked immune-sorbent assay). Results: 4 out of 60 patients (6.7%) had lower IgG-levels for age. Ages ranged from 1 year 8 months to 11 years, 2 boys, 2 girls. Three patients were delF508 homozygotes, one heterozygote composite delF508/G542X. All were pancreatic insufficient. FEV1 ranged from 74 to 108%. One patient never had colonization by PA, 2 had intermittent PA colonization and one was chronically infected. After conjugated vaccination all patients had protective antibodies against serotypes 14, 19, 23F. For serotypes not included in the vaccine, only one patient had protective titers for 1 out of 3 serotypes. None of the patients had received unconjugated pneumococcal vaccine. There was no significant clinical difference in FEV1, PA colonization or number of exacerbations according to IgG and vaccination antibody levels. Conclusion: Cystic Fibrosis patients with low immunoglobulin levels have normal antibody response to protein antigens. However, despite recurrent infections, there seems to be delayed or deficient antibody response to polysaccharide antigens. Prospective studies are needed to evaluate the development of polysaccharide antibody responses in CF-patients to monitor for CVID. With early detection of CF by newborn screening program, long term follow up could be started early in childhood.

Comparisons of Estimates of Annual Exceedance-Probability Discharges for Small Drainage Basins in Iowa, Based on Data through Water Year 2013, TR-678, 2015

Traditionally, the Iowa Department of Transportation has used the Iowa Runoff Chart and single-variable regional-regression equations (RREs) from a U.S. Geological Survey report (published in 1987) as the primary methods to estimate annual exceedance-probability discharge (AEPD) for small (20 square miles or less) drainage basins in Iowa. With the publication of new multi- and single-variable RREs by the U.S. Geological Survey (published in 2013), the Iowa Department of Transportation needs to determine which methods of AEPD estimation provide the best accuracy and the least bias for small drainage basins in Iowa. Twenty five streamgages with drainage areas less than 2 square miles (mi2) and 55 streamgages with drainage areas between 2 and 20 mi2 were selected for the comparisons that used two evaluation metrics. Estimates of AEPDs calculated for the streamgages using the expected moments algorithm/multiple Grubbs-Beck test analysis method were compared to estimates of AEPDs calculated from the 2013 multivariable RREs; the 2013 single-variable RREs; the 1987 single-variable RREs; the TR-55 rainfall-runoff model; and the Iowa Runoff Chart. For the 25 streamgages with drainage areas less than 2 mi2, results of the comparisons seem to indicate the best overall accuracy and the least bias may be achieved by using the TR-55 method for flood regions 1 and 3 (published in 2013) and by using the 1987 single-variable RREs for flood region 2 (published in 2013). For drainage basins with areas between 2 and 20 mi2, results of the comparisons seem to indicate the best overall accuracy and the least bias may be achieved by using the 1987 single-variable RREs for the Southern Iowa Drift Plain landform region and for flood region 3 (published in 2013), by using the 2013 multivariable RREs for the Iowan Surface landform region, and by using the 2013 or 1987 single-variable RREs for flood region 2 (published in 2013). For all other landform or flood regions in Iowa, use of the 2013 single-variable RREs may provide the best overall accuracy and the least bias. An examination was conducted to understand why the 1987 single-variable RREs seem to provide better accuracy and less bias than either of the 2013 multi- or single-variable RREs. A comparison of 1-percent annual exceedance-probability regression lines for hydrologic regions 1–4 from the 1987 single-variable RREs and for flood regions 1–3 from the 2013 single-variable RREs indicates that the 1987 single-variable regional-regression lines generally have steeper slopes and lower discharges when compared to 2013 single-variable regional-regression lines for corresponding areas of Iowa. The combination of the definition of hydrologic regions, the lower discharges, and the steeper slopes of regression lines associated with the 1987 single-variable RREs seem to provide better accuracy and less bias when compared to the 2013 multi- or single-variable RREs; better accuracy and less bias was determined particularly for drainage areas less than 2 mi2, and also for some drainage areas between 2 and 20 mi2. The 2013 multi- and single-variable RREs are considered to provide better accuracy and less bias for larger drainage areas. Results of this study indicate that additional research is needed to address the curvilinear relation between drainage area and AEPDs for areas of Iowa.

Alternative genotyping method for the single nucleotide polymorphism A2959G (AF159246) of the bovine CAST gene

The objective of this work was to genotype the single nucleotide polymorphism (SNP) A2959G (AF159246) of bovine CAST gene by PCR-RFLP technique, and to report its use for the first time. For this, 147 Bos indicus and Bos taurus x Bos indicus animals were genotyped. The accuracy of the method was confirmed through the direct sequencing of PCR products of nine individuals. The lowest frequency of the meat tenderness favorable allele (A) in Bos indicus was confirmed. The use of PCR-RFLP for the genotyping of the bovine CAST gene SNP was shown to be robust and inexpensive, which will greatly facilitate its analysis by laboratories with basic structure.

A treatment planning method for sequentially combining radiopharmaceutical therapy and external radiation therapy.

PURPOSE: Effective cancer treatment generally requires combination therapy. The combination of external beam therapy (XRT) with radiopharmaceutical therapy (RPT) requires accurate three-dimensional dose calculations to avoid toxicity and evaluate efficacy. We have developed and tested a treatment planning method, using the patient-specific three-dimensional dosimetry package 3D-RD, for sequentially combined RPT/XRT therapy designed to limit toxicity to organs at risk. METHODS AND MATERIALS: The biologic effective dose (BED) was used to translate voxelized RPT absorbed dose (D(RPT)) values into a normalized total dose (or equivalent 2-Gy-fraction XRT absorbed dose), NTD(RPT) map. The BED was calculated numerically using an algorithmic approach, which enabled a more accurate calculation of BED and NTD(RPT). A treatment plan from the combined Samarium-153 and external beam was designed that would deliver a tumoricidal dose while delivering no more than 50 Gy of NTD(sum) to the spinal cord of a patient with a paraspinal tumor. RESULTS: The average voxel NTD(RPT) to tumor from RPT was 22.6 Gy (range, 1-85 Gy); the maximum spinal cord voxel NTD(RPT) from RPT was 6.8 Gy. The combined therapy NTD(sum) to tumor was 71.5 Gy (range, 40-135 Gy) for a maximum voxel spinal cord NTD(sum) equal to the maximum tolerated dose of 50 Gy. CONCLUSIONS: A method that enables real-time treatment planning of combined RPT-XRT has been developed. By implementing a more generalized conversion between the dose values from the two modalities and an activity-based treatment of partial volume effects, the reliability of combination therapy treatment planning has been expanded.

The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.

The M-Coffee server is a web server that makes it possible to compute multiple sequence alignments (MSAs) by running several MSA methods and combining their output into one single model. This allows the user to simultaneously run all his methods of choice without having to arbitrarily choose one of them. The MSA is delivered along with a local estimation of its consistency with the individual MSAs it was derived from. The computation of the consensus multiple alignment is carried out using a special mode of the T-Coffee package [Notredame, Higgins and Heringa (T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 2000; 302: 205-217); Wallace, O'Sullivan, Higgins and Notredame (M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 2006; 34: 1692-1699)] Given a set of sequences (DNA or proteins) in FASTA format, M-Coffee delivers a multiple alignment in the most common formats. M-Coffee is a freeware open source package distributed under a GPL license and it is available either as a standalone package or as a web service from www.tcoffee.org.

The diagnosis of chronic inflammatory demyelinating polyneuropathy: a Delphi-method approach.

The diagnosis of chronic inflammatory demyelinating polyneuropathy (CIDP) is based on a set of clinical and neurophysiological parameters. However, in clinical practice, CIDP remains difficult to diagnose in atypical cases. In the present study, 32 experts from 22 centers (the French CIDP study group) were asked individually to score four typical, and seven atypical, CIDP observations (TOs and AOs, respectively) reported by other physicians, according to the Delphi method. The diagnoses of CIDP were confirmed by the group in 96.9 % of the TO and 60.1 % of the AO (p < 0.0001). There was a positive correlation between the consensus of CIDP diagnosis and the demyelinating features (r = 0.82, p < 0.004). The European CIDP classification was used in 28.3 % of the TOs and 18.2 % of the AOs (p < 0.002). The French CIDP study group diagnostic strategy was used in 90 % of the TOs and 61 % of the AOs (p < 0.0001). In 3 % of the TOs and 21.6 % of the AOs, the experts had difficulty determining a final diagnosis due to a lack of information. This study shows that a set of criteria and a diagnostic strategy are not sufficient to reach a consensus for the diagnosis of atypical CIDP in clinical practice.

A simple halide-to-anion exchange method for heteroaromatic salts and ionic liquids

A broad and simple method permitted halide ions in quaternary heteroaromatic and ammonium salts to be exchanged for a variety of anions using an anion exchange resin (A− form) in non-aqueous media. The anion loading of the AER (OH− form) was examined using two different anion sources, acids or ammonium salts, and changing the polarity of the solvents. The AER (A− form) method in organic solvents was then applied to several quaternary heteroaromatic salts and ILs, and the anion exchange proceeded in excellent to quantitative yields, concomitantly removing halide impurities. Relying on the hydrophobicity of the targeted ion pair for the counteranion swap, organic solvents with variable polarity were used, such as CH3OH, CH3CN and the dipolar nonhydroxylic solvent mixture CH3CN:CH2Cl2 (3:7) and the anion exchange was equally successful with both lipophilic cations and anions.

TraumaHawk: Improving Treatment for Crash Victims Using Photos and a Smartphone App

Photographic documentation of crashed vehicles at the scene can be used to improve triage of crash victims. A U.S. expert panel developed field triage rules to determine the likelihood of occupants sustaining serious injuries based on vehicle damage that would require transport to a trauma center (Sasser et al., 2011). The use of photographs for assessing vehicle damage and occupant compartment intrusion as it correlates to increased injury severity has been validated (Davidson et al., 2014). Providing trauma staff with crash scene photos remotely could assist them in predicting injuries. This would allow trauma care providers to assess the appropriate transport, as well as develop mental models of treatment options prior to patient arrival at the emergency department (ED). Crash-scene medical response has improved tremendously in the past 20-30 years. This is in part due to the increasing number of paramedics who now have advanced life support (ALS) training that allows independence in the field. However, while this advanced training provides a more streamlined field treatment protocol, it also means that paramedics focused on treating crash victims may not have time to communicate with trauma centers regarding crash injury mechanisms. As a result, trauma centers may not learn about severe trauma patients until just a few minutes before they arrive. The information transmitted by the TraumaHawk app allows interpretation of injury mechanisms from crash scene photos at the trauma center, providing clues about the type and severity of injury. With strategic crash scene photo documentation, trained trauma professionals can assess the severity and patterns of injury based on exterior crush and occupant intrusion. Intrusion increases the force experienced by vehicle occupants, which translates into a higher level of injury severity (Tencer et al., 2005; Assal et al., 2002; Mandell et al., 2010). First responders have the unique opportunity to assess the damaged vehicle at the crash scene, but often the mechanism of injury is limited or not even relayed to ED trauma staff. To integrate photographic and scene information, an app called TraumaHawk was created to capture images of crash vehicles and send them electronically to the trauma center. If efficiently implemented, it provides the potential advantage of increasing lead-time for preparation at the trauma center through the crash scene photos. Ideally, the result is better treatment outcomes for crash victims. The objective of this analysis was to examine if the extra lead-time granted by the TraumaHawk app could improve trauma team activation time over the current conventional communication method.

Analysis of Markers for Recent Alcohol Consumption by Capillary Zone Electrophoresis and an Immunochemical Method

Le but de ce travail doctoral était le développement de méthodes analytiques pour la détermination dethyl glucuronide et dethyl sulfate. Ces deux substances sont des métabolites directs de lethanol qui peuvent être détectées pendant des heures jusqu'à des jours dans des fluides corporels, après que léthanol ait été complètement éliminé du corps humain. Ce sont donc des marqueurs de consommation récente d'alcool.La majorité des expériences ont été effectuées en utilisant l'électrophorèse capillaire. Il était envisagé de fournir des méthodes utilisables dans des laboratoires de routine. Des méthodes électrophorétiques ont été développées et optimisées pour la détermination dethyl sulfate dans le sérum et l'urine ainsi que pour lethyl glucuronide dans le sérum. Lethyl glucuronide urinaire a pu être déterminé par un immunoassay commerciale qui a en plus été adapté avec succès pour des échantillons de sérum. Avec toutes ces méthodes d'analyse il était possible d'observer les deux marqueurs de consommation d'alcool récente, même une consommation aussi basse qu'un verre de boissons alcooliques.Finalement, une étude englobant plus de 100 échantillons aété effectuée avec l'ambition de déterminer les valeurs de référence pour lethyl glucuronide dans le sérum et l'urine. De plus, la nécessité de normaliser les échantillons d'urine par rapport à la dilution a été investiguée. Grâce à cette étude des valeurs de cut-off et une base statistique pour l'interprétation probabiliste ont pu être proposées.

A new method to simulate the hydrological state of soil under natural conditions

Micro, macro and mesofauna in the soil often respond to fluctuating environmental conditions, resulting in changes of abundance and community structure. Effects of changing soil parameters are normally determined with samples taken in the field and brought to the laboratory, i.e. where natural environmental conditions may not apply. We devised a method (STAFD - soil tubes for artificial flood and drought), which simulates the hydrological state of soil in situ using implanted cores. Control tubes were compared with treatment tubes in which floods of 15, 30, 60 and 90 days, and droughts of 60, 90 and 120 days were simulated in the field. Flooding and drought were found to reduce number of individuals in all soil faunal groups, but the response to drought was slower and not in proportion to the expected decrease of the water content. The results of the simulated floods in particular show the value of the STAFD method for the investigation of such extreme events in natural habitats.

Suprachoroidal electrotransfer: a nonviral gene delivery method to transfect the choroid and the retina without detaching the retina.

Photoreceptors and retinal pigment epithelial cells (RPE) targeting remains challenging in ocular gene therapy. Viral gene transfer, the only method having reached clinical evaluation, still raises safety concerns when administered via subretinal injections. We have developed a novel transfection method in the adult rat, called suprachoroidal electrotransfer (ET), combining the administration of nonviral plasmid DNA into the suprachoroidal space with the application of an electrical field. Optimization of injection, electrical parameters and external electrodes geometry using a reporter plasmid, resulted in a large area of transfected tissues. Not only choroidal cells but also RPE, and potentially photoreceptors, were efficiently transduced for at least a month when using a cytomegalovirus (CMV) promoter. No ocular complications were recorded by angiographic, electroretinographic, and histological analyses, demonstrating that under selected conditions the procedure is devoid of side effects on the retina or the vasculature integrity. Moreover, a significant inhibition of laser induced-choroidal neovascularization (CNV) was achieved 15 days after transfection of a soluble vascular endothelial growth factor receptor-1 (sFlt-1)-encoding plasmid. This is the first nonviral gene transfer technique that is efficient for RPE targeting without inducing retinal detachment. This novel minimally invasive nonviral gene therapy method may open new prospects for human retinal therapies.

Iowa Fen Rapid Assessment Method for Wetlands v. 1 Quantitative Rating, 2016

Rapid assessment methods are valuable tools for collecting information about the quality and status of natural systems. However, they are not a substitute for detailed surveys of those systems. Users of this method should consider that the method may under-score or over-score the site that’s assessed, especially when the site is not a typical fen (i.e. a sedge meadow could score lower than fens, but in-fact be a relatively high quality sedge meadow). This assessment can be used throughout most of the spring, summer and fall period, however the ideal “index period” would be from late May through early October when native plant communities, as well as invasive species, are most apparent.