Evaluation of algorithms used to order markers on genetic maps

When building genetic maps, it is necessary to choose from several marker ordering algorithms and criteria, and the choice is not always simple. In this study, we evaluate the efficiency of algorithms try (TRY), seriation (SER), rapid chain delineation (RCD), recombination counting and ordering (RECORD) and unidirectional growth (UG), as well as the criteria PARF (product of adjacent recombination fractions), SARF (sum of adjacent recombination fractions), SALOD (sum of adjacent LOD scores) and LHMC (likelihood through hidden Markov chains), used with the RIPPLE algorithm for error verification, in the construction of genetic linkage maps. A linkage map of a hypothetical diploid and monoecious plant species was simulated containing one linkage group and 21 markers with fixed distance of 3 cM between them. In all, 700 F(2) populations were randomly simulated with and 400 individuals with different combinations of dominant and co-dominant markers, as well as 10 and 20% of missing data. The simulations showed that, in the presence of co-dominant markers only, any combination of algorithm and criteria may be used, even for a reduced population size. In the case of a smaller proportion of dominant markers, any of the algorithms and criteria (except SALOD) investigated may be used. In the presence of high proportions of dominant markers and smaller samples (around 100), the probability of repulsion linkage increases between them and, in this case, use of the algorithms TRY and SER associated to RIPPLE with criterion LHMC would provide better results. Heredity (2009) 103, 494-502; doi:10.1038/hdy.2009.96; published online 29 July 2009

A Survey for Diclofop-Methyl Resistance in Italian Ryegrass from Tennessee and How To Manage Resistance in Wheat

Italian ryegrass resistance to diclofop has been documented in several countries, including the United States. The purpose of this research was to screen selected putative resistant populations of Italian ryegrass for resistance to the acetyl-CoA carboxylase (ACCase)-inhibiting herbicides diclofop and pinoxaden and the acetolactate synthase (ALS)-inhibiting herbicides imazamox, pyroxsulam, and mesosulfuron in the greenhouse and to use field experiments to develop herbicide programs for Italian ryegrass control. Resistance to diclofop was confirmed in eight populations from Tennessee. These eight populations did not show cross-resistance to pinoxaden. One additional population (R1) from Union County, North Carolina, was found to be resistant to both diclofop and pinoxaden. The level of resistance to pinoxaden of the R1 population was 15 times that of the susceptible population. No resistance was confirmed to any of the ALS-inhibiting herbicides examined in this research. Field experiments demonstrated PRE Italian ryegrass control with chlorsulfuron (71 to 94%) and flufenacet + metribuzin (84 to 96%). Italian ryegrass control with pendimethalin applied PRE or delayed preemergence (DPRE) was variable (0 to 85%). POST control of Italian ryegrass was acceptable with pinoxaden, mesosulfuron, flufenacet + metribuzin, and chlorsulfuron + flucarbazone (> 80%). Application timing and herbicide treatment had no effect on wheat yield, except for diclofop and pendimethalin treatments, in which uncontrolled Italian ryegrass reduced wheat yield.

Adaptation of an apple sooty blotch and flyspeck warning system for the Upper Midwest United States

A warning system for sooty blotch and flyspeck (SBFS) of apple, developed in the southeastern United States, uses cumulative hours of leaf wetness duration (LWD) to predict the timing of the first appearance of signs. In the Upper Midwest United States, however, this warning system has resulted in sporadic disease control failures. The purpose of the present study was to determine whether the warning system`s algorithm could be modified to provide more reliable assessment of SBFS risk. Hourly LWD, rainfall, relative humidity (RH), and temperature data were collected from orchards in Iowa, North Carolina, and Wisconsin in 2005 and 2006. Timing of the first appearance of SBFS signs was determined by weekly scouting. Preliminary analysis using scatterplots and boxplots suggested that Cumulative hours of RH >= 97% could be a useful predictor of SBFS appearance. Receiver operating characteristic curve analysis was used to compare the predictive performance of cumulative LWD and cumulative hours of RH >= 97%. Cumulative hours of RH >= 97% was a more conservative and accurate predictor than cumulative LWD for 15 site years in the Upper Midwest, but not for four site years in North Carolina. Performance of the SBFS warning system in the Upper Midwest and climatically similar regions may be improved if cumulative hours of RH >= 97% were substituted for cumulative LWD to predict the first appearance of SBFS.

Spatial heterogeneity of leaf wetness duration in apple trees and its influence on performance of a warning system for sooty blotch and flyspeck

To determine the effect of sensor placement on the performance of a disease-warning system for sooty blotch and flyspeck (SBFS), we measured leaf wetness duration (LWD) at 12 canopy positions in apple trees, then simulated operation of the disease-warning system using LWD measurements from different parts of the canopy. LWD sensors were placed in four trees within one Iowa orchard during two growing seasons, and in one tree in each of four orchards during a single growing season. The LWD measurements revealed substantial heterogeneity among sensor locations. In all data sets, the upper, eastern portion of the canopy had the longest mean daily LWD, and was the first site to form dew and the last to dry. The lower, western portion of the canopy averaged about 3 It less LWD per day than the top of the canopy, and was the last zone where dew formed and the first to dry off. On about 25% of nights when dew occurred in the top of the canopy, no dew formed in the lower, western canopy. Intracanopy variability of LWD was more pronounced when dew was the sole source of wetness than on days when rainfall occurred. Daily LWD in the upper, eastern portion of the canopy was slightly less than reference measurements made at a 0.7-m height over turfgrass located near the orchard. When LWD measurements from several canopy positions were input to the SBFS warning system, timing of occurrence of a fungicide-spray threshold varied by as much as 30 days among canopy positions. Under Iowa conditions, placement of an LWD sensor at an unobstructed site over turfgrass was a fairly accurate surrogate for the wettest part of the canopy. Therefore, such an extra-canopy LWD sensor might be substituted for a within-canopy sensor to enhance operational reliability of the SBFS warning system.

Monitoring the authenticity of Brazilian UHT milk: A chemometric approach

In this work, chemometric methods are reported as potential tools for monitoring the authenticity of Brazilian ultra-high temperature (UHT) milk processed in industrial plants located in different regions of the country. A total of 100 samples were submitted to the qualitative analysis of adulterants such as starch, chlorine, formal. hydrogen peroxide and urine. Except for starch, all the samples reported, at least, the presence of one adulterant. The use of chemometric methodologies such as the Principal Component Analysis (PCA) and Hierarchical Cluster Analysis (HCA) enabled the verification of the occurrence of certain adulterations in specific regions. The proposed multivariate approaches may allow the sanitary agency authorities to optimise materials, human and financial resources, as they associate the occurrence of adulterations to the geographical location of the industrial plants. (c) 2010 Elsevier Ltd. All rights reserved.

Exploratory Approach to the use of Techniques of Regression Analysis and Pooled Analysis in Studies of Consumer Behavior

This paper is part of a large study to assess the adequacy of the use of multivariate statistical techniques in theses and dissertations of some higher education institutions in the area of marketing with theme of consumer behavior from 1997 to 2006. The regression and conjoint analysis are focused on in this paper, two techniques with great potential of use in marketing studies. The objective of this study was to analyze whether the employement of these techniques suits the needs of the research problem presented in as well as to evaluate the level of success in meeting their premisses. Overall, the results suggest the need for more involvement of researchers in the verification of all the theoretical precepts of application of the techniques classified in the category of investigation of dependence among variables.

Host preference of the bean weevil Zabrotes subfasciatus

It is largely known that the range of an insect diet is mostly determined by oviposition behavior, mainly in species with endophytic larvae such as Zabrotes subfasciatus. However, the proximate factors determining host choice and the subsequent steps leading to the expansion or reduction of the host number and occasional host shifts are largely unknown. We analyzed various factors determining host preference of Z. subfasciatus through the evaluation of: (i) oviposition preference of a wild population of Z subfasciatus on the usual host (bean) and unusual hosts (lentil, chickpea and soy), and the performance of the offspring; (ii) artificial selection for increasing preference for hosts initially less frequently chosen; (iii) comparison of oviposition behavior between two different populations (reared for similar to 30 generations in beans or chickpeas, respectively); (iv) oviposition timing on usual and unusual hosts; and (v) identification of preference hierarchies. We found that when using unusual hosts, there is no correlation between performance and preference and that the preference hierarchy changes only slightly when the population passes through several generations on the less frequently accepted host. We also found a positive response to artificial selection for increasing oviposition on the less preferred host; however, when the host-choice experiment involved two varieties of the usual host, the response was faster than when the choice involved usual and unusual hosts. Finally, beetles reared on an unusual host (chickpea) for 26 generations showed similar good fitness on both usual and unusual hosts, indicating that the use of a new host does not necessarily result in the loss of performance on the original host. Nevertheless, this population showed lower fitness on the usual host than that of the original population, suggesting an underlying partial trade-off phenomenon which may contribute to a broadening of diet of this insect species.

The Effect of Expectancy of a Threatening Event on Time Perception in Human Adults

Two experiments were conducted to investigate the effect of a threatening stimulus in human adults in a temporal bisection task. In Experiment I. for two anchor duration conditions (400/800 vs. 800/1600 ms), the participants completed trials in which the probe duration was followed by an aversive stimulus or a nonaversive stimulus. The results showed that the duration was judged longer when the participants expected an aversive rather than a nonaversive stimulus. In Experiment 2, the effect of the temporal localization of the aversive stimulus was also tested, with the aversive stimulus being presented at the beginning or at the end of the probe duration. The results revealed a temporal overestimation in each condition compared to the trials in which no aversive stimulus was presented. Furthermore, the temporal overestimation was greater when the expectation for the forthcoming threatening stimulus was longer. This temporal overestimation is explained in terms of a speeding-up of the neural timing system in response to the increase in the arousal level produced by the expectation of a threatening stimulus.

Contextual politics of service delivery reforms: Lessons from Delhi, Mexico city and Sao Paulo comparison

Little attention has been given to the contextual politics of service delivery reforms. By focusing on cases of reform in the healthcare sector and, to a lesser extent, in the main policies in the social service sector in India, Mexico and Brazil, this article explores two dimensions of analysis which have enormous relevance in understanding the reach and effectiveness of service delivery reforms: (1) the historical timing of reforms and sectorial baselines, and (2) the degree and institutional locus of local discretion in policy. Findings show that depending on both dimensions, there is an extraordinary variation as to the degree, interests involved and meaning of changes which, in theory, correspond to these countries` commitment to the service delivery reforms, However, consideration of the contextual politics is relevant not for the sake of diversity but for the similarities that this diversity reveals, pointing to underlying analytic dimensions that receive attention in this article.

Abatacept in children with juvenile idiopathic arthritis: a randomised, double-blind, placebo-controlled withdrawal trial

Background Some children with juvenile idiopathic arthritis either do not respond, or are intolerant to, treatment with disease-modifying antirheumatic drugs, including anti-tumour necrosis factor (TNF) drugs. We aimed to assess the safety and efficacy of abatacept, a selective T-cell costimulation modulator, in children with juvenile idiopathic arthritis who had failed previous treatments. Methods We did a double-blind, randomised controlled withdrawal trial between February, 2004, and June, 2006. We enrolled 190 patients aged 6-17 years, from 45 centres, who had a history of active juvenile idiopathic arthritis; at least five active joints; and an inadequate response to, or intolerance to, at least one disease-modifying antirheumatic drug. All 190 patients were given 10 mg/kg of abatacept intravenously in the open-label period of 4 months. Of the 170 patients who completed this lead-in course, 47 did not respond to the treatment according to predefined American College of Rheumatology (ACR) paediatric criteria and were excluded. Of the patients who did respond to abatacept, arthritis, and 62 were randomly assigned to receive placebo at the same dose and timing. The primary endpoint was time to flare of arthritis. Flare was defined as worsening of 30% or more in at least three of six core variables, with at least 30% improvement in no more than one variable. We analysed all patients who were treated as per protocol. This trial is registered, number NCT00095173. Findings Flares of arthritis occurred in 33 of 62 (53%) patients who were given placebo and 12 of 60 (20%) abatacept patients during the double-blind treatment (p=0.0003). Median time to flare of arthritis was 6 months for patients given placebo (insufficient events to calculate IQR); insufficient events had occurred in the abatacept group for median time to flare to be assessed (p=0.0002). The risk of flare in patients who contined abatacept was less than a third of that for controls during that double-blind period (hazard ratio 0.31, 95% CI 0.16-0.95). During the double-blind period, the frequency of adverse events did not differ in the two treatment groups, Adverse events were recorded in 37 abatacept recipients (62%) and 34 (55%) placebo recipients (p=0.47); only two serious adverse events were reported, bouth in controls (p=0.50). Interpretation Selective modulation of T-cell costimulation with abatacept is a rational alternative treatment for children with juvenile idiopathic arthritis. Funding Bristol-Myers Squibb.

When Should Renal Replacement Therapy be Initiated for Acute Kidney Injury?

Acute kidney injury (AKI) is now well recognized as an independent risk factor for increased morbidity and mortality particularly when dialysis is needed. Although renal replacement therapy (RRT) has been used in AKI for more than five decades, there is no standard methodology to predict which AKI patients will need dialysis and who will recover renal function without requiring dialysis. The lack of consensus on what parameters should guide the decision to start dialysis has led to a wide variation in dialysis utilization. A contributing factor is the lack of studies in the modern era evaluating the relationship of timing of dialysis initiation and outcomes. Although listed as one of the top priorities in research on AKI, timing of dialysis initiation has not been included as a factor in large, randomized controlled trials in this area. In this review we will discuss the criteria that have been used to define early vs. late initiation in previous studies on dialysis initiation. In addition, we propose a patient-centered approach to define early and late initiation that could serve as framework for managing patients and for future studies in this area.

Risk Profiles and Penetrance Estimations in Multiple Endocrine Neoplasia Type 2A Caused by Germline RET Mutations Located in Exon 10

Multiple endocrine neoplasia type 2 is characterized by germline mutations in RET. For exon 10, comprehensive molecular and corresponding phenotypic data are scarce. The International RET Exon 10 Consortium, comprising 27 centers from 15 countries, analyzed patients with RET exon 10 mutations for clinical-risk profiles. Presentation, age-dependent penetrance, and stage at presentation of medullary thyroid carcinoma (MTC), pheochromocytoma, and hyperparathyroidism were studied. A total of 340 subjects from 103 families, age 4-86, were registered. There were 21 distinct single nucleotide germline mutations located in codons 609 (45 subjects), 611 (50), 618 (94), and 620 (151). MTC was present in 263 registrants, pheochromocytoma in 54, and hyperparathyroidism in 8 subjects. Of the patients with MTC, 53% were detected when asymptomatic, and among those with pheochromocytoma, 54%. Penetrance for MTC was 4% by age 10, 25% by 25, and 80% by 50. Codon-associated penetrance by age 50 ranged from 60% (codon 611) to 86% (620). More advanced stage and increasing risk of metastases correlated with mutation in codon position (609-620) near the juxtamembrane domain. Our data provide rigorous bases for timing of premorbid diagnosis and personalized treatment/prophylactic procedure decisions depending on specific RET exon 10 codons affected. Hum Mutat 32:51-58, 2011. (C) 2010 Wiley-Liss, Inc.

The surgical repair of half-nose

Absence of half-nose is an extremely rare congenital malformation, which has a devastating impact on the patient and the family. A review of indexed English-language literature found 91 cases of half-nose, including 50 patients with proboscis lateralis. Pathogenesis is not clear, and the reported cases have sporadically occurred. Many aspects must be considered when reconstructing a congenital half-nose, such as timing of surgery, type of tissue to be used and the need to reconstruct nasal airway. The aim of this article is to present personal experience in seven cases of half-nose reconstruction, in order to review the literature regarding to this rare entity, highlighting aspects of incidence, pathogenesis and surgical treatment. Nasal reconstruction was performed at ages of 5-7 years to minimise psychological trauma. Forehead skin demonstrated to be an excellent donor site to re-surface the nose. For the inner lining, contralateral cutaneous nasal flap was our preference. Concerning the nasal framework reconstruction, alar contour was restored using a cartilage graft from the lower portion of ear tragus and concha. (C) 2008 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.

Challenges in Using Stem Cells for Cardiac Repair

Of the many diseases discussed in the context of stem cell therapy, those concerning the heart account for almost one-third of the publications in the field. However, the long-term clinical outcomes have been disappointing, in part because of preclinical studies failing to optimize the timing, number, type, and method of cell delivery and to account for shape changes that the heart undergoes during failure. In situations in which cardiomyocytes have been used in cell therapy, their alignment and integration with host tissue have not been realized. Here we review the present status of direct delivery of stem cells or their derivative cardiomyocytes to the heart and the particular challenges each cell type brings, and consider where we should go from here.

Effect of the Novel Thienopyridine Prasugrel Compared With Clopidogrel on Spontaneous and Procedural Myocardial Infarction in the Trial to Assess Improvement in Therapeutic Outcomes by Optimizing Platelet Inhibition With Prasugrel-Thrombolysis in Myocardial Infarction 38 An Application of the Classification System From the Universal Definition of Myocardial Infarction

Background-Prasugrel is a novel thienopyridine that reduces new or recurrent myocardial infarctions (MIs) compared with clopidogrel in patients with acute coronary syndrome undergoing percutaneous coronary intervention. This effect must be balanced against an increased bleeding risk. We aimed to characterize the effect of prasugrel with respect to the type, size, and timing of MI using the universal classification of MI. Methods and Results-We studied 13 608 patients with acute coronary syndrome undergoing percutaneous coronary intervention randomized to prasugrel or clopidogrel and treated for 6 to 15 months in the Trial to Assess Improvement in Therapeutic Outcomes by Optimizing Platelet Inhibition With Prasugrel-Thrombolysis in Myocardial Infarction (TRITON-TIMI 38). Each MI underwent supplemental classification as spontaneous, secondary, or sudden cardiac death (types 1, 2, and 3) or procedure related (Types 4 and 5) and examined events occurring early and after 30 days. Prasugrel significantly reduced the overall risk of MI (7.4% versus 9.7%; hazard ratio [HR], 0.76; 95% confidence interval [CI], 0.67 to 0.85; P < 0.0001). This benefit was present for procedure-related MIs (4.9% versus 6.4%; HR, 0.76; 95% CI, 0.66 to 0.88; P = 0.0002) and nonprocedural (type 1, 2, or 3) MIs (2.8% versus 3.7%; HR, 0.72; 95% CI, 0.59 to 0.88; P = 0.0013) and consistently across MI size, including MIs with a biomarker peak >= 5 times the reference limit (HR. 0.74; 95% CI, 0.64 to 0.86; P = 0.0001). In landmark analyses starting at 30 days, patients treated with prasugrel had a lower risk of any MI (2.9% versus 3.7%; HR, 0.77; P = 0.014), including nonprocedural MI (2.3% versus 3.1%; HR, 0.74; 95% CI, 0.60 to 0.92; P = 0.0069). Conclusion-Treatment with prasugrel compared with clopidogrel for up to 15 months in patients with acute coronary syndrome undergoing percutaneous coronary intervention significantly reduces the risk of MIs that are procedure related and spontaneous and those that are small and large, including new MIs occurring during maintenance therapy. (Circulation. 2009; 119: 2758-2764.)