Gene filtering with optimal threshold selection

Gene filtering is a useful preprocessing technique often applied to microarray datasets. However, it is no common practice because clear guidelines are lacking and it bears the risk of excluding some potentially relevant genes. In this work, we propose to model microarray data as a mixture of two Gaussian distributions that will allow us to obtain an optimal filter threshold in terms of the gene expression level.

Near-optimal mean value estimates for multidimensional Weyl sums

We obtain sharp estimates for multidimensional generalisations of Vinogradov’s mean value theorem for arbitrary translation-dilation invariant systems, achieving constraints on the number of variables approaching those conjectured to be the best possible. Several applications of our bounds are discussed.

An improved estimate of leaf area index based on the histogram analysis of hemispherical photographs

Leaf area index (LAI) is a key parameter that affects the surface fluxes of energy, mass, and momentum over vegetated lands, but observational measurements are scarce, especially in remote areas with complex canopy structure. In this paper we present an indirect method to calculate the LAI based on the analyses of histograms of hemispherical photographs. The optimal threshold value (OTV), the gray-level required to separate the background (sky) and the foreground (leaves), was analytically calculated using the entropy crossover method (Sahoo, P.K., Slaaf, D.W., Albert, T.A., 1997. Threshold selection using a minimal histogram entropy difference. Optical Engineering 36(7) 1976-1981). The OTV was used to calculate the LAI using the well-known gap fraction method. This methodology was tested in two different ecosystems, including Amazon forest and pasturelands in Brazil. In general, the error between observed and calculated LAI was similar to 6%. The methodology presented is suitable for the calculation of LAI since it is responsive to sky conditions, automatic, easy to implement, faster than commercially available software, and requires less data storage. (C) 2008 Elsevier B.V. All rights reserved.

Blood glucose and prognosis in children with presumed severe malaria: is there a threshold for 'hypoglycaemia'?

OBJECTIVES: Hypoglycaemia (glucose <2.2 mmol/l) is a defining feature of severe malaria, but the significance of other levels of blood glucose has not previously been studied in children with severe malaria. METHODS: A prospective study of 437 consecutive children with presumed severe malaria was conducted in Mali. We defined hypoglycaemia as <2.2 mmol/l, low glycaemia as 2.2-4.4 mmol/l and hyperglycaemia as >8.3 mmol/l. Associations between glycaemia and case fatality were analysed for 418 children using logistic regression models and a receiver operator curve (ROC). RESULTS: There was a significant difference between blood glucose levels in children who died (median 4.6 mmol/l) and survivors (median 7.6 mmol/l, P < 0.001). Case fatality declined from 61.5% of the hypoglycaemic children to 46.2% of those with low glycaemia, 13.4% of those with normal glycaemia and 7.6% of those with hyperglycaemia (P < 0.001). Logistic regression showed an adjusted odds ratio (AOR) of 0.75 (0.64-0.88) for case fatality per 1 mmol/l increase in baseline blood glucose. Compared to a normal blood glucose, hypoglycaemia and low glycaemia both significantly increased the odds of death (AOR 11.87, 2.10-67.00; and 5.21, 1.86-14.63, respectively), whereas hyperglycaemia reduced the odds of death (AOR 0.34, 0.13-0.91). The ROC [area under the curve at 0.753 (95% CI 0.684-0.820)] indicated that glycaemia had a moderate predictive value for death and identified an optimal threshold at glycaemia <6.1 mmol/l, (sensitivity 64.5% and specificity 75.1%). CONCLUSIONS: If there is a threshold of blood glucose which defines a worse prognosis, it is at a higher level than the current definition of 2.2 mmol/l.

Blood glucose and prognosis in children with presumed severe malaria: is there a threshold for 'hypoglycaemia'?

OBJECTIVES: Hypoglycaemia (glucose <2.2 mmol/l) is a defining feature of severe malaria, but the significance of other levels of blood glucose has not previously been studied in children with severe malaria. METHODS: A prospective study of 437 consecutive children with presumed severe malaria was conducted in Mali. We defined hypoglycaemia as <2.2 mmol/l, low glycaemia as 2.2-4.4 mmol/l and hyperglycaemia as >8.3 mmol/l. Associations between glycaemia and case fatality were analysed for 418 children using logistic regression models and a receiver operator curve (ROC). RESULTS: There was a significant difference between blood glucose levels in children who died (median 4.6 mmol/l) and survivors (median 7.6 mmol/l, P < 0.001). Case fatality declined from 61.5% of the hypoglycaemic children to 46.2% of those with low glycaemia, 13.4% of those with normal glycaemia and 7.6% of those with hyperglycaemia (P < 0.001). Logistic regression showed an adjusted odds ratio (AOR) of 0.75 (0.64-0.88) for case fatality per 1 mmol/l increase in baseline blood glucose. Compared to a normal blood glucose, hypoglycaemia and low glycaemia both significantly increased the odds of death (AOR 11.87, 2.10-67.00; and 5.21, 1.86-14.63, respectively), whereas hyperglycaemia reduced the odds of death (AOR 0.34, 0.13-0.91). The ROC [area under the curve at 0.753 (95% CI 0.684-0.820)] indicated that glycaemia had a moderate predictive value for death and identified an optimal threshold at glycaemia <6.1 mmol/l, (sensitivity 64.5% and specificity 75.1%). CONCLUSIONS: If there is a threshold of blood glucose which defines a worse prognosis, it is at a higher level than the current definition of 2.2 mmol/l.

Systematic analysis of the intravoxel incoherent motion threshold separating perfusion and diffusion effects: Proposal of a standardized algorithm

PURPOSE To systematically evaluate the dependence of intravoxel-incoherent-motion (IVIM) parameters on the b-value threshold separating the perfusion and diffusion compartment, and to implement and test an algorithm for the standardized computation of this threshold. METHODS Diffusion weighted images of the upper abdomen were acquired at 3 Tesla in eleven healthy male volunteers with 10 different b-values and in two healthy male volunteers with 16 different b-values. Region-of-interest IVIM analysis was applied to the abdominal organs and skeletal muscle with a systematic increase of the b-value threshold for computing pseudodiffusion D*, perfusion fraction Fp , diffusion coefficient D, and the sum of squared residuals to the bi-exponential IVIM-fit. RESULTS IVIM parameters strongly depended on the choice of the b-value threshold. The proposed algorithm successfully provided optimal b-value thresholds with the smallest residuals for all evaluated organs [s/mm2]: e.g., right liver lobe 20, spleen 20, right renal cortex 150, skeletal muscle 150. Mean D* [10(-3) mm(2) /s], Fp [%], and D [10(-3) mm(2) /s] values (±standard deviation) were: right liver lobe, 88.7 ± 42.5, 22.6 ± 7.4, 0.73 ± 0.12; right renal cortex: 11.5 ± 1.8, 18.3 ± 2.9, 1.68 ± 0.05; spleen: 41.9 ± 57.9, 8.2 ± 3.4, 0.69 ± 0.07; skeletal muscle: 21.7 ± 19.0; 7.4 ± 3.0; 1.36 ± 0.04. CONCLUSION IVIM parameters strongly depend upon the choice of the b-value threshold used for computation. The proposed algorithm may be used as a robust approach for IVIM analysis without organ-specific adaptation. Magn Reson Med, 2014. © 2014 Wiley Periodicals, Inc.

Private valuation of carbon sequestration in forest plantations

Approval of the Clean Development Mechanism, provided for in the Kyoto Protocol, enables countries with afforested land to trade in carbon emissions reduction certificates related to carbon dioxide equivalent quantities (CO(2-e)) stored within a certain forest area. Potential CO(2-e) above base line sequestration was determined for two forest sites on commercial eucalyptus plantations in northern Brazil (Bahia). Compensation values for silvicultural regimes involving rotation lengths greater than economically optimal were computed using the Faustmann formula. Mean values obtained were US$8.16 (MgCO(2-e))(-1) and US $7.19 (MgCO(2-e))(-1) for average and high site indexes, respectively. Results show that carbon supply is more cost-efficient in highly productive sites. Annuities of US$18.8 Mg C(-1) and US$35.1 Mg C(-1) and yearly payments of US$4.4 m(-3) and US$8.2 m(-3) due for each marginal cubic meter produced were computed for high and average sites, respectively. The estimated value of the tonne of carbon defines minimum values to be paid to forest owners, in order to induce a change in silvicultural management regimes. A reduction of carbon supply could be expected as a result of an increase in wood prices, although it would not respond in a regular manner. For both sites, price elasticity of supply was found to be inelastic and increased as rotation length moved further away from economically optimal: 0.24 and 0.27 for age 11 years in average- and high-productivity sites, respectively. This would be due to biomass production potential as a limiting factor; beyond a certain threshold value. an increase in price does not sustain a proportional change in carbon storage supply. The environmental service valuation model proposed might be adequate for assessing potential supply in plantation forestry, from a private landowner perspective, with an economic opportunity cost. The model is not applicable to low commercial value forest plantations. (C) 2009 Elsevier B.V. All rights reserved.

Diffusion-weighted MR imaging of the spine at 3-T: feasibility, optimization of b-value and utility to differentiate benign from pathological vertebral compression fractures

Purpose: To evaluate the feasibility, determine the optimal b-value, and assess the utility of 3-T diffusion-weighted MR imaging (DWI) of the spine in differentiating benign from pathologic vertebral compression fractures.Methods and Materials: Twenty patients with 38 vertebral compression fractures (24 benign, 14 pathologic) and 20 controls (total: 23 men, 17 women, mean age 56.2years) were included from December 2010 to May 2011 in this IRB-approved prospective study. MR imaging of the spine was performed on a 3-T unit with T1-w, fat-suppressed T2-w, gadolinium-enhanced fat-suppressed T1-w and zoomed-EPI (2D RF excitation pulse combined with reduced field-of-view single-shot echo-planar readout) diffusion-w (b-values: 0, 300, 500 and 700s/mm2) sequences. Two radiologists independently assessed zoomed-EPI image quality in random order using a 4-point scale: 1=excellent to 4=poor. They subsequently measured apparent diffusion coefficients (ADCs) in normal vertebral bodies and compression fractures, in consensus.Results: Lower b-values correlated with better image quality scores, with significant differences between b=300 (mean±SD=2.6±0.8), b=500 (3.0±0.7) and b=700 (3.6±0.6) (all p<0.001). Mean ADCs of normal vertebral bodies (n=162) were 0.23, 0.17 and 0.11×10-3mm2/s with b=300, 500 and 700s/mm2, respectively. In contrast, mean ADCs were 0.89, 0.70 and 0.59×10-3mm2/s for benign vertebral compression fractures and 0.79, 0.66 and 0.51×10-3mm2/s for pathologic fractures with b=300, 500 and 700s/mm2, respectively. No significant difference was found between ADCs of benign and pathologic fractures.Conclusion: 3-T DWI of the spine is feasible and lower b-values (300s/mm2) are recommended. However, our preliminary results show no advantage of DWI in differentiating benign from pathologic vertebral compression fractures.

Growth in a Cross-Section of Cities: Location, Increasing Returns or Random Growth?

This article analyzes empirically the main existing theories on income and population city growth: increasing returns to scale, locational fundamentals and random growth. To do this we implement a threshold nonlinearity test that extends standard linear growth regression models to a dataset on urban, climatological and macroeconomic variables on 1,175 U.S. cities. Our analysis reveals the existence of increasing returns when per-capita income levels are beyond $19; 264. Despite this, income growth is mostly explained by social and locational fundamentals. Population growth also exhibits two distinct equilibria determined by a threshold value of 116,300 inhabitants beyond which city population grows at a higher rate. Income and population growth do not go hand in hand, implying an optimal level of population beyond which income growth stagnates or deteriorates

Optimal perfusion computed tomographic thresholds for ischemic core and penumbra are not time dependent in the clinically relevant time window.

BACKGROUND AND PURPOSE: This study aims to determine whether perfusion computed tomographic (PCT) thresholds for delineating the ischemic core and penumbra are time dependent or time independent in patients presenting with symptoms of acute stroke. METHODS: Two hundred seventeen patients were evaluated in a retrospective, multicenter study. Patients were divided into those with either persistent occlusion or recanalization. All patients received admission PCT and follow-up imaging to determine the final ischemic core, which was then retrospectively matched to the PCT images to identify optimal thresholds for the different PCT parameters. These thresholds were assessed for significant variation over time since symptom onset. RESULTS: In the persistent occlusion group, optimal PCT parameters that did not significantly change with time included absolute mean transit time, relative mean transit time, relative cerebral blood flow, and relative cerebral blood volume when time was restricted to 15 hours after symptom onset. Conversely, the recanalization group showed no significant time variation for any PCT parameter at any time interval. In the persistent occlusion group, the optimal threshold to delineate the total ischemic area was the relative mean transit time at a threshold of 180%. In patients with recanalization, the optimal parameter to predict the ischemic core was relative cerebral blood volume at a threshold of 66%. CONCLUSIONS: Time does not influence the optimal PCT thresholds to delineate the ischemic core and penumbra in the first 15 hours after symptom onset for relative mean transit time and relative cerebral blood volume, the optimal parameters to delineate ischemic core and penumbra.

Climate Change and the Cost of Carbon Sequestration: The Case of Forest Management

The Kyoto protocol allows Annex I countries to deduct carbon sequestered by land use, land-use change and forestry from their national carbon emissions. Thornley and Cannell (2000) demonstrated that the objectives of maximizing timber and carbon sequestration are not complementary. Based on this finding, this paper determines the optimal selective management regime taking into account the underlying biophysical and economic processes. The results show that the net benefits of carbon storage only compensate the decrease in net benefits of timber production once the carbon price has exceeded a certain threshold value. The sequestration costs are significantly lower than previous estimates

Threshold Selection Criteria for Quantification of Lumbosacral Cerebrospinal Fluid and Root Volumes from MRI

BACKGROUND AND PURPOSE: The high variability of CSF volumes partly explains the inconsistency of anesthetic effects, but may also be due to image analysis itself. In this study, criteria for threshold selection are anatomically defined. METHODS: T2 MR images (n = 7 cases) were analyzed using 3-dimentional software. Maximal-minimal thresholds were selected in standardized blocks of 50 slices of the dural sac ending caudally at the L5-S1 intervertebral space (caudal blocks) and middle L3 (rostral blocks). Maximal CSF thresholds: threshold value was increased until at least one voxel in a CSF area appeared unlabeled and decreased until that voxel was labeled again: this final threshold was selected. Minimal root thresholds: thresholds values that selected cauda equina root area but not adjacent gray voxels in the CSF-root interface were chosen. RESULTS: Significant differences were found between caudal and rostral thresholds. No significant differences were found between expert and nonexpert observers. Average max/min thresholds were around 1.30 but max/min CSF volumes were around 1.15. Great interindividual CSF volume variability was detected (max/min volumes 1.6-2.7). CONCLUSIONS: The estimation of a close range of CSF volumes which probably contains the real CSF volume value can be standardized and calculated prior to certain intrathecal procedures

Gestion adaptative des ressources dans les réseaux maillés sans fil à multiples-radios multiples-canaux

Depuis quelques années, la recherche dans le domaine des réseaux maillés sans fil ("Wireless Mesh Network (WMN)" en anglais) suscite un grand intérêt auprès de la communauté des chercheurs en télécommunications. Ceci est dû aux nombreux avantages que la technologie WMN offre, telles que l'installation facile et peu coûteuse, la connectivité fiable et l'interopérabilité flexible avec d'autres réseaux existants (réseaux Wi-Fi, réseaux WiMax, réseaux cellulaires, réseaux de capteurs, etc.). Cependant, plusieurs problèmes restent encore à résoudre comme le passage à l'échelle, la sécurité, la qualité de service (QdS), la gestion des ressources, etc. Ces problèmes persistent pour les WMNs, d'autant plus que le nombre des utilisateurs va en se multipliant. Il faut donc penser à améliorer les protocoles existants ou à en concevoir de nouveaux. L'objectif de notre recherche est de résoudre certaines des limitations rencontrées à l'heure actuelle dans les WMNs et d'améliorer la QdS des applications multimédia temps-réel (par exemple, la voix). Le travail de recherche de cette thèse sera divisé essentiellement en trois principaux volets: le contrôle d‟admission du trafic, la différentiation du trafic et la réaffectation adaptative des canaux lors de la présence du trafic en relève ("handoff" en anglais). Dans le premier volet, nous proposons un mécanisme distribué de contrôle d'admission se basant sur le concept des cliques (une clique correspond à un sous-ensemble de liens logiques qui interfèrent les uns avec les autres) dans un réseau à multiples-sauts, multiples-radios et multiples-canaux, appelé RCAC. Nous proposons en particulier un modèle analytique qui calcule le ratio approprié d'admission du trafic et qui garantit une probabilité de perte de paquets dans le réseau n'excédant pas un seuil prédéfini. Le mécanisme RCAC permet d‟assurer la QdS requise pour les flux entrants, sans dégrader la QdS des flux existants. Il permet aussi d‟assurer la QdS en termes de longueur du délai de bout en bout pour les divers flux. Le deuxième volet traite de la différentiation de services dans le protocole IEEE 802.11s afin de permettre une meilleure QdS, notamment pour les applications avec des contraintes temporelles (par exemple, voix, visioconférence). À cet égard, nous proposons un mécanisme d'ajustement de tranches de temps ("time-slots"), selon la classe de service, ED-MDA (Enhanced Differentiated-Mesh Deterministic Access), combiné à un algorithme efficace de contrôle d'admission EAC (Efficient Admission Control), afin de permettre une utilisation élevée et efficace des ressources. Le mécanisme EAC prend en compte le trafic en relève et lui attribue une priorité supérieure par rapport au nouveau trafic pour minimiser les interruptions de communications en cours. Dans le troisième volet, nous nous intéressons à minimiser le surcoût et le délai de re-routage des utilisateurs mobiles et/ou des applications multimédia en réaffectant les canaux dans les WMNs à Multiples-Radios (MR-WMNs). En premier lieu, nous proposons un modèle d'optimisation qui maximise le débit, améliore l'équité entre utilisateurs et minimise le surcoût dû à la relève des appels. Ce modèle a été résolu par le logiciel CPLEX pour un nombre limité de noeuds. En second lieu, nous élaborons des heuristiques/méta-heuristiques centralisées pour permettre de résoudre ce modèle pour des réseaux de taille réelle. Finalement, nous proposons un algorithme pour réaffecter en temps-réel et de façon prudente les canaux aux interfaces. Cet algorithme a pour objectif de minimiser le surcoût et le délai du re-routage spécialement du trafic dynamique généré par les appels en relève. Ensuite, ce mécanisme est amélioré en prenant en compte l‟équilibrage de la charge entre cliques.

The accuracy of HADS and GHQ-12 in detecting psychiatric morbidity in breast cancer patients

Objective: Psychological problems should be identified in breast cancer patients proactively if doctors and nurses are to help them cope with the challenges imposed by their illness. Screening is one possible way to identify emotional problems proactively. Self-report questionnaires can be useful alternatives to carrying out psychiatric interviews during screening, because interviewing a large number of patients can be impractical due to limited resources. Two such measures are the Hospital Anxiety and Depression Scale (HADS) and the General Health Questionnaire-12 (GHQ-12). Method: The present study aimed to compare the performance of the GHQ-12, and the HADS Unitary Scale and its subscales to that of the Schedule for Affective Disorders and Schizophrenia (SADS) in identifying patients with affective disorders, including DSM major depression and generalized anxiety disorder. The sample consisted of 296 female breast cancer patients who underwent surgery for breast cancer a year previously. Results: A small number of patients (11%) were identified as having DSM major depression or generalized anxiety disorder based on SADS score. The findings indicate that the optimal thresholds in detecting generalized anxiety disorder and DSM major depression with the HADS anxiety and depression subscales were ≥ 8 and ≥ 7, with 93.3% and 77.3% sensitivity, respectively, and 77.9% and 87.1% specificity, respectively. They also had a 21% and 36% positive predictive value, respectively. Using the HADS Unitary Scale the optimal threshold for detecting affective disorders was ≥ 12, with 88.9% sensitivity, 80.7% specificity, and a 35% positive predictive value. In detecting affective disorders, the optimal threshold on the GHQ-12 was ≥ 2, with 77.8% sensitivity and 70.2% specificity. This scale also had a 24% positive predictive value. In detecting generalized anxiety disorder and DSM major depression, the optimal thresholds on the GHQ-12 were ≥ 2 and ≥ 4 with 73.3% and 77.3% sensitivity, respectively, and 67.5% and 82% specificity, respectively. The scale also had 12% and 29% positive predictive values, respectively. Conclusion: The HADS Unitary Scale and its subscales were effective in identifying affective disorders. They can be used as screening measures in breast cancer patients. The GHQ-12 was less accurate in detecting affective disorders than the HADS, but it can also be used as a screening instrument to detect affective disorders, generalized anxiety disorder, and DSM major depression.

Instantaneous Phase Threshold for Reflector Detection in Ultrasonic Images

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)