Algorithmic aspects of bio-inspired string operations

We present building blocks for algorithms for the efficient reduction of square factor, i.e. direct repetitions in strings. So the basic problem is this: given a string, compute all strings that can be obtained by reducing factors of the form zz to z. Two types of algorithms are treated: an offline algorithm is one that can compute a data structure on the given string in advance before the actual search for the square begins; in contrast, online algorithms receive all input only at the time when a request is made. For offline algorithms we treat the following problem: Let u and w be two strings such that w is obtained from u by reducing a square factor zz to only z. If we further are given the suffix table of u, how can we derive the suffix table for w without computing it from scratch? As the suffix table plays a key role in online algorithms for the detection of squares in a string, this derivation can make the iterated reduction of squares more efficient. On the other hand, we also show how a suffix array, used for the offline detection of squares, can be adapted to the new string resulting from the deletion of a square. Because the deletion is a very local change, this adaption is more eficient than the computation of the new suffix array from scratch.

Phase I/IIa study of cilengitide and temozolomide with concomitant radiotherapy followed by cilengitide and temozolomide maintenance therapy in patients with newly diagnosed glioblastoma.

Purpose: Invasion and migration are key processes of glioblastoma and are tightly linked to tumor recurrence. Integrin inhibition using cilengitide has shown synergy with chemotherapy and radiotherapy in vitro and promising activity in recurrent glioblastoma. This multicenter, phase I/IIa study investigated the efficacy and safety of cilengitide in combination with standard chemoradiotherapy in newly diagnosed glioblastoma. Patients and Methods: Patients (age >= 18 to >= 70 years) were treated with cilengitide (500 mg) administered twice weekly intravenously in addition to standard radiotherapy with concomitant and adjuvant temozolomide. Treatment was continued until disease progression or for up to 35 weeks. The primary end point was progression-free survival (PFS) at 6 months. Results: Fifty-two patients ( median age, 57 years; 62% male) were included. Six- and 12-month PFS rates were 69% (95% CI, 54% to 80%) and 33% ( 95% CI, 21% to 46%). Median PFS was 8 months ( 95% CI, 6.0 to 10.7 months). Twelve- and 24-month overall survival ( OS) rates were 68% ( 95% CI, 53% to 79%) and 35% ( 95% CI, 22% to 48%). Median OS was 16.1 months ( 95% CI, 13.1 to 23.2 months). PFS and OS were longer in patients with tumors with O-6-methylguanine-DNA methyltransferase (MGMT) promoter methylation (13.4 and 23.2 months) versus those without MGMT promoter methylation (3.4 and 13.1 months). The combination of cilengitide with temozolomide and radiotherapy was well tolerated, with no additional toxicity. No pharmacokinetic interactions between temozolomide and cilengitide were identified. Conclusion: Compared with historical controls, the addition of concomitant and adjuvant cilengitide to standard chemoradiotherapy demonstrated promising activity in patients with glioblastoma with MGMT promoter methylation. J Clin Oncol 28:2712-2718. (C) 2010 by American Society of Clinical Oncology

Heterozygote advantage and the maintenance of polymorphism for multilocus traits.

Explaining how polymorphism is maintained in the face of selection remains a puzzle since selection tends to erode genetic variation. Provided an infinitely large unsubdivided population and no frequency-dependance of selective values, heterozygote advantage is the text book explanation for the maintenance of polymorphism when selection acts at a diallelic locus. Here, we investigate whether this remains true when selection acts at multiple diallelic loci. We use five different definitions of heterozygote advantage that largely cover this concept for multiple loci. Using extensive numerical simulations, we found no clear associations between the presence of any of the five definitions of heterozygote advantage and the maintenance of polymorphism at all loci. The strength of the association decreases as the number of loci increases or as recombination decreases. We conclude that heterozygote advantage cannot be a general mechanism for the maintenance of genetic polymorphism at multiple loci. These findings suggest that a correlation between the number of heterozygote loci and fitness is not warranted on theoretical ground.

Phenotypes influencing low physical activity in maintenance dialysis.

OBJECTIVE: The "Pas à Pas" initiative aimed at evaluating the weekly physical activity (PA) and its determinants in a large cohort of dialysis patients. SETTING: Physical inactivity is a risk factor for mortality in maintenance dialysis patients and is still poorly documented in this population. DESIGN: A prospective national epidemiological study was performed. SUBJECTS: A total of 1,163 patients on maintenance dialysis (hemodialysis and peritoneal dialysis) were included. INTERVENTION AND MAIN OUTCOME MEASURE: PA was recorded during seven consecutive days using a pedometer to measure daily step numbers. RESULTS: Median age was 63 years (Q1 51-Q3 75). Sixty-three percent were sedentary (<5000 steps/day) with a median of 3,688 steps/day (1,866-6,271)]. PA level was similar between hemodialysis patients and those on peritoneal dialysis (3,693 steps [1,896-6,307] vs. 3,320 [1,478-5,926], P = .33). In hemodialysis patients, PA was lower on dialysis days compared with nondialysis days (2,912 [1,439-5,232] vs. 4,054 [2,136-7,108], respectively, P < .01). PA gradually decreased with age, 57% being sedentary between 50 and 65 years and 83% of patients after 80 years. Beyond this age effect, we identified, for the first time, specific phenotypes of patients with lower PA, such as inflammation, cardiovascular disease, protein energy wasting, obesity, and diabetes. By contrast, previous kidney transplantation and a higher muscle mass were associated with higher PA. CONCLUSIONS: Dialysis patients present a very low level of PA with high sedentary. Acting on patient's modifiable phenotypes may help to increase PA to improve morbidity, mortality, and quality of life.

Local Roads Maintenance Workers’ Manual, June 2006

This manual describes best roadway maintenance practices for Iowa's local roads and streets, from the center line to shoulders, ditches, and drainage, with chapters on public relations, bridge maintenance, and snow and ice control. Each chapter contains safety tips, information(as appropriate) on managing quality control, and a list of references for further information.

Evolutionary games on complex networks : the emergence and maintenance of cooperation

Abstract The object of game theory lies in the analysis of situations where different social actors have conflicting requirements and where their individual decisions will all influence the global outcome. In this framework, several games have been invented to capture the essence of various dilemmas encountered in many common important socio-economic situations. Even though these games often succeed in helping us understand human or animal behavior in interactive settings, some experiments have shown that people tend to cooperate with each other in situations for which classical game theory strongly recommends them to do the exact opposite. Several mechanisms have been invoked to try to explain the emergence of this unexpected cooperative attitude. Among them, repeated interaction, reputation, and belonging to a recognizable group have often been mentioned. However, the work of Nowak and May (1992) showed that the simple fact of arranging the players according to a spatial structure and only allowing them to interact with their immediate neighbors is sufficient to sustain a certain amount of cooperation even when the game is played anonymously and without repetition. Nowak and May's study and much of the following work was based on regular structures such as two-dimensional grids. Axelrod et al. (2002) showed that by randomizing the choice of neighbors, i.e. by actually giving up a strictly local geographical structure, cooperation can still emerge, provided that the interaction patterns remain stable in time. This is a first step towards a social network structure. However, following pioneering work by sociologists in the sixties such as that of Milgram (1967), in the last few years it has become apparent that many social and biological interaction networks, and even some technological networks, have particular, and partly unexpected, properties that set them apart from regular or random graphs. Among other things, they usually display broad degree distributions, and show small-world topological structure. Roughly speaking, a small-world graph is a network where any individual is relatively close, in terms of social ties, to any other individual, a property also found in random graphs but not in regular lattices. However, in contrast with random graphs, small-world networks also have a certain amount of local structure, as measured, for instance, by a quantity called the clustering coefficient. In the same vein, many real conflicting situations in economy and sociology are not well described neither by a fixed geographical position of the individuals in a regular lattice, nor by a random graph. Furthermore, it is a known fact that network structure can highly influence dynamical phenomena such as the way diseases spread across a population and ideas or information get transmitted. Therefore, in the last decade, research attention has naturally shifted from random and regular graphs towards better models of social interaction structures. The primary goal of this work is to discover whether or not the underlying graph structure of real social networks could give explanations as to why one finds higher levels of cooperation in populations of human beings or animals than what is prescribed by classical game theory. To meet this objective, I start by thoroughly studying a real scientific coauthorship network and showing how it differs from biological or technological networks using divers statistical measurements. Furthermore, I extract and describe its community structure taking into account the intensity of a collaboration. Finally, I investigate the temporal evolution of the network, from its inception to its state at the time of the study in 2006, suggesting also an effective view of it as opposed to a historical one. Thereafter, I combine evolutionary game theory with several network models along with the studied coauthorship network in order to highlight which specific network properties foster cooperation and shed some light on the various mechanisms responsible for the maintenance of this same cooperation. I point out the fact that, to resist defection, cooperators take advantage, whenever possible, of the degree-heterogeneity of social networks and their underlying community structure. Finally, I show that cooperation level and stability depend not only on the game played, but also on the evolutionary dynamic rules used and the individual payoff calculations. Synopsis Le but de la théorie des jeux réside dans l'analyse de situations dans lesquelles différents acteurs sociaux, avec des objectifs souvent conflictuels, doivent individuellement prendre des décisions qui influenceront toutes le résultat global. Dans ce cadre, plusieurs jeux ont été inventés afin de saisir l'essence de divers dilemmes rencontrés dans d'importantes situations socio-économiques. Bien que ces jeux nous permettent souvent de comprendre le comportement d'êtres humains ou d'animaux en interactions, des expériences ont montré que les individus ont parfois tendance à coopérer dans des situations pour lesquelles la théorie classique des jeux prescrit de faire le contraire. Plusieurs mécanismes ont été invoqués pour tenter d'expliquer l'émergence de ce comportement coopératif inattendu. Parmi ceux-ci, la répétition des interactions, la réputation ou encore l'appartenance à des groupes reconnaissables ont souvent été mentionnés. Toutefois, les travaux de Nowak et May (1992) ont montré que le simple fait de disposer les joueurs selon une structure spatiale en leur permettant d'interagir uniquement avec leurs voisins directs est suffisant pour maintenir un certain niveau de coopération même si le jeu est joué de manière anonyme et sans répétitions. L'étude de Nowak et May, ainsi qu'un nombre substantiel de travaux qui ont suivi, étaient basés sur des structures régulières telles que des grilles à deux dimensions. Axelrod et al. (2002) ont montré qu'en randomisant le choix des voisins, i.e. en abandonnant une localisation géographique stricte, la coopération peut malgré tout émerger, pour autant que les schémas d'interactions restent stables au cours du temps. Ceci est un premier pas en direction d'une structure de réseau social. Toutefois, suite aux travaux précurseurs de sociologues des années soixante, tels que ceux de Milgram (1967), il est devenu clair ces dernières années qu'une grande partie des réseaux d'interactions sociaux et biologiques, et même quelques réseaux technologiques, possèdent des propriétés particulières, et partiellement inattendues, qui les distinguent de graphes réguliers ou aléatoires. Entre autres, ils affichent en général une distribution du degré relativement large ainsi qu'une structure de "petit-monde". Grossièrement parlant, un graphe "petit-monde" est un réseau où tout individu se trouve relativement près de tout autre individu en termes de distance sociale, une propriété également présente dans les graphes aléatoires mais absente des grilles régulières. Par contre, les réseaux "petit-monde" ont, contrairement aux graphes aléatoires, une certaine structure de localité, mesurée par exemple par une quantité appelée le "coefficient de clustering". Dans le même esprit, plusieurs situations réelles de conflit en économie et sociologie ne sont pas bien décrites ni par des positions géographiquement fixes des individus en grilles régulières, ni par des graphes aléatoires. De plus, il est bien connu que la structure même d'un réseau peut passablement influencer des phénomènes dynamiques tels que la manière qu'a une maladie de se répandre à travers une population, ou encore la façon dont des idées ou une information s'y propagent. Ainsi, durant cette dernière décennie, l'attention de la recherche s'est tout naturellement déplacée des graphes aléatoires et réguliers vers de meilleurs modèles de structure d'interactions sociales. L'objectif principal de ce travail est de découvrir si la structure sous-jacente de graphe de vrais réseaux sociaux peut fournir des explications quant aux raisons pour lesquelles on trouve, chez certains groupes d'êtres humains ou d'animaux, des niveaux de coopération supérieurs à ce qui est prescrit par la théorie classique des jeux. Dans l'optique d'atteindre ce but, je commence par étudier un véritable réseau de collaborations scientifiques et, en utilisant diverses mesures statistiques, je mets en évidence la manière dont il diffère de réseaux biologiques ou technologiques. De plus, j'extrais et je décris sa structure de communautés en tenant compte de l'intensité d'une collaboration. Finalement, j'examine l'évolution temporelle du réseau depuis son origine jusqu'à son état en 2006, date à laquelle l'étude a été effectuée, en suggérant également une vue effective du réseau par opposition à une vue historique. Par la suite, je combine la théorie évolutionnaire des jeux avec des réseaux comprenant plusieurs modèles et le réseau de collaboration susmentionné, afin de déterminer les propriétés structurelles utiles à la promotion de la coopération et les mécanismes responsables du maintien de celle-ci. Je mets en évidence le fait que, pour ne pas succomber à la défection, les coopérateurs exploitent dans la mesure du possible l'hétérogénéité des réseaux sociaux en termes de degré ainsi que la structure de communautés sous-jacente de ces mêmes réseaux. Finalement, je montre que le niveau de coopération et sa stabilité dépendent non seulement du jeu joué, mais aussi des règles de la dynamique évolutionnaire utilisées et du calcul du bénéfice d'un individu.

Study of Iowa's Current Road Use Tax Funds (RUTF) and Future Road Maintenance and Construction Needs, 2006

The 81st General Assembly of the Iowa Legislature, in Section 85 of House File 868, required the Iowa Department of Transportation (DOT) to conduct a study of current Road Use Tax Fund (RUTF)revenues, and projected roadway construction and maintenance needs.

Toolbox to Address Safety and Operations on School Grounds and Public Streets Adjacent to Elementary and Middle Schools in Iowa, August 2006

This study identified transportation safety issues at existing Iowa school sites through on-site observations, traffic data collection, and through interviews with schools, law enforcement, and traffic engineers. Frequently observed problems, such as crossing at unmarked crosswalks, unloading and loading students on the street side, inattentive student safety patrols, and illegal parking, were documented and solutions were recommended for implementation. The results of the study also conclude that regular communications between school officials, traffic engineers, law enforcement, parents, and school transportation personnel are all critical to promoting safe operations within school zones.

Study of Iowa’s Current Road Use Tax Funds (RUTF) and Future Road Maintenance and Construction Needs, 2006

The 81st General Assembly of the Iowa legislature, in Section 85 of House File 868, required the Iowa Department of Transportation (Iowa DOT) to conduct a study of current Road Use Tax Fund (RUTF) revenues, and projected roadway construction and maintenance needs. With input from Iowa’s cities, counties and other interested groups, the Iowa DOT completed this report for submittal to the legislature.

Study of Iowa’s Current Road Use Tax Funds (RUTF) and Future Road Maintenance and Construction Needs, 2006

The 81st General Assembly of the Iowa legislature, in Section 85 of House File 868, required the Iowa Department of Transportation (Iowa DOT) to conduct a study of current Road Use Tax Fund (RUTF) revenues, and projected roadway construction and maintenance needs.

Effective Shoulder Design and Maintenance, 2007

Granular shoulders are an important element of the transportation system and are constantly subjected to performance problems due to wind- and water-induced erosion, rutting, edge drop-off, and slope irregularities. Such problems can directly affect drivers’ safety and often require regular maintenance. The present research study was undertaken to investigate the factors contributing to these performance problems and to propose new ideas to design and maintain granular shoulders while keeping ownership costs low. This report includes observations made during a field reconnaissance study, findings from an effort to stabilize the granular and subgrade layer at six shoulder test sections, and the results of a laboratory box study where a shoulder section overlying a soft foundation layer was simulated. Based on the research described in this report, the following changes are proposed to the construction and maintenance methods for granular shoulders: • A minimum CBR value for the granular and subgrade layer should be selected to alleviate edge drop-off and rutting formation. • For those constructing new shoulder sections, the design charts provided in this report can be used as a rapid guide based on an allowable rut depth. The charts can also be used to predict the behavior of existing shoulders. • In the case of existing shoulder sections overlying soft foundations, the use of geogrid or fly ash stabilization proved to be an effective technique for mitigating shoulder rutting.

Salt subtraction in patients on maintenance hemodialysis. Efficacy and limitations.

In 6 hypertensive patients with terminal renal failure maintained on hemodialysis, the effects of 'salt subtraction' and of sequential ultrafiltrating were evaluated. Following each of 3 weekly hemodialysis sessions, salt subtraction was carried out by ultrafiltrating 1 liter and simultaneously infusing an equal volume of 5% dextrose. This resulted in a net sodium loss without hypovolemia. After a 2-week period of this procedure, the blood pressure prior to dialysis was lower (156/76 +/- 12/5 mm Hg) than after a comparable number of sequential ultrafiltration sessions (181/88 +/- 10/6 mm Hg; mean +/- SEM). This difference was not statistically significant. At the same time, body weight was comparable at 64.4 +/- 3 and 64.7 +/- 4 kg, respectively. Neither plasma renin activity nor plasma catecholamines responded with a clear increase to either procedure. The limited effect on blood pressure and the renin system of a marked sodium removal during salt subtraction suggests that sodium must still be present in excess in these patients. The procedure of salt subtraction appears safe and subjectively well tolerated, but it can probably not be used as the sole means of decreasing total body sodium without associating dietary measures to reduce sodium intake.

Income maintenance programs and multidimensional screening

This paper examines properties of optimal poverty assistance programs under different informational environments using an income maintenanceframework. To that end, we make both the income generating ability andthe disutility of labor of individuals unobservable, and compare theresulting benefit schedules with those of programs found in the UnitedStates since Welfare Reform (1996). We find that optimal programs closelyresemble a Negative Income Tax with a Benefit Reduction rate that dependson the distribution of population characteristics. A policy of workfare(unpaid public sector work) is inefficient when disutility of labor isunobservable, but minimum work requirements (for paid work) may be usedin that same environment. The distortions to work incentives and thepresence of minimum work requirements depend on the observability andrelative importance of the population's characteristics.

LRF-mediated Dll4 repression in erythroblasts is necessary for hematopoietic stem cell maintenance.

Hematopoietic stem cells (HSCs) are the most primitive cells in the hematopoietic system and are under tight regulation for self-renewal and differentiation. Notch signals are essential for the emergence of definitive hematopoiesis in mouse embryos and are critical regulators of lymphoid lineage fate determination. However, it remains unclear how Notch regulates the balance between HSC self-renewal and differentiation in the adult bone marrow (BM). Here we report a novel mechanism that prevents HSCs from undergoing premature lymphoid differentiation in BM. Using a series of in vivo mouse models and functional HSC assays, we show that leukemia/lymphoma related factor (LRF) is necessary for HSC maintenance by functioning as an erythroid-specific repressor of Delta-like 4 (Dll4) expression. Lrf deletion in erythroblasts promoted up-regulation of Dll4 in erythroblasts, sensitizing HSCs to T-cell instructive signals in the BM. Our study reveals novel cross-talk between HSCs and erythroblasts, and sheds a new light on the regulatory mechanisms regulating the balance between HSC self-renewal and differentiation.

Maintenance Service Level Map, October 13, 2006

Maintenance Service Level Map