Approximate Deadline-Scheduling with Precedence Constraints

We consider the classic problem of scheduling a set of n jobs non-preemptively on a single machine. Each job j has non-negative processing time, weight, and deadline, and a feasible schedule needs to be consistent with chain-like precedence constraints. The goal is to compute a feasible schedule that minimizes the sum of penalties of late jobs. Lenstra and Rinnoy Kan [Annals of Disc. Math., 1977] in their seminal work introduced this problem and showed that it is strongly NP-hard, even when all processing times and weights are 1. We study the approximability of the problem and our main result is an O(log k)-approximation algorithm for instances with k distinct job deadlines

Singularly Perturbed Monotone Systems and an Application to Double Phosphorylation Cycles

The theory of monotone dynamical systems has been found very useful in the modeling of some gene, protein, and signaling networks. In monotone systems, every net feedback loop is positive. On the other hand, negative feedback loops are important features of many systems, since they are required for adaptation and precision. This paper shows that, provided that these negative loops act at a comparatively fast time scale, the main dynamical property of (strongly) monotone systems, convergence to steady states, is still valid. An application is worked out to a double-phosphorylation ``futile cycle'' motif which plays a central role in eukaryotic cell signaling.Comment: 21 pages, 3 figures, corrected typos, references remove

Testing non-uniform k-wise independent distributions over product spaces (extended abstract)

A distribution D over Σ1× ⋯ ×Σ n is called (non-uniform) k-wise independent if for any set of k indices {i 1, ..., i k } and for any z1zki1ik, PrXD[Xi1Xik=z1zk]=PrXD[Xi1=z1]PrXD[Xik=zk]. We study the problem of testing (non-uniform) k-wise independent distributions over product spaces. For the uniform case we show an upper bound on the distance between a distribution D from the set of k-wise independent distributions in terms of the sum of Fourier coefficients of D at vectors of weight at most k. Such a bound was previously known only for the binary field. For the non-uniform case, we give a new characterization of distributions being k-wise independent and further show that such a characterization is robust. These greatly generalize the results of Alon et al. [1] on uniform k-wise independence over the binary field to non-uniform k-wise independence over product spaces. Our results yield natural testing algorithms for k-wise independence with time and sample complexity sublinear in terms of the support size when k is a constant. The main technical tools employed include discrete Fourier transforms and the theory of linear systems of congruences.National Science Foundation (U.S.) (NSF grant 0514771)National Science Foundation (U.S.) (grant 0728645)National Science Foundation (U.S.) (Grant 0732334)Marie Curie International Reintegration Grants (Grant PIRG03-GA-2008-231077)Israel Science Foundation (Grant 1147/09)Israel Science Foundation (Grant 1675/09)Massachusetts Institute of Technology (Akamai Presidential Fellowship

An operational overview of the EXport processes in the ocean from RemoTe sensing (EXPORTS) northeast pacific field deployment

The goal of the EXport Processes in the Ocean from RemoTe Sensing (EXPORTS) field campaign is to develop a predictive understanding of the export, fate, and carbon cycle impacts of global ocean net primary production. To accomplish this goal, observations of export flux pathways, plankton community composition, food web processes, and optical, physical, and biogeochemical (BGC) properties are needed over a range of ecosystem states. Here we introduce the first EXPORTS field deployment to Ocean Station Papa in the Northeast Pacific Ocean during summer of 2018, providing context for other papers in this special collection. The experiment was conducted with two ships: a Process Ship, focused on ecological rates, BGC fluxes, temporal changes in food web, and BGC and optical properties, that followed an instrumented Lagrangian float; and a Survey Ship that sampled BGC and optical properties in spatial patterns around the Process Ship. An array of autonomous underwater assets provided measurements over a range of spatial and temporal scales, and partnering programs and remote sensing observations provided additional observational context. The oceanographic setting was typical of late-summer conditions at Ocean Station Papa: a shallow mixed layer, strong vertical and weak horizontal gradients in hydrographic properties, sluggish sub-inertial currents, elevated macronutrient concentrations and low phytoplankton abundances. Although nutrient concentrations were consistent with previous observations, mixed layer chlorophyll was lower than typically observed, resulting in a deeper euphotic zone. Analyses of surface layer temperature and salinity found three distinct surface water types, allowing for diagnosis of whether observed changes were spatial or temporal. The 2018 EXPORTS field deployment is among the most comprehensive biological pump studies ever conducted. A second deployment to the North Atlantic Ocean occurred in spring 2021, which will be followed by focused work on data synthesis and modeling using the entire EXPORTS data set

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

BIKMAS: A Knowledge Engineering System for Bioinformatics

ABSTRACT We present the functional and architectural specification of BIKMAS, a Bioinformatics Knowledge Management System. BIKMAS contains an interactive user interface, a database in which several sources of knowledge are registered and a nucleus of knowledge management implemented with an algorithm that filters scientific information and assists the user in the task of using knowledge. BIKMAS is an active information system capable of retrieving, processing and filtering scientific information, checking for consistency and structuring the relevant information for its efficient distribution and convenient use. Two of the most important aspects of BIKMAS are that the system is based on an object-oriented database and it has been developed in JAVA tightly integrated in Internet

Influence of suction matrica the flow and conditions slope stability Dam Fishing

Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgicoA importÃncia do comportamento de solos nÃo saturados tem sido reconhecida no Ãmbito da mecÃnica dos solos, de forma que, nas Ãltimas dÃcadas a geotecnia tem evoluÃdo muito no sentido de compreender-se o comportamento dos solos com o objetivo de melhoria e aperfeiÃoamento dos projetos de engenharia. Uma das particularidades dos solos nÃo saturados consiste no acrÃscimo de tensÃes internas devido ao fenÃmeno da sucÃÃo. Este acrÃscimo de tensÃes tem influÃncia comprovada em muitas caracterÃsticas do solo como na sua permeabilidade, compressibilidade, resistÃncia ao cisalhamento, etc., porÃm muitos estudos realizados atualmente utilizam os conceitos da mecÃnica dos solos tradicional, nÃo levando em consideraÃÃo o comportamento dos solos nÃo saturados, dentre eles estÃo as anÃlises de estabilidade em barragens de terra. Este trabalho tem como principal meta avaliar a influÃncia da nÃo saturaÃÃo dos solos em anÃlises de estabilidade de taludes em barragens de terra durante o enchimento. Para este fim, foi realizado um estudo de fluxo e estabilidade na Barragem Pesqueiro-CE. Para a determinaÃÃo dos parÃmetros geotÃcnicos do maciÃo, foram obtidas amostras deformadas e indeformadas para a realizaÃÃo de ensaios de caracterizaÃÃo, compactaÃÃo, permeabilidade e cisalhamento direto. TambÃm foram realizados ensaios para a determinaÃÃo da curva caracterÃstica do solo por meio do mÃtodo do papel-filtro. A partir dos resultados dos ensaios geotÃcnicos, foram feitos simulaÃÃes transientes para um perÃodo de 60 (sessenta meses) de operaÃÃo da barragem Pesqueiro. Pelas simulaÃÃes de fluxo, foi possÃvel conhecer as condiÃÃes de fluxo durante o perÃodo analisado. Com base nos resultados do estudo de percolaÃÃo transiente, foram realizadas anÃlises de estabilidade no talude de jusante para o perÃodo de enchimento do reservatÃrio. As simulaÃÃes de estabilidade foram feitas por duas metodologias: levando em consideraÃÃo a sucÃÃo presente no maciÃo e outra baseada na metodologia tradicional. Nos resultados obtidos foi constatada a influÃncia na estabilidade de talude ao considerar a sucÃÃo, visualizando uma reduÃÃo no fator de seguranÃa conforme ocorre o avanÃo da frente de saturaÃÃo. TambÃm foi constatado que nos resultados em que foi considerada a sucÃÃo nas anÃlises de estabilidade, os valores dos fatores de seguranÃa foram mais elevados que os apresentados pela metodologia tradicional, constatando o conservadorismo da metodologia tradicional.The importance of the unsaturated soil behavior has been recognized within the soil mechanics, so that in recent decades the geotechnical has much evolved in order to understand the behavior of soils with the objective of improving and improvement of engineering projects. One of the soil characteristics not saturated is the increase of internal stresses due to the suction phenomenon. This one voltage increase has proven influence on many characteristics of the soil as in its permeability, compressibility, shear strength, etc., but many studies currently performed using the concepts of the mechanics of traditional soil, not taking into account the behavior of unsaturated soils, among them are Stability analysis on earth dams. This work has as main goal to evaluate the influence of non-soil saturation on slope stability analysis in dam ground during filling. To this end, it conducted a flow analysis and stability in Fishing dam-CE. To determine the geotechnical parameters of the massif, were Soil samples taken for performing characterization tests, compression, permeability and direct shear. Also tests were performed for determining soil characteristic curve by the method of the filter paper. Starting from results of geotechnical, transient simulations were made for a period of 60 (sixty months) of operation Fishing dam. For flow simulations, it was possible know the flow conditions over the analysis period. Based on the results of the transient percolation study were performed stability analysis in the downstream slope period for filling the reservoir. The stability simulations were made by two methodologies: taking into account the suction present in massive and one based on traditional methodology. The results obtained was found to influence the stability of slope to consider suction, seeing a reduction in safety factor as It is the advance of the saturation front. It was also found that the results it was suction considered in stability analysis, the values of the factors of safety were higher than that provided by traditional methodology, noting the conservatism of traditional methodology