Serial and parallel kernelization of Multiple Hitting Set parameterized by the Dilworth number, implemented on the GPU

The NP-hard Multiple Hitting Set problem is finding a minimum-cardinality set intersecting each of the sets in a given input collection a given number of times. Generalizing a well-known data reduction algorithm due to Weihe, we show a problem kernel for Multiple Hitting Set parameterized by the Dilworth number, a graph parameter introduced by Foldes and Hammer in 1978 yet seemingly so far unexplored in the context of parameterized complexity theory. Using matrix multiplication, we speed up the algorithm to quadratic sequential time and logarithmic parallel time. We experimentally evaluate our algorithms. By implementing our algorithm on GPUs, we show the feasability of realizing kernelization algorithms on SIMD (Single Instruction, Multiple Date) architectures.Comment: Added experiments on one more data se

Survival Estimates of Western Gray Whales \u3ci\u3eEschrichtius robustus\u3c/i\u3e Incorporating Individual Heterogeneity and Temporary Emigration

Gray whales Eschrichtius robustus exist as a 2 geographically and genetically distinct populations in the eastern and western North Pacific. Subjected to intensive commercial whaling during the 19th and 20th centuries, the western population presently numbers approximately 100 individuals and is regarded as one of the most endangered baleen whale populations in the world

Evaluation of the United States National Air Quality Forecast Capability experimental real-time predictions in 2010 using Air Quality System ozone and NO₂ measurements

The National Air Quality Forecast Capability (NAQFC) project provides the US with operational and experimental real-time ozone predictions using two different versions of the three-dimensional Community Multi-scale Air Quality (CMAQ) modeling system. Routine evaluation using near-real-time AIRNow ozone measurements through 2011 showed better performance of the operational ozone predictions. In this work, quality-controlled and -assured Air Quality System (AQS) ozone and nitrogen dioxide (NO₂) observations are used to evaluate the experimental predictions in 2010. It is found that both ozone and NO₂ are overestimated over the contiguous US (CONUS), with annual biases of +5.6 and +5.1 ppbv, respectively. The annual root mean square errors (RMSEs) are 15.4 ppbv for ozone and 13.4 ppbv for NO₂. For both species the overpredictions are most pronounced in the summer. The locations of the AQS monitoring sites are also utilized to stratify comparisons by the degree of urbanization. Comparisons for six predefined US regions show the highest annual biases for ozone predictions in Southeast (+10.5 ppbv) and for NO₂ in the Lower Middle (+8.1 ppbv) and Pacific Coast (+7.1 ppbv) regions. The spatial distributions of the NO₂ biases in August show distinctively high values in the Los Angeles, Houston, and New Orleans areas. In addition to the standard statistics metrics, daily maximum eight-hour ozone categorical statistics are calculated using the current US ambient air quality standard (75 ppbv) and another lower threshold (70 ppbv). Using the 75 ppbv standard, the hit rate and proportion of correct over CONUS for the entire year are 0.64 and 0.96, respectively. Summertime biases show distinctive weekly patterns for ozone and NO₂. Diurnal comparisons show that ozone overestimation is most severe in the morning, from 07:00 to 10:00 local time. For NO₂, the morning predictions agree with the AQS observations reasonably well, but nighttime concentrations are overpredicted by around 100%

Survival Estimates of Western Gray Whales \u3ci\u3eEschrichtius robustus\u3c/i\u3e Incorporating Individual Heterogeneity and Temporary Emigration

Gray whales Eschrichtius robustus exist as a 2 geographically and genetically distinct populations in the eastern and western North Pacific. Subjected to intensive commercial whaling during the 19th and 20th centuries, the western population presently numbers approximately 100 individuals and is regarded as one of the most endangered baleen whale populations in the world

Conventional Anti-glioblastoma Chemotherapy Affects Proteoglycan Composition of Brain Extracellular Matrix in Rat Experimental Model in vivo

Temozolomide (TMZ) is a conventional chemotherapy drug for adjuvant treatment of glioblastoma multiforme (GBM), often accompanied by dexamethasone (DXM) to prevent brain oedema and alleviate clinical side effects. Here, we aimed to investigate an ability of the drugs to affect normal brain tissue in terms of proteoglycan (PG) composition/content in experimental rat model in vivo. Age- and brain zone-specific transcriptional patterns of PGs were demonstrated for 8, 60, and 120 days old rats, and syndecan-1, glypican-1, decorin, biglycan, and lumican were identified as the most expressed PGs. DXM treatment affected both PG core proteins expression (mainly syndecan-1, glypican-1, decorin, biglycan, lumican, versican, brevican, and NG2) and heparan sulphate (HS)/chondroitin sulphate (CS) content in organotypic brain slice culture ex vivo and experimental animals in vivo in a dose-dependent manner. TMZ treatment did not result in the significant changes in PG core proteins expression both in normal rat brain hippocampus and cortex in vivo (although generics did), but demonstrated significant effects onto polysaccharide HS/CS content in the brain tissue. The effects were age- and brain zone-specific and similar with the age-related PGs expression changes in rat brain. Combination of TMZ with DXM resulted in the most profound deterioration in PGs composition and content in the brain tissue both at core protein and glycosaminoglycan levels. Taken together, the obtained results demonstrate that conventional anti-glioblastoma therapy affects proteoglycan structure and composition in normal brain tissue, potentially resulting in deterioration of brain extracellular matrix and formation of the favourable tumorigenic niche for the expansion of the residual glioma cells. During the TMZ chemotherapy, dose and regimen of DXM treatment matter, and repetitive low DXM doses seem to be more sparing treatment compared with high DXM dose(s), which should be avoided where possible, especially in combination with TMZ

Влияние дексаметазона на экспрессию и содержание гликозилированных компонентов в ткани головного мозга мышей

Introduction. Glucocorticoids are actively used in the treatment of various diseases, however their long-term use leads to numerous negative side-effects, the molecular mechanisms of which remain poorly understood.Aim. Study of the short-term (1–10 days) effects of various doses of dexamethasone (Dex) (0,1–10 mg/kg) on the expression of the glucocorticoid receptor (GR, Nr3c1), core proteins of main proteoglycans and heparan sulfate metabolism-involved genes, as well as the content of carbohydrate macromolecules of glycosaminoglycans in the brain tissue of experimental animals.Materials and methods. In the study, C57Bl/6 mice were used. The expression of GR, proteoglycan core proteins and heparan sulfate metabolism-involved genes was determined by real-time polymerase chain reaction with reverse transcription. The content and localization of GR protein molecule were studied by Western blot and immunohistochemical analysis, and the glycosaminoglycan content was determined by dot-blot analysis and Alcian Blue staining.Results. It was shown that a single Dex administration leads to fast (1–3 days) short-term activation of GR expression (+1.5 times, p <0.05), proteoglycan’s genes (syndecan-3, Sdc3; perlecan, Hspg2; phosphacan, Ptprz1; neurocan, Ncan; +2–3-fold; p <0.05) and heparan sulfate-metabolism-involved genes (Ndst1, Glce, Hs2st1, Hs6st1, Sulf1 / 2; +1.5–2-fold; p <0.05) in the mouse brain, with a return to control values by 7–10 days after Dex administration. At the same time, the effect of Dex on carbohydrate macromolecules of glycosaminoglycans was more delayed and stable, increasing the content of low-sulfated glycosaminoglycans in the brain tissue in a dose-dependent manner starting from day 1 after Dex administration. Highly-sulfated glycosaminoglycans showed more delayed response to Dex administration, and an increase in their content was observed only at higher doses (2.5 and 10 mg/kg) and only on 7–10 days after its administration, apparently, mainly due to an increase in heparan sulfate content.Conclusion. In general, the effect of a single injection of Dex on the transcriptional activity of GR, proteoglycan core proteins and heparan sulfate metabolism-involved genes were short-termed, and the genes expression quickly returned to the normal levels. However, even a single use of Dex significantly increased the content of total as well as highly sulfated glycosaminoglycans in the mouse brain tissue, which can lead to the changes in the composition and structure of the brain tissue, as well as its functional characteristics.Введение. Глюкокортикоиды активно используются при лечении различных заболеваний, однако их длительное применение приводит ко множеству побочных эффектов, молекулярные механизмы развития которых остаются недостаточно изученными.Цель исследования – изучение краткосрочного (1–10 сут) влияния различных доз дексаметазона (Dex) (0,1–10 мг/кг) на экспрессию глюкокортикоидного рецептора (GR, Nr3c1), коровых белков основных протеогликанов и ферментов биосинтеза углеводных цепей гепарансульфата, а также содержание углеводных макромолекул гликозаминогликанов в ткани головного мозга экспериментальных животных.Материалы и методы. В исследовании использовали мышей линии C57Bl/6. Экспрессию GR, коровых белков протеогликанов и генов, кодирующих ферменты биосинтеза гепарансульфата, определяли с помощью полимеразной цепной реакции с обратной транскрипцией в реальном времени. Содержание и локализация белковой молекулы GR были изучены методами Вестерн-блоттинга и иммуногистохимического анализа, а содержание гликозаминогликанов – с помощью дот-блот анализа и окраски альциановым синим.Результаты. Было показано, что однократное введение Dex приводило к быстрой (на 1–3-и сутки) кратковременной активации экспрессии GR (+1,5 раза; p <0,05) некоторых генов коровых белков протеогликанов (синдекан-3, Sdc3; перлекан, Hspg2; фосфакан, Ptprz1; нейрокан, Ncan; +2–3 раза; p <0,05) и генов ферментов биосинтеза гепарансульфатов (Ndst1, Glce, Hs2st1, Hs6st1, Sulf1 / 2; +1,5–2 раза; p <0,05) в мозге мышей с возвращением к контрольным показателям к 7–10-м суткам после введения Dex. При этом влияние данного препарата на углеводные макромолекулы гликозаминогликанов имело более отсроченный и стабильный характер, дозозависимо увеличивая содержание общих гликозаминогликанов в ткани мозга, начиная с 1-х суток после введения Dex. Высокосульфатированные гликозаминогликаны демонстрировали более медленный ответ на введение препарата, повышение их содержания наблюдалось только при более высоких дозах (2,5 и 10 мг/кг) и только на 7–10-е сутки после его введения в основном за счет повышения содержания гепарансульфата.Заключение. Влияние однократного применения Dex на транскрипционную активность GR, протеогликанов и ферментов биосинтеза гепарансульфата носит кратковременный характер, и экспрессия генов быстро возвращается к нормальному уровню. Однако даже однократное применение Dex значительно повышает содержание общих и высокосульфатированных гликозаминогликанов в ткани головного мозга мышей, что может привести к изменению состава и структуры ткани головного мозга, а также его функциональных характеристик

MEP: a 3D PIC Code for the Simulation of the Dynamics of a Non-Neutral Plasma

The three-dimensional evolution of a pure electron plasma is studied by means of a newly developed particle-in-cell code which solves the drift-Poisson system where kinetic effects in the motion parallel to the magnetic field are taken into account. Different results relevant to the non-linear dynamics of trapped plasmas and low-energy electron beams are presented. [All rights reserved Elsevier]

Influence of seismic surveys on western gray whales off Sakhalin Island, Russia in 2001

Western gray whales (Eschrichtius robustus) aggregate off the northeastern coast of Sakhalin Island, Russia during summer-autumn to feed on benthic and near-benthic prey. During summer 2001, 3D seismic surveys were conducted during a six-week period in known gray whale foraging areas off Sakhalin Island. To test the hypothesis that the distribution of gray whales on the feeding ground would shift away from nearby seismic surveying, we examined the number of whales and number of pods (dependent variables) sighted during systematic scans in relation to three independent variables (i.e. preseismic, seismic, post-seismic). Results showed the main effect of condition was significant, with both the number of whales and the number of pods during pre- and post-seismic conditions significantly differing from the seismic condition. Although the relationship between the seismic survey operation period and the observed change in distribution of whales is only a correlation at this time, we strongly believe that it warrants an appropriate management response. The western gray whale population is critically endangered and depends on the northeastern Sakhalin Island feeding ground for the majority of its annual food intake. Disruption of feeding in preferred areas is a biologically significant event that could have major negative effects on individual whales, their reproductive success, and thus the population as a whole

Three-dimensional PIC simulation of electron plasmas

The three-dimensional evolution of a pure electron plasma is studied by means of a particle-in-cell code which solves the drift-Poisson system where kinetic effects in the motion parallel to the magnetic field are taken into account. Different results relevant to the nonlinear dynamics of trapped plasmas and low-energy electron beams are presented