Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel

Single T4-DNA molecules were confined in rectangular-shaped channels with a depth of 300 nm and a width in the range 150-300 nm casted in a poly(dimethylsiloxane) nanofluidic chip. The extensions of the DNA molecules were measured with fluorescence microscopy as a function of the ionic strength and composition of the buffer as well as the DNA intercalation level by the YOYO-1 dye. The data were interpreted with scaling theory for a wormlike polymer in good solvent, including the effects of confinement, charge, and self-avoidance. It was found that the elongation of the DNA molecules with decreasing ionic strength can be interpreted in terms of an increase of the persistence length. Self-avoidance effects on the extension are moderate, due to the small correlation length imposed by the channel cross-sectional diameter. Intercalation of the dye results in an increase of the DNA contour length and a partial neutralization of the DNA charge, but besides effects of electrostatic origin it has no significant effect on the bare bending rigidity. In the presence of divalent cations, the DNA molecules were observed to contract, but they do not collapse into a condensed structure. It is proposed that this contraction results from a divalent counterion mediated attractive force between the segments of the DNA molecule.Comment: 38 pages, 10 figures, accepted for publication in The Journal of Chemical Physic

The aspartic proteinase family of three Phytophthora species

Background: Phytophthora species are oomycete plant pathogens with such major social and economic impact that genome sequences have been determined for Phytophthora infestans, P. sojae and P. ramorum. Pepsin-like aspartic proteinases (APs) are produced in a wide variety of species (from bacteria to humans) and contain conserved motifs and landmark residues. APs fulfil critical roles in infectious organisms and their host cells. Annotation of Phytophthora APs would provide invaluable information for studies into their roles in the physiology of Phytophthora species and interactions with their hosts. Results: Genomes of Phytophthora infestans, P. sojae and P. ramorum contain 11-12 genes encoding APs. Nine of the original gene models in the P. infestans database and several in P. sojae and P. ramorum (three and four, respectively) were erroneous. Gene models were corrected on the basis of EST data, consistent positioning of introns between orthologues and conservation of hallmark motifs. Phylogenetic analysis resolved the Phytophthora APs into 5 clades. Of the 12 sub-families, several contained an unconventional architecture, as they either lacked a signal peptide or a propart region. Remarkably, almost all APs are predicted to be membrane-bound. Conclusions: One of the twelve Phytophthora APs is an unprecedented fusion protein with a putative G-protein coupled receptor as the C-terminal partner. The others appear to be related to well-documented enzymes from other species, including a vacuolar enzyme that is encoded in every fungal genome sequenced to date. Unexpectedly, however, the oomycetes were found to have both active and probably-inactive forms of an AP similar to vertebrate BACE, the enzyme responsible for initiating the processing cascade that generates the Aβ peptide central to Alzheimer's Disease. The oomycetes also encode enzymes similar to plasmepsin V, a membrane-bound AP that cleaves effector proteins of the malaria parasite Plasmodium falciparum during their translocation into the host red blood cell. Since the translocation of Phytophthora effector proteins is currently a topic of intense research activity, the identification in Phytophthora of potential functional homologues of plasmepsin V would appear worthy of investigation. Indeed, elucidation of the physiological roles of the APs identified here offers areas for future study. The significant revision of gene models and detailed annotation presented here should significantly facilitate experimental design.Fil: Kay, John. Cardiff University; Reino UnidoFil: Meijer, Harold J. G.. Wageningen University; Reino UnidoFil: Ten Have, Arjen. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Mar del Plata. Instituto de Investigaciones Biológicas; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales; ArgentinaFil: van Kan, Jan A. L.. Wageningen University; Reino Unid

Sensitivity Analysis of List Scheduling Heuristics

When jobs have to be processed on a set of identical parallel machines so as to minimize the makespan of the schedule, list scheduling rules form a popular class of heuristics. The order in which jobs appear on the list is assumed here to be determined by the relative size of their processing times; well known special cases are the LPT rule and the SPT rule, in which the jobs are ordered according to non-increasing and non-decreasing processing time respectively. When one of the job processing times is gradually increased, the schedule produced by a list scheduling rule will be affected in a manner reflecting its sensitivity to data perturbations. We analyze this phenomenon and obtain analytical support for the intuitively plausible notion that the sensitivity of a list scheduling rule increases with the quality of the schedule produced

Optics-less smart sensors and a possible mechanism of cutaneous vision in nature

Optics-less cutaneous (skin) vision is not rare among living organisms, though its mechanisms and capabilities have not been thoroughly investigated. This paper demonstrates, using methods from statistical parameter estimation theory and numerical simulations, that an array of bare sensors with a natural cosine-law angular sensitivity arranged on a flat or curved surface has the ability to perform imaging tasks without any optics at all. The working principle of this type of optics-less sensor and the model developed here for determining sensor performance may be used to shed light upon possible mechanisms and capabilities of cutaneous vision in nature

"Narrow" Graphene Nanoribbons Made Easier by Partial Hydrogenation

It is a challenge to synthesize graphene nanoribbons (GNRs) with narrow widths and smooth edges in large scale. Our first principles study on the hydrogenation of GNRs shows that the hydrogenation starts from the edges of GNRs and proceeds gradually toward the middle of the GNRs so as to maximize the number of carbon-carbon $\pi$-$\pi$ bonds. Furthermore, the partially hydrogenated wide GNRs have similar electronic and magnetic properties as those of narrow GNRs. Therefore, it is not necessary to directly produce narrow GNRs for realistic applications because partial hydrogenation could make wide GNRs "narrower"

Order statistics and the linear assignment problem

Under mild conditions on the distribution functionF, we analyze the asymptotic behavior in expectation of the smallest order statistic, both for the case thatF is defined on (–, +) and for the case thatF is defined on (0, ). These results yield asymptotic estimates of the expected optiml value of the linear assignment problem under the assumption that the cost coefficients are independent random variables with distribution functionF

The asymptotic behaviour of a distributive sorting method

In the distributive sorting method of Dobosiewicz, both the interval between the minimum and the median of the numbers to be sorted and the interval between the median and the maximum are partitioned inton/2 subintervals of equal length; the procedure is then applied recursively on each subinterval containing more than three numbers. We refine and extend previous analyses of this method, e.g., by establishing its asymptotic linear behaviour under various probabilistic assumptions

On-ward participation of a hospital pharmacist in a Dutch intensive care unit reduces prescribing errors and related patient harm: an intervention study

Introduction: Patients admitted to an intensive care unit (ICU) are at high risk for prescribing errors and related adverse drug events (ADEs). An effective intervention to decrease this risk, based on studies conducted mainly in North America, is on-ward participation of a clinical pharmacist in an ICU team. As the Dutch Healthcare System is organized differently and the on-ward role of hospital pharmacists in Dutch ICU teams is not well established, we conducted an intervention study to investigate whether participation of a hospital pharmacist can also be an effective approach in reducing prescribing errors and related patient harm (preventable ADEs) in this specific setting. Methods: A prospective study compared a baseline period with an intervention period. During the intervention period, an ICU hospital pharmacist reviewed medication orders for patients admitted to the ICU, noted issues related to prescribing, formulated recommendations and discussed those during patient review meetings with the attending ICU physicians. Prescribing issues were scored as prescribing errors when consensus was reached between the ICU hospital pharmacist and ICU physicians. Results: During the 8.5-month study period, medication orders for 1,173 patients were reviewed. The ICU hospital pharmacist made a total of 659 recommendations. During the intervention period, the rate of consensus between the ICU hospital pharmacist and ICU physicians was 74%. The incidence of prescribing errors during the intervention period was significantly lower than during the baseline period: 62.5 per 1,000 monitored patient-days versus 190.5 per 1,000 monitored patient-days, respectively (P < 0.001). Preventable ADEs (patient harm, National Coordinating Council for Medication Error Reporting and Prevention severity categories E and F) were reduced from 4.0 per 1,000 monitored patient-days during the baseline period to 1.0 per 1,000 monitored patient-days during the intervention period (P = 0.25). Per monitored patient-day, the intervention itself cost (sic)3, but might have saved (sic)26 to (sic)40 by preventing ADEs. Conclusions: On-ward participation of a hospital pharmacist in a Dutch ICU was associated with significant reductions in prescribing errors and related patient harm (preventable ADEs) at acceptable costs per monitored patient-da

Kondo effect in Ce(x)La(1-x)Cu(2.05)Si(2) intermetallics

The magnetic susceptibility and susceptibility anisotropy of the quasi-binary alloy system Ce(x)La(1-x)Cu(2.05)Si(2) have been studied for low concentration of Ce ions. The single-ion desc ription is found to be valid for x < 0.1. The experimental results are discussed in terms of t he degenerate Coqblin-Schrieffer model with a crystalline electric field splitting Delta = 330 K. The properties of the model, obtained by combining the lowest-order scaling and the pertur bation theory, provide a satisfactory description of the experimental data down to 30 K. The e xperimental results between 20 K and 2 K are explained by the exact solution of the Kondo mode l for an effective doublet.Comment: 11 pages, 13 Postscript figures, 1 tabl

Multimorbidity patterns in hospitalized older patients: Associations among chronic diseases and geriatric syndromes

Background/Objectives The clinical status of older individuals with multimorbidity can be further complicated by concomitant geriatric syndromes. This study explores multimorbidity patterns, encompassing both chronic diseases and geriatric syndromes, in geriatric patients attended in an acute hospital setting. Design Retrospective observational study. Setting Unit of Social and Clinical Assessment (UVSS), Miguel Servet University Hospital (HUMS), Zaragoza (Spain). Year, 2011. Participants A total of 924 hospitalized patients aged 65 years or older. Measurements Data on patients'' clinical, functional, cognitive and social statuses were gathered through comprehensive geriatric assessments. To identify diseases and/or geriatric syndromes that cluster into patterns, an exploratory factor analysis was applied, stratifying by sex. The factors can be interpreted as multimorbidity patterns, i.e., diseases non-randomly associated with each other within the study population. The resulting patterns were clinically assessed by several physicians. Results The mean age of the study population was 82.1 years (SD 7.2). Multimorbidity burden was lower in men under 80 years, but increased in those over 80. Immobility, urinary incontinence, hypertension, falls, dementia, cognitive decline, diabetes and arrhythmia were among the 10 most frequent health problems in both sexes, with prevalence rates above 20%. Four multimorbidity patterns were identified that were present in both sexes: Cardiovascular, Induced Dependency, Falls and Osteoarticular. The number of conditions comprising these patterns was similar in men and women. Conclusion The existence of specific multimorbidity patterns in geriatric patients, such as the Induced Dependency and Falls patterns, may facilitate the early detection of vulnerability to stressors, thus helping to avoid negative health outcomes such as functional disability