Counting approximately-shortest paths in directed acyclic graphs

Given a directed acyclic graph with positive edge-weights, two vertices s and t, and a threshold-weight L, we present a fully-polynomial time approximation-scheme for the problem of counting the s-t paths of length at most L. We extend the algorithm for the case of two (or more) instances of the same problem. That is, given two graphs that have the same vertices and edges and differ only in edge-weights, and given two threshold-weights L_1 and L_2, we show how to approximately count the s-t paths that have length at most L_1 in the first graph and length at most L_2 in the second graph. We believe that our algorithms should find application in counting approximate solutions of related optimization problems, where finding an (optimum) solution can be reduced to the computation of a shortest path in a purpose-built auxiliary graph

DomSVR: Domain boundary prediction with support vector regression from sequence information alone

Protein domains are structural and fundamental functional units of proteins. The information of protein domain boundaries is helpful in understanding the evolution, structures and functions of proteins, and also plays an important role in protein classification. In this paper, we propose a support vector regression-based method to address the problem of protein domain boundary identification based on novel input profiles extracted from AA-index database. As a result, our method achieves an average sensitivity of ∼36.5% and an average specificity of ∼ 81% for multi-domain protein chains, which is overall better than the performance of published approaches to identify domain boundary. As our method used sequence information alone, our method is simpler and faster.© Springer-Verlag 2010

First comparison of French and Australian OsHV-1 µvars by bath exposure

Economically devastating mortality events of farmed and wild shellfish due to infectious disease have been reported globally. Currently, one of the most significant disease threats to Pacific oyster Crassostrea gigas culture is the ostreid herpesvirus 1 (OsHV-1), in particular the emerging OsHV-1 microvariant genotypes. OsHV-1 microvariants (OsHV-1 μvars) are spreading globally, and concern is high among growers in areas unaffected by OsHV-1. No study to date has compared the relative virulence among variants. We provide the first challenge study comparing survival of naïve juvenile Pacific oysters exposed to OsHV-1 μvars from Australia (AUS μvar) and France (FRA μvar). Oysters challenged with OsHV-1 μvars had low survival (2.5% exposed toAUS μvar and 10% to FRA μvar), and high viral copy number as compared to control oysters(100% survival and no virus detected). As our study was conducted in a quarantine facility located~320 km from the ocean, we also compared the virulence of OsHV-1 μvars using artificial seawater made from either facility tap water (3782 μmol kg−1seawater total alkalinity) or purchased distilled water (2003 μmol kg−1). Although no differences in survival or viral copy number were detected in oysters exposed to seawater made using tap or distilled water, more OsHV-1 was detected in tanks containing the lower-alkalinity seawater, indicating that water quality may be important for virus transmission, as it may influence the duration of viral viability outside of the hos

Valuing informal carers' quality of life using best-worst scaling-Finnish preference weights for the Adult Social Care Outcomes Toolkit for carers (ASCOT-Carer)

This study developed Finnish preference weights for the seven-attribute Adult Social Care Outcomes Toolkit for carers (ASCOT-Carer) and investigated survey fatigue and learning in best-worst scaling (BWS) experiments. An online survey that included a BWS experiment using the ASCOT-Carer was completed by a sample from the general population in Finland. A block of eight BWS profiles describing different states from the ASCOT-Carer were randomly assigned to each respondent, who consecutively made four choices (best, worst, second best and second worst) per profile. The analysis panel data had 32,160 choices made by 1005 respondents. A scale multinomial logit (S-MNL) model was used to estimate preference weights for 28 ASCOT-Carer attribute levels. Fatigue and learning effects were examined as scale heterogeneity. Several specifications of the generalised MNL model were employed to ensure the stability of the preference estimates. The most and least-valued states were the top and bottom levels of the control over daily life attribute. The preference weights were not on a cardinal scale. We observed the position effect of the attributes on preferences associated with the best or second-best choices. A learning effect was found. The established preference weights can be used in evaluations of the effects of long-term care services and interventions on the quality of life of service users and caregivers. The learning effect implies a need to develop study designs that ensure equal consideration to all profiles (choice tasks) in a sequential choice experiment

Standing in a Garden of Forking Paths

According to the Path Principle, it is permissible to expand your set of beliefs iff (and because) the evidence you possess provides adequate support for such beliefs. If there is no path from here to there, you cannot add a belief to your belief set. If some thinker with the same type of evidential support has a path that they can take, so do you. The paths exist because of the evidence you possess and the support it provides. Evidential support grounds propositional justification. The principle is mistaken. There are permissible steps you may take that others may not even if you have the very same evidence. There are permissible steps that you cannot take that others can even if your beliefs receive the same type of evidential support. Because we have to assume almost nothing about the nature of evidential support to establish these results, we should reject evidentialism

Braveheart, a Long Noncoding RNA Required for Cardiovascular Lineage Commitment

Long noncoding RNAs (lncRNAs) are often expressed in a development-specific manner, yet little is known about their roles in lineage commitment. Here, we identified Braveheart (Bvht), a heart-associated lncRNA in mouse. Using multiple embryonic stem cell (ESC) differentiation strategies, we show that Bvht is required for progression of nascent mesoderm toward a cardiac fate. We find that Bvht is necessary for activation of a core cardiovascular gene network and functions upstream of mesoderm posterior 1 (MesP1), a master regulator of a common multipotent cardiovascular progenitor. We also show that Bvht interacts with SUZ12, a component of polycomb-repressive complex 2 (PRC2), during cardiomyocyte differentiation, suggesting that Bvht mediates epigenetic regulation of cardiac commitment. Finally, we demonstrate a role for Bvht in maintaining cardiac fate in neonatal cardiomyocytes. Together, our work provides evidence for a long noncoding RNA with critical roles in the establishment of the cardiovascular lineage during mammalian development.Damon Runyon Cancer Research Foundation (DRG 2032-09)Damon Runyon Cancer Research Foundation (DFS 04-12)European Molecular Biology Organization (Long-term Fellowship)National Heart, Lung, and Blood Institute. Bench to Bassinet Program (U01HL098179)National Heart, Lung, and Blood Institute. Bench to Bassinet Program (U01HL098188)Smith Family FoundationPew Charitable Trusts. Program in the Biomedical Science

Dissect: detection and characterization of novel structural alterations in transcribed sequences

Motivation: Computational identification of genomic structural variants via high-throughput sequencing is an important problem for which a number of highly sophisticated solutions have been recently developed. With the advent of high-throughput transcriptome sequencing (RNA-Seq), the problem of identifying structural alterations in the transcriptome is now attracting significant attention

Understanding the UK hospital supply chain in an era of patient choice

Author Posting © Westburn Publishers Ltd, 2011. This is a post-peer-review, pre-copy-edit version of an article which has been published in its definitive form in the Journal of Marketing Management, and has been posted by permission of Westburn Publishers Ltd for personal use, not for redistribution. The article was published in Journal of Marketing Management, 27(3-4), 401 - 423, doi:10.1080/0267257X.2011.547084 http://dx.doi.org/10.1080/0267257X.2011.547084The purpose of this paper is to investigate the UK hospital supply chain in light of recent government policy reform where patients will have, inter alia, greater choice of hospital for elective surgery. Subsequently, the hospital system should become far more competitive with supply chains having to react to these changes as patient demand becomes less predictable. Using a qualitative case study methodology, hospital managers are interviewed on a range of issues. Views on the development of the hospital supply chain in different phases are derived, and are used to develop a map of the current hospital chain. The findings show hospital managers anticipating some significant changes to the hospital supply chain and its workings as Patient Choice expands. The research also maps the various aspects of the hospital supply chain as it moves through different operational phases and highlights underlying challenges and complexities. The hospital supply chain, as discussed and mapped in this research, is original work given there are no examples in the literature that provide holistic representations of hospital activity. At the end, specific recommendations are provided that will be of interest to service to managers, researchers, and policymakers