bluuebunny/crossref_metadata_2025_split huggingface dataset:
Why process safety programs sometimes fail
Authors: Kelly Brian D. 
Published: October 2011

AbstractProcess safety management (PSM) failures are common across industry. Many of these failures trace their roots back to lack of understanding and support by senior management. Inadequate resources, improper metrics and unrealistic expectations are some of the reasons for such failures. Formal audits often fail to disclose the reasons why PSM may not provide its full intended benefits. This article discusses some of the principal reasons for process safety shortcomings. © 2011 American Institute of Chemical Engineers Process Saf Prog, 2011
Network resource stocks and flows: how do alliance portfolios affect the value of new alliance formations?
Authors: Wassmer Ulrich , Dussauge Pierre 
Published: October 2011

AbstractWe examine how new network resources accessed through alliance formations interact with network resources present in a firm's alliance portfolio. We test our theoretical model using event study methodology and data from the global air transportation industry. We find that the market rewards firms forming alliances that contribute resources that can be synergistically combined with firms' own resources as well as with network resources accessed through their alliance portfolios. Our results also indicate that the market penalizes firms entering into alliances that create resource combinations that are substitutes to resource combinations deployed by existing alliance partners. Copyright © 2011 John Wiley & Sons, Ltd.
CoFeed: privacy‐preserving Web search recommendation based on collaborative aggregation of interest feedback
Authors: Felber Pascal , Kropf Peter , Leonini Lorenzo , Luu Toan , Rajman Martin , Rivière Etienne , Schiavoni Valerio , Valerio José 
Published: October 2011

SUMMARYSearch engines essentially rely on the structure of the graph of hyperlinks. Although accurate for the main trend, this is not effective when some query is ambiguous. Leveraging semantic information by the mean of interest matching allows proposing complementary results that are tailored to the user's expectations. This paper proposes a collaborative search companion system, CoFeed, that collects user search queries and that considers feedback to build user‐centric and document‐centric profiling information. Over time, the system constructs ranked collections of elements that maintain the required information diversity and enhance the user search experience by presenting additional results tailored to the user's interest space. This collaborative search companion requires a supporting architecture adapted to large user populations generating high request loads. To that end, it integrates mechanisms for ensuring scalability and load balancing of the service under varying loads and user interest distributions. Moreover, collecting the recommendation data poses the problem of users’ privacy, and the bias one peer can induce to the system by sending fake recommendations. To that end, CoFeed ensures both publisher anonymity and rate limitation. With the former, the origin of the data is never known by the server that processes it, even if several servers collude to spy on some user. The latter, combined with decoupled authentication, allows to minimize the influence of cheating peers sending fake recommendations. Experiments with a deployed prototype highlight the efficiency of the system by analyzing improvement in search relevance, computational cost, scalability and load balancing. Copyright © 2011 John Wiley & Sons, Ltd.
Joint detection and estimation for cooperative communications in cluster‐based networks
Authors: Wang Tsang‐Yi , Pu Jyun‐Wei , Li Chih‐Peng 
Published: October 2011

ABSTRACTA joint data detection and channel estimation scheme is proposed for cooperative communications in cluster‐based networks. In the proposed approach, each relay detects the source information using its joint detection and estimation rules and then compresses this information and forwards it to the destination node. The source information received from all the relays in the network is combined at the destination node in accordance with a fusion decision rule in order to determine the corresponding symbol vector. The joint detection and estimation rule at the relays and the fusion rule at the destination node are both processed using an expectation maximization algorithm. In order to reliably avoid poor local maxima, we utilized one pilot symbol per signal block to obtain a better initial starting point for the expectation maximization algorithm. The simulation results show that the feedback mechanism accelerates the convergence of the local channel estimates toward the Cramer–Rao lower bound. Copyright © 2011 John Wiley & Sons, Ltd.
Evolution of vortex-surface fields in viscous Taylor–Green and Kida–Pelz flows
Authors: Yang Yue , Pullin D. I. 
Published: October 2011

AbstractIn order to investigate continuous vortex dynamics based on a Lagrangian-like formulation, we develop a theoretical framework and a numerical method for computation of the evolution of a vortex-surface field (VSF) in viscous incompressible flows with simple topology and geometry. Equations describing the continuous, timewise evolution of a VSF from an existing VSF at an initial time are first reviewed. Non-uniqueness in this formulation is resolved by the introduction of a pseudo-time and a corresponding pseudo-evolution in which the evolved field is ‘advected’ by frozen vorticity onto a VSF. A weighted essentially non-oscillatory (WENO) method is used to solve the pseudo-evolution equations in pseudo-time, providing a dissipative-like regularization. Vortex surfaces are then extracted as iso-surfaces of the VSFs at different real physical times. The method is applied to two viscous flows with Taylor–Green and Kida–Pelz initial conditions respectively. Results show the collapse of vortex surfaces, vortex reconnection, the formation and roll-up of vortex tubes, vorticity intensification between anti-parallel vortex tubes, and vortex stretching and twisting. A possible scenario for understanding the transition from a smooth laminar flow to turbulent flow in terms of topology of vortex surfaces is discussed.
Seasonal Synechococcus and Thaumarchaeal population dynamics examined with high resolution with remote in situ instrumentation
Authors: Robidart Julie C , Preston Christina M , Paerl Ryan W , Turk Kendra A , Mosier Annika C , Francis Christopher A , Scholin Christopher A , Zehr Jonathan P 
Published: October 2011

Abstract
Monterey Bay, CA is an Eastern boundary upwelling system that is nitrogen limited much of the year. In order to resolve population dynamics of microorganisms important for nutrient cycling in this region, we deployed the Environmental Sample Processor with quantitative PCR assays targeting both ribosomal RNA genes and functional genes for subclades of cyanobacteria (Synechococcus) and ammonia-oxidizing Archaea (Thaumarchaeota) populations. Results showed a strong correlation between Thaumarchaea abundances and nitrate during the spring upwelling but not the fall sampling period. In relatively stratified fall waters, the Thaumarchaeota community reached higher numbers than in the spring, and an unexpected positive correlation with chlorophyll concentration was observed. Further, we detected drops in Synechococcus abundance that occurred on short (that is, daily) time scales. Upwelling intensity and blooms of eukaryotic phytoplankton strongly influenced Synechococcus distributions in the spring and fall, revealing what appear to be the environmental limitations of Synechococcus populations in this region. Each of these findings has implications for Monterey Bay biogeochemistry. High-resolution sampling provides a better-resolved framework within which to observe changes in the plankton community. We conclude that controls on these ecosystems change on smaller scales than are routinely assessed, and that more predictable trends will be uncovered if they are evaluated within seasonal (monthly), rather than on annual or interannual scales.
Characterization of the cellular action of the MSK inhibitor SB-747651A
Authors: Naqvi Shaista , Macdonald Andrew , McCoy Claire E. , Darragh Joanne , Reith Alastair D. , Arthur J. Simon C. 
Published: October 2011

MSK1 (mitogen- and stress-activated kinase 1) and MSK2 are nuclear protein kinases that regulate transcription downstream of the ERK1/2 (extracellular-signal-regulated kinase 1/2) and p38α MAPKs (mitogen-activated protein kinases) via the phosphorylation of CREB (cAMP-response-element-binding protein) and histone H3. Previous studies on the function of MSKs have used two inhibitors, H89 and Ro 31-8220, both of which have multiple off-target effects. In the present study, we report the characterization of the in vitro and cellular properties of an improved MSK1 inhibitor, SB-747651A. In vitro, SB-747651A inhibits MSK1 with an IC50 value of 11 nM. Screening of an in vitro panel of 117 protein kinases revealed that, at 1 μM, SB-747651A inhibited four other kinases, PRK2 (double-stranded-RNA-dependent protein kinase 2), RSK1 (ribosomal S6 kinase 1), p70S6K (S6K is S6 kinase) (p70RSK) and ROCK-II (Rho-associated protein kinase 2), with a similar potency to MSK1. In cells, SB-747651A fully inhibited MSK activity at 5–10 μM. SB-747651A was found to inhibit the production of the anti-inflammatory cytokine IL-10 (interleukin-10) in wild-type, but not MSK1/2-knockout, macrophages following LPS (lipopolysaccharide) stimulation. Both SB-747651A and MSK1/2 knockout resulted in elevated pro-inflammatory cytokine production by macrophages in response to LPS. Comparison of the effects of SB-747651A, both in vitro and in cells, demonstrated that SB-747651A exhibited improved selectivity over H89 and Ro 31-8220 and therefore represents a useful tool to study MSK function in cells.
Stocking Success of Paddlefish in Lake Francis Case, South Dakota: Population Characteristics and Sport Fishery Potential
Authors: Pierce Landon L. , Graeb Brian D. S. , Willis David W. , Sorensen Jason S. , Pegg Mark A. 
Published: October 2011

AbstractLake Francis Case, South Dakota, a Missouri River reservoir, supported a paddlefish Polyodon spathula sport fishery shortly after impoundment, but this fishery closed in 1986 owing to a lack of natural recruitment. Lake Francis Case has been stocked intermittently since 1974 and annually since 1990 to maintain the population and potentially sustain a sport harvest. To evaluate the success of these stockings, we assessed the current status of the Lake Francis Case paddlefish population (i.e., population characteristics and dynamics) and evaluated the potential effects of exploitation on this population. Advanced fingerling stockings have been effective, as 56% of sampled fish were of hatchery origin (indicated by coded wire tags), and may sustain a harvestable population. Year‐class strength was negatively correlated to water temperature inputs from Big Bend Dam and positively correlated to White River discharge. Downstream emigration is probably responsible for most of the variability in year‐class strength, and the rate of downstream emigration may be greater during years with warmer water temperatures. Harvest simulations suggested that growth overfishing was possible under a 660‐mm minimum length limit but not under 840‐mm and 1,016‐mm minimum length limits. The proportional size distribution of memorable‐length fish (PSD‐M) was reduced 28.6% and 14.3%, respectively, by 5% exploitation under simulated 660‐mm and 840‐mm minimum length limits. Under a simulated 1,016‐mm minimum length limit, PSD‐M was unchanged by 10% exploitation. At 5% exploitation, broodstock availability was reduced by more than 30% under the simulated 660‐mm and 840‐mm minimum length regulations and was reduced 16% under the 1,016‐mm minimum length limit. Our results suggest that this population could support a limited (e.g., 5% exploitation) sport fishery under a high (e.g., 1,016‐mm) minimum length limit without substantial changes in size structure or the availability of broodstock if stockings are continued.
RNA-Seq analysis in MeV
Authors: Howe Eleanor A. , Sinha Raktim , Schlauch Daniel , Quackenbush John 
Published: October 2011

Abstract
Summary: RNA-Seq is an exciting methodology that leverages the power of high-throughput sequencing to measure RNA transcript counts at an unprecedented accuracy. However, the data generated from this process are extremely large and biologist-friendly tools with which to analyze it are sorely lacking. MultiExperiment Viewer (MeV) is a Java-based desktop application that allows advanced analysis of gene expression data through an intuitive graphical user interface. Here, we report a significant enhancement to MeV that allows analysis of RNA-Seq data with these familiar, powerful tools. We also report the addition to MeV of several RNA-Seq-specific functions, addressing the differences in analysis requirements between this data type and traditional gene expression data. These tools include automatic conversion functions from raw count data to processed RPKM or FPKM values and differential expression detection and functional annotation enrichment detection based on published methods.
Availability: MeV version 4.7 is written in Java and is freely available for download under the terms of the open-source Artistic License version 2.0. The website (http://mev.tm4.org/) hosts a full user manual as well as a short quick-start guide suitable for new users.
Contact: johnq@jimmy.harvard.edu
Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection
Authors: Hamada Michiaki , Wijaya Edward , Frith Martin C. , Asai Kiyoshi 
Published: October 2011

Abstract
Motivation: Recent studies have revealed the importance of considering quality scores of reads generated by next-generation sequence (NGS) platforms in various downstream analyses. It is also known that probabilistic alignments based on marginal probabilities (e.g. aligned-column and/or gap probabilities) provide more accurate alignment than conventional maximum score-based alignment. There exists, however, no study about probabilistic alignment that considers quality scores explicitly, although the method is expected to be useful in SNP/indel callers and bisulfite mapping, because accurate estimation of aligned columns or gaps is important in those analyses.
Results: In this study, we propose methods of probabilistic alignment that consider quality scores of (one of) the sequences as well as a usual score matrix. The method is based on posterior decoding techniques in which various marginal probabilities are computed from a probabilistic model of alignments with quality scores, and can arbitrarily trade-off sensitivity and positive predictive value (PPV) of prediction (aligned columns and gaps). The method is directly applicable to read mapping (alignment) toward accurate detection of SNPs and indels. Several computational experiments indicated that probabilistic alignments can estimate aligned columns and gaps accurately, compared with other mapping algorithms e.g. SHRiMP2, Stampy, BWA and Novoalign. The study also suggested that our approach yields favorable precision for SNP/indel calling.
Availability: The method described in this article is implemented in LAST, which is freely available from: http://last.cbrc.jp.
Contact: mhamada@k.u-tokyo.ac.jp
Supplementary Information: Supplementary data are available at Bioinformatics online.
Estimation of variance components for postpartum dysgalactia syndrome in sows
Authors: Preissler R. , Hinrichs D. , Reiners K. , Looft H. , Kemper N. 
Published: October 2011

SummaryThe postpartum dysgalactia syndrome (PDS) represents one of the most important diseases after parturition in sows. The genetic background of the disease has been investigated some time ago and heritability estimates around 0.10 have been obtained. To compute current estimates, a dataset of 1680 sampled sows and their 2001 clinically examined litters was used for variance components estimation with a threshold liability model. Affected sows were defined through clinical examination 12–48 h after parturition. Posterior mean of additive genetic variance was 0.10 and estimated heritability for PDS averaged 0.0879 with a 95% confidence interval of 0.0876 and 0.0881. The results are in agreement with those of other studies and emphasize the importance of considering the genetic predisposition for susceptibility to PDS as well as of additional factors including hygiene and management conditions.
Effects of a single post‐partum injection of a high dose of vitamin D on glucose tolerance and insulin resistance in mothers with first‐time gestational diabetes mellitus
Authors: Mozaffari‐Khosravi H. , Hosseinzadeh‐Shamsi‐Anar M. , Salami M.‐A. , Hadinedoushan H. , Mozayan M. R. 
Published: October 2011

Diabet. Med. 29, 36–42 (2012)AbstractAim  This study was performed to determine the effect of a single, large, intramuscular injection of vitamin D post‐partum on glucose tolerance and insulin resistance in women with gestational diabetes.Methods  Forty‐five participants in a randomized controlled trial on gestational diabetes mellitus were divided into an intervention group and a control group. Only subjects in the intervention group received one intramuscular injection of 300 000 IU of vitamin D3. HbA1c, serum 25‐hydroxyvitamin D3, fasting insulin and blood glucose, C‐peptide, homeostasis model assessment insulin resistance index (HOMA‐IR), β‐cell function, insulin sensitivity and the Quantitative Insulin Sensitivity Check Index (QUICKI) were measured at baseline and after 3 months of intervention.Results  Approximately 80% of the mothers had a degree of vitamin D deficiency. Post‐intervention, this was found in 4.2 and 71.4% in the intervention and control groups, respectively. The medians of HOMA‐IR indices before and after intervention were 0.6 and 0.5 (P = 0.7), respectively, in subjects in the intervention group, and 0.5 and 0.9 (P = 0.01) in subjects in the control group. The mean of the QUICKI fell only in the control group (P = 0.008). In the control group, β‐cell function increased by ∼8% (P = 0.01) and insulin sensitivity decreased after 3 months (P = 0.002). Post‐intervention, the median C‐peptide decreased in the intervention group and increased in the control group, but the change was significant only in the control group (P = 0.03).Conclusions  A single injection of 300 000 IU of vitamin D3 achieves a 3‐month serum 25‐hydroxyvitamin D range of 50–80 nmol/l and is an efficient, effective and safe procedure for improving the vitamin status and indices of insulin resistance in mothers with gestational diabetes after delivery.
Neural response to the second stimulus associated with poor speed discrimination performance in schizophrenia
Authors: Wang Jun , Dobkins Karen R. , McDowell Jennifer E. , Clementz Brett A. 
Published: October 2011

AbstractVisual motion processing is compromised in schizophrenia (SZ), but it is uncertain what neural deviations account for their motion analysis abnormalities. Neural activations were measured with dense‐array electroencephalography while 14 medicated SZ and 14 healthy persons performed a paired‐stimuli forced choice speed discrimination task. SZ had (a) worse‐at‐speed discrimination, replicating previous findings, (b) normal early extrastriate neural activity (N1) to both motion stimuli, (c) reduced later extrastriate activity (P2) specifically to the second stimulus, and (d) following P2, an enhanced later N2 over parietal cortex. Stronger P2 and N2 responses were associated with better speed discrimination performance across groups. These findings indicate that the neural correlates of poor motion analysis in SZ may not be an early visual analysis abnormality but a problem with efficient use of speed information later in cognitive processing.
Edentulism trends among middle‐aged and older adults in the United States: comparison of five racial/ethnic groups
Authors: Wu Bei , Liang Jersey , Plassman Brenda L. , Remle Corey , Luo Xiao 
Published: October 2011

Wu B, Liang J, Plassman BL, Remle C, Luo X. Edentulism trends among middle‐aged and older adults in the United States: comparison of five racial/ethnic groups. Community Dent Oral Epidemiol 2012; 40: 145–153. © 2011 John Wiley & Sons A/SAbstract –  Objectives:  This study examined edentulism trends among adults aged 50 and above in five ethnic groups in the United States: Asians, African Americans, Hispanics, Native Americans, and non‐Hispanic Caucasians.Methods:  Data came from the National Health Interview Surveys between 1999 and 2008. Respondents included 616 Native Americans, 2,666 Asians, 15,295 African Americans, 13,068 Hispanics, and 86,755 Caucasians.Results:  In 2008, Native Americans had the highest predicated rate of edentulism (23.98%), followed by African Americans (19.39%), Caucasians (16.90%), Asians (14.22%), and Hispanics (14.18%). Overall, there was a significant downward trend in edentulism rates between 1999 and 2008 (OR = 0.97, 95% CI: 0.96, 0.98). However, compared with Caucasians, Native Americans showed a significantly less decline of edentulism during this period (OR = 1.10, 95% CI: 1.02, 1.19).Conclusions:  While there was a downward trend in edentulism between 1999 and 2008, significant variations existed across racial/ethnic groups. Innovative public health programs and services are essential to prevent oral health diseases and conditions for minority populations who lack access to adequate dental care. Additionally, given the increasing numbers of adults retaining their natural teeth, interventions designed to assist individuals in maintaining healthy teeth becomes more critical.
Restricted expression of chromatin remodeling associated factor Chd3 during tooth root development
Authors: Date Y. , Yokoyama Y. , Kondo H. , Kuroda S. , Ohya K. , Ota M. S. , Iseki S. , Kasugai S. 
Published: October 2011

Date Y, Yokoyama Y, Kondo H, Kuroda S, Ohya K, Ota MS, Iseki S, Kasugai S. Restricted expression of chromatin remodeling associated factor Chd3 during tooth root development. J Periodont Res 2012; 47: 180–187. © 2011 John Wiley & Sons A/SBackground and Objective:  The tooth root is one of the critical parts to maintain tooth function; however, the molecular mechanisms of root development remain unknown. We aimed to identify specific factors for root morphogenesis using a newly developed experimental system.Material and Methods:  Tentative cementoblasts and periodontal ligament cells from mouse mandibular molars were isolated using laser capture microdissection. More than 500 cementoblasts and periodontal ligament cells were separately captured. After RNA extraction and amplification, mRNA expression in isolated cementoblasts was compared with that of periodontal ligament cells by cDNA microarray analysis. Then, putative cementoblast‐specific genes were subjected to in situ hybridization analysis to confirm the results in mouse mandible.Results:  Approximately 2000 genes were differentially expressed between these tissues. Among those genes, zinc finger helicase (ZFH), also termed chromodomain‐helicase‐DNA‐binding protein 3 (Chd3), was one of the highly expressed transcripts in tentative cementoblasts. In situ hybridization revealed that ZFH/Chd3 was strongly expressed in Hertwig’s epithelial root sheath rather than in cementum. Moreover, its expression disappeared when root formation was advanced in the first molar. In contrast, Chd3 was continuously expressed in dental epithelial cells of the cervical loop, in which root extension is never terminated.Conclusion:  These results suggest that ZFH/Chd3 might play an important role in tooth root development and subsequent cementogenesis.