bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance analysis of channel estimation in amplify‐and‐forward multi‐hop direct forwarding wireless networks
Authors: Choi Jeong‐Min , Baek Jong‐Seob , Han Jae‐Shin , Seo Jong‐Soo 
Published: July 2014

AbstractIn this paper, we study the performance of a training‐based least square (LS) and linear minimum mean‐square‐error (LMMSE) channel estimation for both hop‐by‐hop and multi‐hop direct forwarding wireless sensor networks over frequency‐selective fading channels. Specifically, to investigate the properties of the channel estimation, we accomplish a theoretical analysis of MSE in terms of various link parameters. From the performance evaluation, we analytically present the effects of the number of hops on the MSE performance for channel estimations in both multi‐hop networks. Interesting observations of MSE behaviors under various conditions are discussed, and the receiver complexity and channel equalization performance are also analyzed. Finally, through the computer simulations, the analytical results and detection performance are demonstrated. Copyright © 2014 John Wiley & Sons, Ltd.
Irinophore C™, a lipid nanoparticle formulation of irinotecan, abrogates the gastrointestinal effects of irinotecan in a rat model of clinical toxicities
Authors: Waterhouse Dawn N. , Sutherland Brent W. , Santos Nancy Dos , Masin Dana , Osooly Maryam , Strutt Dita , Ostlund Christina , Anantha Malathi , Harasym Natashia , Manisali Irina , Wehbe Mohamed , Bally Marcel B. , Webb Murray S. 
Published: July 2014

SummaryIrinotecan is a water-soluble camptothecin derivative with clinical activity against colorectal and small cell lung cancers and is currently a standard of care therapeutic in the treatment of colorectal cancer in combination with 5-fluorouracil. One of the major clinical issues limiting the use of irinotecan is gastrointestinal toxicity manifested as life-threatening diarrhea which is reported in up to 45 % of treated patients. The studies summarized here tested, in a rat model of irinotecan-associated gastro-intestinal toxicity, whether a lipid nanoparticle formulation of irinotecan, Irinophore C™, mitigated early-onset or late-onset diarrhea when given at doses equivalent to unformulated irinotecan that engenders both early- and late-onset diarrhea. Specifically, rats administered intravenously on two consecutive days with unformulated irinotecan at 170 mg/kg then 160 mg/kg experienced transient early-onset diarrhea after each administration and then experienced significant late-onset diarrhea peaking 4 days after treatment. Irinophore C™ given at the identical dose and schedule did not elicit either early- or late-onset diarrhea in any animals. When Irinophore C™ was combined with 5-fluorouracil there was also no early- or late-onset diarrhea observed. Histopathological analysis of the gastro-intestinal tract confirmed that the effects associated with irinotecan treatment were absent in rats given Irinophore C™ at the identical dose. Pharmacokinetic analysis demonstrated significantly higher systemic concentrations of irinotecan in rats given the nanoparticle formulation compared to those given unformulated irinotecan. These results demonstrate that the Irinophore C™ formulation is significantly less toxic than irinotecan, used either as a single agent or in combination with 5-fluorouracil, in a rat model of irinotecan-induced gastrointestinal toxicity.
A Historical Perspective of the Effect of the Great Recession on Hospitals
Authors: Shortt Janet 
Published: July 2014

AbstractAt 18 months, the Great Recession of December 2007 to June 2009 is the longest recession since World War II. The recession led to soaring unemployment, resulting in loss of employment‐based health insurance for millions of people. In addition to seeing increases in uninsured patients, hospitals experienced losses in their investment portfolios, which in turn increased bad debt, charity care, and uncompensated care nationwide. Hospital executives began to devise cost‐cutting strategies to balance the rising debt, such as standardizing medical equipment, cutting staff positions, and delaying construction projects and capital expenditures as well as implementing value analysis strategies. The recession is officially over, and, although economic recovery has been slow and unemployment continues to be an issue, hospitals’ net revenue started improving as of 2009 and hospital construction started increasing in 2010. Still, caution is warranted in the postrecession climate, because it is unknown what effects will be seen when the Baby Boomer generation begins using Medicare.
How Hemostatic Agents Interact With the Coagulation Cascade
Authors: Overbey Douglas M. , Jones Edward L. , Robinson Thomas N. 
Published: July 2014

AbstractHemostasis is a critical component of the preservation of hemodynamic stability and operative visibility during surgery. Initially, hemostasis is achieved via the careful application of direct pressure to allow time for the coagulation cascade to create a fibrin and platelet plug. Other first‐line methods of hemostasis in surgery include repair or ligation of the bleeding vessel with sutures, clips, or staples and coagulation of the bleeding site with a thermal energy‐based device. When these methods are insufficient to provide adequate hemostasis, topical hemostatic agents can be used to augment the creation of a clot during surgery. A basic understanding of how and where these products interact with the coagulation cascade is essential to achieving optimal hemostasis outcomes.
Hemostatic Agents: A Guide to Safe Practice for Perioperative Nurses
Authors: Camp Margaret A. 
Published: July 2014

AbstractPerioperative hemostasis, the effective management of bleeding during operative and other invasive procedures, can involve the use of blood, blood products, and hemostatic agents to augment the patient's natural clotting abilities. Currently, more than 50 hemostatic products are available in the marketplace and dozens more are in development. It is important for perioperative nurses to understand each of the hemostatic agent categories and their actions, properties, applications, and limitations. This article provides an overview of the normal coagulation process (ie, clotting cascade) that is activated by the body when there is a bleeding episode; the management of blood products and the rationale for reducing their use; the financial implications of hemostatic agent use; and how these agents are used, their clinical indications, and potential complications from their use.
Safety and Usability of Hemostats, Sealants, and Adhesives
Authors: Burks Sandra , Spotnitz William 
Published: July 2014

AbstractHemostats, sealants, and adhesives are an integral part of surgical patient care. Nurses who have knowledge about these agents can better help ensure safe, efficient surgical patient care. As a caregiver and patient advocate, the perioperative nurse must understand the most current information about these agents and be prepared to facilitate the transfer of this knowledge to all caregivers. Information about these agents, including the contraindications, warnings, and precautions associated with their use as well as their preparation and application, is provided here. Algorithms designed to clarify the best options for using hemostats, sealants, and adhesives are included as well.
Clinical Issues‐August 2014
Authors: Wood Amber , Conner Ramona L. , Bruley Mark E. , Lavanchy Chris , Horvath Gail M. 
Published: July 2014

This MonthCyanoacrylate microbial sealantsKey words: sealant, microbial sealant, surgical site infections, SSIs.Enhanced environmental cleaningKey words: cleaning, enhanced cleaning, multidrug‐resistant organisms, MDROs, infection transmission.Antibiotic stewardship programsKey words: stewardship, stewardship programs, antibiotics, multidrug‐resistant organisms, MDROs, Clostridium difficile, C diff.Blanket‐warming cabinet temperature settingsKey words: blankets, warming, temperature settings, warming cabinets.
Dependence in Alzheimer's disease and service use costs, quality of life, and caregiver burden: The DADE study
Authors: Jones Roy W. , Romeo Renee , Trigg Richard , Knapp Martin , Sato Azusa , King Derek , Niecko Timothy , Lacey Loretto ,   DADE Investigator Group
Published: July 2014

AbstractBackgroundMost models determining how patient and caregiver characteristics and costs change with Alzheimer's disease (AD) progression focus on one aspect, for example, cognition. AD is inadequately defined by a single domain; tracking progression by focusing on a single aspect may mean other important aspects are insufficiently addressed. Dependence has been proposed as a better marker for following disease progression.MethodsThis was a cross‐sectional observational study (18 UK sites). Two hundred forty‐nine community or institutionalized patients, with possible/probable AD, Mini‐Mental State Examination (3–26), and a knowledgeable informant participated.ResultsSignificant associations noted between dependence (Dependence Scale [DS]) and clinical measures of severity (cognition, function, and behavior). Bivariate and multivariate models demonstrated significant associations between DS and service use cost, patient quality of life, and caregiver perceived burden.ConclusionThe construct of dependence may help to translate the combined impact of changes in cognition, function, and behavior into a more readily interpretable form. The DS is useful for assessing patients with AD in clinical trials/research.
Psychosocial telephone intervention for dementia caregivers: A randomized, controlled trial
Authors: Tremont Geoffrey , Davis Jennifer D. , Papandonatos George D. , Ott Brian R. , Fortinsky Richard H. , Gozalo Pedro , Yue Mun Sang , Bryant Kimberly , Grover Christine , Bishop Duane S. 
Published: July 2014

AbstractBackgroundIdentifying effective and accessible interventions for dementia caregivers is critical as dementia prevalence increases.ObjectiveExamine the effects of a telephone‐based intervention on caregiver well‐being.DesignRandomized, controlled trial.SettingAcademic medical center.ParticipantsTwo hundred and fifty distressed, family, dementia caregivers.InterventionCaregivers randomized to receive 16 telephone contacts over 6 months of either the Family Intervention: Telephone Tracking—Caregiver (FITT‐C) or Telephone Support (TS).OutcomePrimary outcome variables were family caregivers' depressive symptoms, burden, and reactions to care recipients' behavior problems at 6 months.ResultsThe FITT‐C intervention resulted in significantly improved caregiver depressive symptoms (P = .003; 27% net improvement) and less severe reactions to care‐recipient depressive behaviors (P = .009; 29% net improvement) compared with the control condition (TS).ConclusionAn entirely telephone‐based intervention improves caregivers' depressive symptoms and reactions to behavior problems in the care recipient and is comparable with reported results of face‐to‐face interventions.
Economies of extremes: Lessons from venture‐capital decision making
Authors: de Treville Suzanne , Petty Jeffrey S. , Wager Stefan 
Published: July 2014

AbstractAn organization's ability to exploit extreme events—such as exceptional opportunities—depends on its capacity strategy. The venture capital industry illustrates the interplay of expensive capacity and negative externalities from high utilization. The cost of adding a venture capitalist provides a strong incentive to run lean, but such leanness may make it impossible to evaluate all interesting investment opportunities. Using concepts from extreme‐value theory, we analyze the trade‐off between the costs and benefits arising from an increase in the number of evaluated deals. We ground our analysis in 11 years of archival data from a venture capital firm, representing 3631 deals, the decisions made, the reasons for those decisions, and the decision lead times. The firm identified 20% of arriving deals as worth evaluating during the screening process, but was not able to evaluate approximately 9% of those interesting deals due to a lack of capacity. We show that the value of increasing the number of deals evaluated increases with the tail weight of the distribution of deal values. When the right tail is light, increasing the number of deals evaluated may provide too modest a benefit to justify the cost. When, however, the right tail is heavy, the value of increasing the number of deals is likely to more than compensate for the cost of capacity. Our results provide new insight into the relative value of a chase capacity strategy that emphasizes responsiveness versus a high‐utilization heuristic that emphasizes productivity. Our approach can be applied to other search operations such as personnel selection, quality circles seeking to identify root causes, and making employee capacity available for innovation.
Orbital Roof Fracture and Orbital Cellulitis Secondary to Halo Pin Penetration: Case Report
Authors: Menon K. Venugopal , Al Rawi Asif Esam , Taif Sawsan , Al Ghafri Khalifa , Mollahalli Kishore Kumar 
Published: July 2014

Study Design Case report. Objective To report and discuss a rare complication after a patient was treated conservatively with a halo vest. Methods A 51-year-old man sustained a hangman's injury of the C2 vertebra following a motor vehicle collision. He was treated conservatively in a halo vest appliance and following mobilization was discharged from the hospital. Two weeks after discharge, the patient presented to the emergency department complaining of proptosis, ptosis, diplopia, and pin loosening. He was readmitted to the hospital, the halo vest was removed, and urgent imaging studies including computed tomography scan and magnetic resonance imaging were performed. They revealed that one of the halo pins had penetrated the orbital roof with active infection of the extraocular soft tissues. In consultation with the ophthalmologist, he was treated conservatively with antibiotics for 10 days. Results His ophthalmologic complaints resolved gradually and his eye returned to normal appearance and function. In the meantime, he was immobilized in a sterno-occipital mandibular immobilizer brace. Conclusion Though rare, penetrating injuries after cranial pin insertion can occur. Halo devices must be applied by, or under close supervision of, experienced personnel to avoid such complications, and halo vests should be reviewed frequently to detect such incidents early.
Big data and other challenges in the quest for orthologs
Authors: Sonnhammer Erik L.L. , Gabaldón Toni , Sousa da Silva Alan W. , Martin Maria , Robinson-Rechavi Marc , Boeckmann Brigitte , Thomas Paul D. , Dessimoz Christophe ,   the Quest for Orthologs consortium
Published: July 2014

Abstract
Given the rapid increase of species with a sequenced genome, the need to identify orthologous genes between them has emerged as a central bioinformatics task. Many different methods exist for orthology detection, which makes it difficult to decide which one to choose for a particular application.
Here, we review the latest developments and issues in the orthology field, and summarize the most recent results reported at the third ‘Quest for Orthologs’ meeting. We focus on community efforts such as the adoption of reference proteomes, standard file formats and benchmarking. Progress in these areas is good, and they are already beneficial to both orthology consumers and providers. However, a major current issue is that the massive increase in complete proteomes poses computational challenges to many of the ortholog database providers, as most orthology inference algorithms scale at least quadratically with the number of proteomes.
The Quest for Orthologs consortium is an open community with a number of working groups that join efforts to enhance various aspects of orthology analysis, such as defining standard formats and datasets, documenting community resources and benchmarking.
Availability and implementation: All such materials are available at http://questfororthologs.org .
Contact: erik.sonnhammer@scilifelab.se or c.dessimoz@ucl.ac.uk
Comparison of the mammalian insulin signalling pathway to invertebrates in the context of FOXO-mediated ageing
Authors: Papatheodorou Irene , Petrovs Rudolfs , Thornton Janet M. 
Published: July 2014

Abstract
Motivation : A large number of experimental studies on ageing focus on the effects of genetic perturbations of the insulin/insulin-like growth factor signalling pathway (IIS) on lifespan. Short-lived invertebrate laboratory model organisms are extensively used to quickly identify ageing-related genes and pathways. It is important to extrapolate this knowledge to longer lived mammalian organisms, such as mouse and eventually human, where such analyses are difficult or impossible to perform. Computational tools are needed to integrate and manipulate pathway knowledge in different species.
Results: We performed a literature review and curation of the IIS and target of rapamycin signalling pathways in Mus Musculus . We compare this pathway model to the equivalent models in Drosophila melanogaster and Caenorhabtitis elegans . Although generally well-conserved, they exhibit important differences. In general, the worm and mouse pathways include a larger number of feedback loops and interactions than the fly. We identify ‘functional orthologues’ that share similar molecular interactions, but have moderate sequence similarity. Finally, we incorporate the mouse model into the web-service NetEffects and perform in silico gene perturbations of IIS components and analyses of experimental results. We identify sub-paths that, given a mutation in an IIS component, could potentially antagonize the primary effects on ageing via FOXO in mouse and via SKN-1 in worm. Finally, we explore the effects of FOXO knockouts in three different mouse tissues.
Availability and implementation: http://www.ebi.ac.uk/thornton-srv/software/NetEffects
Contact: ip8@sanger.ac.uk or thornton@ebi.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Compression and fast retrieval of SNP data
Authors: Sambo Francesco , Di Camillo Barbara , Toffolo Gianna , Cobelli Claudio 
Published: July 2014

Abstract
Motivation: The increasing interest in rare genetic variants and epistatic genetic effects on complex phenotypic traits is currently pushing genome-wide association study design towards datasets of increasing size, both in the number of studied subjects and in the number of genotyped single nucleotide polymorphisms (SNPs). This, in turn, is leading to a compelling need for new methods for compression and fast retrieval of SNP data.
Results: We present a novel algorithm and file format for compressing and retrieving SNP data, specifically designed for large-scale association studies. Our algorithm is based on two main ideas: (i) compress linkage disequilibrium blocks in terms of differences with a reference SNP and (ii) compress reference SNPs exploiting information on their call rate and minor allele frequency. Tested on two SNP datasets and compared with several state-of-the-art software tools, our compression algorithm is shown to be competitive in terms of compression rate and to outperform all tools in terms of time to load compressed data.
Availability and implementation: Our compression and decompression algorithms are implemented in a C++ library, are released under the GNU General Public License and are freely downloadable from http://www.dei.unipd.it/~sambofra/snpack.html .
Contact: sambofra@dei.unipd.it or cobelli@dei.unipd.it .
Biocellion
: accelerating computer simulation of multicellular biological system models
Authors: Kang Seunghwa , Kahan Simon , McDermott Jason , Flann Nicholas , Shmulevich Ilya 
Published: July 2014

Abstract
Motivation: Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming.
Results: We have developed Biocellion , a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion , modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies.
Availability and implementation: Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information.
Contact: seunghwa.kang@pnnl.gov
e-Driver: a novel method to identify protein regions driving cancer
Authors: Porta-Pardo Eduard , Godzik Adam 
Published: July 2014

Abstract
Motivation: Most approaches used to identify cancer driver genes focus, true to their name, on entire genes and assume that a gene, treated as one entity, has a specific role in cancer. This approach may be correct to describe effects of gene loss or changes in gene expression; however, mutations may have different effects, including their relevance to cancer, depending on which region of the gene they affect. Except for rare and well-known exceptions, there are not enough data for reliable statistics for individual positions, but an intermediate level of analysis, between an individual position and the entire gene, may give us better statistics than the former and better resolution than the latter approach.
Results: We have developed e-Driver, a method that exploits the internal distribution of somatic missense mutations between the protein’s functional regions (domains or intrinsically disordered regions) to find those that show a bias in their mutation rate as compared with other regions of the same protein, providing evidence of positive selection and suggesting that these proteins may be actual cancer drivers. We have applied e-Driver to a large cancer genome dataset from The Cancer Genome Atlas and compared its performance with that of four other methods, showing that e-Driver identifies novel candidate cancer drivers and, because of its increased resolution, provides deeper insights into the potential mechanism of cancer driver genes identified by other methods.
Availability and implementation: A Perl script with e-Driver and the files to reproduce the results described here can be downloaded from https://github.com/eduardporta/e-Driver.git
Contact: adam@godziklab.org or eppardo@sanfordburnham.org
Supplementary information: Supplementary data are available at Bioinformatics online.