bluuebunny/crossref_metadata_2025_split huggingface dataset:
New York City's Healthcare Transportation during a Disaster: A Preparedness Framework for a Wicked Problem
Authors: Sternberg Ernest , Lee George C. 
Published: November 2014

AbstractDuring a disaster, victims with varied morbidities are located at incident sites, while healthcare facilities with varied healthcare resources are distributed elsewhere. Transportation serves an essential equilibrating role: it helps balance the patients' need for care with the supply of care. Studying the special case of New York City, this article sets out the healthcare transportation components as: (1) incident morbidity; (2) transportation assets; and (3) healthcare capacity. The relationship between these three components raises an assignment problem: the management of healthcare transportation within a dynamic and partly unpredictable incident-transportation-healthcare nexus, under urban disruption. While the routine dispatch problem can be tackled through better geographic allocation software and technical algorithms, the disaster assignment problem must be confronted through real-time, mutual adjustment between institutions. This article outlines institutional alternatives for managing the assignment problem and calls for further research on the merits of alternative institutional models.
The Influence of Experimental Parameters and Specimen Geometry on the Mass Spectra of Copper During Pulsed-Laser Atom-Probe Tomography
Authors: Kolli R. Prakash , Meisenkothen Frederick 
Published: November 2014

AbstractWe have studied the influence of experimental factors and specimen geometry on the quality of the mass spectra in copper (Cu) during pulsed-laser atom-probe tomography. We have evaluated the effects of laser pulse energy, laser pulse frequency, specimen base temperature, specimen tip radius, and specimen tip shank half-angle on the effects of mass resolving power, (m/Δm), at full-width at half-maximum and at full-width at tenth-maximum, the tail size after the major mass-to-charge state (m/n) ratio peaks, and the mass spectra. Our results indicate that mass resolving power improves with decreasing pulse energy between 40 and 80 pJ and decreasing base temperature between 20 and 80 K. The mass resolving power also improves with increasing tip radius and shank half-angle. A pulse frequency of 250 kHz slightly improves the mass resolving power relative to 100 or 500 kHz. The tail size decreases with increasing pulse energy. The mass resolving power improves when the cooling time is reduced, which is influenced by the thermal diffusivity of Cu and the specimen base temperature.
A Study on the Digestive Physiology of a Marine Polychaete (Eulalia viridis) through Microanatomical Changes of Epithelia During the Digestive Cycle
Authors: Rodrigo Ana P. , Costa Maria H. , Alves de Matos António Pedro , Carrapiço Francisco , Costa Pedro M. 
Published: November 2014

AbstractAs for many invertebrates, the gut of marine polychaete species has key physiological functions. However, studies integrating microanatomical descriptions with physiological processes are scarce. The present investigates histological, histochemical and cytological changes in the alimentary canal during the digestive cycle of the marine annelid Eulalia viridis, a species that combines opportunist scavenging, predation and cannibalistic behavior. The gut is comprised of an eversible pharynx, esophagus, intestine and rectum. Three main phases of digestion were identified, namely, resting/secretory, absorptive and excretory. The intestinal epithelium is complex and exhibited the most significant changes regarding intracellular digestion, excretion and storage. Conversely, the pharynx and esophagus were chiefly important for enzyme secretion. The results also indicate the existence of two distinct types of secretory cells in the intestine, with likely distinct physiological roles. Some similarities have been found between the intestinal epithelia and the molluscan (especially cephalopod) digestive gland, as, for instance, the shedding of apical corpuscles by digestive cells at posterior stages of digestion. The findings indicate that the digestive process in this worm is complex and related to the many physiological roles that cells need to play in the presence of reduced organ differentiation.
Linking the Population Pharmacokinetics of Tenofovir and Its Metabolites With Its Cellular Uptake and Metabolism
Authors: Madrasi K , Burns R N , Hendrix C W , Fossler M J , Chaturvedula A 
Published: November 2014

Empirical pharmacokinetic models are used to explain the pharmacokinetics of the antiviral drug tenofovir (TFV) and its metabolite TFV diphosphate (TFV‐DP) in peripheral blood mononuclear cells. These empirical models lack the ability to explain differences between the disposition of TFV‐DP in HIV‐infected patients vs. healthy individuals. Such differences may lie in the mechanisms of TFV transport and phosphorylation. Therefore, we developed an exploratory model based on mechanistic mass transport principles and enzyme kinetics to examine the uptake and phosphorylation kinetics of TFV. TFV‐DP median Cmax from the model was 38.5 fmol/106 cells, which is bracketed by two reported healthy volunteer studies (38 and 51 fmol/106 cells). The model presented provides a foundation for exploration of TFV uptake and phosphorylation kinetics for various routes of TFV administration and can be updated as more is known on actual mechanisms of cellular transport of TFV.CPT Pharmacometrics Syst. Pharmacol. (2014) 3, e147; doi:10.1038/psp.2014.46; published online 12 November 2014
Effects of UV radiation on aquatic ecosystems and interactions with other environmental factors
Authors: Häder Donat-P. , Williamson Craig E. , Wängberg Sten-Åke , Rautio Milla , Rose Kevin C. , Gao Kunshan , Helbling E. Walter , Sinha Rajeshwar P. , Worrest Robert 
Published: November 2014

Abstract
Interactions between climate change and UV radiation are having strong effects on aquatic ecosystems due to feedback between temperature, UV radiation, and greenhouse gas concentration. Higher air temperatures and incoming solar radiation are increasing the surface water temperatures of lakes and oceans, with many large lakes warming at twice the rate of regional air temperatures. Warmer oceans are changing habitats and the species composition of many marine ecosystems. For some, such as corals, the temperatures may become too high. Temperature differences between surface and deep waters are becoming greater. This increase in thermal stratification makes the surface layers shallower and leads to stronger barriers to upward mixing of nutrients necessary for photosynthesis. This also results in exposure to higher levels of UV radiation of surface-dwelling organisms. In polar and alpine regions decreases in the duration and amount of snow and ice cover on lakes and oceans are also increasing exposure to UV radiation. In contrast, in lakes and coastal oceans the concentration and colour of UV-absorbing dissolved organic matter (DOM) from terrestrial ecosystems is increasing with greater runoff from higher precipitation and more frequent extreme storms. DOM thus creates a refuge from UV radiation that can enable UV-sensitive species to become established. At the same time, decreased UV radiation in such surface waters reduces the capacity of solar UV radiation to inactivate viruses and other pathogens and parasites, and increases the difficulty and price of purifying drinking water for municipal supplies. Solar UV radiation breaks down the DOM, making it more available for microbial processing, resulting in the release of greenhouse gases into the atmosphere. In addition to screening solar irradiance, DOM, when sunlit in surface water, can lead to the formation of reactive oxygen species (ROS). Increases in carbon dioxide are in turn acidifying the oceans and inhibiting the ability of many marine organisms to form UV-absorbing exoskeletons. Many aquatic organisms use adaptive strategies to mitigate the effects of solar UV-B radiation (280-315 nm), including vertical migration, crust formation, synthesis of UV-absorbing substances, and enzymatic and non-enzymatic quenching of ROS. Whether or not genetic adaptation to changes in the abiotic factors plays a role in mitigating stress and damage has not been determined. This assessment addresses how our knowledge of the interactive effects of UV radiation and climate change factors on aquatic ecosystems has advanced in the past four years.
Epithelial MUC1 promotes cell migration, reduces apoptosis and affects levels of mucosal modulators during acetylsalicylic acid (aspirin)-induced gastropathy
Authors: Banerjee Debashish , Fernandez Harvey Robert , Patil Pradeep Bhatu , Premaratne Pushpa , Quiding-Järbrink Marianne , Lindén Sara Katarina 
Published: November 2014

MUC1 is a transmembrane mucin highly expressed in the stomach. Although extensive research has uncovered many of its roles in cancer, knowledge about the functions of MUC1 in normal tissues is limited. In the present study, we showed that acetylsalicylic acid (ASA; aspirin) up-regulated MUC1/Muc1 expression in the gastric mucosa of humans and wild-type (WT) mice. ASA induced mucosal injury in all mice to a similar extent; however, WT animals and those chimaeras with Muc1 on the epithelia recovered faster than Muc1-knockout (KO) mice and chimaeras carrying Muc1 on haemopoietic but not epithelial cells. MUC1 enhanced proliferation and migration of the human gastric cell line MKN-7 and increased resistance to apoptosis. The repeated treatment regime used caused a reduction in cyclo-oxygenase-1 (Cox-1) expression, though WT animals returned faster towards pre-treatment levels and had increased Cox-2 and vascular endothelial growth factor levels during recovery. Thus we found that epithelial Muc1 is more important for the healing process than haemopoietic Muc1 and Muc1/MUC1 facilitates wound healing by enhancing cell migration and proliferation, protecting against apoptosis and mediating expression of mucosal modulators. Thus MUC1 plays essential roles during wound healing and development of treatment modalities targeting enhanced expression of MUC1 may be beneficial to treat mucosal wounds.
Teaching Active Listening Skills to Pre-Service Speech-Language Pathologists: A First Step in Supporting Collaboration With Parents of Young Children Who Require AAC
Authors: Thistle Jennifer J. , McNaughton David 
Published: November 2014

Purpose
This study examined the effect of instruction in an active listening strategy on the communication skills of pre-service speech-language pathologists (SLPs).

Method
Twenty-three pre-service SLPs in their 2nd year of graduate study received a brief strategy instruction in active listening skills. Participants were videotaped during a simulated parent meeting before and after the strategy instruction. Simulated parent meetings addressed issues that parents of children who use augmentative and alternative communication (AAC) may face. Social validity measures were gathered from the participants and from parents of children who use AAC.

Results
Pre- and postinstruction use of the active listening strategy was scored and compared using a Wilcoxon signed-ranks test, with statistically significant results. Postinstruction scores were significantly higher than preinstruction scores, providing evidence of the effectiveness of the instruction. Furthermore, participants and parents of children who use AAC described the postinstruction interactions more positively than the preinstruction interactions, suggesting that the pre-service SLPs benefited from the instruction.

Conclusion
The current study provides evidence of the effectiveness of strategy instruction in active listening skills that may be incorporated into SLP preparation programs.
Consequences of Co-Occurring Attention-Deficit/Hyperactivity Disorder on Children's Language Impairments
Authors: Redmond Sean M. , Ash Andrea C. , Hogan Tiffany P. 
Published: November 2014

Purpose
Co-occurring attention-deficit/hyperactivity disorder (ADHD) and communication disorders represent a frequently encountered challenge for school-based practitioners. The purpose of the present study was to examine in more detail the clinical phenomenology of co-occurring ADHD and language impairments (LIs).

Method
Measures of nonword repetition, sentence recall, and tense marking were collected from 57 seven- to nine-year-old children. The performances of children with ADHD+LI status were compared with those of children with specific language impairment (SLI) and children with typical development (TD).

Results
ADHD status had no independent detrimental impact on the affected children's LIs (SLI = ADHD+LI < TD). A modest positive correlation was found between the severity of children's ADHD symptoms and their sentence recall performance, suggesting a tendency for affected children who had higher levels of ADHD symptoms to perform better than those children with lower levels.

Conclusion
These outcomes are difficult to reconcile with attention-deficit/information-processing accounts of the core deficits associated with SLI. Potential protective mechanisms associated with ADHD status are discussed.
Improved successive multiuser detection initial ranging algorithm with interference cancellation for orthogonal frequency division multiple access systems
Authors: Xia Yujie , Ren Guangliang , Zhang Huining 
Published: November 2014

An improved successive multiuser detection (SMUD) initial ranging (IR) algorithm with interference cancellation is presented for orthogonal frequency division multiple access systems followed by IEEE 802.16 m standard. The proposed method detects all the valid paths of IR subscriber stations, selects the path with the maximum signal‐to‐interference‐plus‐noise ratio, and estimates the parameters of the path by least‐square method. The estimated parameters are further processed by the parallel interference cancellation processing to improve their accuracy, and then the signal of the selected valid path is removed from the received signal in the successive interference cancellation (SIC) process. The proposed scheme can efficiently improve the parameter estimation accuracy of the selected valid path and reduce the residual multiple access interference in the SIC process. Simulation results show that the proposed method has a much better performance than the SMUD algorithm.
GlycoRDF: an ontology to standardize glycomics data in RDF
Authors: Ranzinger Rene , Aoki-Kinoshita Kiyoko F. , Campbell Matthew P. , Kawano Shin , Lütteke Thomas , Okuda Shujiro , Shinmachi Daisuke , Shikanai Toshihide , Sawaki Hiromichi , Toukach Philip , Matsubara Masaaki , Yamada Issaku , Narimatsu Hisashi 
Published: November 2014

Abstract
Motivation: Over the last decades several glycomics-based bioinformatics resources and databases have been created and released to the public. Unfortunately, there is no common standard in the representation of the stored information or a common machine-readable interface allowing bioinformatics groups to easily extract and cross-reference the stored information.
Results: An international group of bioinformatics experts in the field of glycomics have worked together to create a standard Resource Description Framework (RDF) representation for glycomics data, focused on glycan sequences and related biological source, publications and experimental data. This RDF standard is defined by the GlycoRDF ontology and will be used by database providers to generate common machine-readable exports of the data stored in their databases.
Availability and implementation: The ontology, supporting documentation and source code used by database providers to generate standardized RDF are available online (http://www.glycoinfo.org/GlycoRDF/).
Contact: rene@ccrc.uga.edu or kkiyoko@soka.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
Development of a robust classifier for quality control of reverse-phase protein arrays
Authors: Ju Zhenlin , Liu Wenbin , Roebuck Paul L. , Siwak Doris R. , Zhang Nianxiang , Lu Yiling , Davies Michael A. , Akbani Rehan , Weinstein John N. , Mills Gordon B. , Coombes Kevin R. 
Published: November 2014

Abstract
Motivation: High-throughput reverse-phase protein array (RPPA) technology allows for the parallel measurement of protein expression levels in approximately 1000 samples. However, the many steps required in the complex protocol (sample lysate preparation, slide printing, hybridization, washing and amplified detection) may create substantial variability in data quality. We are not aware of any other quality control algorithm that is tuned to the special characteristics of RPPAs.
Results: We have developed a novel classifier for quality control of RPPA experiments using a generalized linear model and logistic function. The outcome of the classifier, ranging from 0 to 1, is defined as the probability that a slide is of good quality. After training, we tested the classifier using two independent validation datasets. We conclude that the classifier can distinguish RPPA slides of good quality from those of poor quality sufficiently well such that normalization schemes, protein expression patterns and advanced biological analyses will not be drastically impacted by erroneous measurements or systematic variations.
Availability and implementation: The classifier, implemented in the “SuperCurve” R package, can be freely downloaded at http://bioinformatics.mdanderson.org/main/OOMPA:Overview or http://r-forge.r-project.org/projects/supercurve/. The data used to develop and validate the classifier are available at http://bioinformatics.mdanderson.org/MOAR.
Contact: Kevin.Coombes@osumc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Mapping a viral phylogeny onto outbreak trees to improve host transmission inference
Authors: Allen Jonathan E , Velsko Stephan P 
Published: November 2014

AbstractBackgroundDeveloping methods to reconstruct transmission histories for viral outbreaks could provide critical information to support locating sources of disease transmission. Phylogenetic methods used to measure the degree of relatedness among sequenced viral samples have proven useful in identifying potential outbreak sources. The complex nature of infectious disease, however, makes it difficult to assign a rigorously defined quantitative confidence value assessing the likelihood of a true direct transmission event using genetic data alone.ResultsA new method is presented to calculate a confidence value assessing the likelihood of a transmission event using both phylogenetic inference and limited knowledge of incubation and infectious duration times. The method is applied to simulations of a foot and mouth disease (FMD) outbreak to demonstrate how the combination of both phylogenetic and epidemiology data can be used to strengthen the assessment of the likelihood of direct transmission over methods using just phylogenetic data or infection timing data alone. The method is applied to a previous FMD outbreak to identify areas where over confidence in previously inferred direct transmission may exist.ConclusionCombining knowledge from viral evolution and epidemiology within a single integrated transmission inference framework is an important approach to assess the potential likelihood of transmission events and makes clear how specific features of a virus’ spread through the course of an outbreak will directly determine the potential for confidence in inferred host transmission links.
RISAP Is a TGN-Associated RAC5 Effector Regulating Membrane Traffic during Polar Cell Growth in Tobacco
Authors: Stephan Octavian , Cottier Stephanie , Fahlén Sara , Montes-Rodriguez Adriana , Sun Jia , Eklund D. Magnus , Klahre Ulrich , Kost Benedikt 
Published: November 2014

AbstractRAC/ROP GTPases coordinate actin dynamics and membrane traffic during polar plant cell expansion. In tobacco (Nicotiana tabacum), pollen tube tip growth is controlled by the RAC/ROP GTPase RAC5, which specifically accumulates at the apical plasma membrane. Here, we describe the functional characterization of RISAP, a RAC5 effector identified by yeast (Saccharomyces cerevisiae) two-hybrid screening. RISAP belongs to a family of putative myosin receptors containing a domain of unknown function 593 (DUF593) and binds via its DUF593 to the globular tail domain of a tobacco pollen tube myosin XI. It also interacts with F-actin and is associated with a subapical trans-Golgi network (TGN) compartment, whose cytoplasmic position at the pollen tube tip is maintained by the actin cytoskeleton. In this TGN compartment, apical secretion and endocytic membrane recycling pathways required for tip growth appear to converge. RISAP overexpression interferes with apical membrane traffic and blocks tip growth. RAC5 constitutively binds to the N terminus of RISAP and interacts in an activation-dependent manner with the C-terminal half of this protein. In pollen tubes, interaction between RAC5 and RISAP is detectable at the subapical TGN compartment. We present a model of RISAP regulation and function that integrates all these findings.
Impacts of climate change on net crop revenue in North and South China
Authors: Wang Jinxia , Huang Jikun , Zhang Lijuan , Li Yumin 
Published: November 2014

Purpose
– The purpose of this paper is to explore the impacts of climate change on crop net revenue by region. Particularly, the authors focus on the impact differences between north and south regions.

Design/methodology/approach
– The authors applied the Ricardian approach which assumes that each farmer wishes to maximize revenue subject to the exogenous conditions of their farm. The climate data are based on actual measurements in 753 national meteorological stations and the socio-economic data covers 8,405 farms across 28 provinces in China.

Findings
– On average, the rise of annual temperature will hurt farms both in the north or south. The impacts of climate change on both precipitation and temperatures have different seasonal impacts on producers in the north and the south of China. As a consequence, the impact on net farm revenues varies with farms in the north and the south being adversely affected (to different degrees) by a rise in the temperature, but both benefiting from an anticipated increase in rainfall. The results also reveal that irrigation is one key adaption measure to dealing with climate change. Whether in the north or south of China, increasing temperature is beneficial to irrigated farms, while for rainfed farms, higher temperature will result in a reduction in net revenues. The results also reveal that farms in the north are more vulnerable to temperature and precipitation variation than that in the south. Irrigated farms in the south are more vulnerable to precipitation variation than that in the north; but rainfed farms in the north are more vulnerable to precipitation variation than that in the south.

Originality/value
– Applying empirical analysis to identify the differences of climate change impacts between north and south regions will help policy makers to design reasonable adaptation policies for various regions.