bluuebunny/crossref_metadata_2025_split huggingface dataset:
Behavioral and Physiological Responses of Largemouth Bass to Rain‐Induced Reductions in Dissolved Oxygen in an Urban System
Authors: Gaulke Greg L. , Wolfe, John R. , Bradley, Douglas L. , Moskus Penelope E. , Wahl David H. , Suski Cory D. 
Published: July 2015

AbstractWaters in urban areas often experience hypoxic events due to combined sewer overflows, which have the potential to negatively affect aquatic biota. Despite these hypoxic events, many urban areas have diverse fish assemblages, suggesting hypoxia has a minimal impact. Data to quantify the impacts of aquatic hypoxia in urban systems are currently lacking. The current study sought to define how rain‐induced hypoxia affected the movement, distribution, and physiology of individual Largemouth Bass Micropterus salmoides residing in the Chicago Area Waterway System (CAWS), an urban area prone to episodes of hypoxia. Following the onset of hypoxic events, the likelihood of Largemouth Bass remaining in hypoxic water was reduced, but fish did not completely avoid hypoxic areas. This suggests that hypoxia exerts only a moderate influence on the movement of Largemouth Bass. Field sampling showed that Largemouth Bass from the site prone to hypoxia were not in poor nutritional condition and were not suffering from chronic stress, relative to compared with those from reference sites. Field sampling also showed that fish from the CAWS displayed an improved capability to transport oxygen in the blood compared with individuals from control sites. Following a low‐oxygen challenge in the laboratory, fish from the CAWS also displayed elevated levels of oxygen transport capabilities compared with fish from some control sites. Together, results suggest that hypoxic events have limited behavioral consequences for Largemouth Bass, and in fact, Largemouth Bass in our study may have developed an improved ability to tolerate hypoxia, which would allow them to persist in hypoxia‐prone areas.
Does Daily Growth Affect the Rate of Manganese Uptake in Juvenile River Herring Otoliths?
Authors: Turner S. M. , Limburg K. E. 
Published: July 2015

AbstractManganese is a commonly found constituent in fish otoliths, yet a direct correlation with ambient water concentrations as observed for other elements has proven elusive. There is compelling evidence that Mn uptake is related to the availability of reduced Mn (Mn2+) resulting from hypoxia (Limburg et al. 2015) but that fish growth rate also plays a role. We tested the latter possibility by examining otoliths from anadromous river herring (Alewife Alosa pseudoharengus and Blueback Herring A. aestivalis) in New York waters. A significant correlation was found between the ages at which shifts in otolith daily growth increments (assumed proportional to somatic growth) and shifts in otolith Mn:Ca ratios were detected. Furthermore, significant positive Spearman's rank correlations were observed between mean otolith daily growth and otolith Mn:Ca. Species‐ and site‐specific differences were evident, but significant positive correlations were found for these relationships within each species and at most sampling sites. Ambient water concentrations were weakly correlated with otolith Mn:Ca, suggesting that both exogenous and endogenous factors influence Mn:Ca in otoliths. Thus, while endogenous mechanisms (i.e., growth rate) likely influence Mn uptake, exogenous availability is the ultimate control.
Development of a PCR Assay Based on a Single–Base Pair Substitution for the Detection of Aeromonas caviae by Targeting the gyrB Gene
Authors: Payattikul Penpan , Longyant Siwaporn , Sithigorngul Paisarn , Chaivisuthangkura Parin 
Published: July 2015

Abstract
Aeromonas caviae is a bacterial pathogen that causes various infectious diseases in both humans and animals. To facilitate its detection, we developed species-specific primer sets targeting polymorphisms in the gyrB gene for use in a PCR assay. The technique was able to detect 100% (29/29) of the A. caviae strains tested using either of two sets of primers (designated ACF1-ACR and ACF3-ACR), which produced 293-bp and 206-bp amplicons, respectively. Another set of primers (designated ACF2-ACR) yielded a 237-bp amplicon and exhibited 90% (26/29) positive results with respect to A. caviae. None of the primer sets exhibited cross-reactivity with 12 non–A. caviae isolates and 52 other non-Aeromonas bacteria. The detection limit using the ACF2-ACR and ACF3-ACR primer sets in pure culture was 1.6 × 103 CFU/mL, or 6 CFU per reaction, whereas that of the ACF1-ACR primer set was 1.6 × 104 CFU/mL, or 60 CFU per reaction. In the case of spiked Nile Tilapia Oreochromis niloticus, the sensitivity of all primer sets without enrichment was 1.8 × 104 CFU/g, or 30 CFU per reaction. Primer set ACF3-ACR was the best for a PCR assay targeting the gyrB gene, and the PCR technique developed was rapid, specific, and sensitive for the identification of A. caviae.
Received December 2, 2014; accepted April 9, 2015
Influence of Dietary Ascorbic Acid on the Immune Responses of Juvenile Korean Rockfish Sebastes schlegelii
Authors: Kim Jun-Hwan , Kang Ju-Chan 
Published: July 2015

Abstract
Juvenile Korean Rockfish Sebastes schlegelii (length, 13.6 ± 1.4 cm [mean ± SD]; weight, 53.6 ± 4.2 g) were fed twice daily with diets containing varying levels of ascorbic acid (0, 50, 100, 200, and 400 mg/kg) for 4 weeks. Significant increases in daily weight and length occurred in fish fed more than 50 mg/kg ascorbic acid. The lysozyme activity of fish fed diets containing ascorbic acid was considerably increased in rockfish plasma at 400 mg/kg ascorbic acid and in kidney at over 50 mg/kg ascorbic acid. Total plasma immunoglobulin M (IgM) levels were markedly elevated in fish fed 400 mg/kg ascorbic acid. The results suggest that dietary ascorbic acid supplementation in juvenile rockfish can induce a significant increase in growth and in immunological features such as lysozyme activity and plasma IgM levels.
Received October 1, 2014; accepted May 2, 2015
The Effect of a Mycotoxin Deactivation Product on Growth of Juvenile Rainbow Trout Fed Distillers Dried Grains
Authors: Sealey Wendy M , Hooley Christopher G , Rosentrater Kurt A , Gaylord T Gibson , Barrows Frederic T 
Published: July 2015

Abstract
Distillers dried grains (DDG) with solubles (DDGS) is a product that has shown potential as a protein source for some fish species, but high inclusion rates of DDGS have not always been successfully achieved for Rainbow Trout Oncorhynchus mykiss. Our objective was to determine whether inclusion of a mycotoxin deactivation product (Biofix Plus) could improve the ability of high-protein DDG (HPDDG) to replace a portion of the fish meal in diets for Rainbow Trout. The 2 × 2 factorial feeding trial examined protein source (menhaden fish meal [MFM] or HPDDG) with or without Biofix Plus. A control diet (42% digestible protein, 20% crude lipid, 25% MFM) was compared to a test diet in which HPDDG replaced 12% of the total MFM on a digestible-protein basis (24% HPDDG inclusion). Diets were fed to juvenile Rainbow Trout (initial weight: mean ± SE = 30.5 ± 1.6 g) in four replicate tanks per treatment for 9 weeks in a 15°C recirculating system. At the conclusion of the feeding trial, we observed no negative effects of fish meal replacement on growth or feed conversion ratio; no benefit of Biofix Plus supplementation was observed. These data indicate that when Rainbow Trout diets containing a high-quality DDGS product are balanced for digestible protein, lysine, methionine, and threonine, dietary fish meal levels can be successfully reduced to 13% without compromising growth and without the need for mycotoxin deactivator inclusion.
SynLinker: an integrated system for designing linkers and synthetic fusion proteins
Authors: Liu Chengcheng , Chin Ju Xin , Lee Dong-Yup 
Published: July 2015

Abstract
Summary: Synthetic fusion proteins have shown great potential in various biotechnological and (bio)pharmaceutical applications. They usually contain more than two protein domains joined by a linker peptide sequence which is often selected intuitively or in ad hoc manner. Thus, we developed an integrated web-based system, SynLinker, to provide appropriate linker candidates for constructing fusion proteins. We compiled a total of 2260 linker sequences comprising of natural linkers extracted from a set of non-redundant multi-domain proteins in Protein Data Bank and artificial/empirical linkers collected from literature and patents. Multiple query interface allows users to search for the desired linker candidates based on selection criteria and their preferences. In addition, a selected linker can be combined with two domain structures which are uploaded and appended at its N and C terminals, thereby predicting a de novo structure of the fusion protein. Hence, SynLinker can serve as a systematic tool for researchers who are interested in designing synthetic fusion proteins.
Availability and implementation: SynLinker is freely available at http://bioinfo.bti.a-star.edu.sg/synlinker.
Contact: cheld@nus.edu.sg
Supplementary information: Supplementary data are available at Bioinformatics online.
Review and evaluation of electronic health records-driven phenotype algorithm authoring tools for clinical and translational research
Authors: Xu Jie , Rasmussen Luke V , Shaw Pamela L , Jiang Guoqian , Kiefer Richard C , Mo Huan , Pacheco Jennifer A , Speltz Peter , Zhu Qian , Denny Joshua C , Pathak Jyotishman , Thompson William K , Montague Enid 
Published: July 2015

Abstract
Objective To review and evaluate available software tools for electronic health record–driven phenotype authoring in order to identify gaps and needs for future development.
Materials and Methods Candidate phenotype authoring tools were identified through (1) literature search in four publication databases (PubMed, Embase, Web of Science, and Scopus) and (2) a web search. A collection of tools was compiled and reviewed after the searches. A survey was designed and distributed to the developers of the reviewed tools to discover their functionalities and features.
Results Twenty-four different phenotype authoring tools were identified and reviewed. Developers of 16 of these identified tools completed the evaluation survey (67% response rate). The surveyed tools showed commonalities but also varied in their capabilities in algorithm representation, logic functions, data support and software extensibility, search functions, user interface, and data outputs.
Discussion Positive trends identified in the evaluation included: algorithms can be represented in both computable and human readable formats; and most tools offer a web interface for easy access. However, issues were also identified: many tools were lacking advanced logic functions for authoring complex algorithms; the ability to construct queries that leveraged un-structured data was not widely implemented; and many tools had limited support for plug-ins or external analytic software.
Conclusions Existing phenotype authoring tools could enable clinical researchers to work with electronic health record data more efficiently, but gaps still exist in terms of the functionalities of such tools. The present work can serve as a reference point for the future development of similar tools.
Learning from the crowd while mapping to LOINC
Authors: Vreeman Daniel J , Hook John , Dixon Brian E 
Published: July 2015

Abstract
Objective To describe the perspectives of Regenstrief LOINC Mapping Assistant (RELMA) users before and after the deployment of Community Mapping features, characterize the usage of these new features, and analyze the quality of mappings submitted to the community mapping repository.
Methods We evaluated Logical Observation Identifiers Names and Codes (LOINC) community members’ perceptions about new “wisdom of the crowd” information and how they used the new RELMA features. We conducted a pre-launch survey to capture users’ perceptions of the proposed functionality of these new features; monitored how the new features and data available via those features were accessed; conducted a follow-up survey about the use of RELMA with the Community Mapping features; and analyzed community mappings using automated methods to detect potential errors.
Results Despite general satisfaction with RELMA, nearly 80% of 155 respondents to our pre-launch survey indicated that having information on how often other users had mapped to a particular LOINC term would be helpful. During the study period, 200 participants logged into the RELMA Community Mapping features an average of 610 times per month and viewed the mapping detail pages a total of 6686 times. Fifty respondents (25%) completed our post-launch survey, and those who accessed the Community Mapping features unanimously indicated that they were useful. Overall, 95.3% of the submitted mappings passed our automated validation checks.
Conclusion When information about other institutions’ mappings was made available, study participants who accessed it agreed that it was useful and informed their mapping choices. Our findings suggest that a crowd-sourced repository of mappings is valuable to users who are mapping local terms to LOINC terms.
Globe Loss From Intraocular Invasion of MIRAgel Scleral Buckle Components
Authors: Rubinstein Tal J. , Choudhary Maria M. , Modi Yasha S. , Ehlers Justis P. , Perry Julian D. 
Published: July 2015

Purpose:
To describe intraocular invasion of MIRAgel scleral buckles requiring evisceration.

Methods:
This is an Institutional Review Board-approved retrospective consecutive case series of eyes requiring evisceration secondary to intraocular intrusion of MIRAgel implants performed at the Cole Eye Institute from 2000 to 2014. Charts were reviewed for age at surgery, gender, laterality, time between MIRAgel placement and evisceration, preoperative examination and imaging results, intraoperative findings, postoperative complications, and duration of follow up.

Results:
Five eyes of 5 patients underwent evisceration due to a blind, painful eye secondary to MIRAgel expansion. The mean time between MIRAgel placement and evisceration was 21 years (range: 17–30 years). Preoperative ultrasound identified intraocular MIRAgel in 3 of 5 cases; however, intraocular MIRAgel was identified during surgery in all 5 cases. A transocular-approach orbitotomy was performed at the time of evisceration in an effort to remove the MIRAgel. Postoperative complications included ptosis and inability to retain an ocular prosthesis. No cases of orbital implant extrusion occurred.

Conclusion:
Scleral invasion and intraocular penetration of MIRAgel may occur decades after placement. This may result in a blind, painful eye requiring evisceration and orbitotomy to remove residual material. Suspicion of intraocular penetration of implant should be high in blind, painful eyes. Surgical removal can be difficult due to MIRAgel fragmentation. Conjunctival insufficiency may result in the need for further surgery after evisceration.
Incidence and etiology of mortality in polytrauma patients in a Dutch level I trauma center
Authors: El Mestoui Zainab , Jalalzadeh Hamid , Giannakopoulos Georgios F. , Zuidema Wietse P. 
Published: July 2015

Background
Earlier studies assessing mortality in polytrauma patients have focused on improving trauma care and reducing complications during hospital stay. The same studies have shown that the complication rate in these patients is high, often resulting in death. The aim of this study was to assess the incidence and causes of mortality in polytrauma patients in our institute. Secondarily, we assessed the donation and autopsy rates and outcome in these patients.

Patients and methods
All polytrauma patients (injury severity score≥16) transported to and treated in our institute during a period of 6 years were retrospectively analyzed. We included all patients who died during hospital stay. Prehospital and in-hospital data were collected on patients’ condition, diagnostics, and treatment. The chance of survival was calculated according to the TRISS methodology. Patients were categorized according to the complications during treatment and causes of death. Logistic regression analysis was used to design a prediction model for mortality in major trauma. A statistical analysis was carried out.

Results
Of the 1073 polytrauma patients who were treated in our institute during the study period, 205 (19.1%) died during hospital stay. The median age of the deceased patients was 58.8 years and 125 patients were men. Their mean injury severity score was 30.4. The most common mechanism of injury involved fall from height, followed by bicycle accidents. Almost 50% of the patients underwent an emergency intervention. Almost 92% of the total population died because of the effects of the accident (primary trauma). Of these, 24% died during primary assessment in the emergency department. Most patients died because of the effects of severe head injury (63.4%), followed by exsanguination (17.6%). The most common type of complications causing death during treatment was respiratory failure (6.3%), followed by multiple organ failure (1.5%). Autopsy was performed in 10.4%. Organ donation procedure was performed in 14.5%. Permission for donation was not provided in almost 20% of the population.

Conclusion
The mortality rate in polytrauma patients in our institute is considerable and comparable with the international literature. Most patients die because of the effects of the accident (primary trauma). Autopsy and organ donation rates are low in our institution and leave room for substantial improvements in the future.
Can Composite Measures Provide a Different Perspective on Provider Performance Than Individual Measures?
Authors: Shwartz Michael , Rosen Amy K. , Burgess James F. 
Published: July 2015

Background:
Composite measures, which aggregate performance on individual measures into a summary score, are increasingly being used to evaluate facility performance. There is little understanding of the unique perspective that composite measures provide.

Objective:
To examine whether high/low (ie, high or low) performers on a composite measures are also high/low performers on most of the individual measures that comprise the composite.

Methods:
We used data from 2 previous studies, one involving 5 measures from 632 hospitals and one involving 28 measures from 112 Veterans Health Administration (VA) nursing homes; and new data on hospital readmissions for 3 conditions from 131 VA hospitals. To compare high/low performers on a composite to high/low performers on the component measures, we used 2-dimensional tables to categorize facilities into high/low performance on the composite and on the individual component measures.

Results:
In the first study, over a third of the 162 hospitals in the top quintile based on the composite were in the top quintile on at most 1 of the 5 individual measures. In the second study, over 40% of the 27 high-performing nursing homes on the composite were high performers on 8 or fewer of the 28 individual measures. In the third study, 20% of the 61 low performers on the composite were low performers on only 1 of the 3 individual measures.

Conclusions:
Composite measures can identify as high/low performers facilities that perform “pretty well” (or “pretty poorly”) across many individual measures but may not be high/low performers on most of them.
Mutations in the Prokaryotic Pathway Rescue the fatty acid biosynthesis1 Mutant in the Cold
Authors: Gao Jinpeng , Wallis James G. , Browse John 
Published: July 2015

Abstract
The Arabidopsis (Arabidopsis thaliana) fatty acid biosynthesis1 (fab1) mutant has increased levels of the saturated fatty acid 16:0 due to decreased activity of 3-ketoacyl-acyl carrier protein (ACP) synthase II. In fab1 leaves, phosphatidylglycerol, the major chloroplast phospholipid, contains up to 45% high-melting-point molecular species (molecules that contain only 16:0, 16:1-trans, and 18:0), a trait associated with chilling-sensitive plants, compared with less than 10% in wild-type Arabidopsis. Although they do not exhibit typical chilling sensitivity, when exposed to low temperatures (2°C–6°C) for long periods, fab1 plants do suffer collapse of photosynthesis, degradation of chloroplasts, and eventually death. A screen for suppressors of this low-temperature phenotype has identified 11 lines, some of which contain additional alterations in leaf-lipid composition relative to fab1. Here, we report the identification of two suppressor mutations, one in act1, which encodes the chloroplast acyl-ACP:glycerol-3-phosphate acyltransferase, and one in lpat1, which encodes the chloroplast acyl-ACP:lysophosphatidic acid acyltransferase. These enzymes catalyze the first two steps of the prokaryotic pathway for glycerolipid synthesis, so we investigated whether other mutations in this pathway would rescue the fab1 phenotype. Both the gly1 mutation, which reduces glycerol-3-phosphate supply to the prokaryotic pathway, and fad6, which is deficient in the chloroplast 16:1/18:1 fatty acyl desaturase, were discovered to be suppressors. Analyses of leaf-lipid compositions revealed that mutations at all four of the suppressor loci result in reductions in the proportion of high-melting-point molecular species of phosphatidylglycerol relative to fab1. We conclude that these reductions are likely the basis for the suppressor phenotypes.
Access over ownership – a typology of shared space
Authors: Brinkø Rikke , Nielsen Susanne Balslev , van Meel Juriaan 
Published: July 2015

Purpose
– This paper aims to explore shared use of space and facilities as a concept, and present and illustrate the use of a typology to help classify and describe the different options for sharing space and facilities within buildings for optimised use of a building portfolio.

Design/methodology/approach
– The content presented is based on a cross-sectional study with an inductive approach. The results are based partly on secondary data in the form of a literature review and a mapping of 20 examples from Europe, USA and Australia, and partly on primary data from observations and interviews with key actors from two cases in Denmark and an illustration case from Ireland.

Findings
– The typology classifies and describes four archetypes of sharing between different people, building owners and organisations, to be used when discussing, planning, establishing and evaluating new and existing shared spaces.

Research limitations/implications
– The typology is the result of a first exploration of shared use of facilities and does not claim to be fully comprehensive or final.

Practical implications
– The typology is intended for both researchers and practitioners, and aims at increasing the understanding of sharing as a way to minimise the need for building new by better utilisation of the existing building stock.

Originality/value
– Shared space and facilities is a relatively new topic with not much research undertaken. This typology provides a language for discussing shared spaces and a base for further developing the research field.