bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resource quality affects carbon cycling in deep-sea sediments
Authors: Mayor Daniel J , Thornton Barry , Hay Steve , Zuur Alain F , Nicol Graeme W , McWilliam Jenna M , Witte Ursula F M 
Published: March 2012

Abstract
Deep-sea sediments cover ∼70% of Earth's surface and represent the largest interface between the biological and geological cycles of carbon. Diatoms and zooplankton faecal pellets naturally transport organic material from the upper ocean down to the deep seabed, but how these qualitatively different substrates affect the fate of carbon in this permanently cold environment remains unknown. We added equal quantities of 13C-labelled diatoms and faecal pellets to a cold water (−0.7 °C) sediment community retrieved from 1080 m in the Faroe-Shetland Channel, Northeast Atlantic, and quantified carbon mineralization and uptake by the resident bacteria and macrofauna over a 6-day period. High-quality, diatom-derived carbon was mineralized &gt;300% faster than that from low-quality faecal pellets, demonstrating that qualitative differences in organic matter drive major changes in the residence time of carbon at the deep seabed. Benthic bacteria dominated biological carbon processing in our experiments, yet showed no evidence of resource quality-limited growth; they displayed lower growth efficiencies when respiring diatoms. These effects were consistent in contrasting months. We contend that respiration and growth in the resident sediment microbial communities were substrate and temperature limited, respectively. Our study has important implications for how future changes in the biochemical makeup of exported organic matter will affect the balance between mineralization and sequestration of organic carbon in the largest ecosystem on Earth.
Scale- and Context-Dependent Selection of Recreational Harvest Estimation Methods: The Australasian Experience
Authors: Hartill Bruce W. , Cryer Martin , Lyle Jeremy M. , Rees Eugene B. , Ryan Karina L. , Steffe Aldo S. , Taylor Stephen M. , West Laurie , Wise Brent S. 
Published: March 2012

Abstract
Fisheries managers are becoming increasingly aware of the need to quantify all forms of harvest, including that by recreational fishers. This need has been driven by both a growing recognition of the potential impact that noncommercial fishers can have on exploited resources and the requirement to allocate catch limits between different sectors of the wider fishing community in many jurisdictions. Marine recreational fishers are rarely required to report any of their activity, and some form of survey technique is usually required to estimate levels of recreational catch and effort. In this review, we describe and discuss studies that have attempted to estimate the nature and extent of recreational harvests of marine fishes in New Zealand and Australia over the past 20 years. We compare studies by method to show how circumstances dictate their application and to highlight recent developments that other researchers may find of use. Although there has been some convergence of approach, we suggest that context is an important consideration, and many of the techniques discussed here have been adapted to suit local conditions and to address recognized sources of bias. Much of this experience, along with novel improvements to existing approaches, have been reported only in “gray” literature because of an emphasis on providing estimates for immediate management purposes. This paper brings much of that work together for the first time, and we discuss how others might benefit from our experience.
Received February 8, 2011; accepted October 13, 2011
Market Structure, Competition from Assisted Living Facilities, and Quality in the Nursing Home Industry
Authors: Bowblis John R. 
Published: March 2012

AbstractThe effort to provide more long‐term care in community‐based settings has caused an expansion in the supply of assisted living beds, yet little is known about the interrelationship between this expansion and nursing home quality. This paper studies data from the State of Ohio to determine if nursing home market structure and the expansion in the supply of assisted living beds impact the quality of care provided by nursing homes. The findings suggest that nursing home quality can be lower in markets with a greater supply of nursing homes. Further, assisted living facility market structure is found to have a mixed effect on nursing home quality. The results of this paper suggest a need for a more integrated approach to regulating long‐term care providers.
Rapid identification of non-human sequences in high-throughput sequencing datasets
Authors: Bhaduri Aparna , Qu Kun , Lee Carolyn S. , Ungewickell Alexander , Khavari Paul A. 
Published: March 2012

Abstract
Summary: Rapid identification of non-human sequences (RINS) is an intersection-based pathogen detection workflow that utilizes a user-provided custom reference genome set for identification of non-human sequences in deep sequencing datasets. In &lt;2 h, RINS correctly identified the known virus in the dataset SRR73726 and is compatible with any computer capable of running the prerequisite alignment and assembly programs. RINS accurately identifies sequencing reads from intact or mutated non-human genomes in a dataset and robustly generates contigs with these non-human sequences (Supplementary Material).
Availability: RINS is available for free download at http://khavarilab.stanford.edu/resources.html
Contact: abhaduri@stanford.edu or kqu@stanford.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Bifidobacteria Isolated From Infants and Cultured on Human Milk Oligosaccharides Affect Intestinal Epithelial Function
Authors: Chichlowski Maciej , De Lartigue Guillaume , German J. Bruce , Raybould Helen E. , Mills David A. 
Published: March 2012

ABSTRACTObjectives:Human milk oligosaccharides (HMOs) are the third most abundant component of breast milk. Our laboratory has previously revealed gene clusters specifically linked to HMO metabolism in selected bifidobacteria isolated from fecal samples of infants. Our objective was to test the hypothesis that growth of selected bifidobacteria on HMO stimulates the intestinal epithelium.Methods:Caco‐2 and HT‐29 cells were incubated with lactose (LAC)‐ or HMO‐grown Bifidobacterium longum subsp infantis (B infantis) or B bifidum. Bacterial adhesion and translocation were measured by real‐time quantitative polymerase chain reaction. Expression of pro‐ and anti‐inflammatory cytokines and tight junction proteins was analyzed by real‐time reverse transcriptase. Distribution of tight junction proteins was measured using immunofluorescent microscopy.Results:We showed that HMO‐grown B infantis had a significantly higher rate of adhesion to HT‐29 cells compared with B bifidum. B infantis also induced expression of a cell membrane glycoprotein, P‐selectin glycoprotein ligand‐1. Both B infantis and B bifidum grown on HMO caused less occludin relocalization and higher expression of anti‐inflammatory cytokine, interleukin‐10 compared with LAC‐grown bacteria in Caco‐2 cells. B bifidum grown on HMO showed higher expression of junctional adhesion molecule and occludin in Caco‐2 cells and HT‐29 cells. There were no significant differences between LAC or HMO treatments in bacterial translocation.Conclusions:The study provides evidence for the specific relation between HMO‐grown bifidobacteria and intestinal epithelial cells. To our knowledge, this is the first study describing HMO‐induced changes in the bifidobacteria–intestinal cells interaction.
Influence of adult age on the total and free clearance and protein binding of (R)‐ and (S)‐warfarin
Authors: Jensen Berit Packert , Chin Paul Ken Leong , Roberts Rebecca Lee , Begg Evan James 
Published: March 2012

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT• Hepatic drug clearance is thought to be reduced with age. However for highly protein bound drugs, which are cleared by capacity‐limited metabolism, studies on total clearance have been conflicting. The hypothesis that protein binding decreases with age has been used to explain this.• Warfarin is a highly protein bound drug, which is cleared by capacity‐limited metabolism. There are conflicting or little data on the relationship between adult age and total and free clearance and protein binding of (R)‐ and (S)‐warfarin.WHAT THIS STUDY ADDS• In a clinical study of 72 patients (18–89 years) on warfarin therapy, both total and free clearance of (R)‐warfarin decreased with age. For (S)‐warfarin there was a stronger signal of a decrease in free than total clearance. Protein binding was found not to correlate with age for (R)‐ and (S)‐warfarin.• In an ex vivo study, in which warfarin was spiked to plasma samples from 60 healthy subjects (19–87 years), no correlation between protein binding and age was found.• These data support the hypothesis that hepatic drug clearance decreases with age. This should be taken into consideration when individualizing dosing, particularly in the elderly.AIMS To test the hypothesis that the clearance (CL) of warfarin, a very highly protein bound drug with capacity‐limited metabolism, decreases with age.METHODS In a clinical study, a steady‐state blood sample was taken from 72 patients (18–89 years) on routine treatment with warfarin. Concentrations of (R)‐ and (S)‐warfarin were determined in plasma (total) and ultrafiltrate (free) by LC‐MS/MS. Total and free CL and protein binding were determined and regressed against age and other covariates. In an ex vivo study, warfarin was spiked to plasma samples from 60 healthy subjects (19–87 years) and protein binding was regressed against age and other covariates.RESULTS For (R)‐warfarin a significant decrease with age was found for both total and free CL (P < 0.001). For (S)‐warfarin there was a stronger signal of a decrease with age in free CL (P= 0.005) vs. total CL (P= 0.045). The decrease in CL of (R)‐ and (S)‐warfarin was 0.3–0.5% per year. Other covariates influencing CL were lean body weight for both (R)‐ and (S)‐warfarin and CYP2C9 genotype and blood sampling time for (S)‐warfarin. Protein binding of (R)‐ and (S)‐warfarin was not found to change significantly with age in either the clinical or the spiked samples, despite a slight decrease in albumin concentration with age.CONCLUSIONS These data support the hypothesis that the CL of (R)‐ and (S)‐warfarin decreases with age. More accurate information was gained when measuring free CL for (S)‐warfarin. Warfarin protein binding did not change significantly with age.
The effect of dicyandiamide on pasture nitrate concentration, yield and N offtake under high N loading in winter and spring
Authors: Moir J. L. , Malcolm B. J. , Cameron K. C. , Di H. J. 
Published: March 2012

AbstractHigh nitrate () concentrations in pastures and forages represent a health risk to grazing livestock. A field trial was conducted on the Lincoln University Dairy Farm, New Zealand, to investigate the effects of applying the nitrification inhibitor dicyandiamide (DCD) on soil extractable N and pasture concentrations in winter and spring. Treatments were control (T1), urea (T2), urea + DCD (T3), May urine + DCD (T4), August urine + DCD (T5), May urine (T6) and August urine (T7). Urine treatments were applied to the ryegrass‐white clover pasture in either May or August. The DCD treatments were applied at 10 kg DCD ha−1 in May and August and urea at 25 kg N ha−1 at selected intervals. Soil samples (0‐ to 75‐ and 75‐ to 150‐mm horizons) were taken regularly to monitor soil and ammonium () levels. Six pasture harvests were conducted from August 2007 to March 2008 and samples analysed for ‐N concentrations and total N content. Application of DCD significantly (P < 0·001) increased total dry‐matter (DM) production by 39 and 42% for the autumn and spring urine treatments, respectively, compared to the urine‐alone treatments. In addition, the application of DCD also significantly (P < 0·001) increased DM yield by 12% on the urea‐only treatment. DCD significantly (P < 0·001) reduced pasture concentrations in both autumn‐ and spring‐applied urine treatments where DCD was applied. This was directly linked to reductions in soil , and increases in soil , from DCD application. The preferential uptake by pasture for ‐N over ‐N may also have been a contributing factor. DCD application can therefore substantially reduce pasture ‐N concentrations to safe levels under high N‐loading (urine patch) conditions.
Functional morphology of the mandibular gland of queens of the ant Monomorium pharaonis (L.)
Authors: Boonen Sofie , Eelen Dieter , Børgesen Lisbeth , Billen Johan 
Published: March 2012

AbstractIn this study, the functional morphology of the mandibular glands of pharaoh ant queens is investigated through histological and behavioural observations. The mandibular glands of queens of different age stages and mating status were examined at the light microscopical as well as the ultrastructural level. The results clearly show a high activity of the gland at the time of hatching, followed by a rapid degeneration independent of the queens' mating status. We therefore hypothesize the glandular secretion serves to stimulate workers to remove the queens' pupal skin. Experiments to compare hatching ability of isolated pupae and pupae assisted by workers confirmed the necessity of worker assistance, which is even more crucial to allow proper wing formation in queens and males. Together with the histological data, this suggests that the mandibular gland may indeed play a role in the social facilitation of hatching, although bioassays are required to give decisive answers about the mandibular gland's function.
Putting twitter to the test: Assessing outcomes for student collaboration, engagement and success
Authors: Junco Reynol , Elavsky C. Michael , Heiberger Greg 
Published: March 2012

AbstractHerein, we present data from two studies of Twitter usage in different postsecondary courses with the goal of analyzing the relationships surrounding student engagement and collaboration as they intersect learning outcomes. Study 1 was conducted with 125 students taking a first‐year seminar course, half of who were required to use Twitter while the other half used Ning. Study 2 was conducted with 135 students taking a large lecture general education course where Twitter participation was voluntary. Faculty in Study 1 engaged with students on Twitter in activities based on an a priori theoretical model, while faculty in Study 2 only engaged students sporadically on the platform. Qualitative analyses of tweets and quantitative outcomes show that faculty participation on the platform, integration of Twitter into the course based on a theoretically driven pedagogical model and requiring students to use Twitter are essential components of improved outcomes.Practitioner notesWhat is already known about this topic
Student use of social media is integrally related to how students engage the world.
Little research exists on how social media use is linked to college student engagement in relation to academic outcomes.
One study using a controlled design demonstrated a relationship between Twitter use and student engagement.
What this paper adds
An empirical comparison of two ways in which Twitter was differently integrated into college courses.
The utilization of quantitative and qualitative data to assess real‐world academic outcomes related to Twitter use.
Evidence‐based best practices for using Twitter in educationally relevant and productive ways.
Implications for practice and/or policy
If integrating Twitter in their courses, faculty should require and structure its use along educationally relevant criteria.
To achieve the most effective results, faculty should have a theoretically driven pedagogical basis for incorporating Twitter.
Faculty should actively engage with students on the platform to obtain maximum benefit.
Integrity—Clarifying and Upgrading an Important Concept for Business Ethics
Authors: TULLBERG JAN 
Published: March 2012

ABSTRACTThis article discusses the concept of integrity. Often, integrity is used as a characteristic of individuals showing a high fidelity to generally praised norms. Here, a more independent meaning is suggested so that the concept implies a clear distance to integration instead of mixing up the two concepts. Integrity implies integration within the individual of beliefs, statements, and action. To what degree can society and companies accommodate a pluralism created by individuals with integrity? Here, it is argued that integrity is a useful virtue and that a more integrity‐friendly environment in companies would be beneficial by stimulating the empowered employee to make improved contributions. The concept is central for business ethics and crucial for the company's choice of such policies. A priority of integrity also affects organizational theory and the practical organizing of the company. Integrity is also vital for society at large for both citizens and companies, providing an ideological support for pluralism and a check on demands for conformism. The article also discusses how a virtue such as integrity can function as guidance for the individual operating in a complex world.
Internal Restructuring and Firm Survival
Authors: Powell Ronan , Yawson Alfred 
Published: March 2012

AbstractWe examine the impact of two common methods of internal restructuring, layoffs and divestitures on the survival of a sample of UK firms. Using a Poisson regression model, we find that divestitures improve survival likelihood by reducing the probability and speed of market exit via takeover or bankruptcy, whereas layoffs increase the probability and speed of market exit via bankruptcy. Surprisingly, classifying firms into financially distressed and healthy groups, we find that distressed firms are less likely to restructure. Furthermore, while divestitures improve survival likelihood in both groups, layoff firms are less likely to survive, irrespective of whether they are distressed or healthy. Our findings are consistent with event studies that examine the market reaction to layoffs and divestiture decisions, and so provide some support for the view that the market correctly values the consequences of these restructuring actions on firm survival. The results are robust to several econometric and modeling issues, including controlling for potential self‐selection bias.
Cystatin C is a strong predictor of survival in patients with cirrhosis: is a cystatin C‐based MELD better?
Authors: Finkenstedt Armin , Dorn Livia , Edlinger Michael , Prokop Wolfgang , Risch Lorenz , Griesmacher Andrea , Graziadei Ivo , Vogel Wolfgang , Zoller Heinz 
Published: March 2012

AbstractBackground/AimsThe model of end stage liver disease (MELD) includes serum creatinine, which is a poor surrogate marker of renal function in patients with cirrhosis. Especially in women and patients with advanced disease creatinine underestimates true renal function. Our objective was to assess whether or not the substitution of creatinine by cystatin C improves the prognostic performance of the model.MethodsThe association between MELD parameters and cystatin C with survival was investigated using a Cox proportional hazards model. A cystatin C‐based MELD score was calculated from the results and compared with creatinine‐based MELD in terms of discrimination and calibration.ResultsFour hundred and twenty‐nine patients were included in the study; 19% died and 12% underwent liver transplantation during a median follow‐up of 602 days. In multivariate Cox regression, cystatin C was an independent predictor of 90‐day mortality with a hazard ratio of 8.0 (95% CI: 2.2–29.6). The median cystatin C‐based MELD was 15, the median creatinine‐based MELD was 12. Calibration and discrimination for 3 month and 1 year mortality was similar between the scores (AUC > 0.85 for both scores). Gender differences in cystatin C‐based MELD were less pronounced than those in the creatinine‐based model, because creatinine but not cystatin C was affected by gender.ConclusionSubstitution of creatinine by cystatin C does not improve the predictive power of MELD.
Role of cytokines in lavage or drainage fluid after hemithyroidectomy in wound healing: Involvement of histamine in the acceleration and delay of wound healing
Authors: Arai Miku , Ogita‐Nakanishi Hiromi , Lee Koutetsu , Yoshimura Katsuhiro , Kawata Ryo , Kanazawa Atsuko , Terada Tetsuya , Takenaka Hiroshi , Sato Tadasu , Endo Yasuo , Kato Ryuji , Ijiri Yoshio , Tanaka Kazuhiko , Tashiro‐Yamaji Junko , Kubota Takahiro , Yoshida Ryotaro 
Published: March 2012

AbstractWound healing is a sophisticated biologic process. In the case of hemithyroidectomy, the operation time is relatively short with small tissue damage and without skin excision, and bacterial contamination before, during, and after the operation is uncommon. Here, we explored which cytokine(s) affected the rates of healing of skin wounds after hemithyroidectomy of 29 patients. We assessed the amounts of cytokines (e.g., interleukin‐6, platelet‐derived growth factor, basic fibroblast growth factor, vascular endothelial growth factor, and tumor necrosis factor‐α) in either the preoperative or postoperative lavage fluids, or in the drainage fluids on postoperative days (PODs) 1–8. All of these cytokines showed a similar pattern; after reaching a peak on POD1, the production fell sharply on POD2–8, revealing that wound healing commenced on POD1. The rates of wound healing were inversely related to the levels of histamine in six patients (i.e., those with the three largest and those with the three smallest total volumes of drainage fluid on POD1): high (or low) levels of histamine in the postoperative lavage fluids with low (or high) levels in the drainage fluids on POD1 caused earlier (or the delay of) wound healing, suggesting involvement of histamine in the acceleration and delay of wound healing.
Green light emitting diodes accelerate wound healing: Characterization of the effect and its molecular basis in vitro and in vivo
Authors: Fushimi Tomohiro , Inui Shigeki , Nakajima Takeshi , Ogasawara Masahiro , Hosokawa Ko , Itami Satoshi 
Published: March 2012

AbstractBecause light‐emitting diodes (LEDs) are low‐coherent, quasimonochromatic, and nonthermal, they are an alternative for low level laser therapy, and have photobiostimulative effects on tissue repair. However, the molecular mechanism(s) are unclear, and potential effects of blue and/or green LEDs on wound healing are still unknown. Here, we investigated the effects of red (638 nm), blue (456 nm), and green (518 nm) LEDs on wound healing. In an in vivo study, wound sizes in the skin of ob/ob mice were significantly decreased on day 7 following exposure to green LEDs, and complete reepithelialization was accelerated by red and green LEDs compared with the control mice. To better understand the molecular mechanism(s) involved, we investigated the effects of LEDs on human fibroblasts in vitro by measuring mRNA and protein levels of cytokines secreted by fibroblasts during the process of wound healing and on the migration of HaCat keratinocytes. The results suggest that some cytokines are significantly increased by exposure to LEDs, especially leptin, IL‐8, and VEGF, but only by green LEDs. The migration of HaCat keratinocytes was significantly promoted by red or green LEDs. In conclusion, we demonstrate that green LEDs promote wound healing by inducing migratory and proliferative mediators, which suggests that not only red LEDs but also green LEDs can be a new powerful therapeutic strategy for wound healing.