bluuebunny/crossref_metadata_2025_split huggingface dataset:
Finding the accelerator and brake in an individual quota fishery: linking ecology, economics, and fleet dynamics of US West Coast trawl fisheries
Authors: Kaplan Isaac C. , Holland Daniel S. , Fulton Elizabeth A. 
Published: September 2013

Abstract
Isaac C. Kaplan, Daniel S. Holland, and Elizabeth A. Fulton. 2014. Finding the accelerator and brake in an individual quota fishery: linking ecology, economics, and fleet dynamics of US West Coast trawl fisheries. – ICES Journal of Marine Science, 71: 308–319. In 2011, the Pacific Fisheries Management Council implemented an individual transferrable quota (ITQ) system for the US West Coast groundfish trawl fleet. Under the ITQ system, each vessel now receives transferrable annual allocations of quota for 29 groundfish species, including target and bycatch species. Here we develop an ecosystem and fleet dynamics model to identify which components of an ITQ system are likely to drive responses in effort, target species catch, bycatch, and overall profitability. In the absence of penalties for discarding over-quota fish, ITQs lead to large increases in fishing effort and bycatch. The penalties fishermen expect for exceeding quota have the largest effect on fleet behaviour, capping effort and total bycatch. Quota prices for target or bycatch species have lesser impacts on fishing dynamics, even up to bycatch quota prices of $50 kg−1. Ports that overlap less with bycatch species can increase effort under individual quotas, while other ports decrease effort. Relative to a prior management system, ITQs with penalties for exceeding quotas lead to increased target species landings and lower bycatch, but with strong variation among species. The model illustrates how alternative fishery management policies affect profitability, sustainability and the ecosystem.
Environmental factors influencing δ13C and δ15N in three Chesapeake Bay fishes
Authors: Davias Lori A. , Kornis Matthew S. , Breitburg Denise L. 
Published: September 2013

AbstractStable isotope analysis has become a common tool for mapping trophic relationships, describing foodweb changes, and assessing ecosystem health. Clear interpretation of stable isotopes is facilitated by understanding how environmental factors can affect isotopic values; in estuarine systems, these factors may include salinity, land use, and shoreline habitat. To evaluate these factors, fish were collected from shallow-water habitats next to hardened (bulkhead and riprap) and unhardened (beach and marsh) shorelines within five subestuaries of the Chesapeake Bay that differed in predominant land use and salinity. This study focused on three common mid-Atlantic fish species: mummichog, Fundulus heteroclitus, Atlantic silverside, Menidia menidia, and white perch, Morone americana. Multiple regression analyses pointed to standard length, salinity, % of watershed as developed or crop land, and shoreline habitat type as important predictors for δ15N in all three species and for δ13C in mummichog and white perch. Further analysis controlling for the effects of salinity, land use, and fish size demonstrated that δ13C and δ15N were lower in tissues of fish collected next to marsh compared with hardened or beach habitat. Habitat effects were strongest for mummichog. This study focused on overarching patterns driving stable isotope signatures in fish; however, it also indicated potentially important interactions between nearshore habitat type and land use or salinity that deserve further analysis. Results have implications for the scale of isotope inquiry and give justification for more detailed follow-up studies of foodweb structure along modified and natural shorelines.
Lack of equivalence in the elemental and stable isotope chemistry within the sagittal otolith pair of the summer flounder, Paralichthys dentatus
Authors: Kajajian Antranik , Schaffler Jason J. , Jones Cynthia M. 
Published: September 2013

AbstractKajajian, A., Schaffler, J. J., and Jones, C. M. 2014. Lack of equivalence in the elemental and stable isotope chemistry within the sagittal otolith pair of the summer flounder, Paralichthys dentatus. – ICES Journal of Marine Science, 71: 356–364. In fish that are not bilaterally symmetrical, the left and right sagittae are often not symmetrical, exhibiting divergent growth patterns and mass, and may have differences in chemical composition. We investigated this in the asymmetrical summer flounder Paralichthys dentatus, collected from different nursery habitats along the US east coast. Significant differences were detected in otolith mass, δ13C, δ18O, Li:Ca, Mg:Ca, and Sr:Ca, and overall chemical signatures. These results refute the hypothesis of left–right equivalence that is prevalent for bilaterally symmetrical fishes. We tested whether a specific side was better suited for classification. The best models differed between sagittae and resulted in different classification accuracies. The left otolith produced better classification accuracies. Simulated samples of randomized sets of left or right otoliths produced mean accuracies intermediate to classification and were often highly variable. We recommend that future otolith chemistry studies involving bilaterally asymmetrical species test the hypothesis of equivalence within the sagittae before randomly choosing an otolith for chemical analyses.
Pseudocollapse and rebuilding of North Sea mackerel (Scomber scombrus)
Authors: Jansen Teunis 
Published: September 2013

Abstract
Jansen, T. 2014. Pseudocollapse and rebuilding of North Sea mackerel (Scomber scombrus). – ICES Journal of Marine Science, 71: 299–307. The largest observed change in mackerel (Scomber scombrus) abundance in the North Atlantic happened when the so-called “North Sea mackerel” collapsed due to overfishing. Despite protection, it has remained in a depleted state. Central to this interpretation was that the “North Sea mackerel” was considered to be a distinct spawning component. However, a recent study has shown that this is not likely. In the light of this study, a review of the history of mackerel spawning in the North Sea found that the traditional explanation of the collapse did not account for a range of unfavourable environmental changes: high fishing pressure was followed by decreasing temperatures that reduced the spawning migration into the North Sea. This was further supplemented by unfavourable changes in food and wind-induced turbulence. On the population level, this was, therefore, not a local stock collapse, but a southwest shift in spawning distribution combined with a reduction in that portion of the population cline with an affinity for spawning in the northeastern part of the spawning area, including the North Sea. No indication of irreversible genetic or behavioural losses caused by the events was found. The previously unexplained lack of rebuilding of spawning in the North Sea consequently seems related to two environmental factors that have remained unfavourable: (i) zooplankton concentration, and (ii) wind-induced turbulence. Furthermore, the large commercial autumn–winter fishery in the North Sea continues to land unknown quantities of mackerel that have an affinity for spawning in the northeastern part of the spawning area, including the North Sea.
Helq acts in parallel to Fancc to suppress replication-associated genome instability
Authors: Luebben Spencer W. , Kawabata Tsuyoshi , Akre Monica K. , Lee Wai Long , Johnson Charles S. , O’Sullivan M. Gerard , Shima Naoko 
Published: September 2013

Abstract
HELQ is a superfamily 2 DNA helicase found in archaea and metazoans. It has been implicated in processing stalled replication forks and in repairing DNA double-strand breaks and inter-strand crosslinks. Though previous studies have suggested the possibility that HELQ is involved in the Fanconi anemia (FA) pathway, a dominant mechanism for inter-strand crosslink repair in vertebrates, this connection remains elusive. Here, we investigated this question in mice using the Helqgt and Fancc− strains. Compared with Fancc−/− mice lacking FANCC, a component of the FA core complex, Helqgt/gt mice exhibited a mild of form of FA-like phenotypes including hypogonadism and cellular sensitivity to the crosslinker mitomycin C. However, unlike Fancc−/− primary fibroblasts, Helqgt/gt cells had intact FANCD2 mono-ubiquitination and focus formation. Notably, for all traits examined, Helq was non-epistatic with Fancc, as Helqgt/gt;Fancc−/− double mutants displayed significantly worsened phenotypes than either single mutant. Importantly, this was most noticeable for the suppression of spontaneous chromosome instability such as micronuclei and 53BP1 nuclear bodies, known consequences of persistently stalled replication forks. These findings suggest that mammalian HELQ contributes to genome stability in unchallenged conditions through a mechanism distinct from the function of FANCC.
Sporulation Capacity and Longevity of Puccinia horiana Teliospores in Infected Chrysanthemum Leaves
Authors: Bonde Morris R. , Palmer Cristi L. , Luster Douglas G. , Nester Susan E. , Revell Jason M. , Berner Dana K. 
Published: September 2013

Puccinia horiana Henn., a quarantine-significant fungal pathogen and causal agent of chrysanthemum white rust (CWR), was first discovered in the United States in 1977 and later believed to have been eradicated. Recently, however, the disease has sporadically reappeared in the northeastern US. Possible explanations for the reappearance include survival of the pathogen in the local environment, and reintroduction from other locations. To determine the possibility that the pathogen might be overwintering in the field, we undertook the study described here. Results from the study showed that P. horiana teliospores, imbedded in infected leaves, were capable of sporulating 2 weeks after inoculation, and this capacity continued until the leaf became necrotic and desiccated. This is the first report of the extreme susceptibility of P. horiana teliospores to leaf necrosis and desiccation and suggests that field infections following winter are unlikely to originate from teliospores. Teliospore germination on excised leaves was shown to be inhibited by light. Accepted for publication 3 April 2013. Published 23 August 2013.
The role of social environment on parental care: offspring benefit more from the presence of female than male helpers
Authors: Brouwer Lyanne , van de Pol Martijn , Cockburn Andrew 
Published: September 2013

Summary

Investment in offspring depends on the costs and benefits to the carer, which can vary with sex and social status. Investment also depends on the effort of others by allowing for compensation (load‐lightening), with biparental care studies showing that this depends on the state and type of the other carer. By contrast, studies on cooperative breeders have solely focussed on the effects of group size rather than its composition (i.e. social environment).
Here we propose and provide the first test of the ‘Social Environment’ hypothesis, that is, how the characteristics (here the sex) of other helpers present in the group affect parental care and how this in turn affects offspring fitness in cooperatively breeding red‐winged fairy‐wrens (Malurus elegans).
Breeders provisioned nestlings at a higher rate than helpers, but there was no sex difference in provisioning rate. Compensation to increasing group size varied little with sex and status, but strongly depended on social environment. All group members reduced their provisioning rates in response to an increasing number of male (load‐lightening), but not female helpers (additive care).
As a result, nestlings received more food and grew faster in the presence of female helpers. The increased nestling growth did convey a fitness advantage due to a higher post‐fledging survival to adulthood.
Our study provides the first evidence that parental care can depend on social environment. This could be an important overlooked aspect to explain variation in parental care in cooperative breeders in general and in particular the enormous variation between the sexes, which we reveal in a literature overview.
Expression analysis and immunohistochemical localization of putative tumor suppressor QM homologue from the cabbage butterfly, Pieris rapae
Authors: Park Bo Mi , Patnaik Bharat Bhusan , Oh Seunghan , Kim Dong Hyun , Jo Yong Hun , Jeong Heon Cheon , Lee Yong Seok , Ko Kisung , Kim Iksoo , Han Yeon Soo 
Published: September 2013

AbstractThe tumor suppressor, QM has been cloned and characterized from eukaryotic organisms including humans, vertebrates, invertebrates, plants and yeast. However, no study on Pieris rapae QM (PrQM) has been reported to date. In this study, cDNA encoding a putative QM protein (PrQM) was obtained from expressed sequence tags (ESTs) of the Pieris rapae cDNA library. Phylogenetic analysis of PrQM showed high similarity of amino acid sequence with other putative homologues identified from Heliothis virescens (95%), Bombyx mori (92%), Plutella xylostella (92%), Drosophila melanogaster (89%) and Polyrhachis vicina (85%), indicating that QM is highly conserved among insects. Semi‐quantitative PCR datasets revealed that PrQM transcripts are highly expressed in head, silk gland, integument and fat body, with pronounced expression observed during the egg stage. The coding region of the PrQM gene was cloned into the pET28 (+) expression vector and the recombinant protein purified by His‐tag affinity chromatography was used for antibody production. Western blotting with the anti‐PrQM antibody detected a single band corresponding to the expected molecular weight of both endogenous (26 kDa) and recombinant (29 kDa) PrQM. Furthermore, immunohistochemical and confocal microscopic analysis with the anti‐PrQM antibody showed that the QM gene is highly expressed in the cytoplasm of fat body, gut and Malpighian tubules in virus‐uninfected control larvae, but down‐regulated at 4 days post Pieris rapae granulovirus (PiraGV) infection. These data show that PrQM is negatively regulated upon virus infection and suggests a putative immunomodulatory function.
Evolutionary engineering of a glycerol‐3‐phosphate dehydrogenase‐negative, acetate‐reducing Saccharomyces cerevisiae strain enables anaerobic growth at high glucose concentrations
Authors: Guadalupe‐Medina Víctor , Metz Benjamin , Oud Bart , van Der Graaf Charlotte M. , Mans Robert , Pronk Jack T. , van Maris Antonius J. A. 
Published: September 2013

SummaryGlycerol production by Saccharomyces cerevisiae, which is required for redox‐cofactor balancing in anaerobic cultures, causes yield reduction in industrial bioethanol production. Recently, glycerol formation in anaerobic S. cerevisiae cultures was eliminated by expressing Escherichia coli (acetylating) acetaldehyde dehydrogenase (encoded by mhpF) and simultaneously deleting the GPD1 and GPD2 genes encoding glycerol‐3‐phosphate dehydrogenase, thus coupling NADH reoxidation to reduction of acetate to ethanol. Gpd– strains are, however, sensitive to high sugar concentrations, which complicates industrial implementation of this metabolic engineering concept. In this study, laboratory evolution was used to improve osmotolerance of a Gpd– mhpF‐expressing S. cerevisiae strain. Serial batch cultivation at increasing osmotic pressure enabled isolation of an evolved strain that grew anaerobically at 1 M glucose, at a specific growth rate of 0.12 h−1. The evolved strain produced glycerol at low concentrations (0.64 ± 0.33 g l−1). However, these glycerol concentrations were below 10% of those observed with a Gpd+ reference strain. Consequently, the ethanol yield on sugar increased from 79% of the theoretical maximum in the reference strain to 92% for the evolved strains. Genetic analysis indicated that osmotolerance under aerobic conditions required a single dominant chromosomal mutation, and one further mutation in the plasmid‐borne mhpF gene for anaerobic growth.
In vivo analysis of dermal and systemic absorption of silver nanoparticles through healthy human skin
Authors: George Robert , Merten Steve , Wang Tim T , Kennedy Peter , Maitz Peter 
Published: September 2013

AbstractBackgroundResearch into nanoparticles has increased markedly during the last decade, especially in light of their potential diagnostic and therapeutic use. While silver has been used since ancient times, a detailed understanding of the kinetics of its dermal absorption requires further study. Thus far, only in vitro and animal models have been used to analyse the absorption characteristics of nanocrystalline silver particles and no in vivo study using intact human skin has demonstrated silver absorption.MethodA nanocrystalline silver dressing was applied to a sample of 16 healthy patients with normal intact skin approximately 5 days prior to surgery. The treated skin samples, removed as surgical waste, were then analysed with a tissue mass spectrometry, light microscopy, scanning electron microscopy (SEM) and an X‐ray diffusion spectrography (XRD). Silver serum levels were also analysed before and after application of the dressing.ResultsA limited amount of silver penetration could be noted even with light microscopy. However, definitive analysis required SEM and XRD confirmation. With SEM, metallic particles could be seen within the dermis. XRD confirmed that these were silver species, possible in oxide form. Furthermore, silver clusters as large as 750 nm could be discerned. In addition, there was no demonstrable rise in serum silver levels post‐treatment with the silver dressing.ConclusionOur results suggest that silver nanoparticles are able to penetrate intact human skin in vivo beyond the stratum corneum and can be found as deep as the reticular dermis. The absorbed silver might be in silver oxide form and the silver species appear to form sizeable clusters once absorbed across the epidermis. However, despite silver deposition into the dermis, the silver nanoparticles did not reach systemic circulation and should thus have no end organ consequences.
Prospective randomized double‐blind multicentre phase II study comparing gemcitabine and cisplatin plus sorafenib chemotherapy with gemcitabine and cisplatin plus placebo in locally advanced and/or metastasized urothelial cancer: SUSE (AUO‐AB 31/05)
Authors: Krege Susanne , Rexer Heidrun , vom Dorp Frank , de Geeter Patrick , Klotz Theodor , Retz Margitte , Heidenreich Axel , Kühn Michael , Kamradt Joern , Feyerabend Susan , Wülfing Christian , Zastrow Stefan , Albers Peter , Hakenberg Oliver , Roigas Jan , Fenner Martin , Heinzer Hans , Schrader Mark 
Published: September 2013

Objective
To evaluate the efficacy and safety of gemcitabine and cisplatin in combination with sorafenib, a tyrosine‐kinase inhibitor, compared with chemotherapy alone as first‐line treatment in advanced urothelial cancer.
Patients and Methods
The study was a randomized phase II trial. Its primary aim was to show an improvement in progression‐free survival (PFS) of 4.5 months by adding sorafenib to conventional chemotherapy. Secondary objectives were objective response rate (ORR), overall survival (OS) and toxicity.
The patients included in the trial had histologically confirmed locally advanced and/or metastatic urothelial cancer of the bladder or upper urinary tract.
Chemotherapy with gemcitabine (1250 mg/qm on days 1 and 8) and cisplatin (70 mg/qm on day 1) repeated every 21 days, was administered to all patients in a double‐blind randomization of additional sorafenib (400 mg twice daily) vs placebo (two tablets twice daily) on days 3–21.
Treatment continued until progression or unacceptable toxicity, the maximum number of cycles was limited to eight. The response assessment was repeated after every two cycles.
Results
Between October 2006 and October 2010, 98 of 132 planned patients were recruited. Nine patients were ineligible. The final analysis included 40 patients in the sorafenib and 49 patients in the placebo arm.
There were no significant differences between the two arms concerning ORR (sorafenib: complete response [CR] 12.5%, partial response [PR] 40%; placebo: CR 12%, PR 35%), median PFS (sorafenib: 6.3 months, placebo: 6.1 months) or OS (sorafenib: 11.3 months, placebo: 10.6 months).
Toxicity was moderately higher in the sorafenib arm. Diarrrhoea occurred significantly more often in the sorafenib arm and hand‐foot syndrome occurred only in the sorafenib arm.
The study was closed prematurely because of slow recruitment.
Conclusion
Although the addition of sorafenib to standard chemotherapy showed acceptable toxicity, the trial failed to show a 4.5 months improvement in PFS.
Bladder outlet obstruction (BOO) in men with castration‐resistant prostate cancer
Authors: Rom Maximilian , Waldert Matthias , Schatzl Georg , Swietek Natalia , Shariat Shahrokh F. , Klatte Tobias 
Published: September 2013

Objective
To evaluate the frequency of bladder outlet obstruction (BOO) and detrusor overactivity (DO) in patients with castration‐resistant prostate cancer (CRPC) and lower urinary tract symptoms (LUTS).
Patients and Methods
Our prospective urodynamics database was queried. Inclusion criteria were CRPC and an International Prostate Symptom Score (IPSS) ≥ 20.
Exclusion criteria were previous local therapy to the prostate gland, known urethral stricture disease, and a neurological component of LUTS.
Twenty‐one patients were identified.
Urodynamic findings were analysed and compared with those of a matched cohort of 42 patients with benign prostatic enlargement (BPE).
Results
The median age of patients in the CRPC group was 74 years, and the median prostate‐specific antigen (PSA) level at the time of the urodynamic study was 90 ng/mL. According to the BOO index, three patients (14%) were obstructed, three were equivocally obstructed (14%) and 15 were unobstructed.
DO was seen in 12 patients (57%).
Compared with the BPE group, patients with CRPC had lower cystometric bladder capacities (P = 0.003), were less likely to have BOO (14 vs 43%, P = 0.009) and more likely to have DO (57 vs 29%, P = 0.028).
Conclusions
This study generates the hypothesis that only a minority of CRPC patients with LUTS have BOO, and that more than half of patients have DO. LUTS in CRPC may therefore be seldom attributable to BOO, but are, at least in part, related to DO and reduced cystometric capacity.
A urodynamic investigation may be necessary before palliative transurethral resection of the prostate to select appropriate candidates.
Larger prospective studies are needed to confirm our findings.