bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selective flatfish seine: a knee-high demersal seine barely catches cod
Authors: Ingólfsson Ólafur Arnar , Humborstad Odd-Børre , Løkkeborg Svein 
Published: December 2018

Abstract
Norwegian coastal cod (Gadus morhua) protection restricts the use of active fishing gears. Demersal seines, acknowledged as being efficient for targeting flatfish, are therefore largely excluded from the fjords. To exploit plaice (Pleuronectes platessa), a species-selective gear that avoids catching cod is needed. We therefore designed a low-rise demersal seine with a 0.6 m vertical opening and tested it on fishing grounds in Lofoten (Northern Norway), comparing it with a conventional seine that had a vertical opening of ∼3.5 m, and fished both during the day and at night. Six to nine hauls were taken with each of the four gear/time-of-day categories (32 hauls in total). The low-rise seine caught no fewer plaice during day-time fishing, but less at night. Cod and haddock (Melanogrammus aeglefinus) catches were reduced by 94% and 98%, respectively, while catches of sole (Solea solea) increased with the low-rise seine. No catch differences were found for halibut (Hippoglossus hippoglossus), common dab (Limanda limanda), or monkfish (Lophius piscatorius). The low-rise seine therefore enables targeting flatfish while avoiding gadoid catches, although loss of plaice during night-time fishing is to be expected.
Plasma membrane sphingomyelin modulates thymocyte development by inhibiting TCR-induced apoptosis
Authors: Toshima Kaoru , Nagafuku Masakazu , Okazaki Toshiro , Kobayashi Toshihide , Inokuchi Jin-ichi 
Published: December 2018

Abstract
Sphingomyelin (SM) in combination with cholesterol forms specialized membrane lipid microdomains in which specific receptors and signaling molecules are localized or recruited to mediate intracellular signaling. SM-microdomain levels in mouse thymus were low in the early CD4+CD8+ double-positive (DP) stage prior to thymic selection and increased &gt;10-fold during late selection. T-cell receptor (TCR) signal strength is a key factor determining whether DP thymocytes undergo positive or negative selection. We examined the role of SM-microdomains in thymocyte development and related TCR signaling, using SM synthase 1 (SMS1)-deficient (SMS1−/−) mice which display low SM expression in all thymocyte populations. SMS1 deficiency caused reduced cell numbers after late DP stages in TCR transgenic models. TCR-dependent apoptosis induced by anti-CD3 treatment was enhanced in SMS1−/− DP thymocytes both in vivo and in vitro. SMS1−/− DP thymocytes, relative to controls, showed increased phosphorylation of TCR-proximal kinase ZAP-70 and increased expression of Bim and Nur77 proteins involved in negative selection following TCR stimulation. Addition of SM to cultured normal DP thymocytes led to greatly increased surface expression of SM-microdomains, with associated reduction of TCR signaling and TCR-induced apoptosis. Our findings indicate that SM-microdomains are increased in late DP stages, function as negative regulators of TCR signaling and modulate the efficiency of TCR-proximal signaling to promote thymic selection events leading to subsequent developmental stages.
Chemotherapy and diffuse low-grade gliomas: a survey within the European Low-Grade Glioma Network
Authors: Darlix Amélie , Mandonnet Emmanuel , Freyschlag Christian F , Pinggera Daniel , Forster Marie-Therese , Voss Martin , Steinbach Joachim , Loughrey Carmel , Goodden John , Banna Giuseppe , Di Blasi Concetta , Foroglou Nicolas , Hottinger Andreas F , Baron Marie-Hélène , Pallud Johan , Duffau Hugues , Rutten Geert-Jan , Almairac Fabien , Fontaine Denys , Taillandier Luc , Pessanha Viegas Catarina , Albuquerque Luisa , von Campe Gord , Urbanic-Purkart Tadeja , Blonski Marie 
Published: December 2018

Abstract

Background
Diffuse low-grade gliomas (DLGGs) are rare and incurable tumors. Whereas maximal safe, functional-based surgical resection is the first-line treatment, the timing and choice of further treatments (chemotherapy, radiation therapy, or combined treatments) remain controversial.

Methods
An online survey on the management of DLGG patients was sent to 28 expert centers from the European Low-Grade Glioma Network (ELGGN) in May 2015. It contained 40 specific questions addressing the modalities of use of chemotherapy in these patients.

Results
The survey demonstrated a significant heterogeneity in practice regarding the initial management of DLGG patients and the use of chemotherapy. Interestingly, radiation therapy combined with the procarbazine, CCNU (lomustine), and vincristine regimen has not imposed itself as the gold-standard treatment after surgery, despite the results of the Radiation Therapy Oncology Group 9802 study. Temozolomide is largely used as first-line treatment after surgical resection for high-risk DLGG patients, or at progression.

Conclusions
The heterogeneity in the management of patients with DLGG demonstrates that many questions regarding the postoperative strategy and the use of chemotherapy remain unanswered. Our survey reveals a high recruitment potential within the ELGGN for retrospective or prospective studies to generate new data regarding these issues.
Substantial Differences in Serum Concentrations of Psychoactive Drugs Measured in Samples Stored for 2 Days or More on Standard Serum Tubes Versus Serum Tubes Containing Gel Separators
Authors: Wollmann Birgit M. , Lunde Hilde A. , Støten Lene K. , Lunder Niclas , Molden Espen 
Published: December 2018

Background:
Drugs may potentially adsorb to blood collection tubes containing gel separators in the preanalytical phase of therapeutic drug monitoring. The aim of this study was to compare measured concentrations of 28 psychoactive drugs and 13 metabolites in spiked serum samples stored on standard (plain) tubes versus barrier gel tubes during a 2–6-day period at room temperature.

Methods:
Drug-free (“blank”) serum samples spiked with mixes of antidepressants, antipsychotics, or mood stabilizers (valproic acid and lamotrigine), including relevant metabolites, were transferred to tubes with and without gel, that is, BD Vacutainer SST II Advance gel tubes and BD Vacutainer Glass Serum Tubes (Becton-Dickinson Company, Plymouth, United Kingdom). Mean serum concentrations of the drugs or metabolites measured by ultra-high performance liquid chromatography–tandem mass spectrometry analyses of protein-precipitated samples were compared after storage on plain or gel tubes at 3 time points (day 0, day 2/48 hours, and day 6/144 hours) in room temperature.

Results:
Mean serum concentrations of all antidepressants, except for one metabolite, and 13 of 18 antipsychotic drugs were significantly lower in gel tubes compared with plain tubes after 2 days of storage (2%–28% lower, P < 0.05). After 6 days of storage, mean serum concentrations of all antipsychotic drugs and antidepressants were significantly lower in gel tubes versus plain tubes (9%–49% lower, P < 0.02), except for amisulpride and O-desmethylvenlafaxine. Serum concentrations of the mood stabilizers were not significantly different in gel tubes compared with plain tubes (P > 0.1). There was a clear relationship between log P (partition coefficient) and residual serum concentrations during gel tube storage (r −0.50 and −0.42 at day 2 and day 6, respectively; P < 0.02).

Conclusions:
This study shows that storage on gel for more than 2 days significantly decreases the serum concentrations of antidepressant and antipsychotic drugs as compared to storage in plain tubes. Thus, using tubes with gel separators in the therapeutic drug monitoring of psychoactive drugs should be reconsidered.
Thermodynamically Consistent Estimation of Gibbs Free Energy from Data: Data Reconciliation Approach
Authors: Salike Saman , Bhatt Nirav 
Published: December 2018

AbstractMotivationThermodynamic analysis of biological reaction networks requires the availability of accurate and consistent values of Gibbs free energies of reaction and formation. These Gibbs energies can be measured directly via the careful design of experiments or can be computed from the curated Gibbs free energy databases. However, the computed Gibbs free energies of reactions and formations do not satisfy the thermodynamic constraints due to the compounding effect of measurement errors in the experimental data. The propagation of these errors can lead to a false prediction of pathway feasibility and uncertainty in the estimation of thermodynamic parameters.ResultsThis work proposes a data reconciliation framework for thermodynamically consistent estimation of Gibbs free energies of reaction, formation and group contributions from experimental data. In this framework, we formulate constrained optimization problems that reduce measurement errors and their effects on the estimation of Gibbs energies such that the thermodynamic constraints are satisfied. When a subset of Gibbs free energies of formations is unavailable, it is shown that the accuracy of their resulting estimates is better than that of existing empirical prediction methods. Moreover, we also show that the estimation of group contributions can be improved using this approach. Further, we provide guidelines based on this approach for performing systematic experiments to estimate unknown Gibbs formation energies.AvailabilityThe MATLAB code for the executing the proposed algorithm is available for free on the GitHub repository:https://github.com/samansalike/DR-thermoContactniravbhatt@iitm.ac.in
Longitudinal prediction of outcome in idiopathic pulmonary fibrosis using automated CT analysis
Authors: Jacob Joseph , Bartholmai Brian J. , van Moorsel Coline H.M. , Rajagopalan Srinivasan , Devaraj Anand , van Es Hendrik W. , Moua Teng , van Beek Frouke T. , Clay Ryan , Veltkamp Marcel , Kokosi Maria , de Lauretis Angelo , Judge Eoin P. , Burd Teresa , Peikert Tobias , Karwoski Ronald , Maldonado Fabien , Renzoni Elisabetta , Maher Toby M. , Altmann Andre , Wells Athol U. 
Published: December 2018

ABSTRACTAIMSTo evaluate computer-derived (CALIPER) CT variables against FVC change as potential drug trials endpoints in IPF.METHODS71 Royal Brompton Hospital (discovery cohort) and 23 Mayo Clinic Rochester and 24 St Antonius Hospital Nieuwegein IPF patients (validation cohort) were analysed. Patients had two CTs performed 5-30 months apart, concurrent FVC measurements and were not exposed to antifibrotics (to avoid confounding of mortality relationships from antifibrotic use). Cox regression analyses (adjusted for patient age and gender) evaluated outcome for annualized FVC and CALIPER vessel-related structures (VRS) change and examined the added prognostic value of thresholded VRS changes beyond standard FVC change thresholds.RESULTSChange in VRS was a stronger outcome predictor than FVC decline when examined as continuous variables, in discovery and validation cohorts. When FVC decline (≥10%) and VRS thresholds were examined together, the majority of VRS change thresholds independently predicted outcome, with no decrease in model fit. When analysed as co-endpoints, a VRS threshold of ≥0·40 identified 30% more patients reaching an endpoint than a ≥10% FVC decline threshold alone.CONCLUSIONSChange in VRS is a strong predictor of outcome in IPF and can increase power in future drug trials when used as a co-endpoint alongside FVC change.Ethics committee approvalApproval for this study of clinically indicated CT and pulmonary function data was obtained from Liverpool Research Ethics Committee (Reference: 14/NW/0028) and the Institutional Ethics Committee of the Royal Brompton Hospital, Mayo Clinic Rochester and St. Antonius Hospital, Nieuwegein. Informed patient consent was not required.Take home messageChange in the vessel-related structures, a computer-derived CT variable, is a strong predictor of outcome in idiopathic pulmonary fibrosis and can increase power in future drug trials when used as a co-endpoint alongside forced vital capacity change.
Stable knockout and complementation of receptor expression using in vitro cell line derived reticulocytes for dissection of host malaria invasion requirements
Authors: Satchwell Timothy J , Wright Katherine E , Haydn-Smith Katy L , Terán Fernando Sánchez-Román , Hawksworth Joseph , Frayne Jan , Toye Ashley M , Baum Jake 
Published: December 2018

AbstractInvasion of and intracellular development within the red blood cell by malaria parasites requires interaction with a multitude of host proteins expressed at the surface of or inside the cell. Perhaps the biggest obstacle to dissection of specific functions of host proteins during invasion is the inability to manipulate protein expression in the genetically intractable anucleate red blood cell. Whilst genetic manipulation and subsequent in vitro differentiation of nucleated erythroid precursors have facilitated progress in this area, such approaches are limited by the finite proliferative capacity of primary hematopoietic stem cells, and a failure of erythroleukemic cell lines to enucleate, respectively. Here, we report that reticulocytes derived through in vitro differentiation of an enucleation competent immortalized erythroblast cell line (BEL-A) support both successful invasion and growth by Plasmodium falciparum. Using CRISPR-mediated gene knockout and lentiviral expression of open reading frames, we validate an essential role for the erythrocyte receptor basigin in P. falciparum invasion and, for the first time, demonstrate that this can be rescued by re-expression of the receptor or of a mutant thereof. Specifically, using sustainable edited clones derived from this line, we exclude a functional role for the cytoplasmic domain of basigin during invasion, and challenge the reported requirement of its associated receptor cyclophilin B. These data establish the use of reticulocytes derived from immortalized erythroblasts as a crucial model system to explore specific hypotheses regarding host receptor requirements and involvement in P. falciparum invasion.
Absorptive capacity and innovation in China
Authors: Reid David McHardy 
Published: December 2018

Purpose
The purpose of this paper is to question the conventional wisdom that China fails to produce distinctive innovation; its capabilities limited merely to copying and reverse engineering. The author postulates that the lack of innovation is a delayed activity since China is undergoing a process of building absorptive capacity (AC) as a precursor to innovation.

Design/methodology/approach
The author probes this question by drawing on the concept of AC, a competence separate from innovativeness and a precursor to it. By drawing on the AC literature three propositions are established. Subsequently, these propositions are examined, in part, with data drawn from 34 interviews conducted in China with CEOs, other senior corporate officers and government officials. In this way, the author explores the challenges to innovating.

Findings
Thomson Reuters 2015 Top Global Innovators report listed no Chinese company among its top 100 list of innovative companies. The author’s belief, however, favors China to become a source of innovation. A positive tilt derived from both interviews and recent reports published by Bain & Company, Booz and Co as well as McKinsey & Co. This evidences, the author argues, China is acquiring AC, a competence independent of innovation but a necessary antecedent to decoding and deploying the intellectual property in its portfolio. The collective effect of this is that the perception of China as a source of innovative activity will show an uptick when the AC threshold is reached.

Research limitations/implications
This is a viewpoint paper grounded on an exploratory study.

Practical implications
Guidance on AC development is valuable to government policy makers promoting innovation in China and those attempting to arbitrage these developments. Similarly, policy makers in competitive nations should also be aware that their innovation-focused industries may need nurturing and bolstering since they may be at risk of being swept away by a tsunami-like innovation wave from China.

Originality/value
This is an original take on the relationship of AC and innovativeness in China. The author argues that in contrast to the conventional wisdom China has the potential for innovativeness.
Effect of post-processing on the dimensional accuracy of small plastic additive manufactured parts
Authors: Nsengimana Joseph , Van der Walt Jacobus , Pei Eujin , Miah Maruf 
Published: December 2018

PurposeThis paper aims to investigate the effect of post-processing techniques on dimensional accuracy of laser sintering (LS) of Nylon and Alumide®and fused deposition modelling (FDM) of acrylonitrile butadiene styrene (ABS) materials.Design/methodology/approachAdditive manufacturing (AM) of test pieces using LS of Nylon and Alumide®powders, as well as the FDM of ABS materials, were first conducted. Next, post-processing of the test pieces involved tumbling, shot peening, hand finishing, spray painting, CNC machining and chemical treatment. Touch probe scanning of the test pieces was undertaken to assess the dimensional deviation, followed by statistical analysis using Chi-square and Z-tests.FindingsThe deviation ranges of the original built parts with those being subjected to tumbling, shot peening, hand finishing, spray painting, CNC machining or chemical treatment were found to be different. Despite the rounding of sharp corners and the removal of small protrusions, the dimensional accuracy of relatively wide surfaces of Nylon or Alumide®test pieces were not significantly affected by the tumbling or shot peening processes. The immersion of ABS test pieces into an acetone bath produced excellent dimensional accuracy.Research limitations/implicationsOnly Nylon PA2200 and Alumide®processed through LS and ABS P400 processed through FDM were investigated. Future work could also examine other materials and using parts produced with other AM processes.Practical implicationsThe service bureaus that produce prototypes and end-use functional parts through AM will be able to apply the findings of this investigation.Originality/valueThis research has outlined the differences of post-processing techniques such as tumbling, shot peening, hand finishing, spray painting, CNC machining and chemical treatment. The paper discusses the advantages and disadvantages of each of those methods and suggests that the immersion of ABS test pieces into an acetone bath produced excellent dimensional accuracy.
Factors influencing cruise vacations: the impact of online reviews and environmental friendliness
Authors: Bahja Frida , Cobanoglu Cihan , Berezina Katerina , Lusby Carolin 
Published: December 2018

Purpose
The purpose of the study was to discover the relative importance of influencing factors toward booking a cruise vacation. Based on a review of literature, this study focused on exploring the relative importance of six influential factors in cruise customers’ decision-making process: cruise vacation price, cruise duration, distance from the cruise port, itineraries, environmental friendliness of cruise line and cruise online reviews.

Design/methodology/approach
The complexity of cruise customers’ decision-making process for involving these six attributes with several levels was examined with choice-based conjoint (CBC) analysis. CBC was selected due to its realistic approach to purchase decisions, in the form of trade-offs. The online survey collected data anonymously. The survey was distributed through Amazon’s Mechanical Turk (Mturk) platform. The sample consisted of 450 cruise customers, who had experienced a cruise vacation before.

Findings
The findings of the study showed that online reviews were the most influential attribute for cruise customers in their cruise decision, followed very closely by the environmental friendliness of the cruise line. The next influential factor was the duration of the cruise vacation, which was followed by distance from the cruise port, cruise itinerary and cruise vacation price. The best and the worst cruise vacation profiles were generated based on the CBC analysis.

Practical implications
The findings of this study provide some insights with regard to cruise customers’ importance about influencing factors when deciding on a cruise vacation.

Originality/value
The research provides insides in understanding the influential factors at the last stage of cruise customers’ decision-making process. In this regard, cruise industry can pay more attention in promoting the attributes of a cruise offer as influential factors. Additionally, the findings of this study contribute to the general knowledge about cruise customers’ decision-making process.
Estimating contributions of pelagic and benthic pathways to consumer production in coupled marine food webs
Authors: Duffill Telsnig Jessica I. , Jennings Simon , Mill Aileen C. , Walker Nicola D. , Parnell Andrew C. , Polunin Nicholas V. C. 
Published: December 2018

Abstract

Pelagic and benthic systems usually interact, but their dynamics and production rates differ. Such differences influence the distribution, reproductive cycles, growth rates, stability and productivity of the consumers they support. Consumer preferences for, and dependence on, pelagic or benthic production are governed by the availability of these sources of production and consumer life history, distribution, habitat, behavioural ecology, ontogenetic stage and morphology.

Diet studies may demonstrate the extent to which consumers feed on prey in pelagic or benthic environments. But they do not discriminate benthic production directly supported by phytoplankton from benthic production recycled through detrital pathways. The former will track the dynamics of phytoplankton production more closely than the latter.

We develop and apply a new analytical method that uses carbon (C) and sulphur (S) natural abundance stable isotope data to assess the relative contribution of pelagic and benthic pathways to fish consumer production.

For 13 species of fish that dominate community biomass in the northern North Sea (estimated >90% of total biomass), relative modal use of pelagic pathways ranged from <25% to >85%. Use of both C and S isotopes as opposed to just C reduced uncertainty in relative modal use estimates. Temporal comparisons of relative modal use of pelagic and benthic pathways revealed similar ranking of species dependency over 4 years, but annual variation in relative modal use within species was typically 10%–40%.

For the total fish consumer biomass in the study region, the C and S method linked approximately 70% and 30% of biomass to pelagic and benthic pathways, respectively. As well as providing a new method to define consumers’ links to pelagic and benthic pathways, our results demonstrate that a substantial proportion of fish biomass, and by inference production, in the northern North Sea is supported by production that has passed through transformations on the seabed.