bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vertical mixing, critical depths, and phytoplankton growth in the Ross Sea
Authors: Smith Walker O. , Jones Randolph M. 
Published: December 2014

AbstractPhytoplankton growth and biomass accumulation vary spatially and temporally in the Ross Sea, largely as a function of ice concentrations, vertical mixing depths, and iron concentrations. To assess the role of vertical mixing in bloom initiation, we used a high-resolution numerical model to estimate changes in mixed layer depths from October 1 through early December, the period where phytoplankton growth begins and biomass accumulates, and estimate critical depths for this period. Mixed layers in October ranged from the complete water column (&gt;600 m) to ca. 200 m; over a 60-day period, the mixed layers decreased on average by 70%. Estimated critical depths were exceeded in October, but would allow growth to proceed in late October due to shoaling of mixed layer depths, consistent with the known onset of the spring bloom in the Ross Sea. We also analysed a series of stations sampled near the Ross Ice Shelf during January 2012. Mean vertical profiles for the stations indicated deep vertical mixing; mixed layer depths averaged 60 m and ranged up to 96 m. Chlorophyll concentrations within the mixed layer averaged 6.60 µg l−1, and the pigment contributions were dominated by Phaeocystis antarctica. We suggest that this mesoscale region near the ice shelf is elevated in phytoplankton biomass due to frequent mixing events that redistribute biomass to depth and replenish nutrients, which in turn are utilized by an assemblage capable of utilizing low mean irradiance levels. Thus, the deep mixed layers and high biomass concentrations represent growth over long periods under reduced mixing punctuated by short periods of deeper vertical mixing that redistribute biomass. Water column vertical mixing and phytoplankton biomass in the Ross Sea are consistent with the critical depth concept as originally proposed by Sverdrup.
FORGE: A tool to discover cell specific enrichments of GWAS associated SNPs in regulatory regions
Authors: Dunham Ian , Kulesha Eugene , Iotchkova Valentina , Morganella Sandro , Birney Ewan 
Published: December 2014

AbstractGenome wide association studies provide an unbiased discovery mechanism for numerous human diseases. However, a frustration in the analysis of GWAS is that the majority of variants discovered do not directly alter protein-coding genes. We have developed a simple analysis approach that detects the tissue-specific regulatory component of a set of GWAS SNPs by identifying enrichment of overlap with DNase I hotspots from diverse tissue samples. Functional element Overlap analysis of the Results of GWAS Experiments (FORGE) is available as a web tool and as standalone software and provides tabular and graphical summaries of the enrichments. Conducting FORGE analysis on SNP sets for 260 phenotypes available from the GWAS catalogue reveals numerous overlap enrichments with tissue–specific components reflecting the known aetiology of the phenotypes as well as revealing other unforeseen tissue involvements that may lead to mechanistic insights for disease.
Piketty's challenge for sociology
Authors: Savage Mike 
Published: December 2014

AbstractThis paper argues that Piketty's book should not simply be seen as that of an economist, but that it contains significant resources for sociologists to draw upon. These are firstly, this approach to social science and his use of visualizations which chime closely with recent claims about the power of description. Secondly I consider his conceptualization of time and history – which in rebutting epochal arguments about the speed of contemporary change allows for a much better appreciation of the ‘long durée’; and finally his conceptualization of social classes and privilege through his elaboration of a sociology of accumulation and inheritance. In all these ways, Piketty's work assists in developing an account of elites and wealth which should be highly productive for future sociology.
Capital in the twenty‐first century: a critique
Authors: Soskice David 
Published: December 2014

AbstractI set out and explain Piketty's model of the dynamics of capitalism based on two equations and the r > g inequality (his central contradiction of capitalism). I then take issue with Piketty's analysis of the rebuilding of inequality from the 1970s to the present on three grounds: First, his model is based on the (neo‐classical) assumption that companies are essentially passive actors who invest the amount savers choose to accumulate at equilibrium output – leading to the counterintuitive result that companies respond to the secular fall in growth (and hence their product markets) from the 1970s on by increasing their investment relative to output; this does indeed imply increased inequality on Piketty's β measure, the ratio of capital to output. I suggest a more realistic model in which businesses determine investment growth based on their expectations of output growth, with monetary policy bringing savings into line with business‐determined investment; the implication of this model is that β does not change at all. And in fact as other recent empirical work which I reference has noted, β has not changed significantly over these recent decades. Hence Piketty's central analysis of the growth of contemporary inequality requires rethinking. Second, despite many references to the need for political economic analysis, Piketty's analysis of the growth of inequality in the period from the 1970s to the present is almost devoid of it, his explanatory framework being purely mathematical. I sketch what a political economic framework might look like during a period when politics was central to inequality. Third, inequality in fact rose on a variety of dimensions apart from β (including poverty which Piketty virtually makes no reference to in this period), but it is unclear what might explain why inequality rose in these other dimensions.
Gendering inequality: a note on Piketty's Capital in the Twenty‐First Century
Authors: Perrons Diane 
Published: December 2014

AbstractThomas Piketty's Capital in the Twenty‐First Century is remarkable for moving inequality from the margins to mainstream debate through detailed analysis of longitudinal statistics and, for an economist, by advocating an interdisciplinary perspective and writing in a witty and accessible style. With reference to the post 1970 period, when wage increases are largely responsible for the increase in inequality, Piketty shows how patrimonial capitalists (elite managers) in the top decile and centile of the distribution appropriate a growing share of social wealth as a consequence of their ‘power to set their own remuneration’ in the context of tolerant social norms rather than through their productive contributions. Piketty raises but defers the question of where these social norms come from to other disciplines. A Feminist Economics perspective indicates that these questions are central to a more inclusive form of economic analysis and such an approach would enrich Piketty's analysis in two main ways. First, by paying greater attention to the processes and social norms through which inequalities are produced and justified and second by highlighting the ways in which inequality is experienced differently depending not only on class, but also on other aspects of identity including gender. This approach also suggests that it is necessary to supplement the ex‐post redistributive policies recommended by Piketty: a global wealth tax and more steeply progressive income tax, with ex‐ante measures to stop the rise in wage inequality in the first place, especially by bridging the huge gulf that exists between those who care for people and those who manage money.
Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics
Authors: Paula Débora P. , Linard Benjamin , Andow David A. , Sujii Edison R. , Pires Carmen S. S. , Vogler Alfried P. 
Published: December 2014

AbstractDNA methods are useful to identify ingested prey items from the gut of predators, but reliable detection is hampered by low amounts of degraded DNA. PCR‐based methods can retrieve minute amounts of starting material but suffer from amplification biases and cross‐reactions with the predator and related species genomes. Here, we use PCR‐free direct shotgun sequencing of total DNA isolated from the gut of the harlequin ladybird Harmonia axyridis at five time points after feeding on a single pea aphid Acyrthosiphon pisum. Sequence reads were matched to three reference databases: Insecta mitogenomes of 587 species, including H. axyridis sequenced here; A. pisum nuclear genome scaffolds; and scaffolds and complete genomes of 13 potential bacterial symbionts. Immediately after feeding, multicopy mtDNA of A. pisum was detected in tens of reads, while hundreds of matches to nuclear scaffolds were detected. Aphid nuclear DNA and mtDNA decayed at similar rates (0.281 and 0.11 h−1 respectively), and the detectability periods were 32.7 and 23.1 h. Metagenomic sequencing also revealed thousands of reads of the obligate Buchnera aphidicola and facultative Regiella insecticola aphid symbionts, which showed exponential decay rates significantly faster than aphid DNA (0.694 and 0.80 h−1, respectively). However, the facultative aphid symbionts Hamiltonella defensa, Arsenophonus spp. and Serratia symbiotica showed an unexpected temporary increase in population size by 1–2 orders of magnitude in the predator guts before declining. Metagenomics is a powerful tool that can reveal complex relationships and the dynamics of interactions among predators, prey and their symbionts.
Who uses methadone services in China? Monitoring the world's largest methadone programme
Authors: Sullivan Sheena G. , Wu Zunyou , Rou Keming , Pang Lin , Luo Wei , Wang Changhe , Cao Xiaobin , Yin Wenyuan , Liu Enwu , Mi Guodong ,   National Methadone Maintenance Treatment Working Group
Published: December 2014

AbstractAimsTo describe the data collected by the Chinese methadone maintenance treatment (MMT) system and the characteristics of clients entering the programme.DesignDescriptive study using routinely collected data from the MMT data management system for the period March 2004 and March 2010.SettingAll MMT clinics in China.ParticipantsClients who enrolled for services between March 2004 and March 2010.MeasurementsRoutinely collected data included: demographic information; drug use, sexual and criminal behaviours; status of infection with human immunodeficiency virus (HIV), hepatitis C virus (HCV) and syphilis; random urine‐opiate test results; and the daily methadone dose received. Differences among clients by year were examined.FindingsDuring the period examined, there were 251 974 clients attending 684 clinics in 27 provinces. Overall, the mean age was 34.4 years, 83.8% were male, 70.2% were unemployed, 75% had ever injected drugs, 17% had shared needles and 7.4% were HIV‐positive. The profile of clients changed over time, with fewer HIV‐positive individuals, fewer injecting drug users, fewer needle‐sharers, fewer females and fewer unemployed. Half the clients dropped out within 6 months. The average final dose received was 49.4 mg. The estimated probability of interrupting treatment before 6 months was 52.5%.ConclusionsThe profile of clients enrolling in methadone maintenance treatment in China is continually changing and appears to be associated with reduced risk of HIV. High dropout in the programme may limit its effectiveness. The availability of a centralized, real‐time data system was extremely useful for monitoring the progress of the Chinese methadone maintenance treatment programme.
Advances in receptor conformation research: the quest for functionally selective conformations focusing on the β2‐adrenoceptor
Authors: Woo Anthony Yiu‐Ho , Song Ying , Zhu Weizhong , Xiao Rui‐Ping 
Published: December 2014

Seven‐transmembrane receptors, also called GPCRs, represent the largest class of drug targets. Upon ligand binding, a GPCR undergoes conformational rearrangement and thereby changes its interaction with effector proteins including the cognate G‐proteins and the multifunctional adaptor proteins, β‐arrestins. These proteins, by initiating distinct signal transduction mechanisms, mediate one or several functional responses. Recently, the concept of ligand‐directed GPCR signalling, also called functional selectivity or biased agonism, has been proposed to explain the phenomenon that chemically diverse ligands exhibit different efficacies towards the different signalling pathways of a single GPCR, and thereby act as functionally selective or ‘biased’ ligands. Current concepts support the notion that ligand‐specific GPCR conformations are the basis of ligand‐directed signalling. Multiple studies using fluorescence spectroscopy, X‐ray crystallography, mass spectroscopy, nuclear magnetic resonance spectroscopy, single‐molecule force spectroscopy and other techniques have provided the evidence to support this notion. It is anticipated that these techniques will ultimately help elucidate the structural basis of ligand‐directed GPCR signalling at a precision meaningful for structure‐based drug design and how a specific ligand molecular structure induces a unique receptor conformation leading to biased signalling. In this review, we will summarize recent advances in experimental techniques applied in the study of functionally selective GPCR conformations and breakthrough data obtained in these studies particularly those of the β2‐adrenoceptor.Linked ArticlesThis article is part of a themed section on Chinese Innovation in Cardiovascular Drug Discovery. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2015.172.issue-23
Novel immunosuppressive agent caerulomycin A exerts its effect by depleting cellular iron content
Authors: Kaur Suneet , Srivastava Gautam , Sharma Amar Nath , Jolly Ravinder S 
Published: December 2014

Background and PurposeRecently, we have described the use of caerulomycin A (CaeA) as a potent novel immunosuppressive agent. Immunosuppressive drugs are crucial for long‐term graft survival following organ transplantation and treatment of autoimmune diseases, inflammatory disorders, hypersensitivity to allergens, etc. The objective of this study was to identify cellular targets of CaeA and decipher its mechanism of action.Experimental ApproachJurkat cells were treated with CaeA and cellular iron content, iron uptake/release, DNA content and deoxyribonucleoside triphosphate pool determined. Activation of MAPKs; expression level of transferrin receptor 1, ferritin and cell cycle control molecules; reactive oxygen species (ROS) and cell viability were measured using Western blotting, qRT‐PCR or flow cytometry.Key ResultsCaeA caused intracellular iron depletion by reducing its uptake and increasing its release by cells. CaeA caused cell cycle arrest by (i) inhibiting ribonucleotide reductase (RNR) enzyme, which catalyses the rate‐limiting step in the synthesis of DNA; (ii) stimulating MAPKs signalling transduction pathways that play an important role in cell growth, proliferation and differentiation; and (iii) by targeting cell cycle control molecules such as cyclin D1, cyclin‐dependent kinase 4 and p21CIP1/WAF1. The effect of CaeA on cell proliferation was reversible.Conclusions and ImplicationsCaeA exerts its immunosuppressive effect by targeting iron. The effect is reversible, which makes CaeA an attractive candidate for development as a potent immunosuppressive drug, but also indicates that iron chelation can be used as a rationale approach to selectively suppress the immune system, because compared with normal cells, rapidly proliferating cells require a higher utilization of iron.
Dietary and Temporal Niche Differentiation in Tropical Ants—Can They Explain Local Ant Coexistence?
Authors: Houadria Mickal , Salas‐Lopez Alex , Orivel Jérôme , Blüthgen Nico , Menzel Florian 
Published: December 2014

AbstractHow species with similar ecological requirements avoid competitive exclusion remains contentious, especially in the species‐rich tropics. Niche differentiation has been proposed as a major mechanism for species coexistence. However, different niche dimensions must be studied simultaneously to assess their combined effects on diversity and composition of a community. In most terrestrial ecosystems, ants are among the most abundant and ubiquitous animals. Since they display direct, aggressive competition and often competitively displace subordinate species from resources, niche differentiation may be especially relevant among ants. We studied temporal and trophic niche differentiation in a ground ant community in a forest fragment in French Guiana. Different baits were presented during day and night to assess the temporal and dietary niches of the local species. They represented natural food resources such as sugars, carrion, excrements, seeds, and live prey. In addition, pitfalls provided a background measure of ant diversity. The communities attracted to the different baits significantly differed from each other, and even less attractive baits yielded additional species. We detected species specialized on living grasshoppers, sucrose, seeds, or dead insects. Community‐level differences between day and night were larger than those between baits, and many species were temporally specialized. In contrast to commonness, foraging efficiency of species was correlated to food specialization. We conclude that many ant species occupy different temporal or dietary niches. However, for many generalized species, the dietary, and temporal niche differentiation brought forward through our sampling effort, cannot alone explain their coexistence.
Foliar Extrafloral Nectar of Humboldtia brunonis (Fabaceae), a Paleotropic Ant‐plant, is Richer than Phloem Sap and More Attractive than Honeydew
Authors: Chanam Joyshree , Kasinathan Srinivasan , Pramanik Gautam K. , Jagdeesh Amaraja , Joshi Kanchan A. , Borges Renee M. 
Published: December 2014

AbstractThe ant‐plant Humboldtia brunonis secretes extrafloral nectar (EFN) despite the lack of antiherbivore protection from most ants. EFN was richer in composition than phloem sap and honeydew from untended Hemiptera on the plant, suggesting that EFN could potentially distract ants from honeydew, since ants rarely tended Hemiptera on this plant.
Analysing and reporting UK CAMHS outcomes: an application of funnel plots
Authors: Fugard Andrew J. B. , Stapley Emily , Ford Tamsin , Law Duncan , Wolpert Miranda , York Ann 
Published: December 2014

BackgroundPatient‐reported outcomes measures are increasingly being used in child and adolescent mental health services (CAMHS). League tables are a common way of comparing organizations across health and education but have limitations that are not well known in CAMHS.MethodParent‐rated Strengths and Difficulties Questionnaire (SDQ) outcomes data from 15,771 episodes of care across 51 UK CAMHS were analysed using funnel plots, an alternative to league tables.ResultsWhile most services were indistinguishable from the national average there was evidence of heterogeneous outcomes and seven services had outcomes below 99.9% limits for SDQ added‐value scores.ConclusionsFunnel plots are powerful tools for navigating national data and can help prompt investigations using clinical theory and local service context. Examples are provided of factors to consider in these investigations. We argue that analyses of the local context are central to the valid application of funnel plots.
Simulated colonoscopy training using a low‐cost physical model improves responsiveness of surgery interns
Authors: Buscaglia J. M. , Fakhoury J. , Loyal J. , Denoya P. I. , Kazi E. , Stein S. A. , Scriven R. , Bergamaschi R. 
Published: December 2014

AbstractAimSurgery residents are required to become proficient in colonoscopy before completing training. The aim of this study was to evaluate the responsiveness of surgery interns to simulated colonoscopy training.MethodInterns, defined as postgraduate year 1 residents without exposure to endoscopy, underwent training in a physical model including colonoscopy, synthetic anatomy trays with luminal tattoos and a hybrid simulator. After baseline testing and mentored training, final testing was performed using five predetermined proficiency criteria. Content‐valid metrics defined by the extent of departure from clinical reality were evaluated by two blinded assessors. Responsiveness was defined as change in performance over time and assessed comparing baseline testing with nonmentored final testing.ResultsTwelve interns (eight male, mean age 26, 80% right‐handed) performed 48 colonoscopies each over 1 year. Improvement was seen in the overall procedure time (24 min 46 s vs 20 min 54 s; P = 0.03), passing the splenic flexure (20 min 33 s vs 10 min 45 s; P = 0.007), passing the hepatic flexure (23 min 31 s vs 12 min 45 s; P = 0.003), caecal intubation time (23 min 38 s vs 13 min 26 s; P = 0.008), the duration of loss of view of the lumen (75% vs 8.3%; P = 0.023), incomplete colonoscopy (100% vs 33.3%; P = 0.042), colonoscope withdrawal < 6 min (16.7% vs 8.3%; P = 0.052). Tattoo identification time (9 min 16 s vs 12 min 25 s; P = 0.50), colon looped time (2 min 12 s vs 1 min 45 s; P = 0.50) and rate of colon perforation (8.3% vs 8.3%; P = 1) remained unchanged. Interrater reliability was 1.0 for all measures.ConclusionSimulated colonoscopy training in a low‐cost physical model improved the performance of surgery interns with decreased procedure time, increased rates of complete colonoscopy and appropriate scope withdrawal.
Ecology and distribution of the Southeast Asian invasive liana Kudzu, Pueraria lobata (Fabaceae), in Southern Switzerland
Authors: Gigon A. , Pron S. , Buholzer S. 
Published: December 2014

Pueraria lobata, Kudzu, is a perennial liana native in temperate to tropical East Asia. Introduced mainly as an ornamental plant into many (sub)tropical regions, and as a forage crop in the South‐Eastern USA, it has spread vegetatively into adjacent forests and grasslands and has also been dispersed with garden waste. The objectives of this paper are: (i) to assess whether the ecology of P. lobata in Southern Switzerland is similar to that in the South‐Eastern USA, where it causes great damage; (ii) to predict its further spread in Southern Switzerland. In Switzerland it already occurs in 32 sites covering 16 200 m2; the shoots grow ≤ 26 cm per day and ≤ 11 m per year, forming ≤ 2 m thick mats. P. lobata infested sites contain about half as many plant species as similar sites without it. This paper shows that the ecology of P. lobata in Southern Switzerland is similar to that described for the USA. The broad climatic requirements of the species suggest that it could establish in many regions of Southern and Central Europe. However, it is not expected to spread on a large scale in Switzerland because there appears to be no establishment from seed and because its stands are always near settlements and thus mostly controlled.
Weight distribution in container loading: a case study
Authors: Costa Maria da Graça , Captivo Maria Eugénia 
Published: December 2014

AbstractThis work addresses a real‐world problem proposed by a Portuguese company. Every day this company needs to define a plan to pack a set of boxes onto a single truck. The truck will have to make as many trips as necessary to deliver the entire set of boxes. In the literature, this is known as the bin‐packing problem. As this is a real‐world application, practical constraints, such as load stability and box orientation constraints, weight limit of the truck, and uniform distribution of weight inside the truck, should be ensured. To solve this problem, we propose a constructive heuristic based on a layer arrangement approach that comprises a corner selection strategy for placing the boxes. Some experiments are conducted with the company's data, and the quality of the solutions is evaluated regarding the occupancy rates and distribution of the cargo weight inside the truck.