bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterising uncertainty in generalised dissimilarity models
Authors: Woolley Skipton N.C. , Foster Scott D. , O'Hara Timothy D. , Wintle Brendan A. , Dunstan Piers K. 
Published: December 2016

Summary

Generalised dissimilarity modelling (GDM) is a statistical method for analysing and predicting patterns of turnover in species composition, usually in response to environmental gradients that vary in space and time. GDM is becoming widely applied in ecology and conservation science to interpret macro‐ecological and biogeographical patterns, to support conservation assessment, predict changes in species distributions under climate change and prioritise biological surveys.

Inferential and predictive uncertainty is difficult to characterise using current implementations of GDM, reducing the utility of GDM in ecological risk assessment and conservation decision‐making. Current practice is to undertake permutation tests to assess the importance of variables in GDM. Permutation testing overcomes the issue of data‐dependence (because dissimilarities are calculated on a smaller number of observations) but it does not give a quantification of uncertainty in predictions. Here, we address this issue by utilising the Bayesian bootstrap, so that the uncertainty in the observations is carried through the entire analysis (including into the predictions).

We tested our Bayesian bootstrap GDM (BBGDM) approach on simulated data sets and two benthic species data sets. We fitted BBGDMs and GDMs to compare the differences in inference and prediction of compositional turnover that resulted from a coherent treatment of model uncertainty. We showed that our BBGDM approach correctly identified the signal within the data, resulting in an improved characterisation of uncertainty and enhanced model‐based inference.

We show that our approach gives appropriate parameter estimates while better representing the underlying uncertainty that arises when conducting inference and making predictions with GDMs. Our approach to fitting GDMs will provide more realistic insights into parameter and prediction uncertainty.
Predation by the carabid beetle Harpalus rufipes on the pest slug Deroceras reticulatum in the laboratory
Authors: El‐Danasoury H. , Cerecedo C. , Córdoba M. , Iglesias‐Piñeiro J. 
Published: December 2016

AbstractThe Harpalini species Harpalus rufipes, as many other generalist carabids, consume a wide variety of prey and it is known to feed on pest slugs such as the grey field slug Deroceras reticulatum, but quantitative data about the predatory activity of H. rufipes on slugs are very scarce. In laboratory experiments, we assessed the capability of male H. rufipes to kill eggs and different‐sized slugs of the pest species D. reticulatum in either the absence or the presence of alternative live prey (dipteran larvae and aphids). We also investigated the preference of H. rufipes for eggs and hatchlings of D. reticulatum in a choice experiment. H. rufipes killed considerable amounts of eggs and small juveniles (≤5.0 mg) of D. reticulatum, both in no‐choice and in choice situations. Medium‐sized juvenile slugs (10–20 mg) were seldom killed only in no‐choice situations, and no large juveniles (50–60 mg) were killed. Dipteran larvae and aphids were killed also in no‐choice and in choice situations. The type of alternative prey presented with slug eggs affected the survival of the eggs to H. rufipes predation. The presence of dipteran larvae as alternative prey did not affect the survival of juvenile slugs. When eggs and small juvenile slugs were offered together, the survivals of both items were similar. The obtained results under laboratory conditions suggest that the generalist predator H. rufipes might realise an important contribution to the control of pest slugs.
Rice demand in Tanzania: an empirical analysis
Authors: Lazaro Edith , Sam Abdoul G. , Thompson Stanley R. 
Published: December 2016

AbstractWe investigate the consumer side of the Tanzania rice market with the primary objective of estimating price elasticities of imported and domestically produced rice. Previous studies of the rice market in Tanzania claim that domestic rice is implicitly protected by consumer preference of its perceived better quality. However, rice producers increasingly complain that imported rice adversely impacts the price of domestic rice. Using household consumer survey data, we estimate price and expenditure elasticities of imported rice, domestic rice, and maize to assess their substitutability in the Tanzanian diet. Our results show that Tanzanian consumers have a preference for domestic rice varieties with weak substitutability between domestic and imported rice varieties.
Leveling the field for biofuels: comparing the economic and environmental impacts of biofuel and other export crops in Malawi
Authors: Schuenemann Franziska , Thurlow James , Zeller Manfred 
Published: December 2016

AbstractBiofuels often raise the specter of food insecurity, water resource depletion, and greenhouse gas emissions from land clearing. These concerns underpin the “sustainability criteria” governing access to European biofuel markets. However, it is unclear if producing biofuels in low‐income countries does exacerbate poverty and food insecurity, and moreover, whether the sustainability criteria should apply to all agricultural exports entering European markets. We develop an integrated modeling framework to simultaneously assess the economic and environmental impacts of producing biofuels in Malawi. We incorporate the effects of land use change on crop water use, and the opportunity costs of using scarce resources for biofuels instead of other crops. We find that biofuel production reduces poverty and food insecurity by raising household incomes. Irrigated outgrower schemes, rather than estate farms, lead to better economic outcomes, fewer emissions, and similar water requirements. Nevertheless, to gain access to European markets, Malawi would need to reduce emissions from ethanol plants. We find that biofuels’ economic and emissions outcomes are generally preferable to tobacco or soybeans. We conclude that the sustainability criteria encourage more sustainable biofuel production in countries like Malawi, but are perhaps overly biased against biofuels since other export crops raise similar concerns about food security and environmental impacts.
Targeting, bias, and expected impact of complex innovations on developing‐country agriculture: evidence from Malawi
Authors: Haile Beliyou , Azzarri Carlo , Roberts Cleo , Spielman David J. 
Published: December 2016

AbstractAgronomic analyses of new technologies are often conducted under carefully controlled research station programs or trials managed by self‐selected farmers. Oftentimes, the technologies are then scaled up with minimal evaluation under real‐world conditions. Yet, the interim step between agronomic trials and large‐scale promotion is crucial to generate evidence on the social and economic impact of technologies that is both internally valid and generalizable. The article focuses on a participatory action research program in Malawi designed to test and identify scalable technology options to intensify the smallholder sector and contribute to poverty reduction and food and nutrition security. We examine the socioeconomic characteristics of farmers testing technologies and find evidence of systematic targeting of better‐endowed farmers. After controlling for observable differences using matching and a doubly robust estimator, we find evidence of early positive effects on maize yield and harvest value, although placebo tests suggest possible selection on unobservables. We note that attention should be given to program design and household characterization to better define and improve targeting criteria, technology selection, and external validity.
Cocoa pricing options and their implications for poverty and industrialization in Ghana
Authors: Mulangu Francis M. , Miranda Mario J. , Maïga Eugenie W.H. 
Published: December 2016

AbstractThis study establishes the cocoa pricing subsidization options that will stabilize processors’ throughput while meeting the multiple, but possibly conflicting, public policy objectives of maximizing government revenue and reducing poverty among Ghanaian cocoa beans producers. To evaluate these options, we construct and numerically simulate a structural dynamic stochastic model of a representative cocoa processor who maximizes the present value of current and expected future profits, given prevailing market conditions and cocoa pricing policies. Our results indicate that, given current processing capacity, the Ghana Cocoa Board would have to offer a 92% discount to processors on main‐crop beans in order to achieve the industrial goal of locally processing 40% of annual production. This would cause light‐crop beans used in processing to be completely displaced by main‐crop beans carried over as inventory. It would also increase mean processor revenues by 167%, but cause the Ghana Cocoa Board to operate at a significant deficit, implying that the stated goal could only be achieved through massive government subsidies.
AllergoOncology – the impact of allergy in oncology: EAACI position paper
Authors: Jensen‐Jarolim E. , Bax H. J. , Bianchini R. , Capron M. , Corrigan C. , Castells M. , Dombrowicz D. , Daniels‐Wells T. R. , Fazekas J. , Fiebiger E. , Gatault S. , Gould H. J. , Janda J. , Josephs D. H. , Karagiannis P. , Levi‐Schaffer F. , Meshcheryakova A. , Mechtcheriakova D. , Mekori Y. , Mungenast F. , Nigro E. A. , Penichet M. L. , Redegeld F. , Saul L. , Singer J. , Spicer J. F. , Siccardi A. G. , Spillner E. , Turner M. C. , Untersmayr E. , Vangelista L. , Karagiannis S. N. 
Published: December 2016

AbstractTh2 immunity and allergic immune surveillance play critical roles in host responses to pathogens, parasites and allergens. Numerous studies have reported significant links between Th2 responses and cancer, including insights into the functions of IgE antibodies and associated effector cells in both antitumour immune surveillance and therapy. The interdisciplinary field of AllergoOncology was given Task Force status by the European Academy of Allergy and Clinical Immunology in 2014. Affiliated expert groups focus on the interface between allergic responses and cancer, applied to immune surveillance, immunomodulation and the functions of IgE‐mediated immune responses against cancer, to derive novel insights into more effective treatments. Coincident with rapid expansion in clinical application of cancer immunotherapies, here we review the current state‐of‐the‐art and future translational opportunities, as well as challenges in this relatively new field. Recent developments include improved understanding of Th2 antibodies, intratumoral innate allergy effector cells and mediators, IgE‐mediated tumour antigen cross‐presentation by dendritic cells, as well as immunotherapeutic strategies such as vaccines and recombinant antibodies, and finally, the management of allergy in daily clinical oncology. Shedding light on the crosstalk between allergic response and cancer is paving the way for new avenues of treatment.
The Consequences of Vagueness in Consent to Organ Donation
Authors: Shaw David M. 
Published: December 2016

AbstractIn this article I argue that vagueness concerning consent to post‐mortem organ donation causes considerable harm in several ways. First, the information provided to most people registering as organ donors is very vague in terms of what is actually involved in donation. Second, the vagueness regarding consent to donation increases the distress of families of patients who are potential organ donors, both during and following the discussion about donation. Third, vagueness also increases the chances that the patient's intention to donate will not be fulfilled due to the family's distress. Fourth, the consequent reduction in the number of donated organs leads to avoidable deaths and increased suffering among potential recipients, and distresses them and their families.There are three strategies which could be used to reduce the harmful effects of this vagueness. First, recategorizing the reasons (commonly referred to as ‘overrules’ under the current system) given by families who refuse donation from registered donors would bring greater clarity to donation discussions. Second, people who wish to donate their organs should be encouraged to discuss their wishes in detail with their families, and to consider recording their wishes in other ways. Finally, the consent system for organ donation could be made more detailed, ensuring both that more information is provided to potential donors and that they have more flexibility in how their intentions are indicated; this last strategy, however, could have the disadvantage of discouraging some potential donors from registering.
Eradication of minimal residual disease improves overall and progression‐free survival in patients with chronic lymphocytic leukaemia, evidence from NCRN CLL207: a phase II trial assessing alemtuzumab consolidation
Authors: Varghese Abraham M. , Howard Dena R. , Pocock Christopher , Rawstron Andy C. , Follows George , McCarthy Helen , Dearden Claire , Fegan Christopher , Milligan Donald , Smith Alexandra F. , Gregory Walter , Hillmen Peter ,   NCRI CLL Sub‐Group
Published: December 2016

SummaryWith immunochemotherapy, remission duration and survival in patients with chronic lymphocytic leukaemia is dependent on the level of minimal residual disease (MRD) after treatment. This phase II trial assessed alemtuzumab consolidation post‐chemotherapy in patients who responded with persistent low levels of detectable disease. Blood was screened for MRD using multi‐parameter flow cytometry, 6–24 months post‐chemotherapy. MRD‐positive participants received alemtuzumab 30 mg subcutaneously 3 times weekly for 6 weeks. Following a marrow assessment, MRD‐negative participants or non‐responders stopped therapy and MRD‐positive participants with 1 + log reduction had 6 more weeks of alemtuzumab. Alemtuzumab consolidation was received by 47 participants. One death and 19 of 22 serious adverse events reported from 17 (36%) participants were alemtuzumab‐related. MRD eradication from blood and bone marrow was achieved in 39 (83%) participants at the end of consolidation, with 18 (38%) remaining MRD‐negative in the blood 6 months later. Of the 18 participants who were MRD‐negative at 6 months, the median time to MRD relapse was 46 months, which was similar to patients who were MRD‐negative at baseline and were followed up. The 5‐year progression‐free survival (PFS) and overall survival (OS) of participants who were MRD‐negative at 6 months was significantly better than MRD‐positive participants [PFS: 78% vs. 39% (P = 0·010), OS: 89% vs. 64% (P = 0·029)].
Synthesis, molecular docking and biological evaluation of 1‐phenylsulphonyl‐2‐(1‐methylindol‐3‐yl)‐benzimidazole derivatives as novel potential tubulin assembling inhibitors
Authors: Wang Yan‐Ting , Cai Xun‐Chao , Shi Tian‐Qi , Zhang Ya‐Liang , Wang Zhong‐Chang , Liu Chang‐Hong , Zhu Hai‐Liang 
Published: December 2016

A series of new 1‐phenylsulphonyl‐2‐(1‐methylindol‐3‐yl)‐benzimidazole derivatives were designed, synthesized and evaluated as potential inhibitors of tubulin polymerization and anthropic cancer cell lines. Among them, compound 33 displayed the most potent tubulin polymerization inhibitory activity in vitro (IC50 = 1.41 μM) and strong antiproliferative activities against A549, Hela, HepG2 and MCF‐7 cell lines in vitro with GI50 value of 1.6, 2.7, 2.9 and 4.3 μM, respectively, comparable with the positive control colchicine (GI50 value of 4.1, 7.2, 9.5 and 14.5 μM, respectively) and CA‐4 (GI50 value of 2.2, 4.3, 6.4 and 11.4 μM, respectively). Simultaneously, we evaluated that compound 33 could effectively induce apoptosis of A549 associated with G2/M phase cell cycle arrest. Immunofluorescence microscopy also clearly indicated compound 33 a potent antimicrotubule agent. Docking simulation showed that compound 33 could bind tightly with the colchicine‐binding site and act as a tubulin inhibitor. Three‐dimensional‐QSAR model was also built to provide more pharmacophore understanding that could be used to design new agents with more potent tubulin assembling inhibitory activity in the future.
Cultivation and characterisation of the surface markers and carbohydrate profile of human corneal endothelial cells
Authors: Nagymihály Richárd , Veréb Zoltán , Albert Réka , Sidney Laura , Dua Harminder , Hopkinson Andrew , Petrovski Goran 
Published: December 2016

AbstractBackgroundThe study aims to characterise human corneal endothelial cell (HCEnC) cultures generated by the peel‐and‐digest method based on their surface protein/carbohydrate expression pattern.MethodsQuantitative polymerase chain reaction was used to compare expression of vimentin, CD90, Cytokeratin‐19, ZO‐1 and Claudin 14 in cultured HCEnC and cell line B4G12 versus stromal cells. Fluorescence‐activated cell sorting was used to assess surface protein distribution of cultured and uncultured HCEnC. Distribution of surface proteins/carbohydrates was visualised by immunofluorescent and lectin staining.ResultsHuman corneal endothelial cell and B4G12 showed lower expression level for vimentin, CD90, Cytokeratin‐19 compared with stromal cells; while ZO‐1 was expressed in endothelial cells, Claudin 14 was detected in B4G12 only. Fluorescence‐activated cell sorting analyses revealed CD166, CD47, CD44, CD54, CD73, CD90, CD105, CD106, CD112, CD146 and CD325 to be present, with CD34 to be absent from cultured HCEnC. Freshly isolated, non‐cultivated HCEnCs were CD90, CD73, CD146 and CD325 positive. Carbohydrates were detected by lectins LCA, PHA E, PHA L, PSA, sWGA, Con A, RCA 120 and WGA, but cultured HCEnC showed negative for GSL I, SBA, DBA, PNA and UEA I.ConclusionCultures established by the peel‐and‐digest method are probably not prone to stromal contamination, but the cells are likely to undergo endothelial‐to mesenchymal transition as suggested by apparent morphological changes.
5‐Hydroxymethylcytosine is a nuclear biomarker to assess biological potential in histologically ambiguous heavily pigmented melanocytic neoplasms
Authors: Lee Jonathan J. , Vilain Ricardo E. , Granter Scott R. , Hu Nina R. , Bresler Scott C. , Xu Shuyun , Frank Alexander H. , Mihm Martin C. , Saw Robyn P.M. , Fletcher Christopher D. , Scolyer Richard A. , Murphy George F. , Lian Christine G. 
Published: December 2016

Background5‐Hydroxymethylcytosine (5‐hmC) is an epigenetic marker detectable through immunohistochemistry (IHC) that has been shown to distinguish benign nevi from melanoma with high sensitivity and specificity. The purpose of the study was to explore its diagnostic utility in a subset of histologically challenging, heavily pigmented cutaneous melanocytic neoplasms.Methods5‐hmC IHC was performed on 54 heavily pigmented melanocytic tumors. Semi‐quantitative analysis of immunoreactivity was correlated with clinical, pathologic and follow‐up data.ResultsBenign melanocytic neoplasms (4 of 4 blue nevi with epithelioid change; 12 of 12 combined nevi; 5 of 5 deep penetrating nevi, DPN) exhibited strong 5‐hmC nuclear reactivity. Eight heavily pigmented blue nevus‐like melanomas and 7 of 8 pigmented epithelioid melanocytomas (PEM) showed significant 5‐hmC loss. Five of 7 atypical DPN cases and 8 of 10 melanocytic tumors of uncertain malignant potential (MELTUMP) showed low to intermediate 5‐hmC immunoreactivity. These differences were statistically significant (P‐value <.0001).ConclusionsLoss of 5‐hmC may be helpful in differentiating benign, diagnostically challenging, heavily pigmented melanocytic tumors from those with malignant potential. The intermediate to low 5‐hmC immunoreactivity in atypical DPNs, PEMs and so‐called MELTUMP categories further underscores the need to consider these neoplasms as having some potential for lethal biological behavior.
Who's my little monkey? Effects of infant‐directed speech on visual retention in infant rhesus macaques
Authors: Slonecker Emily M. , Simpson Elizabeth A. , Suomi Stephen J. , Paukner Annika 
Published: December 2016

AbstractBoth human and nonhuman primate adults use infant‐directed facial and vocal expressions across many contexts when interacting with infants (e.g., feeding, playing). This infant‐oriented style of communication, known as infant‐directed speech (IDS), seems to benefit human infants in numerous ways, including facilitating language acquisition. Given the variety of contexts in which adults use IDS, we hypothesized that IDS supports learning beyond the linguistic domain and that these benefits may extend to nonhuman primates. We exposed 2.5‐month‐old rhesus macaque infants (N = 15) to IDS, adult‐directed speech (ADS), and a non‐social control (CTR) during a video presentation of unrelated stimuli. After a 5‐ or 60‐minute delay, infants were shown the familiar video side‐by‐side with a novel video. Infants exhibited a novelty preference after the 5‐minute delay, but not after the 60‐minute delay, in the ADS and CTR conditions, and a novelty preference in the IDS condition only after the 60‐minute delay. These results are the first to suggest that exposure to IDS affects infants’ long‐term memory, even in non‐linguistic animals.
A Look at Uganda's Early HIV Prevention Strategies Through a Moderate ‘African’ Communitarian Lens
Authors: Wathuta Jane 
Published: December 2016

AbstractThis paper seeks to highlight the benefits of prioritizing moderate African communitarian principles as partly demonstrated in the HIV prevention strategies implemented in Uganda in the late 1980s. Pertinent lessons could be drawn so as to achieve the HIV prevention targets envisioned in the post‐2015 development era. Communitarianism emphasizes the importance of communities as part of healthy human existence. Its core ethical values include the virtues of generosity, compassion, and solidarity. Persuasion through communication, consensus through dialogue, and the awareness and commitment to responsibilities towards other members of the community, are chief practices relied upon to achieve appropriate social behaviour. All these elements signify individual rootedness in communities and contribute to the healthy existence of its members. Communitarianism is usually classified as either authoritarian/radical or responsive/moderate, depending on the primacy given to either community interests or the individual will and rights. Moderate communitarianism recognizes the individual's capacity for moral reasoning, virtue and free choice. The ensuing form of society is deemed more ethical as it relies on education in the virtues, moral persuasion and informal social controls, without stifling individual identity, agency, and capacity for self‐determination. If moderate African communitarianism, in particular, can to a certain extent be associated with the significant aspects of Uganda's HIV prevention strategies in the stated period, then its present‐day relevance for HIV prevention and other public health interventions may be emphasized accordingly. This applies especially in view of the ongoing efforts to achieve a balance between individual and collective interests in bioethics.