bluuebunny/crossref_metadata_2025_split huggingface dataset:
Count transformation models
Authors: Siegfried Sandra , Hothorn Torsten 
Published: March 2020

Abstract

The effect of explanatory environmental variables on a species' distribution is often assessed using a count regression model. Poisson generalized linear models or negative binomial models are common, but the traditional approach of modelling the mean after log or square root transformation remains popular and in some cases is even advocated.

We propose a novel framework of linear models for count data. Similar to the traditional approach, the new models apply a transformation to count responses; however, this transformation is estimated from the data and not defined a priori. In contrast to simple least‐squares fitting and in line with Poisson or negative binomial models, the exact discrete likelihood is optimized for parameter estimation and inference. Simple interpretation of effects in the linear predictors is possible.

Count transformation models provide a new approach to regressing count data in a distribution‐free yet fully parametric fashion, obviating the need to a priori commit to a specific parametric family of distributions or to a specific transformation. The models are a generalization of discrete Weibull models for counts and are thus able to handle over‐ and underdispersion. We demonstrate empirically that the models are more flexible than Poisson or negative binomial models but still maintain interpretability of multiplicative effects. A re‐analysis of deer–vehicle collisions and the results of artificial simulation experiments provide evidence of the practical applicability of the model framework.

In ecology studies, uncertainties regarding whether and how to transform count data can be resolved in the framework of count transformation models, which were designed to simultaneously estimate an appropriate transformation and the linear effects of environmental variables by maximizing the exact count log‐likelihood. The application of data‐driven transformations allows over‐ and underdispersion to be addressed in a model‐based approach. Models in this class can be compared to Poisson or negative binomial models using the in‐ or out‐of‐sample log‐likelihood. Extensions to nonlinear additive or interaction effects, correlated observations, hurdle‐type models and other more complex situations are possible. A free software implementation is available in the cotram add‐on package to the R system for statistical computing.
Thermal evaluation of a hermetic transcutaneous energy transfer system to power mechanical circulatory support devices in destination therapy
Authors: Au Shun Long Cyril , McCormick Daniel , Lever Nigel , Budgett David 
Published: March 2020

AbstractCurrent generation left ventricular assist devices (LVADs) are powered by a percutaneous driveline. The high prevalence of driveline infections has motivated the development of transcutaneous energy transfer (TET) systems which eliminate driveline associated complications by wirelessly delivering power across the skin. Destination therapy (DT) requires long‐term reliable operation of the TET electronics suggesting the use of hermetic packaging techniques as used in all other chronically implanted devices. TET coils dissipate heat during operation and in order for the technology to be suitable for patient use, sufficient power must be delivered while maintaining temperatures at levels deemed safe. The heating of a TET system designed for DT which uses hermetic packaging technology was evaluated in silico and in vivo. A numerical model was used to evaluate the temperature of the TET coils. The TET system was fabricated and assessed in vivo using an ovine model. The receiving coil was implanted subcutaneously in a sheep and the transmission coil placed in contact with the skin and concentric to the implanted coil. Temperatures of the system were measured using sensors fixed to the surface of the coils. Numerical modeling indicated that the maximum temperatures of the primary and secondary coil surfaces were 38.13°C and 38.41°C, respectively, when delivering 10 W continuously. Stable temperatures were observed in vivo after 70 minutes and the maximum skin and implant surface temperatures were 37.73°C and 38.31°C, respectively. This study showed that a hermetic, chronically implantable TET system is thermally safe when continuously delivering 10 W of power, sufficient to power modern LVADs.
Earnings management: A new paradigm of corporate social responsibility
Authors: Ehsan Sadaf , Nurunnabi Mohammad , Tahir Samya , Hashmi Maaida H. 
Published: March 2020

AbstractThe study adopted a systematic review approach to review the existing studies on the relationship between corporate social responsibility (CSR) and Earnings Management (EM). The aim of this study is to determine whether CSR is an effective tool to promote healthy relationships with stakeholders or CSR is used as an effective strategy by firm's mangers to hide out their involvement in (EM) practices. Results revealed that prior research on the CSR‐EM relationship is limited. The majority of the studies found an inverse relationship between CSR and EM. Moreover, mixed results were reported because of the lack of sufficient theoretical support, inappropriate research designs, and varying approaches to measure CSR and EM. This study also synthesizes the various consistencies and inconsistencies in the existing literature of CSR‐EM and future research agenda. Policymakers should reward organizations that pursue CSR purely for social and environmental concerns and at the same time they should be vigilant for those which use CSR for shielding their EM practices.
Assessing the goodness of fit of logistic regression models in large samples: A modification of the Hosmer‐Lemeshow test
Authors: Nattino Giovanni , Pennell Michael L. , Lemeshow Stanley 
Published: March 2020

AbstractEvaluating the goodness of fit of logistic regression models is crucial to ensure the accuracy of the estimated probabilities. Unfortunately, such evaluation is problematic in large samples. Because the power of traditional goodness of fit tests increases with the sample size, practically irrelevant discrepancies between estimated and true probabilities are increasingly likely to cause the rejection of the hypothesis of perfect fit in larger and larger samples. This phenomenon has been widely documented for popular goodness of fit tests, such as the Hosmer‐Lemeshow test. To address this limitation, we propose a modification of the Hosmer‐Lemeshow approach. By standardizing the noncentrality parameter that characterizes the alternative distribution of the Hosmer‐Lemeshow statistic, we introduce a parameter that measures the goodness of fit of a model but does not depend on the sample size. We provide the methodology to estimate this parameter and construct confidence intervals for it. Finally, we propose a formal statistical test to rigorously assess whether the fit of a model, albeit not perfect, is acceptable for practical purposes. The proposed method is compared in a simulation study with a competing modification of the Hosmer‐Lemeshow test, based on repeated subsampling. We provide a step‐by‐step illustration of our method using a model for postneonatal mortality developed in a large cohort of more than 300 000 observations.
Plasmin improves blood–gas barrier function in oedematous lungs by cleaving epithelial sodium channels
Authors: Zhao Runzhen , Ali Gibran , Nie Hong‐Guang , Chang Yongchang , Bhattarai Deepa , Su Xuefeng , Zhao Xiaoli , Matthay Michael A. , Ji Hong‐Long 
Published: March 2020

Background and PurposeLung oedema in association with suppressed fibrinolysis is a hallmark of lung injury. Here, we have tested whether plasmin cleaves epithelial sodium channels (ENaC) to resolve lung oedema fluid.Experimental ApproachHuman lungs and airway acid‐instilled mice were used for analysing fluid resolution. In silico prediction, mutagenesis, Xenopus oocytes, immunoblotting, voltage clamp, mass spectrometry, and protein docking were combined for identifying plasmin cleavage sites.Key ResultsPlasmin improved lung fluid resolution in both human lungs ex vivo and injured mice. Plasmin activated αβγENaC channels in oocytes in a time‐dependent manner. Deletion of four consensus proteolysis tracts (αΔ432‐444, γΔ131‐138, γΔ178‐193, and γΔ410‐422) eliminated plasmin‐induced activation significantly. Further, immunoblotting assays identified 7 cleavage sites (K126, R135, K136, R153, K168, R178, K179) for plasmin to trim both furin‐cleaved C‐terminal fragments and full‐length human γENaC proteins. In addition, 9 new sites (R122, R137, R138, K150, K170, R172, R180, K181, K189) in synthesized peptides were found to be cleaved by plasmin. These cleavage sites were located in the finger and the thumb, particularly the GRIP domain of human ENaC 3D model composed of two proteolytic centres for plasmin. Novel uncleaved sites beyond the GRIP domain in both α and γ subunits were identified to interrupt the plasmin cleavage‐induced conformational change in ENaC channel complexes. Additionally, plasmin could regulate ENaC activity via the G protein signal.Conclusion and ImplicationsPlasmin can cleave ENaC to improve blood‐gas exchange by resolving oedema fluid and could be a potent therapy for oedematous lungs.
Activation of the MET receptor attenuates doxorubicin‐induced cardiotoxicity in vivo and in vitro
Authors: Gallo Simona , Spilinga Martina , Albano Raffaella , Ferrauto Giuseppe , Di Gregorio Enza , Casanova Elena , Balmativola Davide , Bonzano Alessandro , Boccaccio Carla , Sapino Anna , Comoglio Paolo Maria , Crepaldi Tiziana 
Published: March 2020

Background and PurposeDoxorubicin anti‐cancer therapy is associated with cardiotoxicity, resulting from DNA damage response (DDR). Hepatocyte growth factor (HGF) protects cardiomyocytes from injury, but its effective use is compromised by low biodistribution. In this study, we have investigated whether the activation of the HGF receptor—encoded by the Met gene—by an agonist monoclonal antibody (mAb) could protect against doxorubicin‐induced cardiotoxicity.Experimental ApproachThe mAb (5 mg·kg−1) was injected in vivo into C57BL/6J mice, before doxorubicin (three doses of 7 mg·kg−1). Cardiac functions were evaluated through MRI after treatment termination. Heart histological staining and mRNA levels of genes associated with heart failure (Acta1 and Nppa), inflammation (IL‐6), and fibrosis (Ctgf, Col1a2, Timp1, and Mmp9) were assessed. MAb (100 nM) was administered in vitro to H9c2 cardiomyoblasts before addition of doxorubicin (25 μM). DDR and apoptosis markers were evaluated by quantitative western blotting, flow cytometry, and immunofluorescence. Stattic was used for pharmacological inactivation of STAT3.Key ResultsIn vivo, administration of the mAb alleviated doxorubicin‐induced cardiac dysfunction and fibrosis. In vitro, mAb mimicked the response to HGF by (a) inhibiting histone H2AX phosphorylation at S139, (b) quenching the expression of the DNA repair enzyme PARP1, and (c) reducing the proteolytic activation of caspase 3. The MET‐driven cardioprotection involved, at least in vitro, the phosphorylation of STAT3.Conclusion and ImplicationsThe MET agonist mAb provides a new tool for cardioprotection against anthracycline cardiotoxicity.
Critical role of OX40 in drug‐induced acute liver injury
Authors: Zhang Chunpan , Jin Hua , Wang Yan , Li Changying , Zhao Xinyan , Li Yanmeng , Shi Wen , Tian Yue , Xu Hufeng , Tian Dan , Liu Kai , Jia Jidong , Sun Guangyong , Zhang Dong 
Published: March 2020

Background and PurposeThe innate and adaptive immune systems both play important roles in drug‐induced liver injury (DILI). However, the crosstalk between the innate and adaptive immunity in DILI is largely unknown. Extensive crosstalk is likely mandated by co‐stimulatory interactions between these immune systems. OX40 is a co‐stimulatory molecule, but whether it regulates the intrahepatic immune response in DILI remains unknown.Experimental ApproachAcute liver injury was induced by paracetamol (acetaminophen), carbon tetrachloride (CCl4), and d‐galactosamine/LPS (GalN/LPS) in wild‐type (WT) and Ox40 knockout (KO) mice, and disease progress was compared.Key ResultsPlasma OX40 levels were significantly increased and were augmented in intrahepatic CD4+ T cells after paracetamol, CCl4, or GalN/LPS administration. Liver injury in Ox40‐deficient mice was attenuated compared with that in WT mice. Compared with WT mice, hepatic infiltration of Th1 and Th17 cells and macrophages in Ox40 KO mice was reduced. Furthermore, adoptive transfer of Ox40 KO‐CD4+ T cells to Rag1−/− mice resulted in alleviated liver injury compared with WT‐CD4+ T‐cell transfer, with reduced liver infiltration of macrophages and pro‐inflammatory cytokine secretion. Moreover, OX40/Fc stimulation in vitro revealed that soluble OX40 enhanced the biological function of murine macrophages, including up‐regulation of genes associated with inflammation and tissue infiltration. Finally, soluble OX40 levels were significantly elevated in DILI patients compared with healthy controls.Conclusion and ImplicationsOX40 is a key molecule that promotes both pro‐inflammatory macrophage and CD4+ T‐cell function, exacerbating paracetamol‐induced liver injury. OX40 could serve as a diagnostic index and therapeutic target of DILI.
Is shadier better? The effect of agroforestry management on small mammal diversity
Authors: Silva Adna Alves de Souza , Alvarez Martin Roberto Del Valle , Mariano‐Neto Eduardo , Cassano Camila Righetto 
Published: March 2020

AbstractAgroforestry systems play fundamental roles for wildlife conservation, but are prone to disturbances from management practices aiming at increasing local productivity. This work investigates the small mammal assemblages present in cacao agroforests, which differ in shade tree density. We tested the prediction that higher tree density increases shade level, analyzed how some environmental variables important for small mammals (vegetation complexity, tree basal area, and invertebrate biomass) vary across the shade level gradient, and how the assemblages respond to these variations. We also tested the effect of the environmental variables on the abundance of the three most common species: Rhipidomys mastacalis, Hylaeamys seuanezi, and Marmosa murina. We captured 651 individuals belonging to 18 species. A positive relationship was observed between an abundance of non‐forest specialists and tree basal area, while species diversity within this group showed positive association with vegetation complexity. Assemblage structure (described by a matrix of species abundance per site) was not affected by our environmental variables, but R. mastacalis was more abundant in sites with lower vegetation complexity. Higher shade levels in cacao agroforest tended to occur in sites with greater tree basal area, which was not a good predictor of small mammal diversity. This suggests that environmental management to reduce shade with the purpose of increasing cacao productivity is not necessarily negative for small mammal conservation. Species diversity was favored by structurally complex systems, a possible response to greater niche diversity.Abstract in Portuguese is available with online material.
Diurnal foraging ant–tree co‐occurrence networks are similar between canopy and understorey in a Neotropical rain forest
Authors: Antoniazzi Reuber , García‐Franco Jose , Janda Milan , Leponce Maurice , Dáttilo Wesley 
Published: March 2020

AbstractDiscussion of the vertical stratification of organisms in tropical forests has traditionally focused on species distribution. Most studies have shown that, due to differences in abiotic conditions and resource distribution, species can be distributed along the vertical gradient according to their ecophysiological needs. However, the network structure between distinct vertical strata remains little‐explored. To fill this gap in knowledge, we used baits to sample ants in the canopy and understorey trees of a Mexican tropical rain forest to record the ant–tree co‐occurrences. We examined the ant–tree co‐occurrences in the canopy and understorey using complementary network metrics (i.e., specialization, interaction diversity, modularity, and nestedness). In addition, we evaluated co‐occurrence patterns between ant species on trees, using C‐score analysis. In general, we found no differences in the network structure, although the interaction diversity was greater in the understorey than in the canopy networks. We also observed that co‐occurrence networks of each vertical stratum featured four ant species in the central core of highly co‐occurring species, with three species unique to each stratum. Moreover, we found a similar trend toward ant species segregation in the both strata. These findings reveal a similar pattern of ant–ant co‐occurrences in both vertical strata, probably due to the presence of arboreal‐nesting ants in the understorey. Overall, we showed that despite the marked differences in species composition and environmental conditions between understorey and canopy strata, ant–tree co‐occurrences in these habitats could be governed by similar mechanisms, related to dominance and resource monopolization by ants.Abstract in Spanish is available with online material.
Coping with branch excision when measuring leaf net photosynthetic rates in a lowland tropical forest
Authors: Verryckt Lore T. , Van Langenhove Leandro , Ciais Philippe , Courtois Elodie A. , Vicca Sara , Peñuelas Josep , Stahl Clément , Coste Sabrina , Ellsworth David S. , Posada Juan M. , Obersteiner Michael , Chave Jérôme , Janssens Ivan A. 
Published: March 2020

AbstractMeasuring leaf gas exchange from canopy leaves is fundamental for our understanding of photosynthesis and for a realistic representation of carbon uptake in vegetation models. Since canopy leaves are often difficult to reach, especially in tropical forests with emergent trees up to 60 m at remote places, canopy access techniques such as canopy cranes or towers have facilitated photosynthetic measurements. These structures are expensive and therefore not very common. As an alternative, branches are often cut to enable leaf gas exchange measurements. The effect of branch excision on leaf gas exchange rates should be minimized and quantified to evaluate possible bias. We compared light‐saturated leaf net photosynthetic rates measured on excised and intact branches. We selected branches positioned at three canopy positions, estimated relative to the top of the canopy: upper sunlit foliage, middle canopy foliage, and lower canopy foliage. We studied the variation of the effects of branch excision and transport among branches at these different heights in the canopy. After excision and transport, light‐saturated leaf net photosynthetic rates were close to zero for most leaves due to stomatal closure. However, when the branch had acclimated to its new environmental conditions—which took on average 20 min—light‐saturated leaf net photosynthetic rates did not significantly differ between the excised and intact branches. We therefore conclude that branch excision does not affect the measurement of light‐saturated leaf net photosynthesis, provided that the branch is recut under water and is allowed sufficient time to acclimate to its new environmental conditions.
Predator–prey interactions in anurans of the tropical dry forests of the Colombian Caribbean: A functional approach
Authors: Blanco‐Torres Argelina , Duré Marta I. , Bonilla Maria Argenis , Cagnolo Luciano 
Published: March 2020

AbstractAnuran–prey selection might be mediated by traits, either by mismatches in predator and prey traits (preventing interactions) or by predator selection of prey traits (encouraging interactions). These effect traits could be summarized in two contrasting foraging strategies: “active” and “sit‐and‐wait” foragers. We evaluated whether anurans could be classified into groups of species sharing traits associated with their diet, and what is the relation between particular effect traits of anurans and their prey. We collected anurans and identified their stomach contents once during dry, minor, and major rain seasons in six dry forest sites in the Colombian Caribbean. For each of the 19 anuran species and 436 prey items, we registered six effect traits. We applied RLQ and fourth‐corner methodologies to relate predator and prey traits through their interaction matrix. Predators were assigned to five groups according to their differences in locomotion, body shape, proportion of the jaw width, mode of tongue protrusion, and strata preferred. Regarding preys, species were assigned to four groups according to their gregariousness, body shape and hardness, defensive traits, and mobility. Body size of both, predators and prey, had a minor contribution in the group assignment. We found that predators using active search target low‐mobility preys, whereas species using sit‐and‐wait strategy target highly nutritive prey that are difficult to manipulate. By linking amphibian diet with foraging strategies, we hope to contribute to the understanding of mechanisms behind anuran–prey food web patterns and to build more realistic models of functional response to changing environments.Abstract in Spanish is available with online material.
Artificial intelligence in oncology
Authors: Shimizu Hideyuki , Nakayama Keiichi I. 
Published: March 2020

AbstractArtificial intelligence (AI) has contributed substantially to the resolution of a variety of biomedical problems, including cancer, over the past decade. Deep learning, a subfield of AI that is highly flexible and supports automatic feature extraction, is increasingly being applied in various areas of both basic and clinical cancer research. In this review, we describe numerous recent examples of the application of AI in oncology, including cases in which deep learning has efficiently solved problems that were previously thought to be unsolvable, and we address obstacles that must be overcome before such application can become more widespread. We also highlight resources and datasets that can help harness the power of AI for cancer research. The development of innovative approaches to and applications of AI will yield important insights in oncology in the coming decade.
Philosophical and Historical Perspectives on Student Boredom
Authors: Scribner Campbell F. 
Published: March 2020

Abstract.In this article, Campbell Scribner applies insights from history, philosophy, and reader theory to marginal inscriptions in nineteenth‐century textbooks, providing a conjectural explanation of student boredom during the period. He contends that boredom was a dialectic and contingent experience, based on shifting notions of childhood and education, in which students navigated between public and private space and between spontaneity and convention. Ultimately, Scribner concludes, despite difficulties in documentation, that boredom constituted a crucial element of children's self‐education.
Educating in the Seventh Fire: Debwewin, Mino‐bimaadiziwin, and Ecological Justice
Authors: Kruse Marc , Tanchuk Nicolas , Hamilton Robert 
Published: March 2020

AbstractThe Anishinaabe Seven Fires Creation Story can be read as a theory on which all human beings share a fundamental love of reflecting reality in what they think and do. In this article, Marc Kruse, Nicolas Tanchuk, and Robert Hamilton argue that this ethical theory is correct but that the colonial ideology taught in our schools can obscure our knowledge of this fact. Specifically, the authors claim that decolonizing education requires teaching students and teachers alike to see the presence of value whenever they encounter other beings animated by a responsiveness to reality. All living things strive to perceive and respond to reality — to live and continue to learn — even if epistemic faculties differ. All living things, then, the authors conclude, are rightly seen as our relatives and kin, as bearers of value to whom we owe moral respect, as Anishinaabe elders have long taught.