bluuebunny/crossref_metadata_2025_split huggingface dataset:
Penalized likelihood methods improve parameter estimates in occupancy models
Authors: Hutchinson Rebecca A. , Valente Jonathon J. , Emerson Sarah C. , Betts Matthew G. , Dietterich Thomas G. 
Published: March 2015

Summary

Occupancy models are employed in species distribution modelling to account for imperfect detection during field surveys. While this approach is popular in the literature, problems can occur when estimating the model parameters. In particular, the maximum likelihood estimates can exhibit bias and large variance for data sets with small sample sizes, which can result in estimated occupancy probabilities near 0 and 1 (‘boundary estimates’).

In this paper, we explore strategies for estimating parameters based on maximizing a penalized likelihood. Penalized likelihood methods augment the usual likelihood with a penalty function that encodes information about what parameter values are undesirable. We introduce penalties for occupancy models that have analogues in ridge regression and Bayesian approaches, and we compare them to a penalty developed for occupancy models in prior work.

We examine the bias, variance and mean squared error of parameter estimates obtained from each method on synthetic data. Across all of the synthetic data sets, the penalized estimation methods had lower mean squared error than the maximum likelihood estimates. We also provide an example of the application of these methods to point counts of avian species. Penalized likelihood methods show similar improvements when tested using empirical bird point count data.

We discuss considerations for choosing among these methods when modelling occupancy. We conclude that penalized methods may be of practical utility for fitting occupancy models with small sample sizes, and we are releasing R code that implements these methods.
A Stepwise Confidence Interval Procedure Under Unknown Variances Based on an Asymmetric Loss Function for Toxicological Evaluation
Authors: Cao Lei , Tao Jian , Shi Ning‐Zhong , Liu Wei 
Published: March 2015

SummaryOne of the most important issues in toxicity studies is the identification of the equivalence of treatments with a placebo. Because it is unacceptable to declare non‐equivalent treatments to be equivalent, it is important to adopt a reliable statistical method to properly control the family‐wise error rate (FWER). In dealing with this issue, it is important to keep in mind that overestimating toxicity equivalence is a more serious error than underestimating toxicity equivalence. Consequently asymmetric loss functions are more appropriate than symmetric loss functions. Recently Tao, Tang & Shi (2010) developed a new procedure based on an asymmetric loss function. However, their procedure is somewhat unsatisfactory because it assumes that the variances of various dose levels are known. This assumption is restrictive for some applications. In this study we propose an improved approach based on asymmetric confidence intervals without the restrictive assumption of known variances. The asymmetry guarantees reliability in the sense that the FWER is well controlled. Although our procedure is developed assuming that the variances of various dose levels are unknown but equal, simulation studies show that our procedure still performs quite well when the variances are unequal.
The group exponential lasso for bi‐level variable selection
Authors: Breheny Patrick 
Published: March 2015

SummaryIn many applications, covariates possess a grouping structure that can be incorporated into the analysis to select important groups as well as important members of those groups. One important example arises in genetic association studies, where genes may have several variants capable of contributing to disease. An ideal penalized regression approach would select variables by balancing both the direct evidence of a feature's importance as well as the indirect evidence offered by the grouping structure. This work proposes a new approach we call the group exponential lasso (GEL) which features a decay parameter controlling the degree to which feature selection is coupled together within groups. We demonstrate that the GEL has a number of statistical and computational advantages over previously proposed group penalties such as the group lasso, group bridge, and composite MCP. Finally, we apply these methods to the problem of detecting rare variants in a genetic association study.
The TRPA1 channel mediates the analgesic action of dipyrone and pyrazolone derivatives
Authors: Nassini Romina , Fusi Camilla , Materazzi Serena , Coppi Elisabetta , Tuccinardi Tiziano , Marone Ilaria M , De Logu Francesco , Preti Delia , Tonello Raquel , Chiarugi Alberto , Patacchini Riccardo , Geppetti Pierangelo , Benemei Silvia 
Published: March 2015

Background and PurposeAlthough still used by hundreds of millions of people worldwide, the mechanism of the analgesic action of the pyrazolone derivatives (PDs), dipyrone, propyphenazone and antipyrine remains unknown. The transient receptor potential ankyrin 1 (TRPA1) channel, expressed by nociceptors, is emerging as a major pain transduction pathway. We hypothesized that PDs target the TRPA1 channel and by this mechanism produce their analgesic effect.Experimental ApproachCalcium responses and currents were studied in cultured TRPA1‐expressing rodent dorsal root ganglion neurons and human cells. Acute nociception and mechanical hypersensitivity were investigated in naïve and genetically manipulated mice.Key ResultsPyrazolone and PDs selectively inhibited calcium responses and currents in TRPA1‐expressing cells and acute nocifensor responses in mice evoked by reactive channel agonists (allyl isothiocyanate, acrolein and H2O2). In line with recent results obtained with TRPA1 antagonists and TRPA1 gene deletion, the two most largely used PDs, dipyrone and propyphenazone, attenuated TRPA1‐mediated nociception and mechanical allodynia in models of inflammatory and neuropathic pain (formalin, carrageenan, partial sciatic nerve ligation and the chemotherapeutic drug, bortezomib). Notably, dipyrone and propyphenazone attenuated carrageenan‐evoked mechanical allodynia, without affecting PGE2 levels. The main metabolites of PDs did not target TRPA1 and did not affect TRPA1‐dependent nociception and allodynia.Conclusions and ImplicationsEvidence that in rodents the nociceptive/hyperalgesic effect produced by TRPA1 activation is blocked by PDs suggests that a similar pathway is attenuated by PDs in humans and that TRPA1 antagonists could be novel analgesics, devoid of the adverse haematological effects of PDs.
Oxidative shielding and the cost of reproduction
Authors: Blount Jonathan D. , Vitikainen Emma I. K. , Stott Iain , Cant Michael A. 
Published: March 2015

ABSTRACTLife‐history theory assumes that reproduction and lifespan are constrained by trade‐offs which prevent their simultaneous increase. Recently, there has been considerable interest in the possibility that this cost of reproduction is mediated by oxidative stress. However, empirical tests of this theory have yielded equivocal support. We carried out a meta‐analysis to examine associations between reproduction and oxidative damage across markers and tissues. We show that oxidative damage is positively associated with reproductive effort across females of various species. Yet paradoxically, categorical comparisons of breeders versus non‐breeders reveal that transition to the reproductive state is associated with a step‐change reduction in oxidative damage in certain tissues and markers. Developing offspring may be particularly sensitive to harm caused by oxidative damage in mothers. Therefore, such reductions could potentially function to shield reproducing mothers, gametes and developing offspring from oxidative insults that inevitably increase as a consequence of reproductive effort. According to this perspective, we hypothesise that the cost of reproduction is mediated by dual impacts of maternally‐derived oxidative damage on mothers and offspring, and that mothers may be selected to diminish such damage. Such oxidative shielding may explain why many existing studies have concluded that reproduction has little or no oxidative cost. Future advance in life‐history theory therefore needs to take account of potential transgenerational impacts of the mechanisms underlying life‐history trade‐offs.
The evolution of acceptance and tolerance in hosts of avian brood parasites
Authors: Medina Iliana , Langmore Naomi E. 
Published: March 2015

ABSTRACTAvian brood parasites lay their eggs in the nests of their hosts, which rear the parasite's progeny. The costs of parasitism have selected for the evolution of defence strategies in many host species. Most research has focused on resistance strategies, where hosts minimize the number of successful parasitism events using defences such as mobbing of adult brood parasites or rejection of parasite eggs. However, many hosts do not exhibit resistance. Here we explore why some hosts accept parasite eggs in their nests and how this is related to the virulence of the parasite. We also explore the extent to which acceptance of parasites can be explained by the evolution of tolerance; a strategy in which the host accepts the parasite but adjusts its life history or other traits to minimize the costs of parasitism. We review examples of tolerance in hosts of brood parasites (such as modifications to clutch size and multi‐broodedness), and utilize the literature on host–pathogen interactions and plant herbivory to analyse the prevalence of each type of defence (tolerance or resistance) and their evolution. We conclude that (i) the interactions between brood parasites and their hosts provide a highly tractable system for studying the evolution of tolerance, (ii) studies of host defences against brood parasites should investigate both resistance and tolerance, and (iii) tolerance and resistance can lead to contrasting evolutionary scenarios.
Difference between patients’ and clinicians’ perception of pouch dysfunction and its impact on quality of life following restorative proctocolectomy
Authors: Brandsborg S. , Chen T. Y. , Nicholls R. J. , Laurberg S. 
Published: March 2015

AbstractAimThe Pouch Dysfunction Score (PDS) is a five‐item instrument that evaluates bowel function and quality of life following restorative proctocolectomy for ulcerative colitis. The PDS includes items that have a significantly negative impact on quality of life from the patient's point of view. The study aimed to establish how pouch dysfunction is perceived by clinicians in relation to patients experience.MethodFifty‐eight leading clinicians in the field of inflammatory bowel disease were invited to complete two PDS‐based exercises. In part 1, they received a list of the 12 bowel symptoms from which the PDS had been developed and were asked to identify and rank (in order of severity) the five they thought had the most significantly negative impact on quality of life. In part 2, they were given the list of symptoms perceived by patients to be most troublesome and were then required to enter a score that they thought was appropriate for each item according to the impact on quality of life.ResultsForty‐three clinicians responded, and each correctly identified one to three items selected by patients and included in the PDS. Severity of urgency was selected by 29 (67%) clinicians, and four (9%) rated it to be the most important. Incomplete emptying after defaecation was selected by 10 (23%). Frequency of defaecation and the use of anti‐diarrhoeal medication were selected by 14 (33%) and three (7%) clinicians, respectively. Twenty‐six (60%) did not include incomplete emptying and 25 (58%) did not include uncontrolled loss of stool in their selection.ConclusionThis study demonstrates that clinicians do not have a great understanding of the symptoms of pouch dysfunction that really matter to the patient.
Safety and effectiveness of non‐insulin glucose‐lowering agents in the treatment of people with type 2 diabetes who observe Ramadan: a systematic review and meta‐analysis
Authors: Gray L. J. , Dales J. , Brady E. M. , Khunti K. , Hanif W. , Davies M. J. 
Published: March 2015

AimTo determine which non‐insulin glucose‐lowering treatment regimens are most appropriate in people with type 2 diabetes who choose to fast during Ramadan.MethodsElectronic databases were searched for randomized controlled trials (RCTs) and observational studies that compared non‐insulin glucose‐lowering agents in people with type 2 diabetes fasting during Ramadan. Those studies which reported hypoglycaemia, weight and glycated haemoglobin (HbA1c) change were included. Data were pooled using random effects models.ResultsA total of 16 studies were included: 9 RCTs and 7 observational studies. There was evidence that dipeptidyl peptidase‐4 (DPP‐4) inhibitors led to fewer hypoglycaemic events compared with sulphonylureas. Sitagliptin significantly reduced the number of patients with ≥1 hypoglycaemic episodes during Ramadan [risk ratio (RR) 0.48, 95% confidence interval (CI) 0.36, 0.64; p > 0.0001]. This was not replicated in the RCTs of vildagliptin, but a significant reduction was found in the observational studies (RR 0.28, 95% CI 0.10, 0.75; p = 0.01) with high heterogeneity (I2 = 86.7%). Significant reductions in HbA1c and weight were seen in the observational studies of vildagliptin versus sulphonylureas. The use of liraglutide led to significant weight loss (−1.81 kg, 95% CI −2.91, −0.71; p = 0.001) compared with sulphonylureas. Pioglitazone significantly increased weight compared with placebo (3.48 kg, 95% CI 2.82, 4.14; p < 0.0001).ConclusionsThe analysis supports the use of DPP‐4 inhibitors during Ramadan rather than sulphonylureas for reduction in hypoglycaemia without a cost to diabetes control and weight. The glucagon‐like peptide (GLP)‐1 agonist liraglutide provides clinical benefits, but more studies are required. RCTs of DPP‐4 inhibitors compared with GLP‐1 agonists and novel therapies including the sodium‐glucose co‐transporter 2 and α‐glucosidase inhibitors are needed to inform evidence‐based guidelines.
Changing fitness of a necrotrophic plant pathogen under increasing temperature
Authors: Sabburg Rosalie , Obanor Friday , Aitken Elizabeth , Chakraborty Sukumar 
Published: March 2015

AbstractWarmer temperatures associated with climate change are expected to have a direct impact on plant pathogens, challenging crops and altering plant disease profiles in the future. In this study, we have investigated the effect of increasing temperature on the pathogenic fitness of Fusarium pseudograminearum, an important necrotrophic plant pathogen associated with crown rot disease of wheat in Australia. Eleven wheat lines with different levels of crown rot resistance were artificially inoculated with F. pseudograminearum and maintained at four diurnal temperatures 15/15°C, 20/15°C, 25/15°C and 28/15°C in a controlled glasshouse. To quantify the success of F. pseudograminearum three fitness measures, these being disease severity, pathogen biomass in stem base and flag leaf node, and deoxynivalenol (DON) in stem base and flag leaf node of mature plants were used. F. pseudograminearum showed superior overall fitness at 15/15°C, and this was reduced with increasing temperature. Pathogen fitness was significantly influenced by the level of crown rot resistance of wheat lines, but the influence of line declined with increasing temperature. Lines that exhibited superior crown rot resistance in the field were generally associated with reduced overall pathogen fitness. However, the relative performance of the wheat lines was dependent on the measure of pathogen fitness, and lines that were associated with one reduced measure of pathogen fitness did not always reduce another. There was a strong correlation between DON in stem base tissue and disease severity, but length of browning was not a good predictor of Fusarium biomass in the stem base. We report that a combination of host resistance and rising temperature will reduce pathogen fitness under increasing temperature, but further studies combining the effect of rising CO2 are essential for more realistic assessments.
A Video Feedback Intervention for Workforce Development: Exploring Staff Perspective Using Longitudinal Qualitative Methodology
Authors: James Deborah Michelle , Hall Alex , Lombardo Chiara , McGovern Will 
Published: March 2015

BackgroundIn this study, we explored the impact of staff training that used video feedback to help staff see the effect of their interactional work with service users. The study was based at a large organization delivering services for children and adults with autism.Materials and MethodsA longitudinal qualitative study with semi‐structured interviews was conducted to explore changes over time in 10 staff participants who received the intervention. Five participants were interviewed twice before they received the video feedback intervention to gauge the degree to which their perspective changed as part of the natural course of their working lives.ResultsThe results showed that the staff talked differently after they had the intervention. The most notable change was their talk about the service user perspective which was evident after the intervention but not before.ConclusionsThe outcomes suggest that the use of video feedback of in situ practice could help staff develop person‐centred work practices.
Perinatally administered losartan augments renal ACE2 expression but not cardiac or renal Mas receptor in spontaneously hypertensive rats
Authors: Klimas Jan , Olvedy Michael , Ochodnicka‐Mackovicova Katarina , Kruzliak Peter , Cacanyiova Sona , Kristek Frantisek , Krenek Peter , Ochodnicky Peter 
Published: March 2015

AbstractSince the identification of the alternative angiotensin converting enzyme (ACE)2/Ang‐(1‐7)/Mas receptor axis, renin‐angiotensin system (RAS) is a new complex target for a pharmacological intervention. We investigated the expression of RAS components in the heart and kidney during the development of hypertension and its perinatal treatment with losartan in young spontaneously hypertensive rats (SHR). Expressions of RAS genes were studied by the RT‐PCR in the left ventricle and kidney of rats: normotensive Wistar, untreated SHR, SHR treated with losartan since perinatal period until week 9 of age (20 mg/kg/day) and SHR treated with losartan only until week 4 of age and discontinued until week 9. In the hypertrophied left ventricle of SHR, cardiac expressions of Ace and Mas were decreased while those of AT1 receptor (Agtr1a) and Ace2 were unchanged. Continuous losartan administration reduced LV weight (0.43 ± 0.02; P < 0.05 versus SHR) but did not influence altered cardiac RAS expression. Increased blood pressure in SHR (149 ± 2 in SHR versus 109 ± 2 mmHg in Wistar; P < 0.05) was associated with a lower renal expressions of renin, Agtr1a and Mas and with an increase in ACE2. Continuous losartan administration lowered blood pressure to control levels (105 ± 3 mmHg; P < 0.05 versus SHR), however, only renal renin and ACE2 were significantly up‐regulated (for both P < 0.05 versus SHR). Conclusively, prevention of hypertension and LV hypertrophy development by losartan was unrelated to cardiac or renal expression of Mas. Increased renal Ace2, and its further increase by losartan suggests the influence of locally generated Ang‐(1‐7) in organ response to the developing hypertension in SHRs.
Adaptive contraction of diet breadth affects sexual maturation and specific nutrient consumption in an extreme generalist omnivore
Authors: Jensen K. , Schal C. , Silverman J. 
Published: March 2015

AbstractAnimals balance their intake of specific nutrients, but little is known about how they do so when foraging in an environment with toxic resources and whether toxic foods promote adaptations that affect life history traits. In German cockroach (Blattella germanica) populations, glucose aversion has evolved in response to glucose‐containing insecticidal baits. We restricted newly eclosed glucose‐averse (GA) and wild‐type (WT) female cockroaches to nutritionally defined diets varying in protein‐to‐carbohydrate (P : C) ratio (3 : 1, 1 : 1, or 1 : 3) or gave them free choice of the 3 : 1 and 1 : 3 diets, with either glucose or fructose as the sole carbohydrate source. We measured consumption of each diet over 6 days and then dissected the females to measure the length of basal oocytes in their ovaries. Our results showed significantly lower consumption by GA compared to WT cockroaches when restricted to glucose‐containing diets, but also lower fructose intake by GA compared to WT cockroaches when restricted to high fructose diets or given choice of fructose‐containing diets. Protein intake was regulated tightly regardless of carbohydrate intake, except by GA cockroaches restricted to glucose‐containing diets. Oocyte growth was completely suppressed in GA females restricted to glucose‐containing diets, but also significantly slower in GA than in WT females restricted to fructose‐containing diets. Our findings suggest that GA cockroaches have adapted to reduced diet breadth through endocrine adjustments which reduce requirements for energetic fuels. Our study illustrates how an evolutionary change in the chemosensory system may affect the evolution of other traits that govern animal life histories.
Autoimmune hepatitis: East meets west
Authors: Yang Fan , Wang Qixia , Bian Zhaolian , Ren Lin‐Lin , Jia Jidong , Ma Xiong 
Published: March 2015

AbstractAutoimmune hepatitis (AIH) is an inflammatory liver disease with diverse clinical spectrum, which predominantly affects females. This review provides detailed comparisons of epidemiology, genetic predispositions, clinical features, risk factors of hepatocellular carcinoma, and mortality in AIH patients between eastern and western countries. AIH prevalence and incidence are lower in Asia‐Pacific area than in Europe and America. European and American patients seem to have more severe disease, characterized with human leukocyte antigen‐DR3 haplotype, younger age, more AIH‐induced “cirrhosis” at diagnosis, higher elevated serum immunoglobulin G levels, and positive rate of antisoluble liver antigen/liver pancreatitis. The overall AIH diagnostic accuracy of revised original criteria and simplified scoring system are similar in European/American populations and Asian. Cirrhosis at presentation and non‐response to immunosuppressive therapy within 1 year are the most important predictors for poor prognosis of AIH patients.
Pharmacokinetics of tulathromycin after subcutaneous injection in North American bison (Bison bison)
Authors: Bachtold K. , Alcorn J. , Matus J. , Boison J. , Woodbury M. 
Published: March 2015

Tulathromycin is approved for the treatment of respiratory disease in cattle and swine. It is intended for long‐acting, single‐dose injection therapy (Draxxin), making it particularly desirable for use in bison due to the difficulty in handling and ease of creating stress in these animals. The pharmacokinetic properties of tulathromycin in bison were investigated. Ten wood bison received a single 2.5 mg/kg subcutaneous injection of Draxxin. Serum concentrations were measured by liquid chromatography–mass spectrometry (LC‐MS) detection. Tulathromycin demonstrated early maximal serum concentrations, extensive distribution, and slow elimination characteristics. The mean maximum serum concentration (Cmax) was 195 ng/mL at 1.04 h (tmax) postinjection. The mean area under the serum concentration–time curve, extrapolated to infinity (AUC0–inf), was 9341 ng·h/mL. The mean apparent volume of distribution (Vd/F) and clearance (Cls/F) was 111 L/kg and 0.4 L/h/kg, respectively, and the mean half‐life (t1/2) was 214 h (8.9 days). Compared to values for cattle, Cmax and AUC0–inf were lower in bison, while the Vd/F was larger and the t1/2 longer. Tissue distribution and clinical efficacy studies in bison are needed to confirm the purported extensive distribution of tulathromycin into lung tissue and to determine whether a 2.5 mg/kg subcutaneous dosage is adequate for bison.