bluuebunny/crossref_metadata_2025_split huggingface dataset:
Update on maintenance therapy for granulomatosis with polyangiitis and microscopic polyangiitis
Authors: Singer Ora , McCune W. Joseph 
Published: March 2017

Purpose of review
The antineutrophilic cytoplasmic antibody (ANCA)-associated vasculitides are a group of rare systemic diseases. The past several years have seen major therapeutic advances in the treatment of granulomatosis with polyangiitis (GPA) and microscopic polyangiitis (MPA). The success rate in induction of remission is high, but reducing the high incidence of relapses remains a therapeutic challenge.

Recent findings
Studies have shown no improvement in relapse rates in GPA and MPA over the past 2 decades. This has prompted a recent focus on therapeutic strategies to maintain remission in these relapsing diseases. Low-dose rituximab (RTX) at fixed intervals has been shown superior to azathioprine for maintenance of remission. Despite this advance, longer follow-up periods have shown late-stage relapses with withdrawal of therapy suggesting a possible need for longer treatment regimens. Evaluation of prognostic indicators is also helpful in stratifying patients who might be more likely to relapse or to respond to a particular therapy.

Summary
Results from recent research have significantly advanced our approach to prevention of relapses in GPA and MPA. Newer maintenance agents have shown benefit in maintenance of remission and relapse-free survival.
Examining Patient Outcome Quality Indicators Based on Wait Time From Referral to Entry Into Cardiac Rehabilitation
Authors: Kehler Dustin Scott , Kent Dave , Beaulac Julie , Strachan Leisha , Wangasekara Nilu , Chapman Soyun , Hiebert Brett , Lamont Darlene , Lerner Neal , Boreskie Sue , Avery Lorraine , Duhamel Todd A. 
Published: March 2017

Purpose:
The purpose of this study was to examine whether meeting the Canadian Cardiovascular Society (CCS) ≤60-day wait time from cardiac rehabilitation (CR) referral to enrollment is associated with CCS patient-level quality indicator outcomes.

Methods:
This pilot observational study consisted of 69 participants entering CR separated into 2 groups based on wait time (≤60-day, n = 45; >60-day, n = 24). Data were collected at baseline, and 1, 4 (CR completion), 6, and 12 months after baseline. Quality indicators for achieving a 0.5 peak metabolic equivalent (MET) improvement at CR completion, physical activity of 150 min/wk of moderate-vigorous physical activity, and CR adherence were assessed. Depressive symptoms were assessed with the Patient Health Questionnaire.

Results:
Sixty participants completed the study (≤60-day, n = 40; >60-day, n = 20). In the ≤60-day group, 92% of participants achieved the 0.5 MET improvement upon CR completion; whereas 60% of the >60-day group met this criteria (P ≤ .05). For the 150 min/wk of moderate-vigorous physical activity and CR adherence, both groups were not significantly different at any time. Elevated depressive symptoms were initially observed in 45% of participants in the ≤60-day group and 35% in the >60-day group (NS) and decreased to 8% in the ≤60-day group compared with 30% in the >60-day group at 12 months (P ≤ .05).

Conclusions:
Meeting the CCS 60-day acceptable wait time is associated with improvements in METs and depressive symptoms, but not with physical activity or CR adherence. A larger observational study is warranted to explore patient-level CCS quality indicators during and after CR.
MICROPERIMETRY IN BEST VITELLIFORM MACULAR DYSTROPHY
Authors: Battaglia Parodi Maurizio , Castellino Niccolò , Iacono Pierluigi , Chowers Itay , Empeslidis Theodoros , Goldstein Michaella , Bandello Francesco 
Published: March 2017

Purpose:
To investigate retinal sensitivity in eyes with all the clinical stages of Best vitelliform macular dystrophy (VMD).

Methods:
Thirty-two patients affected by VMD in subclinical, vitelliform, pseudohypopyon, vitelliruptive, and atrophic stages were enrolled in this prospective cross-sectional study. Patients underwent a complete ophthalmologic examination, including determination of best-corrected visual acuity (BCVA), staging of the disease (Gass's classification), and microperimetry by means of the macular integrity assessment microperimeter. The primary outcome measure was to describe the alterations in the retinal sensitivity of eyes affected by VMD in different stages. Secondary outcome measures included correlations between retinal sensitivity and best-corrected visual acuity and the correlation between the VMD stage and the specific microperimetry pattern.

Results:
Mean retinal sensitivity was reduced in all the VMD stages. Nevertheless, vitelliform, pseudohypopyon, and vitelliruptive stages turned out to be very similar, especially within 10°. Fixation was classified as stable in 27 eyes (44.2%), relatively unstable in 16 eyes (26.2%), and unstable in 18 eyes (29.5%). Fixation stability correlated both with the disease stage and best-corrected visual acuity.

Conclusion:
VMD is characterized by complex microperimetric abnormalities, involving the whole macular area. Microperimetry may contribute to the global clinical assessment of patients affected by VMD and could be used in future therapeutic approaches.
News on the molecular regulation and function of hepatic low-density lipoprotein receptor and LDLR-related protein 1
Authors: van de Sluis Bart , Wijers Melinde , Herz Joachim 
Published: March 2017

Purpose of review
Clearing of atherogenic lipoprotein particles by the liver requires hepatic low-density lipoprotein receptor (LDLR) and LDLR-related protein 1 (LRP1). This review highlights recent studies that have expanded our understanding of the molecular regulation and metabolic functions of LDLR and LRP1 in the liver.

Recent findings
Various proteins orchestrate the intracellular trafficking of LDLR and LRP1. After internalization, the receptors are redirected via recycling endosomes to the cell surface. Several new endocytic proteins that facilitate the endosomal trafficking of LDLR and consequently the clearance of circulating LDL cholesterol have recently been reported. Mutations in some of these proteins cause hypercholesterolemia in human. In addition, LRP1 controls cellular cholesterol efflux by modulating the expression of ABCA1 and ABCG1, and hepatic LRP1 protects against diet-induced hepatic insulin resistance and steatosis through the regulation of insulin receptor trafficking.

Summary
LDLR and LRP1 have prominent roles in cellular and organismal cholesterol homeostasis. Their functioning, including their trafficking in the cell, is controlled by numerous proteins. Comprehensive studies into the molecular regulation of LDLR and LRP1 trafficking have advanced our fundamental understanding of cholesterol homeostasis, and these insights may lead to novel therapeutic strategies for atherosclerosis, hyperlipidemia and insulin resistance in the future.
Rediscovering scavenger receptor type BI: surprising new roles for the HDL receptor
Authors: Hoekstra Menno , Sorci-Thomas Mary 
Published: March 2017

Purpose of review
Scavenger receptor BI (SR-BI) is classically known for its role in antiatherogenic reverse cholesterol transport as it selectively takes up cholesterol esters from HDL. Here, we have highlighted recent literature that describes novel functions for SR-BI in physiology and disease.

Recent findings
A large population-based study has revealed that patients heterozygous for the P376L mutant form of SR-BI showed significantly increased levels of plasma HDL-cholesterol and had increased risk of cardiovascular disease, demonstrating that SR-BI in humans is a significant determinant of cardiovascular disease. Furthermore, SR-BI has been shown to modulate the susceptibility to LPS-induced tissue injury and the ability of sphingosine 1 phosphate to interact with its receptor, linking SR-BI to the regulation of inflammation. In addition, important domains within the molecule (Trp-415) as well as novel regulators (procollagen C-endopeptidase enhancer protein 2) of SR-BI's selective uptake function have recently been identified. Moreover, relatively high expression levels of the SR-BI protein have been observed in a variety of cancer tissues, which is associated with a reduced overall survival rate.

Summary
The HDL receptor SR-BI is a potential therapeutic target not only in the cardiovascular disease setting, but also in inflammatory conditions as well as in cancer.
Applying Mondrian Cross-Conformal Prediction to Estimate Prediction Confidence on Large Imbalanced Bioactivity Datasets
Authors: Sun Jiangming , Carlsson Lars , Ahlberg Ernst , Norinder Ulf , Engkvist Ola , Chen Hongming 
Published: March 2017

ABSTRACTConformal prediction has been proposed as a more rigorous way to define prediction confidence compared to other application domain concepts that have earlier been used for QSAR modelling. One main advantage of such a method is that it provides a prediction region potentially with multiple predicted labels, which contrasts to the single valued (regression) or single label (classification) output predictions by standard QSAR modelling algorithms. Standard conformal prediction might not be suitable for imbalanced datasets. Therefore, Mondrian cross-conformal prediction (MCCP) which combines the Mondrian inductive conformal prediction with cross-fold calibration sets has been introduced. In this study, the MCCP method was applied to 18 publicly available datasets that have various imbalance levels varying from 1:10 to 1:1000 (ratio of active/inactive compounds). Our results show that MCCP in general performed well on cheminformatics datasets with various imbalance levels. More importantly, the method not only provides confidence of prediction and prediction regions compared to standard machine learning methods, but also produces valid predictions for the minority class. In addition, a compound similarity based nonconformity measure was investigated. Our results demonstrate that although it gives valid predictions, its efficiency is much worse than nonconformity measures obtained from supervised learning.
Accounting for technical noise in single-cell RNA sequencing analysis
Authors: Jia Cheng , Kelly Derek , Kim Junhyong , Li Mingyao , Zhang Nancy R. 
Published: March 2017

ABSTRACTRecent technological breakthroughs have made it possible to measure RNA expression at the single-cell level, thus paving the way for exploring expression heterogeneity among individual cells. Current single-cell RNA sequencing (scRNA-seq) protocols are complex and introduce technical biases that vary across cells, which can bias downstream analysis without proper adjustment. To account for cell-to-cell technical differences, we propose a statistical framework, TASC (Toolkit for Analysis of Single Cell RNA-seq), an empirical Bayes approach to reliably model the cell-specific dropout rates and amplification bias by use of external RNA spike-ins. TASC incorporates the technical parameters, which reflect cell-to-cell batch effects, into a hierarchical mixture model to estimate the biological variance of a gene and detect differentially expressed genes. More importantly, TASC is able to adjust for covariates to further eliminate confounding that may originate from cell size and cell cycle differences. In simulation and real scRNA-seq data, TASC achieves accurate Type I error control and displays competitive sensitivity and improved robustness to batch effects in differential expression analysis, compared to existing methods. TASC is programmed to be computationally efficient, taking advantage of multi-threaded parallelization. We believe that TASC will provide a robust platform for researchers to leverage the power of scRNA-seq.
Agency cost of debt: evidence from Kansas farm operations
Authors: Brewer Brady , Featherstone Allen M. 
Published: March 2017

Purpose
The purpose of this paper is to examine how debt affects the cost structure of a farm. Agency costs arise when stakeholders of a farm manage their farm differently to obtain debt which results in inefficiencies. These inefficiencies cause a farm to deviate from cost minimization strategies.

Design/methodology/approach
This study uses the non-parametric technique of data envelopment analysis. Through this method, a non-stochastic cost frontier is constructed where all farms must lie on or above the frontier. This allows for the analysis of how debt affects the shape of the cost frontier and for how debt affects deviations away from cost-minimizing strategy. The shadow costs of the debt constraints in the linear programming problem are used to analyze the effect of debt at the cost frontier while a series of Tobit models are estimated to examine the effect of debt on deviations away from the frontier.

Findings
The findings of this paper support the existence of agency costs associated with debt for Kansas farms. The addition of debt and capital constraints lowered the minimum cost frontier increasing the average efficient cost under variable returns to scale. However, for those farms on the frontier, the shadow cost of debt was negative meaning an increase in debt would lower the overall variable cost. The increase of debt was found to be negatively correlated to the efficiency score of the farms.

Originality/value
This paper provides value by supporting the existence of agency costs which has been disagreed upon in the literature and also providing new insights for how to analyze agency costs. Since debt was found to have a negative shadow value for those farms on the frontier but negatively correlated with efficiency scores, this suggests that agency costs affect firms differently depending on where the farm is on the cost frontier.
Farm and lender structural change: implications for federal credit
Authors: Dodson Charles B. , Ahrendsen Bruce L. 
Published: March 2017

Purpose
The purpose of this paper is to examine changes in the structures of US farms and lenders and identify prospective implications for federal credit.

Design/methodology/approach
Data from US farm operations for 1996-2014 were adjusted to 2014 values using commodity price indices. Farm size groups were constructed by value of farm production to analyze changes in farm numbers, production, assets, debt, leverage, liquidity, profitability, land tenure, commodity type, contract production, organization type, and use of Farm Service Agency (FSA) direct and guaranteed loans by farm size. Bank, Farm Credit System (FCS), and FSA data from 1996 to 2015 were adjusted to 2014 values. Lender size groups were constructed to analyze changes in bank and association numbers, farm loans, and use of FSA guaranteed loans by lender size.

Findings
The greatest consolidation has been by farms with over $2 million in production. More farm debt is held by large, complex organizations, frequently with multiple operators, more variable income, and greater reliance on production contracts and operating and nonreal estate credit. Large farms have greater leverage, are more profitable, and have a larger share of household income from the farm. Banks and FCS institutions are fewer and larger, yet smaller institutions use FSA guarantees to a greater extent. Larger farms tend to be more reliant on both direct and guaranteed FSA loans and are likely to become more dependent on FSA credit.

Originality/value
Changing farm and lender structure together with softening farm income may require FSA farm loan program changes to meet any increase in loan demand. Policy alternatives are provided to meet changing demand for farm credit.
Modeling debt choice in agriculture: the effect of endogenous asset values
Authors: Bampasidou Maria , Mishra Ashok K. , Moss Charles B. 
Published: March 2017

Purpose
The purpose of this paper is to investigate the endogeneity of asset values and how it relates to farm financial stress in US agriculture. The authors conceptualize an implied measure of farm financial stress as a function of debt position. The authors posit that there are variations in the asset values that are beyond the farmer’s control and therefore have implications on farm debt.

Design/methodology/approach
The framework recognizes the endogeneity of return on assets (ROA). It uses a non-parametric technique to approximate the variance of expected ROA (VEROA). The authors model the rate of return on agricultural assets and interest rate with a formulation that focuses on macroeconomic policy. Further, the authors use a dynamic balanced panel data set from 1960 to 2011 for 15 US agricultural states from the Agricultural Resource Management Survey, and information from traditional state-level financial statements.

Findings
Estimation of linear dynamic debt panel data models accounting for the endogeneity of ROA and VEROA is a challenging task. Estimated variances are unstable. Hence, the authors focus on variance specification that uses the residuals squared from the ARIMA specification and non-parametric estimators. Arellano-Bover/Blundell-Bond generalized method of moments estimation procedures, although may be biased, show that VEROA has a negative and significant effect on the total amount of debt in the agricultural sector.

Research limitations/implications
The instruments used in this analysis are lagged regressors which may be weakly correlated with the relevant first-order condition, hence not properly identifying the parameters of interest. Future research could include the identification of better instruments, potentially use of sequential moment conditions.

Originality/value
Unlike previous study, the authors use non-parametric approximation of VEROA. The authors model the rate of return on agricultural assets and interest rate with a formulation that focuses on macroeconomic policy. Second, the authors make use of a large dynamic balanced panel data set from 1960 to 2011 for 15 agricultural states in the USA. To the best of the authors’ knowledge, this study is one of the few that provides evidence on risk-balancing behavior at the agricultural sector level, of the USA.
Empirical analysis of the main factors influencing rice harvest losses based on sampling survey data of ten provinces in China
Authors: Wu Linhai , Hu Qipeng , Wang Jianhua , Zhu Dian 
Published: March 2017

Purpose
In China, a major grain producer, rice losses during harvest cannot be ignored. The purpose of this paper is to assess the extent of rice harvest losses in major grain-producing areas in China by a sampling survey, and to further analyze the main factors influencing rice harvest losses using an ordered multinomial logistic model.

Design/methodology/approach
In this study, data were collected using a multi-stage sampling method from ten major rice-producing provinces/regions in China. On this basis, five counties were selected from each of these provinces/regions. In the actual survey, house numbers were randomly selected, and then corresponding farmer households were visited by trained investigators.

Findings
The survey found that 56.22 percent of respondents believed that rice harvest losses were 4 percent or lower in China, though there were differences among the provinces. The proportion of family business income, planting scale, mechanization level, timely harvest, and operational meticulousness had negative effects on rice harvest losses. On the other hand, farmers’ experience of employment as migrant workers had a positive effect on rice harvest losses. In addition, bad weather and short handedness during harvest significantly increased rice harvest losses.

Originality/value
The meaning of rice harvest losses was defined based on previous research findings on the definition of grain harvest losses and the realities in China. The current rice harvest losses in different areas in China were analyzed based on sampling survey data from 957 farmers in ten provinces in China.
Organic farming
Authors: Ma Wanglin , Ma Chunbo , Su Ye , Nie Zihan 
Published: March 2017

Purpose
The purpose of this paper is to explore the factors that influence Chinese apple farmers’ willingness to adopt organic farming, paying a special attention to the role of information acquisition.

Design/methodology/approach
Given that the selection bias may occur when farmers themselves decide whether or not to acquire the information to understand the essence of organic farming, this study employs a recursive bivariate probit model to address the issue of the selection bias.

Findings
The empirical results indicate that farmers’ decision to acquire information is positively affected by farmers’ environmental awareness, access to credit and access to information. In particular, information acquisition appears to increase the likelihood of farmers’ willingness to adopt organic farming by 35.9 percentage points on average.

Practical implications
The findings suggest that measures increasing farmers’ information exposure can be promising policy interventions to induce adoption of organic farming.

Originality/value
While considerable evidence indicates that organic farming provides more benefits than conventional production practice, little is known about farmers’ willingness to adopt in China. This paper provides a first attempt by examining the role of information acquisition in determining Chinese apple farmers’ willingness to adopt.
Rubber specialization vs crop diversification: the roles of perceived risks
Authors: Min Shi , Huang Jikun , Waibel Hermann 
Published: March 2017

PurposeThe purpose of this paper is to examine the impact of farmers’ risk perceptions regarding rubber farming on their land use choices, including rubber specialization and crop diversification.Design/methodology/approachA cross-sectional survey data of some 600 smallholder rubber farmers in Xishuangbanna in Southwest China is employed. This paper develops a general conceptual framework that incorporates a subjective risk item into a model of farmers’ land use choices, thereby developing four econometric models to estimate the role of risk perceptions, and applies instrumental variables to control for the endogeneity of risk perceptions.FindingsThe results demonstrate that risk perceptions play an important role in smallholders’ decision-making regarding land use strategies to address potential risks in rubber farming. Smallholders with higher risk perceptions specialize in rubber farming less often and are more likely to diversify their land use, thereby contributing to local environmental conservation in terms of agrobiodiversity. The land use choices of smallholder rubber farmers are also associated with ethnicity, household wealth, off-farm employment, land tenure status, altitude and rubber farming experience.Originality/valueThis study contributes to a better understanding of the implications of farmers’ risk perceptions and shows entry points for improving the sustainability of rubber-based land use systems.