bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel metrics for growth model selection
Authors: Grigsby Matthew R. , Di Junrui , Leroux Andrew , Zipunnikov Vadim , Xiao Luo , Crainiceanu Ciprian , Checkley William 
Published: February 2018

Abstract
Background
Literature surrounding the statistical modeling of childhood growth data involves a diverse set of potential models from which investigators can choose. However, the lack of a comprehensive framework for comparing non-nested models leads to difficulty in assessing model performance. This paper proposes a framework for comparing non-nested growth models using novel metrics of predictive accuracy based on modifications of the mean squared error criteria.

Methods
Three metrics were created: normalized, age-adjusted, and weighted mean squared error (MSE). Predictive performance metrics were used to compare linear mixed effects models and functional regression models. Prediction accuracy was assessed by partitioning the observed data into training and test datasets. This partitioning was constructed to assess prediction accuracy for backward (i.e., early growth), forward (i.e., late growth), in-range, and on new-individuals. Analyses were done with height measurements from 215 Peruvian children with data spanning from near birth to 2 years of age.

Results
Functional models outperformed linear mixed effects models in all scenarios tested. In particular, prediction errors for functional concurrent regression (FCR) and functional principal component analysis models were approximately 6% lower when compared to linear mixed effects models. When we weighted subject-specific MSEs according to subject-specific growth rates during infancy, we found that FCR was the best performer in all scenarios.

Conclusion
With this novel approach, we can quantitatively compare non-nested models and weight subgroups of interest to select the best performing growth model for a particular application or problem at hand.
Responses to mechanically and visually cued water waves in the nervous system of the medicinal leech
Authors: Lehmkuhl Andrew M. , Muthusamy Arunkumar , Wagenaar Daniel A. 
Published: February 2018

ABSTRACT
Sensitivity to water waves is a key modality by which aquatic predators can detect and localize their prey. For one such predator – the medicinal leech, Hirudo verbana – behavioral responses to visual and mechanical cues from water waves are well documented. Here, we quantitatively characterized the response patterns of a multisensory interneuron, the S cell, to mechanically and visually cued water waves. As a function of frequency, the response profile of the S cell replicated key features of the behavioral prey localization profile in both visual and mechanical modalities. In terms of overall firing rate, the S cell response was not direction selective, and although the direction of spike propagation within the S cell system did follow the direction of wave propagation under certain circumstances, it is unlikely that downstream neuronal targets can use this information. Accordingly, we propose a role for the S cell in the detection of waves but not in the localization of their source. We demonstrated that neither the head brain nor the tail brain are required for the S cell to respond to visually cued water waves.
Using regulatory genomics data to interpret the function of disease variants and prioritise genes from expression studies
Authors: Ferrero Enrico 
Published: February 2018

The identification of therapeutic targets is a critical step in the research and developement of new drugs, with several drug discovery programmes failing because of a weak linkage between target and disease. Genome-wide association studies and large-scale gene expression experiments are providing insights into the biology of several common diseases, but the complexity of transcriptional regulation mechanisms often limits our understanding of how genetic variation can influence changes in gene expression. Several initiatives in the field of regulatory genomics are aiming to close this gap by systematically identifying and cataloguing regulatory elements such as promoters and enhacers across different tissues and cell types. In this Bioconductor workflow, we will explore how different types of regulatory genomic data can be used for the functional interpretation of disease-associated variants and for the prioritisation of gene lists from gene expression experiments.
Serological Surveys for complementing assessments of vaccination coverage in sub-Saharan Africa: A systematic review
Authors: Wanjiku Hannah W. , Adetifa Ifedayo M.O. 
Published: February 2018

Background: Serosurveys of biomarkers of infection/vaccination are widely used for evaluating vaccine-induced immunity and monitoring the effectiveness of immunisation programmes in developed countries. In sub-Saharan Africa (sSA) where vaccination coverage (VC) estimates are often incomplete, inaccurate and overestimate effective population immunity, the use of serosurveys is limited. Methods: We conducted a review of the use of serosurveys to assess/complement assessments of VC in sSA by searching electronic databases (PubMed, Embase, Web of Science, Popline, Ovid and Africa Wide Information) for English language articles published from 1st January 1940 to 31st January 2017. We also searched the references of retrieved articles. SSA was defined as all of Africa excluding the countries in North Africa. We included only articles that measured VC and assessed the quality of these studies using the Newcastle-Ottawa Scale. Results: We found 1056 unique records, reviewed 20 eligible studies of which just 12 met our inclusion criteria. These 12 studies were serosurveys of measles, tetanus, polio and yellow fever. Antibodies induced by natural infection confounded serological test results and there was significant discordance between vaccination history and the presence of antibodies in all except for tetanus vaccine. No study looked at Hepatitis B. Conclusions: Serosurveys for tetanus or tetanus containing vaccines may be directly useful for ascertainment of vaccination exposure or reliably complement current survey methods that measure VC. Given the limited experience in using serosurveys for this purpose in sSA, well-designed serosurveys of tetanus and possibly hepatitis B are required to further validate/evaluate their performance.
Status Assessment of Agricultural Drainage Ditches
Authors: Avilés Daniel , Wesström Ingrid , Joel Abraham 
Published: February 2018

Abstract. Poor maintenance, environmental concerns, land use changes, and adaptation to climate change are creating a growing need for better agricultural drainage. The objectives of this study were to identify ditch properties that can be evaluated visually on-site and related soil erosion processes, and to define parameters requiring more intensive study and estimate these using simplified methods. The study included surveys of ditches in various soils using MADRAS (Minnesota Agricultural Ditch Research Assessment for Stability) to classify ditch status. To explain why some ditch segments were in poor condition, additional field and laboratory studies were carried out. Soil samples were taken for analysis of particle size distribution, unsaturated direct shear strength, and critical stress for erosion. The HEC-RAS data model was used for simulation of hydraulic forces acting at different flow rates. Digital maps of land use in the catchment area in different years were used to estimate changes in runoff conditions over time. MADRAS proved to be a suitable tool for rapid assessment of stability problems in ditches. The HEC-RAS simulations were a good complement to MADRAS in assessing how changes in land use affected the hydraulic load and in highlighting bottlenecks in the system. However, the hydraulic load did not adequately explain the degree of degradation in some ditch segments. Measurements of soil shear strength were a good aid to understanding existing degradation. Thus, assessment of soil erodibility and bank stability is essential in anticipating the risk of future erosion processes in ditches. Keywords: Cohesive strength meter, HEC-RAS, MADRAS, Unsaturated direct shear strength.
An Investigation into the Fertilizer Potential of Slaughterhouse Cattle Paunch
Authors: Antille Diogenes L. , McCabe Bernadette K. , Van Der Spek Wilmer , Baillie Craig P. 
Published: February 2018

Abstract. In Australia, recycling of paunch waste to farmland has been suggested as a cost-effective and practicable environmental option, but little is known about its agronomic value. Experimental work was undertaken to assess potential risks due to weed seed contamination, determine the agronomic response of ryegrass ( L.) to soil incorporation of paunch, and investigate short-term greenhouse gas (GHG) emissions. Five types of paunch with compost ages between 2 and 16 weeks were compared with urea (46% N) and applied at field equivalent rates of 0 (control), 150, and 300 kg ha-1 N. The risk of weed contamination from paunch applied to soil appeared to be negligible; however, techniques that enable seed viability to be determined may be required to fully discard such risk. Average dry matter yield with paunch was ~30% higher than untreated grass, but ~35% lower than with urea. Dry matter yield in paunch-treated grass was between 2500 and 3250 kg ha-1 over five cuts conducted at 25-day intervals. Paunch N responses were between 1.12 and 3.25 kg DM kg-1 N depending on compost age, but lower than with urea N (~6.5 kg DM kg-1 N). Nitrogen use efficiency of paunch ranged between 3% and 20%, compared to about 35% with urea. Nitrogen fertilizer replacement value (NFRV) of paunch was highest in the 6-week-old compost (~60%) and ranged between 20% and 55% across all other organic materials. Short-term N2O emissions were similar (p &gt; 0.05) with both mineral and organic amendments; however, CH4 emissions were higher (p &lt; 0.05) from paunch compared with urea-treated soil. Overall, there appears to be potential for paunch-derived products to be used as a source of C and nutrients in crop production. Industry quality specifications for compost are available, but they need to be expanded to incorporate guidelines relevant to paunch. There is a requirement for the value proposition to industry to be determined, including reduced cost of paunch disposal via gate fees. Keywords: Byproducts, Composting, Fertilizer replacement value, Nutrient recovery, Nutrient use efficiency, Recycling of abattoir-derived waste.
Design and Testing of a Kiwifruit Harvester End-Effector
Authors: Graham Sean S. , Zong Wangyuan , Feng Jun , Tang Shengping 
Published: February 2018

Abstract. Mechanisms to aid fruit harvesting are undergoing constant development with increasing available technologies. However, fruits grown on vines, such as kiwifruit, have complex tree architectures and present difficulties in confirming design parameters. The objective of this research was to develop an end-effector for a kiwifruit harvester based on integrating the physical characteristics of the fruit, such as stem length, the space between mature fruits, and the growing environment provided by a trellised system into the design. These properties contribute to developing a mechanism that is lightweight, battery operated, and requires only one translational joint for positioning. Scissor cutting actuated by a linear solenoid is used to provide the required torque of 1.38 Nm to completely sever Hayward variety kiwifruit at the stem using a curved blade with a 20° relief angle. The cutting of the stem is actuated by a force sensor located on the device that enables cutting at less than 10 N, preventing premature detachment of the fruit and damage to the vine. The cutting time was measured to be 0.1 s ±0.03 s per cut. This end-effector design adds to the body of research aimed at developing a fully mechanized kiwifruit harvester. Keywords: Detachment force, End-effector, Fruit harvester, Kiwifruit, Linear solenoid.
Mitigating Ammonia and PM Generation of Cage-Free Henhouse Litter with Solid Additive and Liquid Spray
Authors: Chai Lilong , Xin Hongwei , Zhao Yang , Wang Tong , Soupir Michelle , Liu Kai 
Published: February 2018

Abstract. A number of chain restaurants, retailers, and grocers in the U.S. have pledged to source only cage-free (CF) eggs in the foreseeable future (e.g., by 2025) due to marketing reasons or concerns over animal welfare. However, CF housing has some inherent challenges, and a predominant one is poor air quality, i.e., ammonia gas (NH3) and particulate matter (PM), and increased emissions. Spraying a liquid agent such as electrolyzed water (EW) can effectively suppress PM generation of CF henhouse litter. However, liquid spray can enhance NH3 generation because it increases the litter moisture content (LMC). Application of acidic liquid to the litter would help control NH3 while suppressing PM, but concerns arise about the potential corrosive effect of acidic liquid on housing equipment. To overcome this dilemma, this study evaluated the effect of applying PLT, a commercial poultry litter additive (LA), on NH3 emissions of CF hen litter while spraying it with neutral EW (NEW) at a rate of 25 mL kg-1 dry litter d-1. The PLT application rates were 0.3, 0.6, and 0.9 kg m-2, denoted as Low-LA, Med-LA, and High-LA, respectively. CF litter was placed inside dynamic emission chambers and automatically stirred to mimic hen scratching. PLT was topically applied onto the litter on day 1; NEW was sprayed daily for 11 d, followed by a 3 d non-spray period (i.e., 14 d per trial); and each regimen was replicated four times. The ammonia emission rate (ER) of the control (no LA), Low-LA, Med-LA, and High-LA regimens (mean ±SE) was, respectively, 0.76 ±0.05, 0.55 ±0.06, 0.37 ±0.04, and 0.16 ±0.02 g kg-1 dry litter d-1, i.e., 28% to 79% reduction by the treatments. The NH3 reduction efficiency was linearly proportional to the PLT application rate, with higher application rate resulting in lower litter pH (p &lt; 0.05). At the end of each trial (d14), the Med-LA and High-LA regimens still showed relatively low NH3 emissions, suggesting the need for a longer measurement period in future studies. The NEW spray increased LMC by up to 60% after 11 once-a-day sprays, which reduced PM2.5, PM10, and TSP levels from 3.83, 6.39, and 7 mg m-3 to 0.07, 0.14, and 0.15 mg m-3, respectively. After a 3 d spray suspension, the PM levels rebounded to 0.72, 1.02, and 1.12 mg m-3 for PM2.5, PM10, and TSP, respectively, due to decreased LMC. Field verification of the mitigation efficacy and an economic assessment of the method are warranted. Keywords: Air quality, Alternative hen housing, Animal and worker health, Litter treatment.
Frottage as inquiry
Authors: Pindyck Maya 
Published: February 2018

Abstract
This article explores the pedagogical and methodological implications of the arts-based practice of frottage: a process of ‘finding’ images by making, and then erasing, an uneven ground. What could this arts practice mean for both research and classroom teaching? The author offers frottage as a mode of inquiry that resists closure, destabilizes solid understandings and treats matter as dynamic energy. Exploring the educational resonances of this practice, the author rubs against her article’s academic language with both written erasures made from the paper itself and visual erasures created by the author from disparate surfaces, times and spaces.
Konstruksi Sosial Komunitas Pesantren mengenai Isu Radikalisme (Studi Kasus Pada Pesantren Salaf & Modern di Kota Malang)
Authors: Alfanani Tsabita Shabrina 
Published: February 2018

Radicalism became a phenomenon widely discussed in inter-religious life. In practice, Islam and pesantren is often associated with acts of terrorism and other violence since the action was perceived as an extension of religious radicalism with jihad and amar ma’ruf nahi mungkar as basic commands. The focus of this study is to analyze how komunitas pesantren (pesantren community) perception about radicalism and how the process of those perceptions is formed. This research was conducted in two komunitas pesantren with different characteristic in Malang City : Alhayatul Islamiyah as salaf (traditional) pesantren and Ma’had Al-Qalam as modern pesantren. By using a qualitative approach and case study, this study resulted in three broad conclusions. First, salaf pesantren community’s perception regarding the issue of radicalism tends to moderate and tolerant. Meanwhile, the perception of modern pesantren community on the issue of radicalism tends to vary; Second. The Construction process could be explained by the dialectical process from Berger & Luckman’s social construction theory consisting of three simultaneous processes: externalization, objectivation and internalization. In the process, the researcher found three types of komunitas pesantren in perceiving radicalism which is contextual moderate and tolerant (as the majority group); fundamental (idealist) and pragmatic. At the salaf pesantren, Kyai was an important figure in constructing value, while at modern pesantren the background, social settings and media give more influence in the construction process about radicalism; Third, the pattern similarity at salaf pesantren motivated by cultural hegemony by constructing value on a single base culturally affiliated to the nahdliyin tradition, while varying perceptions of modern pesantren arise from it’s heterogeneous base. However, both of pesantren does not encourage their santri to act radically.Keywords: Social Construction, Pesantren Community, Radicalism
Autonomy: A Missing Ingredient of a Successful Program?
Authors: Halperin Israel , Wulf Gabriele , Vigotsky Andrew D. , Schoenfeld Brad J. , Behm David G. 
Published: February 2018

ABSTRACT
SUPPORTING AN ATHLETE'S NEED FOR AUTONOMY BY ALLOWING HIM/HER TO MAKE CHOICES CONCERNING TRAINING VARIABLES CAN BE AN EFFECTIVE COACHING STRATEGY BY STRENGTH AND CONDITIONING (S&C) PROFESSIONALS. HOWEVER, THIS COACHING STRATEGY HAS RECEIVED LITTLE ATTENTION IN THE S&C FIELD DESPITE BEING EXTENSIVELY STUDIED IN THE FIELDS OF SPORT PSYCHOLOGY AND MOTOR LEARNING. AUTONOMY SUPPORT HAS BEEN SHOWN TO IMPROVE MOTOR LEARNING, PERFORMANCE, AND MOTIVATION. IN THIS REVIEW, THE POSITIVE EFFECTS OF PROVIDING CHOICES ARE DISCUSSED AS THEY APPLY TO ATHLETES AND S&C PROFESSIONALS. MOREOVER, POSSIBLE MECHANISMS FOR THESE EFFECTS ARE DESCRIBED AND PRACTICAL RECOMMENDATIONS ARE PROVIDED.
A Novel Retrieval-Dependent Memory Process Revealed by the Arrest of ERK1/2 Activation in the Basolateral Amygdala
Authors: Merlo Emiliano , Milton Amy L. , Everitt Barry J. 
Published: February 2018

Fully consolidated fear memories can be maintained or inhibited by retrieval-dependent mechanisms depending on the degree of re-exposure to fear cues. Short exposures promote memory maintenance through reconsolidation, and long exposures promote inhibition through extinction. Little is known about the neural mechanisms by which increasing cue exposure overrides reconsolidation and instead triggers extinction. Using auditory fear conditioning in male rats, we analyzed the role of a molecular mechanism common to reconsolidation and extinction of fear, ERK1/2 activation within the basolateral amygdala (BLA), after intermediate conditioned stimulus (CS) exposure events. We show that an intermediate re-exposure (four CS presentations) failed to activate ERK1/2 in the BLA, suggesting the absence of reconsolidation or extinction mechanisms. Supporting this hypothesis, pharmacologically inhibiting the BLA ERK1/2-dependent signaling pathway in conjunction with four CS presentations had no effect on fear expression, and the NMDA receptor partial agonistd-cycloserine, which enhanced extinction and ERK1/2 activation in partial extinction protocols (seven CSs), had no behavioral or molecular effect when given in association with four CS presentations. These molecular and behavioral data reveal a novel retrieval-dependent memory phase occurring along the transition between conditioned fear maintenance and inhibition. CS-dependent molecular events in the BLA may arrest reconsolidation intracellular signaling mechanism in an extinction-independent manner. These findings are critical for understanding the molecular underpinnings of fear memory persistence after retrieval both in health and disease.SIGNIFICANCE STATEMENTConsolidated fear memories can be altered by retrieval-dependent mechanisms. Whereas a brief conditioned stimulus (CS) exposure promotes fear memory maintenance through reconsolidation, a prolonged exposure engages extinction and fear inhibition. The nature of this transition and whether an intermediate degree of CS exposure engages reconsolidation or extinction is unknown. We show that an intermediate cue exposure session (four CSs) produces the arrest of ERK1/2 activation in the basolateral amygdala, a common mechanism for reconsolidation and extinction. Amnestic or hypermnestic treatments given in association with four CSs had no behavioral or molecular effects, respectively. This evidence reveals a novel retrieval-dependent memory phase. Intermediate degrees of CS exposure fail to trigger reconsolidation or extinction, leaving the original memory in an insensitive state.
Systematic Complex Haploinsufficiency-Based Genetic Analysis ofCandida albicansTranscription Factors: Tools and Applications to Virulence-Associated Phenotypes
Authors: Glazier Virginia E , Murante Thomas , Koselny Kristy , Murante Daniel , Esqueda Marisol , Wall Gina A , Wellington Melanie , Hung Chiung-Yu , Kumar Anuj , Krysan Damian J 
Published: February 2018

AbstractGenetic interaction analysis is a powerful approach to the study of complex biological processes that are dependent on multiple genes. Because of the largely diploid nature of the human fungal pathogen Candida albicans, genetic interaction analysis has been limited to a small number of large-scale screens and a handful for gene-by-gene studies. Complex haploinsufficiency, which occurs when a strain containing two heterozygous mutations at distinct loci shows a phenotype that is distinct from either of the corresponding single heterozygous mutants, is an expedient approach to genetic interactions analysis in diploid organisms. Here, we describe the construction of a barcoded-library of 133 heterozygous TF deletion mutants and deletion cassettes for designed to facilitate complex haploinsufficiency-based genetic interaction studies of the TF networks in C. albicans. We have characterized the phenotypes of these heterozygous mutants under a broad range of in vitro conditions using both agar-plate and pooled signature tag-based assays. Consistent with previous studies, haploinsufficiency is relative uncommon. In contrast, a set of 12 TFs enriched in mutants with a role in adhesion were found to have altered competitive fitness at early time points in a murine model of disseminated candidiasis. Finally, we characterized the genetic interactions of a set of biofilm related TFs in the first two steps of biofilm formation, adherence and filamentation of adherent cells. The genetic interaction networks at each stage of biofilm formation are significantly different indicating that the network is not static but dynamic.