bluuebunny/crossref_metadata_2025 huggingface dataset:
The Pleasure Principle of Magic Mike XXL: Sonic Visibility Toward Female Audiences
Authors: Warner Kristen J
Published: April 2019

A key difference between Magic Mike (2012) and Magic Mike XXL (MMXL, 2015) is the latter films narrative shift toward the viewing experience of its targeted female audience. The hyper-lean storyline that streamlined all the indulgences of Steven Soderbergh’s original transformed the franchise into a spectacle for women. The goal of this article, then, is to examine how MMXXL’s sonic and visual structures create the resonance that then translates to pleasure and a more holistic kind of representation for female viewers. By exploring how this film deploys not only the visual cues of beautiful male bodies to create bodily responses in its largely female audience but also querying how the sound cues create sonic visibility, I aim to illustrate how MMXXL enables women viewers from a cross section of intersectional identities the opportunity to not only feel seen but also desired.
Human leucocyte antigen-associated anti-glomerular basement membrane disease in siblings
Authors: Durcan Martin E , Nair Beena , Anderton John G
Published: April 2019

We report a case of anti-glomerular basement membrane (GBM) disease in association with human leucocyte antigen (HLA) DRB1 15:01. A 71-year-old woman presented with oligoanuric acute kidney injury accompanied by high titre anti-GBM antibodies. Renal biopsy revealed a severe crescentic glomerulonephritis. Her brother had presented 6 years earlier with oligoanuric acute kidney injury. He was dual positive for MPO ANCA and anti-GBM antibodies. Renal biopsy was not performed. Both had an absence of pulmonary involvement. Tissue typing confirmed both were heterozygous for HLA DRB1 15:01 and DRB1 04:03.
Conceptualizing, Organizing, and Positing Moderation in Communication Research
Authors: Holbert R Lance , Park Esul
Published: April 2019

Meta-theoretical focus is given to how communication researchers are approaching and hypothesizing moderation. A moderation typology is offered and an evaluation of the field’s common practices for positing moderation reveals an inability to discern between three overarching classifications (Contributory, Contingent, Cleaved). A content analysis of eight communication journals reveals moderation hypotheses lacking a level of precision that can best aid the field’s knowledge generation. In addition, vague hypothesizing is leaving communication researchers vulnerable to the commitment of Type III error (i.e., correctly rejecting a null hypothesis for the wrong reason). Recommendations are provided in an effort to improve the field’s conceptualization and presentation of moderation.
Algorithmic Personalization and the Two-Step Flow of Communication
Authors: Soffer Oren
Published: April 2019

This study examines the relevance of traditional mass communication’s two-step flow-of-communication theory in relation to algorithmic personalization. I compare the two-step flow theory’s concept of personalized content through opinion leaders with the current notion of personalized algorithms, arguing that opinion leaders and algorithms both function as gatekeeping agents. I also discuss the nature and role of peer groups in the two cases, arguing that while in the original theory, groups were seen as relatively solid (family, friends, and work colleagues), groups in the algorithmic era are much more liquid, transforming according to data inputs and users’ behavior. Finally, the article also considers differences in the source of authority of opinion leaders and algorithms in both eras, as well as the different social settings and public awareness in the second step of the communication flow.
Dryland Organic Farming Partially Offsets Negative Effects of Highly Simplified Agricultural Landscapes on Forbs, Bees, and Bee–Flower Networks
Authors: Adhikari Subodh , Burkle Laura A , O’Neill Kevin M , Weaver David K , Delphia Casey M , Menalled Fabian D
Published: April 2019

Industrialized farming practices result in simplified agricultural landscapes, reduced biodiversity, and degraded species-interaction networks. Thus far, most research assessing the combined effects of farming systems and landscape complexity on beneficial insects has been conducted in relatively diversified and mesic systems and may not represent the large-scale, monoculture-based dryland agriculture that dominates many regions worldwide. Specifically, the effects of farming systems on forbs, bees, and their interactions are poorly understood in highly simplified dryland landscapes such as those in the Northern Great Plains, United States, an area globally important for conventional and organic small grain, pulse, forage, and oilseed production. During a 3-yr (2013–2015) study, we assessed 1) the effects of dryland no-till conventional and tilled organic farming on forbs, bees, and bee–flower networks and 2) the relationship between natural habitat and bee abundance. Flower density and richness were greater in tilled organic fields than in no-till conventional fields, and forb community composition differed between farming systems. We observed high bee diversity (109 taxa) in this highly simplified landscape, and bee abundance, richness, and community composition were similar between systems. Compared with tilled organic fields, bee–flower interactions in no-till conventional fields were poorly connected, suggesting these systems maintain relatively impoverished plant-pollinator networks. Natural habitat (11% of the landscape) did not affect small-bodied bee abundance in either farming system but positively affected large-bodied bees within 2,000 m of crop-field centers. In highly simplified agricultural landscapes, dryland organic farming and no-till conventional farming together support relatively high bee diversity, presumably because dryland organic farming enhances floral resources and bee–flower networks, and no-till management in conventional farming provides undisturbed ground-nesting habitats for wild bees (Hymenoptera: Apoidea).
Basal area and diameter growth in high-graded eastern temperate mixedwood forests: the influence of acceptable growing stock, species, competition and climate
Authors: Power Hugues , Raymond Patricia , Prévost Marcel , Roy Vincent , Berninger Frank
Published: April 2019

Harvesting practices in temperate mixedwoods of eastern North America have a history of diameter-limit cuts, which have often resulted in degraded residual stands. In this study, we examined the factors influencing stand basal area (BA) and tree diameter growth in previously high-graded mixedwood forests, to understand which stands are more likely to recover from high-grading. Over 15 years, we monitored tree growth, recruitment and stem quality of 532 sample plots that were located in high-graded stands of Quebec’s mixedwood forest. We found that diameter growth rates were positively correlated with precipitation-related variables for balsam fir (Abies balsamea) and for yellow birch (Betulla alleghaniensis) but opposing trends for temperature-related variables were found. Conversely to balsam fir, yellow birch growth was positively correlated to temperature variables. Our results also show that BA growth was greater for plots with a larger acceptable growing stock (AGS: trees with potential sawlog production) and that the increase in AGS was greater for plots with larger amount of conifer BA. These result highlights the importance to maintain a proportion of conifer trees in these mixed stands. Moreover, the significant effect of asymmetric competition in our study underscores the relevance of considering the spatial distribution when choosing crop trees.
Exploring coarse- to fine-scale approaches for mapping and estimating forest volume from Brazilian National Forest Inventory data
Authors: David Hassan C , MacFarlane David W , Péllico Netto Sylvio , Corte Ana Paula Dalla , Piotto Daniel , de Oliveira Yeda M M , Morais Vinicius A , Sanquetta Carlos R , Neto Rorai P M
Published: April 2019

The aim of this study was to explore methods to: (1) enhance coarse-scale estimates of wood volume from National Forest Inventories (NFIs) data and (2) map them at finer scales. The ‘standard’ coarse-scale estimation extrapolates wood volume from clusters to the grid cell they represent, using the cluster’s represented forested area (RFA) to predict the cell’s forested area. Data from a subset of Brazil’s NFI clusters were combined with Landsat-8 imagery to explore a new coarse-scale method, where forested area derived from image classification (FADIC) is used instead of RFA. The RFA- and FADIC-derived estimates of total volume were, respectively, 197.4 million m3 and 116.3 million m3. For fine-scale methods, volume was estimated and mapped at pixel level using: (i) surface reflectance-based models (SRMs), and (ii) regression-kriging (RK) and a RK model (RKM) whose inputs were latitude and longitude of pixels. The SRM-based method captured the mean and the general spatial trend of the volume well. The RK-based method also estimated the mean well, but it failed to predict higher and lower volumes. The SRM- and RK-based estimates of total volume were 211.7 million m3 and 203.3 million m3, an overestimate of 7 per cent and 3 per cent, respectively, of the ‘standard’ NFI estimate (197.4 million m3), though both estimates were within the 95 per cent confidence interval, meaning that both fine-scale methods yield total volume statistically similar to the ‘standard’ coarse-scale method.
Positive Selection Evidence in Xylose-Related Genes Suggests Methylglyoxal Reductase as a Target for the Improvement of Yeasts’ Fermentation in Industry
Authors: Borelli Guilherme , Fiamenghi Mateus Bernabe , dos Santos Leandro Vieira , Carazzolle Marcelo Falsarella , Pereira Gonçalo Amarante Guimarães , José Juliana
Published: April 2019

Xylose assimilation and fermentation are important traits for second generation ethanol production. However, some genomic features associated with this pentose sugar’s metabolism remain unknown in yeasts. Comparative genomics studies have led to important insights in this field, but we are still far from completely understanding endogenous yeasts’ xylose metabolism. In this work, we carried out a deep evolutionary analysis suited for comparative genomics of xylose-consuming yeasts, searching for of positive selection on genes associated with glucose and xylose metabolism in the xylose-fermenters’ clade. Our investigation detected positive selection fingerprints at this clade not only among sequences of important genes for xylose metabolism, such as xylose reductase and xylitol dehydrogenase, but also in genes expected to undergo neutral evolution, such as the glycolytic gene phosphoglycerate mutase. In addition, we present expansion, positive selection marks, and convergence as evidence supporting the hypothesis that natural selection is shaping the evolution of the little studied methylglyoxal reductases. We propose a metabolic model suggesting that selected codons among these proteins caused a putative change in cofactor preference from NADPH to NADH that alleviates cellular redox imbalance. These findings provide a wider look into pentose metabolism of yeasts and add this previously overlooked piece into the intricate puzzle of oxidative imbalance. Although being extensively discussed in evolutionary works the awareness of selection patterns is recent in biotechnology researches, rendering insights to surpass the reached status quo in many of its subareas.
Fast and accurate relatedness estimation from high-throughput sequencing data in the presence of inbreeding
Authors: Hanghøj Kristian , Moltke Ida , Andersen Philip Alstrup , Manica Andrea , Korneliussen Thorfinn Sand
Published: April 2019

Background

The estimation of relatedness between pairs of possibly inbred individuals from high-throughput sequencing (HTS) data has previously not been possible for samples where we cannot obtain reliable genotype calls, as in the case of low-coverage data.

Results

We introduce ngsRelateV2, a major revision of ngsRelateV1, a program that originally allowed for estimation of relatedness from HTS data among non-inbred individuals only. The new revised version takes into account the possibility of individuals being inbred by estimating the 9 condensed Jacquard coefficients along with various other relatedness statistics. The program is threaded and scales linearly with the number of cores allocated to the process.

Conclusion

The program is available as an open source C/C++ program under the GPL license and hosted at https://github.com/ANGSD/ngsRelate. To facilitate easy analysis, the program is able to work directly on the most commonly used container formats for raw sequence (BAM/CRAM) and summary data (VCF/BCF).
A Tissue Comparison of DNA Methylation of the Glucocorticoid Receptor Gene (Nr3c1) in European Starlings
Authors: Siller Stefanie J , Rubenstein Dustin R
Published: April 2019

Negative feedback of the vertebrate stress response via the hypothalamic–pituitary–adrenal (HPA) axis is regulated by glucocorticoid receptors in the brain. Epigenetic modification of the glucocorticoid receptor gene (Nr3c1), including DNA methylation of the promoter region, can influence expression of these receptors, impacting behavior, physiology, and fitness. However, we still know little about the long-term effects of these modifications on fitness. To better understand these fitness effects, we must first develop a non-lethal method to assess DNA methylation in the brain that allows for multiple measurements throughout an organism’s lifetime. In this study, we aimed to determine if blood is a viable biomarker for Nr3c1 DNA methylation in two brain regions (hippocampus and hypothalamus) in adult European starlings (Sturnus vulgaris). We found that DNA methylation of CpG sites in the complete Nr3c1 putative promoter varied among tissue types and was lowest in blood. Although we identified a similar cluster of correlated Nr3c1 putative promoter CpG sites within each tissue, this cluster did not show any correlation in DNA methylation among tissues. Additional studies should consider the role of the developmental environment in producing epigenetic modifications in different tissues.
Identifying the species of harvested tuna and billfish using deep convolutional neural networks
Authors: Lu Yi-Chin , Tung Chen , Kuo Yan-Fu
Published: April 2019

Fish catch species provide essential information for marine resource management. Some international organizations demand fishing vessels to report the species statistics of fish catch. Conventionally, the statistics are recorded manually by observers or fishermen. The accuracy of these statistics is, however, questionable due to the possibility of underreporting or misreporting. This paper proposes to automatically identify the species of common tuna and billfish using machine vision. The species include albacore (Thunnus alalunga), bigeye tuna (Thunnus obesus), yellowfin tuna (Thunnus albacares), blue marlin (Makaira nigricans), Indo-pacific sailfish (Istiophorus platypterus), and swordfish (Xiphias gladius). In this approach, the images of fish catch are acquired on the decks of fishing vessels. Deep convolutional neural network models are then developed to identify the species from the images. The proposed approach achieves an accuracy of at least 96.24%.
Consequences of Performing Parallel Dose Finding Trials in Heterogeneous Groups of Patients
Authors: Horton Bethany Jablonski , O'Quigley John , Conaway Mark R
Published: April 2019

Patient heterogeneity, in which patients can be grouped by risk of toxicity, is a design challenge in early phase dose finding trials. Carrying out independent trials for each group is a readily available approach for dose finding. However, this often leads to dose recommendations that violate the known order of toxicity risk by group, or reversals in dose recommendation. In this manuscript, trials for partially ordered groups are simulated using four approaches: independent parallel trials using the continual reassessment method (CRM), Bayesian optimal interval design, and 3 + 3 methods, as well as CRM for partially ordered groups. Multiple group order structures are considered, allowing for varying amounts of group frailty order information. These simulations find that parallel trials in the presence of partially ordered groups display a high frequency of trials resulting in reversals. Reversals occur when dose recommendations do not follow known order of toxicity risk by group, such as recommending a higher dose level in a group of patients known to have a higher risk of toxicity. CRM for partially ordered groups eliminates the issue of reversals, and simulation results indicate improved frequency of maximum tolerated dose selection as well as treating a greater proportion of trial patients at this dose compared with parallel trials. When information is available on differences in toxicity risk by patient subgroup, methods designed to account for known group ordering should be considered to avoid reversals in dose recommendations and improve operating characteristics.
Soil depth- and root diameter-related variations affect root decomposition in temperate pine and oak forests
Authors: Han Seung Hyun , Kim Seongjun , Chang Hanna , Kim Hyun-Jun , Khamzina Asia , Son Yowhan
Published: April 2019

Aims

Assessment of factors regulating root decomposition is needed to understand carbon and nutrient cycling in forest ecosystems. The objective of this study is to examine the effects of soil depth and root diameter on root decomposition and to analyze the relationship of root decomposition with factors such as soil environmental conditions and initial litter quality.

Methods

Two decomposition experiments were conducted in natural pine (Pinus densiflora) and oak (Quercus serrata) forests over a 2-year period using the litterbag technique. For the soil depth experiment, 216 litterbags containing fine roots (∅ = 0–2 mm) were buried at 0–10-, 10–20- and 20–30-cm soil depths. Soil properties and soil enzyme activities and microbial biomass at each soil depth were analyzed. For the root diameter experiment, 216 litterbags containing roots 0–1-, 1–2- and 2–3-mm in diameter were buried at 10-cm soil depth. The initial litter qualities (carbon (C), nitrogen (N), calcium (Ca) and phosphorus (P) concentrations) for each of the root diameter classes were analyzed. Litterbags were retrieved after 3, 6, 12 and 24 months in each forest type.

Important Findings

The root decomposition rate was significantly altered by soil depth and root diameter. After 2 years, the root decay constant at 0–10-cm depth (pine: 0.35 and oak: 0.41) was significantly higher than that at 10–20-cm (0.31 and 0.37) and 20–30-cm (0.32 and 0.33) depths in the P. densiflora and Q. serrata forests. Enzyme activities and microbial biomass declined with soil depth, which may be associated with decreasing soil moisture and organic matter. The decay constant for the 0–1-mm roots (pine: 0.32 and oak: 0.37) was higher than that of 1–2-mm (0.29 and 0.33) and 2–3-mm roots (0.26 and 0.33) for the P. densiflora and Q. serrata forests. Difference in initial P concentration and C/N ratio among the different diameter roots were linearly related with root decomposition. In particular, the increasing C/N ratio with root diameter resulted in decreases in the decomposition rate. These results indicate the surface soil microbial activities and initial C/N ratio of root litter as important drivers of C dynamics in temperate pine and oak forests.
Efficacy of Probiotic Prophylaxis After The First Febrile Urinary Tract Infection in Children With Normal Urinary Tracts
Authors: Sadeghi-bojd S , Naghshizadian R , Mazaheri M , Ghane Sharbaf F , Assadi F
Published: April 2019

Background

Growing antibiotic resistance and debates over their efficacy for urinary tract infection (UTI) recurrence warrants studying nonantibiotic prophylaxis for preventing UTI recurrences.

Methods

We randomly assigned 181 children, aged 4 months to 5 years, with a normal urinary tract after recovery from their first febrile UTI in a 1:1 ratio to receive a probiotic mixture of Lactobacillus acidophilus, Lactobacillus rhamnosus, Bifidobacterium bifidum, and Bifidobacterium lactis (n = 91) or placebo (n = 90) for a total of 18 months of therapy. The primary objective was to show the superiority of probiotic prophylaxis to placebo. The primary end point was composite cure (UTI-free survival) at 18 months, and the secondary end point was the median time to first UTI recurrence.

Results

The probiotics were superior to placebo with respect to the primary efficacy end point. At 18 months, composite cure was observed in 96.7% (3 of 91) of the patients in the probiotic group and 83.3% (15 of 90) of those in the placebo group (P = .02). The median time to the first incidence of UTI recurrence was 3.5 months (range, 1–4 months) and 6.5 months (range, 2–14 months) in the probiotic and placebo groups, respectively (P = .04). The main microorganism that caused recurrent UTI was Escherichia coli, followed by Klebsiella pneumoniae, and these results were not significantly different between the 2 groups. We found no specific adverse events among the participants who received the probiotic mixture during the course of therapy.

Conclusions

The probiotics were more effective than placebo at reducing the risk of recurrent UTI in children with a normal urinary tract after their first episode of febrile UTI.
The clavipectoral fascia as the unique anatomical criteria for distinguishing breast parenchymal lesions from axillary lymph node metastasis
Authors: Patrinos Antonios , Zarokosta Maria , Tsiaoussis John , Noussios George , Piperos Τheodoros , Zoulamoglou Menelaos , Flessas Ioannis , Mariolis–Sapsakos Theodoros
Published: April 2019

Diagnosing primary breast tumors of the axillary tail of Spence may be extremely challenging, since several lesions may be located in the axillary fossa. In the presented case, a 54-year-old post-menopausal Caucasian female patient presented to our institution complaining about a lump in her left axilla. The preoperative imaging modalities could not clarify whether the tumor is part of the tail of Spence or metastasis of the axillary lymph nodes. The diagnosis of primary adenocarcinoma of the axillary tail of Spence was made during a quadrantectomy of the left breast after the clavipectoral fascia, which constitutes the sole anatomical boundary between breast and axilla, was identified.
On Examining the Quality of Spanish Translation in Telephone Surveys: A Novel Test-Retest Approach
Authors: Agans Robert P , Vallejos Quirina M , Benefield Thad S
Published: April 2019

Past research has shown that commonly reported cultural group disparities in health-related indices may be attributable to culturally mediated differences in the interpretation of translated survey questions and response scales. This problem may be exacerbated when administering single-item survey questions, which typically lack the reliability seen in multi-item scales. We adapt the test-retest approach for single-item survey questions that have been translated from English into Spanish and demonstrate how to use this approach as a quick and efficient pilot test before fielding a major survey. Three retest conditions were implemented (English-Spanish, Spanish-English, and English-English) on a convenience sample (n = 109) of Latinos and non-Latinos where translated items were compared against an English-English condition that served as our control. Several items were flagged for investigation using this approach. Discussion centers on the utility of this approach for evaluating the Spanish translation of single-item questions in population-based surveys.
Global Health Outreach by United States Ophthalmology Residency Programs: Understanding of Host Country Systems-Based Practice
Authors: Justin Grant A , Custer Benjamin L , Ward Jane B , Colyer Marcus H , Waller Stephen G , Legault Gary L
Published: April 2019

Introduction

For medical residents, global health outreach is the first experience of learning how to develop partnerships with foreign medical systems. The overall objective of this project was to develop an overview of global health programs in U.S. ophthalmology residencies. The investigation focused on characterizing the goals and services offered, the didactics taught to residents, and the program director’s understanding of systems-based practice gained in the host country.

Materials and Methods

An online survey was sent to all U.S. ophthalmology residency program directors. The two outcome measures of the study were characterization of global health outreach and didactics completed by U.S. ophthalmology residency programs and review of program director understanding of host country systems of care.

Results

Twelve program directors of 117 (10.26%) answered the survey. 100% of programs from the Department of Defense responded. Countries served included Ecuador, Panama, Honduras, Dominican Republic, India, Tanzania, Nepal, Bhutan, Guatemala, Micronesia, Haiti, Mongolia, Bolivia. Sixty five percent worked at a free-standing public hospital. Many programs offered resident participation with only 41.87% giving residents ACGME credit. Most programs (91.67%) offered fewer than 5 hours of global health didactics. When program directors were asked about their knowledge of host country systems of care, most noted understanding of the hospital functions like the referral system, transitions of care, hospital funding, and medical supply chain, but not of the perception of patients with chronic or congenital ophthalmic diseases, host country general or ophthalmic medical education, patient research safeguards and host country malpractice system.

Conclusion

From the small sample of program directors, Ophthalmology residency program global health outreach varies in faculty and resident participation, and in goals and services offered. In addition, there was a wide variation in ophthalmology program director understanding of host country systems of care.
Fitness Landscape of the Fission Yeast Genome
Authors: Grech Leanne , Jeffares Daniel C , Sadée Christoph Y , Rodríguez-López María , Bitton Danny A , Hoti Mimoza , Biagosch Carolina , Aravani Dimitra , Speekenbrink Maarten , Illingworth Christopher J R , Schiffer Philipp H , Pidoux Alison L , Tong Pin , Tallada Victor A , Allshire Robin , Levin Henry L , Bähler Jürg
Published: April 2019

The relationship between DNA sequence, biochemical function, and molecular evolution is relatively well-described for protein-coding regions of genomes, but far less clear in noncoding regions, particularly, in eukaryote genomes. In part, this is because we lack a complete description of the essential noncoding elements in a eukaryote genome. To contribute to this challenge, we used saturating transposon mutagenesis to interrogate the Schizosaccharomyces pombe genome. We generated 31 million transposon insertions, a theoretical coverage of 2.4 insertions per genomic site. We applied a five-state hidden Markov model (HMM) to distinguish insertion-depleted regions from insertion biases. Both raw insertion-density and HMM-defined fitness estimates showed significant quantitative relationships to gene knockout fitness, genetic diversity, divergence, and expected functional regions based on transcription and gene annotations. Through several analyses, we conclude that transposon insertions produced fitness effects in 66–90% of the genome, including substantial portions of the noncoding regions. Based on the HMM, we estimate that 10% of the insertion depleted sites in the genome showed no signal of conservation between species and were weakly transcribed, demonstrating limitations of comparative genomics and transcriptomics to detect functional units. In this species, 3′- and 5′-untranslated regions were the most prominent insertion-depleted regions that were not represented in measures of constraint from comparative genomics. We conclude that the combination of transposon mutagenesis, evolutionary, and biochemical data can provide new insights into the relationship between genome function and molecular evolution.
Sequencing Disparity in the Genomic Era
Authors: David Kyle T , Wilson Alan E , Halanych Kenneth M
Published: April 2019

Advances in sequencing technology have resulted in the expectation that genomic studies will become more representative of organismal diversity. To test this expectation, we explored species representation of nonhuman eukaryotes in the Sequence Read Archive. Though species richness has been increasing steadily, species evenness is decreasing over time. Moreover, the top 1% most studied organisms increasingly represent a larger proportion of total experiments, demonstrating growing bias in favor of a small minority of species. To better understand molecular processes and patterns, genomic studies should reverse current trends by adopting more comparative approaches.
On the Asset Market View of Exchange Rates
Authors: Burnside A Craig , Graveline Jeremy J
Published: April 2019

If the asset market is complete, then the difference between foreign and domestic agents’ log intertemporal marginal rates of substitution (IMRSs) equals the log change in the real exchange rate. This equation is frequently used to argue that changes in real exchange rates reflect differences between agents’ required compensation for exposure to asset return uncertainty. We show that the relative returns on frictionlessly traded assets are only reflected in the common component of agents’ IMRSs, not in differences. Instead, when this equation does offer insights, frictions in the goods market are the source of economic distinction between agents.

Received December 10, 2013; editorial decision November 5, 2018 by Editor Geert Bekaert. Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
Tokenized structures and assets in Liechtenstein law
Authors: Nägele Thomas , Bont Patrick
Published: April 2019

With the ever-growing popularity of the blockchain technology in business and utilizing a token-based economy as a pillar for various recent projects, the legal aspect of tokenized structures and assets poses a significant and relevant challenge. This contribution seeks to outline the legal handling of tokenized structures in Liechtenstein as well as issues with the tokenization of assets from a legal point of view, while drawing an outlook on the potential future situation in view of the upcoming Liechtenstein Trustworthy Technologies Act (TTA) and future European Union legislation. The TTA is set to come into force in late 2019.
Drilling Technique Can Minimize Plunging
Authors: Ding Anthony , Marmor Meir
Published: April 2019

Purpose:

Vibratory and acoustic feedback, drill sharpness, and material density have each been shown to influence the depth of plunging when drilling through bicortical bone. We hypothesized that drilling technique can also influence the depth of plunging.

Methods:

Six subjects of various training levels (PGY1 to 16-year experienced surgeon) were asked to drill through a cortical bone surrogate, third-generation Sawbones tube with similar density and compressive modulus of healthy cortical bone. Using a sharp 4.5-mm drill bit and System 6 drill, each participant drilled 30 holes wearing surgical gloves to mimic tactile feedback and using 3 different techniques (10 holes each). The techniques were single-handed smooth, single-handed bounce, and 2-handed smooth drilling. A 60 frame-per-second high-definition video recorder was placed a standard distance from the model and used to calculate the depth of plunging. Analysis of variance with Fisher PLSD post hoc was used to compare techniques (significance P < 0.05).

Results:

The average ± SD plunge depths were 13.0 ± 4.2 mm (range 6.2–26.8 mm) for single-handed smooth, 17.2 ± 5.0 mm (range 8.0–28.8 mm) for single-handed bounce, and 10.6 ± 3.5 mm (range 5.8–19.2) for 2-handed smooth techniques. Difference among all 3 groups reached statistical significance.

Conclusion:

Bounce technique had the greatest average depth and variance. The 2-handed technique demonstrated the least plunge and the lowest variance, indicating the highest degree of control. This study supports the use of a 2-handed technique for drilling when intraoperative circumstances permit.
Double plastic stenting for inoperable malignant biliary stricture among cirrhotic patients as a possible cost-effective treatment: a pilot study
Authors: Radwan Mohamed I. , Emara Mohamed H. , Zaghloul Mariam S. , Zaghloul Abdallah M.S.
Published: April 2019

Background and study aim

Endoscopic retrograde cholangiopancreatography (ERCP) has evolved as the main therapeutic intervention for hepatobiliary disorders. Palliative stenting for inoperable cases is associated with better morbidity and mortality than surgery. This work aimed at assessing the effect of insertion of two plastic stents in inoperable malignant biliary stricture among cirrhotic patients regarding stent patency, quality of life (QOL), and cost.

Patients and methods

This multicenter study included 72 cirrhotic patients presented for ERCP with an inoperable malignant biliary stricture. All patients underwent ERCP after preoperative optimization with sphincterotomy, balloon dilatation, and insertion of two plastic stents of 10 Fr. Evaluation included stent patency at 6 months, effect on the QOL using EORTC QLQ-C30 (version 3), adverse events, and the cost.

Results

Patients included 67% of males and had an age range of 48–88 years (mean: 70 years). In all, 92% of stents were patent at 6 months. Significant improvement in serum total bilirubin and all items of QOL questionnaire at 6 months after the procedure was reported. Cholangitis and pancreatitis were reported in 25 and 8% of cases, respectively. The cost of insertion of two plastic stents and the daily cost of the procedure regarding the effect on QOL were low.

Conclusion

Double plastic stenting of the common bile duct seems effective at 6 months of follow-up among cirrhotic patients with inoperable malignant biliary obstruction. Furthermore, it seems also valuable in improving laboratory findings and QOL among those patients with an acceptable cost.
How to best measure quality of life in coeliac disease? A validation and comparison of disease-specific and generic quality of life measures
Authors: Burger Jordy P.W. , van Middendorp H. , Drenth Joost P.H. , Wahab Peter J. , Evers Andrea W.M.
Published: April 2019

Objective

Health-related quality of life (HRQoL) is an important outcome in chronic disease. Generic HRQoL questionnaires may not adequately reflect disease-specific challenges in coeliac disease. We investigated whether disease-specific HRQoL questionnaires add relevant information to generic measures that will better help to identify patients experiencing problems.

Patients and methods

We performed a cross-cultural validation of the Celiac Disease Quality Of Life-survey (CD-QOL), next we developed and validated a new disease-specific HRQoL questionnaire, and finally compared their predictive validity with the disease-generic RAND SF-36/SF-12 in 825 patients (mean age: 56.1±15.8 years) with (reported) biopsy-proven coeliac disease. Internal consistency and convergent, discriminative and predictive validity of the questionnaires was determined.

Results

Two Dutch versions of the CD-QOL were validated, consisting of 14 and six items, respectively (CD-QOL-14-NL, CD-QOL-6-NL). We developed and validated the CeliacQ-27, which has 27-items across three subscales (Limitations, Worries and Impact on daily life), and a short seven-item version, the CeliacQ-7. All questionnaires had excellent psychometric properties and differentiated well between active disease and clinical remission and strict versus poor dietary adherence. The added value of the disease-specific questionnaires to the generic HRQoL measure to the explained variance of symptom burden and dietary adherence was limited.

Conclusion

HRQoL in patients with coeliac disease can easily be assessed by brief generic as well as disease-specific measures. Disease-specific questionnaires, however, provide more explicit information on disease-relevant areas of functioning.
Risk Factors for Adverse Birth Outcomes in the PROMISE 1077BF/1077FF Trial
Authors: Sebikari Dorothy , Farhad Mona , Fenton Terry , Owor Maxensia , Stringer Jeffrey S. A. , Qin Min , Chakhtoura Nahida , Chi Benjamin H. , Saidi Friday , Nevrekar Neetal , Violari Avy , Chipato Tsungai , McIntyre James A. , Moodley Dhayendre , Taha Taha E. , Theron Gerhard , Fowler Mary Glenn
Published: April 2019

Background:

In the multicountry PROMISE 1077BF/1077FF trial, the risk of low birth weight (LBW; <2500 g) and preterm delivery (PTD; <37 weeks) was significantly higher among women initiating a protease inhibitor–based antiretroviral treatment (ART) regimen than those receiving ZDV alone. Among those assigned to a protease inhibitor regimen, tenofovir/emtricitabine was associated with the more severe outcomes of very LBW (<1500 g) and very PTD (<34 weeks) compared with zidovudine/lamivudine.

Methods:

We used multivariate logistic regression to further explore these treatment findings, taking into account demographic baseline clinical and postentry obstetrical factors. We evaluated individual adverse outcomes and composites that included stillbirth and early loss/spontaneous abortion.

Results:

Among 3333 women delivering at least 1 live infant, median maternal age at enrollment was 26 years; 661 (20%) were primiparous, and 110 (3.3%) reported at least 1 previous PTD. Seventeen percent of newborns were LBW, 1% were very LBW, 17% had PTD, and 3% had very PTD. Treatment allocation remained strongly associated with multiple adverse outcomes after controlling for other risk factors with both ART regimens exhibiting increased risk relative to ZDV alone. Other risk factors remaining significant in at least one of the multivariate models included the following: country, gestational age at entry, maternal age, maternal body mass index, previous PTD, history of alcohol use, baseline HIV viral titer, multiple gestation, and several obstetric risk factors.

Conclusions:

ART effects on adverse pregnancy outcomes reported in the randomized PROMISE trial remained strongly significant even after controlling for demographic, baseline clinical, and obstetrical risk factors, which were also associated with these outcomes.
Accurate ethnicity prediction from placental DNA methylation data
Authors: Yuan Victor , Price E Magda , Del Gobbo Giulia F , Mostafavi Sara , Cox Brian , Binder Alexandra M. , Michels Karin B. , Marsit Carmen , Robinson Wendy P.
Published: April 2019

Background

The influence of genetics on variation in DNA methylation (DNAme) is well documented. Yet confounding from population stratification is often unaccounted for in DNAme association studies. Existing approaches to address confounding by population stratification using DNAme data may not generalize to populations or tissues outside those in which they were developed. To aid future placental DNAme studies in assessing population stratification, we developed an ethnicity classifier, PlaNET (Placental DNAme Elastic Net Ethnicity Tool), using five cohorts with Infinium Human Methylation 450k BeadChip array (HM450k) data from placental samples that is also compatible with the newer EPIC platform.

Results

Data from 509 placental samples was used to develop PlaNET and show that it accurately predicts (accuracy = 0.938, kappa = 0.823) major classes of self-reported ethnicity/race (African: n = 58, Asian: n = 53, Caucasian: n = 389), and produces ethnicity probabilities that are highly correlated with genetic ancestry inferred from genome-wide SNP arrays (>2.5 million SNP) and ancestry informative markers (n = 50 SNPs). PlaNET’s ethnicity classification relies on 1860 HM450K microarray sites, and over half of these were linked to nearby genetic polymorphisms (n = 955). Our placental-optimized method outperforms existing approaches in assessing population stratification in placental samples from individuals of Asian, African, and Caucasian ethnicities.

Conclusion

PlaNET provides an improved approach to address population stratification in placental DNAme association studies. The method can be applied to predict ethnicity as a discrete or continuous variable and will be especially useful when self-reported ethnicity information is missing and genotyping markers are unavailable. PlaNET is available as an R package at (https://github.com/wvictor14/planet).
Total RNA-sequencing reveals multi-level microbial community changes and functional responses to wood ash application in agricultural and forest soil
Authors: Bang-Andreasen Toke , Anwar Muhammad Zohaib , Lanzén Anders , Kjøller Rasmus , Rønn Regin , Ekelund Flemming , Jacobsen Carsten Suhr
Published: April 2019

Recycling of wood ash from energy production may counteract soil acidification and return essential nutrients to soils. However, wood ash amendment affects soil physicochemical parameters that control composition and functional expression of the soil microbial community. Here, we applied Total RNA-sequencing to simultaneously assess the impact of wood ash amendment on the active soil microbial communities and the expression of functional genes from all microbial taxa. Wood ash significantly affected the taxonomic (rRNA) as well as functional (mRNA) profiles of both agricultural and forest soil. Increase in pH, electrical conductivity, dissolved organic carbon and phosphate were the most important physicochemical drivers for the observed changes. Wood ash amendment increased the relative abundance of the copiotrophic groups Chitinonophagaceae (Bacteroidetes) and Rhizobiales (Alphaproteobacteria) and resulted in higher expression of genes involved in metabolism and cell growth. Finally, Total RNA-sequencing allowed us to show that some groups of bacterial feeding protozoa increased concomitantly to the enhanced bacterial growth, which shows their pivotal role in the regulation of bacterial abundance in soil.
Systematic sequencing of chloroplast transcript termini fromArabidopsis thalianareveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures
Authors: Castandet Benoît , Germain Arnaud , Hotto Amber M. , Stern David B.
Published: April 2019

Chloroplast transcription requires numerous quality control steps to generate the complex but selective mixture of accumulating RNAs. To gain insight into how this RNA diversity is achieved and regulated, we systematically mapped transcript ends by developing a protocol called Terminome-Seq. UsingArabidopsis thalianaas a model, we catalogued >215 primary 5’ ends corresponding to transcription start sites (TSS), as well as 1,628 processed 5’ ends and 1,299 3’ ends. While most termini were found in intergenic regions, numerous abundant termini were also found within coding regions and introns, including several major TSS at unexpected locations. A consistent feature was the clustering of both 5’ and 3’ ends, contrasting with the prevailing description of discrete 5’ termini, suggesting an imprecision of the transcription and/or RNA processing machinery. Numerous termini correlated with the extremities of small RNA footprints or predicted stem-loop structures, in agreement with the model of passive RNA protection. Terminome-Seq was also implemented forpnp1-1, a mutant lacking the processing enzyme polynucleotide phosphorylase. Nearly 2,000 termini were altered inpnp1-1, revealing a dominant role in shaping the transcriptome. In summary, Terminome-Seq permits precise delineation of the roles and regulation of the many factors involved in organellar transcriptome quality control.
psupertime: supervised pseudotime inference for single cell RNA-seq data with sequential labels
Authors: Macnair Will , Claassen Manfred
Published: April 2019

Single cell RNA-seq has been successfully combined with pseudotime inference methods to investigate biological processes which have sequential labels, such as time series studies of development and differentiation. Pseudotime methods developed to date ignore the labels, and where there is substantial variation in the data not associated with the labels (such as cell cycle variation or batch effects), they can fail to find relevant genes. We introducepsupertime, a supervised pseudotime approach which outperforms benchmark pseudotime methods by explicitly using the sequential labels as input.psupertimeuses a simple, regression-based model, which by acknowledging the labels assures that genes relevant to the process, rather than to major drivers of variation, are found.psupertimeis applicable to the wide range of single cell RNA-seq datasets with sequential labels, derived from either experimental design or user-selected cell cluster sequences, and provides a tool for targeted identification of genes regulated along biological processes.
How much do you perceive this? An analysis on perceptions of geometric features, personalities and emotions in virtual humans (Extended Version)
Authors: Araujo Victor , Favaretto Rodolfo Migon , Knob Paulo , Musse Soraia Raupp , Vilanova Felipe , Costa Angelo Brandelli
Published: April 2019

Abstract

This work aims to evaluate people’s perception regarding geometric features, personalities and emotions characteristics in virtual humans. For this, we use as a basis, a dataset containing the tracking files of pedestrians captured from spontaneous videos and visualized them as identical virtual humans. The goal is to focus on their behavior and not being distracted by other features. In addition to tracking files containing their positions, the dataset also contains pedestrian emotions and personalities detected using Computer Vision and Pattern Recognition techniques. We proceed with our analysis in order to answer the question if subjects can perceive geometric features as distances/speeds as well as emotions and personalities in video sequences when pedestrians are represented by virtual humans. Regarding the participants, an amount of 73 people volunteered for the experiment. The analysis was divided in two parts: i) evaluation on perception of geometric characteristics, such as density, angular variation, distances and speeds, and ii) evaluation on personality and emotion perceptions. Results indicate that, even without explaining to the participants the concepts of each personality or emotion and how they were calculated (considering geometric characteristics), in most of the cases, participants perceived the personality and emotion expressed by the virtual agents, in accordance with the available ground truth.