bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

AbstractFish 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

Abstract
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

ABSTRACT

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

Abstract

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

Abstract
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

Abstract
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

AbstractIntroductionFor 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 MethodsAn 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.ResultsTwelve 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.ConclusionFrom 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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

ObjectiveHealth-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 methodsWe 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.ResultsTwo 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.ConclusionHRQoL 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.