bluuebunny/crossref_metadata_2025_split huggingface dataset:
The CCL-K11 ongoing key comparison. Final report for the year 2015
Authors: Matus Michael , Berg Steven van den , Czulek Dariusz , Seppä Jeremias , Robertsson Lennart 
Published: November 2016

Lasers from two national metrological institutes (NMIs) were compared in 2015 as part of the CCL-K11 ongoing key comparison, initiated by the 13th meeting of the Comité Consultative des Longuers (CCL) in 2007. The absolute frequency of R(127) 11-5 transitions of molecular iodine was measured for these lasers following the technical protocol for CCL-K11. The results of these measurements are compiled in the present report. The comparison reports, as communicated by each participant, are included as appendices.
This document constitutes the seventh final report for the ongoing key comparison CCL-K11.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCL, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Efficiency Impacts of Utilizing Soil Data in the Pricing of the Federal Crop Insurance Program
Authors: Woodard Joshua D. , Verteramo‐Chiu Leslie J. 
Published: November 2016

AbstractSince the Agricultural Act of 2014, the federal crop insurance program (FCIP) has been the cornerstone agricultural policy in the United States, and is the largest such program globally, with about $100 billion in coverage annually. Given its scale and scope, the FCIP has the potential to have pervasive impacts on incentives and policy functioning if not designed and priced properly. Surprisingly, soil data are not considered by the government when establishing insurance guarantees or rates. Using soil data that could easily and feasibly be scaled nationally, we find that the pricing differentials caused by the government′s failure to handle soil information leads to large errors in rating.
Role of Nitric Oxide Synthase on Blood Pressure Regulation and Vascular Function in Pregnant Rats on a High-Fat Diet
Authors: Palei Ana C. , Spradley Frank T. , Granger Joey P. 
Published: November 2016

Abstract

BACKGROUND
While obesity is a leading risk factor for preeclampsia, the mechanisms whereby obese women are more susceptible to pregnancy-induced hypertension are unclear. As high-fat diet (HFD) is an important contributor to the development of obesity, we tested the hypothesis that pregnant rats on HFD have hypertension and endothelial dysfunction due to reduced nitric oxide synthase (NOS).

METHODS
Twelve-week-old Sprague-Dawley female rats were fed normal diet (ND, 13% fat kcal) or HFD (40% fat kcal) for 9 weeks. Timed-pregnant rats were then generated and the effect of HFD on mean arterial blood pressure (MAP) and vascular function was assessed on gestational day (GD) 19.

RESULTS
MAP was not different between HFD and ND pregnant rats. Intriguingly, sensitivity to acetylcholine-induced endothelium-dependent vasorelaxation was enhanced in small mesenteric arteries of HFD dams compared to ND controls (logEC50 −7.9 ± 0.3 vs. −6.7 ± 0.3 M; P &lt; 0.05). Additionally, HFD dams exhibited higher mesenteric artery expression of NOS3 and plasma levels of NO metabolites than ND controls (1738.0 ± 316.4 vs. 1094.0 ± 82.5 pg/mg and 72.5 ± 8.7 vs. 39.7 ± 4.5 µM, respectively; both P &lt; 0.05). Further, to determine the role of NOS in modulating blood pressure in HFD pregnant rats, animals were treated with the nonselective inhibitor Nω-Nitro-l-arginine methyl ester hydrochloride (100 mg/l, drinking water) from GD 14 to 19. It was found that NOS inhibition increased MAP equally in HFD and ND groups.

CONCLUSIONS
Contrary to our initial hypothesis, HFD dams were normotensive and presented increased endothelial function and NO/NOS3 levels. This enhanced NOS-mediated vascular function does not appear to have a major impact on blood pressure regulation of HFD-fed pregnant rats.
DACE: a scalable DP-means algorithm for clustering extremely large sequence data
Authors: Jiang Linhao , Dong Yichao , Chen Ning , Chen Ting 
Published: November 2016

AbstractMotivationAdvancements in next-generation sequencing technology have produced large amounts of reads at low cost in a short time. In metagenomics, 16S and 18S rRNA gene have been widely used as marker genes to profile diversity of microorganisms in environmental samples. Through clustering of sequencing reads we can determine both number of OTUs and their relative abundance. In many applications, clustering of very large sequencing data with high efficiency and accuracy is essential for downstream analysis.ResultsHere, we report a scalable Dirichlet Process Means (DP-means) algorithm for clustering extremely large sequencing data, termed DACE. With an efficient random projection partition strategy for parallel clustering, DACE can cluster billions of sequences within a couple of hours. Experimental results show that DACE runs between 6 and 80 times faster than state-of-the-art programs, while maintaining overall better clustering accuracy. Using 80 cores, DACE clustered the Lake Taihu 16S rRNA gene sequencing data (∼316M reads, 30 GB) in 25 min, and the Ocean TARA Eukaryotic 18S rRNA gene sequencing data (∼500M reads, 88 GB) into ∼100 000 clusters within an hour. When applied to the IGC gene catalogs in human gut microbiome (∼10M genes), DACE produced 9.8M clusters with 52K redundant genes in 1.5 hours of running time.Availability and ImplementationDACE is available at https://github.com/tinglab/DACE.Supplementary informationSupplementary data are available at Bioinformatics online.
A comprehensive benchmark of RNA–RNA interaction prediction tools for all domains of life
Authors: Umu Sinan Uğur , Gardner Paul P 
Published: November 2016

Abstract

Motivation
The aim of this study is to assess the performance of RNA–RNA interaction prediction tools for all domains of life.

Results
Minimum free energy (MFE) and alignment methods constitute most of the current RNA interaction prediction algorithms. The MFE tools that include accessibility (i.e. RNAup, IntaRNA and RNAplex) to the final predicted binding energy have better true positive rates (TPRs) with a high positive predictive values (PPVs) in all datasets than other methods. They can also differentiate almost half of the native interactions from background. The algorithms that include effects of internal binding energies to their model and alignment methods seem to have high TPR but relatively low associated PPV compared to accessibility based methods.

Availability and Implementation
We shared our wrapper scripts and datasets at Github (github.com/UCanCompBio/RNA_Interactions_Benchmark). All parameters are documented for personal use.

Supplementary information
Supplementary data are available at Bioinformatics online.
Systemic Elevation of Proinflammatory Interleukin-18 in Human Immunodeficiency Virus (HIV)/Hepatitis C Virus (HCV) Coinfection Versus HIV or HCV Monoinfection
Authors: Veenhuis Rebecca T. , Astemborski Jacquie , Chattergoon Michael A. , Greenwood Paige , Jarosinski Marissa , Moore Richard D. , Mehta Shruti H. , Cox Andrea L. 
Published: November 2016

Abstract

Background.
Human immunodeficiency virus (HIV)/hepatitis C virus (HCV) coinfection and elevated interleukin (IL)-18 levels are both associated with enhanced progression of hepatic inflammation and increased risk of diabetes, kidney disease, and cardiovascular disease. IL-18 is a proinflammatory cytokine made upon activation of the inflammasome, an innate sensing system. We assessed whether increased IL-18 could explain the increased incidence and progression of inflammatory conditions seen with HIV/HCV coinfection.

Methods.
Serum samples from 559 subjects with HIV monoinfection, HCV monoinfection, HIV/HCV coinfection, or people who inject drugs with neither infection were tested for IL-18 by enzyme-linked immunosorbent assay and for 16 other analytes by electrochemiluminescence immunoassay. IL-18 levels were measured in 14 additional chronically HCV-infected subjects who developed incident HIV infection to determine if IL-18 increases with coinfection.

Results.
IL-18 was significantly elevated in coinfected individuals vs both monoinfections (P &lt; .0001) independent of age, sex, and race. IL-18 levels were significantly higher in HIV monoinfection than in HCV monoinfection. High IL-18 levels were correlated with detectable HIV viremia and inversely with CD4 cell count (P &lt; .0001), consistent with HIV activation of the inflammasome resulting in CD4 T-cell depletion. Incident HIV infection of chronically HCV-infected subjects resulted in increased IL-18 (P &lt; .001), while HIV suppression was associated with normal IL-18 levels. Four additional analytes (IP-10, IL-12/23p40, IFN-γ, IL-15) were found to be elevated in HIV/HCV coinfection when compared to both monoinfections.

Conclusions.
HIV/HCV coinfection results in significantly elevated serum IL-18. The elevated levels of this proinflammatory cytokine may explain the increased incidence and progression of inflammatory illnesses seen in coinfected individuals.
A ghostly damped Ly α system revealed by metal absorption lines
Authors: Fathivavsari H. , Petitjean P. , Zou S. , Noterdaeme P. , Ledoux C. , Krühler T. , Srianand R. 
Published: November 2016

Abstract
We report the discovery of the first ‘ghostly’ damped Ly α absorption system (DLA), which is identified by the presence of absorption from strong low-ion species at zabs = 1.704 65 along the line of sight to the quasar SDSS J113341.29−005740.0 with zem = 1.704 41. No Ly α absorption trough is seen associated with these absorptions because the DLA trough is filled with the leaked emission from the broad emission-line region of the quasar. By modelling the quasar spectrum and analysing the metal lines, we derive log N(H i)(cm−2) ∼21.0 ± 0.3. The DLA cloud is small (≤0.32 pc), thus not covering entirely the broad-line region and is located at ≥39 pc from the central active galactic nucleus (AGN). Although the DLA is slightly redshifted relative to the quasar, its metallicity ([S/H] = −0.41 ± 0.30) is intermediate between what is expected from infalling and outflowing gas. It could be possible that the DLA is part of some infalling material accreting on to the quasar host galaxy through filaments, and that its metallicity is raised by mixing with the enriched outflowing gas emanating from the central AGN. Current DLA surveys miss these ‘ghostly’ DLAs, and it would be important to quantify the statistics of this population by searching the Sloan Digital Sky Survey (SDSS) data base using metal absorption templates.
Shukla–Spatschek diffusion effects on surface plasma waves in astrophysical turbulent plasmas
Authors: Lee Myoung-Jae , Jung Young-Dae 
Published: November 2016

Abstract
The effects of Shukla–Spatschek turbulent diffusion on a temporal mode of surface waves propagating at the interface of an astrophysical turbulent plasma are investigated. The damping rates for high and low modes of surface wave are kinetically derived by employing the Vlasov–Poisson equation and the specular reflection boundary condition. We found that the diffusion caused by the fluctuating electric fields leads to damping for both high and low modes of surface waves. The high-mode damping is enhanced with an increase of the wavenumber and the diffusion coefficient, but suppressed by an increase of electron thermal energy. By contrast, the low-mode damping is suppressed as the wavenumber and the thermal energy increase although it is enhanced as the diffusion increases. The variation of the damping rate due to the Shukla–Spatschek turbulent diffusion is also discussed.
Analyses of Yield and Economic Response from Foliar Fungicide and Insecticide Applications to Soybean in the North Central United States
Authors: Kandel Yuba R. , Mueller Daren S. , Hart Chad E. , Bestor Nathan R. C. , Bradley Carl A. , Ames Keith A. , Giesler Loren J. , Wise Kiersten A. 
Published: November 2016

Foliar disease and insect management on soybean (Glycine max L. Merrill) in the North Central region of the United States has been increasingly accomplished through foliar fungicide and insecticide application. Data from research trials conducted in Illinois, Indiana, Iowa, and Nebraska were compiled from 2008 to 2014 to determine the impact of fungicide, insecticide, and fungicide + insecticide applications on soybean yield and profitability. In each state, field experiments occurred each year in two to seven locations. All treatments were applied at the R3 growth stage. Disease and insect pressure were very low in all states and years. A foliar application of fungicide, insecticide, or the combination, increased yield in seven out of 14 total site-years (P < 0.10). Economic analysis using an average soybean price of $0.42 per kilogram and average application cost of $62 per hectare indicated that fungicide applications were only profitable in 14% of the trial site-years. Insecticide alone and fungicide + insecticide was profitable in 39% and 45% of site-years, respectively. Effect of fungicide class on yield was inconsistent. Our results indicate that although yield increases can occur with foliar fungicide and/or insecticide treatments, current market prices and application costs may limit profitability when disease and/or insect pressure is low. Accepted for publication 22 September 2016.
Identifying Soybean Rust-resistant and Susceptible Populations of Kudzu to Increase Disease Monitoring Efficiency in Alabama
Authors: Sikora Edward J. , Delaney Mary A. 
Published: November 2016

Soybean rust (SBR), caused by Phakopsora pachyrhizi, is considered to be one of the most damaging diseases of soybean worldwide. Monitoring for the disease in Alabama relies heavily on scouting kudzu on a biweekly basis in south and central portions of the state from late January through the end of July in areas where soybean production is minimal and is critical to help growers avoid significant yield losses from SBR. Previous studies have reported that some kudzu populations are naturally resistant or immune to infection from the pathogen which can complicate early disease detection. This study will apply that knowledge to determine locations of kudzu populations that are either resistant or susceptible to P. pachyrhizi in order to increase monitoring efficiency and reduce costs associated with the scouting program. Results show that approximately 34% of the 162 kudzu sites tested in Alabama were resistant to P. pachyrhizi. By focusing scouting efforts on SBR-susceptible kudzu sites, we will reduce costs associated with the monitoring program by approximately 25% which is critical at a time when funding for such efforts is decreasing. Accepted for publication 24 October 2016.
Quality Assessment of the Commercially Available Predator Amblyseius swirskii (Acari: Phytoseiidae)
Authors: Lopez Lorena , Smith Hugh A. 
Published: November 2016

Amblyseius swirskii Athias-Henriot (Acari: Phytoseiidae) is a commercially available predatory mite used to control thrips, whiteflies, and broad mites in horticultural production. The inconsistent quality of mass-produced biocontrol agents is a major concern in augmentative biological control and only a few studies have tested the post-shipment quality of commercial phytoseiids. We evaluated the post-shipment quality of A. swirskii purchased from a commercial provider in the United States. Guidelines for quality control of commercially produced natural enemies, established by the International Organization for Biological Control (IOBC), were followed. Quantity, survival, fecundity, and establishment in ornamenttal peppers (‘Explosive Ember’) were measured. The estimated quantity of A. swirskii motiles (immatures and adults) was quite variable among bran containers (20,968 ± 7,391 mites) but close to the number claimed in the label. Numbers of living A. swirskii females evaluated (n = 30) declined by less than 40% (26 ± 1.25 females) within two days of arrival and declined more than 50% by day eight (15 ± 1.23 females). No significant differences among days sampled were identified for female fecundity; however, fecundity varied considerably among containers. There was no population increase in the ornamental peppers during the two weeks following inoculation with A. swirskii. Accepted for publication 3 September 2016.
The Development of an Indigenous Health Curriculum for Medical Students
Authors: Lewis Melissa , Prunuske Amy 
Published: November 2016

Indigenous populations experience dramatic health disparities; yet, few medical schools equip students with the skills to address these inequities. At the University of Minnesota Medical School, Duluth campus, a project to develop an Indigenous health curriculum began in September 2013. This project used collaborative and decolonizing methods to gather ideas and opinions from multiple stakeholders, including students, community members, faculty, and administration, to guide the process of adding Indigenous health content to the curriculum to prepare students to work effectively with Indigenous populations. A mixed-methods needs assessment was implemented to inform the instructional design of the curriculum. In June 2014, stakeholders were invited to attend a retreat and complete a survey to understand their opinions of what should be included in the curriculum and in what way. Retreat feedback and survey responses indicated that the most important topics to include were cultural humility, Indigenous culture, social/political/economic determinants of health, and successful tribal health interventions. Stakeholders also emphasized that this content should be taught by tribal members, medical school faculty, and faculty in complementary departments (e.g., American Indian Studies, Education, Social Work) in a way that incorporates experiential learning.
Preliminary outcomes include the addition of a seven-hour block of Indigenous content for first-year students taught primarily by Indigenous faculty from several departments. To address the systemic barriers to health and well-being and provider bias that Indigenous patients experience, this project sought to gather data and opinions regarding the training of medical students through a process of Indigenizing research and education.
The Correlation Between Recordable MEPs and Motor Function During Spinal Surgery for Resection of Thoracic Spinal Cord Tumor
Authors: Guo LanJun , Li Yan , Han Ruquan , Gelb Adrian W. 
Published: November 2016

Background:
Motor evoked potentials (MEPs) are commonly used during surgery for spinal cord tumor resection. However, it can be difficult to record reliable MEPs from the muscles of the lower extremities during surgery in patients with preoperative weakness due to spinal cord compression. In this study, motor function of patients’ lower extremities and their association with intraoperative MEP recording were compared.

Patients and Methods:
Patients undergoing thoracic spinal cord tumor resection were studied. Patients’ motor function was checked immediately before the surgical procedure. MEP responses were recorded from the tibialis anterior and foot muscles, and the hand muscles were used as control. Electrical current with train of eight pulses, 200 to 500 V was delivered through 2 corkscrews placed at C3’ and C4’ sites. Anesthesia was maintained by total intravenous anesthesia using a combination of propofol and remifentanil after induction with intravenous propofol, remifentanil, and rocuronium. Rocuronium was not repeated. Bispectral Index was maintained between 40 to 50.

Results:
From 178 lower limbs of 89 patients, myogenic MEPs could be recorded from 100% (105/105) of the patients with 5 of 5 motor strength in lower extremity; 90% (36/40) from the patients with 4/5 motor strength; only 25% (5/20) with 3/5; and 12.5% (1/8) with 2/5 motor strength; none (0/5) were able to be recorded if the motor strength was 1/5.

Summary:
The ability to record myogenic MEPs is closely associated with the patient’s motor function. They are difficult to obtain if motor function is 3/5 motor strength in the lower extremity. They are almost impossible to record if motor function is worse than 3/5.
Which Technique Is Better Option for C3 Segment in Multilevel Open-Door Laminoplasty of the Cervical Spine?
Authors: Lee Gun Woo , Cho Chang Woo , Shin Ji-Hoon , Ahn Myun-Whan 
Published: November 2016

Study Design.
A post-hoc comparative study.

Objective.
To evaluate postoperative clinical, radiological, and surgical outcomes after laminoplasty (LP) involving the C3 segment and to compare outcomes with those of patients who underwent LP with C3 laminectomy (LN).

Summary of Background Data.
In many of the pathologies that require LP involving C3 segment, most spine surgeons perform LP at C3 and other cervical segments. Considering the peculiarities of the C2-C3 level, spine surgeons should take into account those in LP involving the C3 segment, but the particular aspects of the C2-C3 levels have not been fully evaluated.

Methods.
Of 93 patients, 66 patients (39 in group A, LP involving C3; 27 in group B, LP with C3 LN) were enrolled in the study. The primary outcome measure was pain intensity of the posterior neck measured with visual analog scale. Secondary endpoints included the following: (1) radiologic outcomes based on the cervical range of motion and rate of bony impingement and spontaneous fusion between C2 and C3, (2) clinical outcomes based on the 12-item short-form health survey and Japanese Orthopedic Association scale, and (3) surgical outcomes.

Results.
The primary end-point of the present study, posterior neck pain, exhibited a greater improvement in the group with C3 LN than in the group with C3 LP at 6 months and 1 year after surgery (P = 0.03 and 0.01, respectively). The cervical range of motion of C3 LN group was significantly greater than C3 LP group at postoperative 1 year (P = 0.02). Radiologic evidences of bony impingement and spontaneous fusion between C2 and C3 were significantly greater in C3 LP group than in C3 LN group. Clinical outcomes and surgical outcomes did not differ significantly between groups.

Conclusion.
We recommend performing LN instead of LP for the C3 segment in cases requiring multilevel LP surgery involving C3.

Level of Evidence: 3