bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bilateral comparison of 1 V and 10 V standards between the NMISA (South Africa) and the BIPM April to June 2017 (part of the ongoing BIPM key comparison BIPM.EM-K11.a and b)
Authors: Solve S , Chayramy R , Matlejoane A M , Magagula L , Stock M 
Published: January 2018

As part of the ongoing BIPM key comparison BIPM.EM-K11.a and b, a comparison of the 1.018 V and 10 V voltage reference standards of the BIPM and the National Metrology Institute of South Africa, NMISA (South Africa), was carried out from April to June 2017. Two BIPM Zener diode-based travelling standards (Fluke 732B), BIPM_A (ZA) and BIPM_B (ZB), were transported by freight to NMISA and back to BIPM. In order to keep the Zeners powered during their transportation phase, a voltage stabilizer developed by BIPM was connected in parallel to the internal battery. It consists of a set of two batteries, electrically protected from surcharge-discharge, easy to recharge and is designed to power two transfer standards for ten consecutive days. At NMISA, the reference standard for DC voltage is a Josephson Voltage Standard. The output EMF (Electromotive Force) of each travelling standard was measured by direct comparison with the primary standard.
At the BIPM, the travelling standards were calibrated, before and after the measurements at NMISA, with the Josephson Voltage Standard. Results of all measurements were corrected for the dependence of the output voltages of the Zener standards on internal temperature and atmospheric pressure.
The final result of the comparison is presented as the difference between the values assigned to DC voltage standards by NMISA, at the level of 1.018 V and 10 V, at NMISA, U
NMISA, and those assigned by the BIPM, at the BIPM, U
BIPM, at the reference dates of the 19th and 18th of May 2017, respectively.

U
NMISA − U
BIPM = + 0.07 μV; u
c = 0.02 μV, at 1.018 V

U
NMISA − U
BIPM = + 0.001 μV; u
c = 0.34 μV, at 10 V
where u
c is the combined standard uncertainty associated with the measured difference, including the uncertainty of the representation of the volt at the BIPM and at NMISA, based on K
J-90, and the uncertainty related to the comparison.

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 CCEM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Final report, on-going key comparison BIPM.QM-K1, ozone at ambient level, comparison with NMISA, June 2017
Authors: Viallon Joële , Idrees Faraz , Moussay Philippe , Wielgosz Robert , Ntsasa Napo G , Tshilongo James , Mphaphuli Gumani E , Norris James E , Hodges Joseph T 
Published: January 2018

As part of the on-going key comparison BIPM.QM-K1, a comparison has been performed between the ozone national standard of South Africa maintained by the National Metrology Institute of South Africa (NMISA) and the common reference standard of the key comparison, maintained by the Bureau International des Poids et Mesures (BIPM), via a transfer standard maintained by the National Institute of Standards and Technology (NIST). The instruments have been compared over a nominal ozone amount-of-substance fraction range of 0 nmol/mol to 500 nmol/mol.

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 CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Economics of Sustainable Development and the Bioeconomy
Authors: Zilberman David , Gordon Ben , Hochman Gal , Wesseler Justus 
Published: January 2018

AbstractSustainable development can be attained by policies that are derived by analyses that integrate biophysical considerations into economic models. We show that policies and incentives that correct market failure can attain sustainable development through enhancing conservation, recycling, the use of renewable resources, and development of the bioeconomy, which relies on biological processes and feedstock to produce renewable products. The design of sustainable development policies and analysis of the bioeconomy pose new challenges to applied economists, who are uniquely qualified to integrate economic analysis with biophysical considerations.
Modeling biological problems in computer science: a case study in genome assembly
Authors: Medvedev Paul 
Published: January 2018

Abstract
As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment and assembly. In this tutorial, we use the example of the genome assembly problem to demonstrate how to go from a question in the biological realm to a solution in the computer science realm. We show the modeling process step-by-step, including all the intermediate failed attempts. Please note this is not an introduction to how genome assembly algorithms work and, if treated as such, would be incomplete and unnecessarily long-winded.
Discovering personalized driver mutation profiles of single samples in cancer by network control strategy
Authors: Guo Wei-Feng , Zhang Shao-Wu , Liu Li-Li , Liu Fei , Shi Qian-Qian , Zhang Lei , Tang Ying , Zeng Tao , Chen Luonan 
Published: January 2018

Abstract

Motivation
It is a challenging task to discover personalized driver genes that provide crucial information on disease risk and drug sensitivity for individual patients. However, few methods have been proposed to identify the personalized-sample driver genes from the cancer omics data due to the lack of samples for each individual. To circumvent this problem, here we present a novel single-sample controller strategy (SCS) to identify personalized driver mutation profiles from network controllability perspective.

Results
SCS integrates mutation data and expression data into a reference molecular network for each patient to obtain the driver mutation profiles in a personalized-sample manner. This is the first such a computational framework, to bridge the personalized driver mutation discovery problem and the structural network controllability problem. The key idea of SCS is to detect those mutated genes which can achieve the transition from the normal state to the disease state based on each individual omics data from network controllability perspective. We widely validate the driver mutation profiles of our SCS from three aspects: (i) the improved precision for the predicted driver genes in the population compared with other driver-focus methods; (ii) the effectiveness for discovering the personalized driver genes and (iii) the application to the risk assessment through the integration of the driver mutation signature and expression data, respectively, across the five distinct benchmarks from The Cancer Genome Atlas. In conclusion, our SCS makes efficient and robust personalized driver mutation profiles predictions, opening new avenues in personalized medicine and targeted cancer therapy.

Availability and implementation
The MATLAB-package for our SCS is freely available from http://sysbio.sibcb.ac.cn/cb/chenlab/software.htm.

Supplementary information
Supplementary data are available at Bioinformatics online.
Enhanced functionalities for annotating and indexing clinical text with the NCBO Annotator+
Authors: Tchechmedjiev Andon , Abdaoui Amine , Emonet Vincent , Melzi Soumia , Jonnagaddala Jitendra , Jonquet Clement 
Published: January 2018

Abstract

Summary
Second use of clinical data commonly involves annotating biomedical text with terminologies and ontologies. The National Center for Biomedical Ontology Annotator is a frequently used annotation service, originally designed for biomedical data, but not very suitable for clinical text annotation. In order to add new functionalities to the NCBO Annotator without hosting or modifying the original Web service, we have designed a proxy architecture that enables seamless extensions by pre-processing of the input text and parameters, and post processing of the annotations. We have then implemented enhanced functionalities for annotating and indexing free text such as: scoring, detection of context (negation, experiencer, temporality), new output formats and coarse-grained concept recognition (with UMLS Semantic Groups). In this paper, we present the NCBO Annotator+, a Web service which incorporates these new functionalities as well as a small set of evaluation results for concept recognition and clinical context detection on two standard evaluation tasks (Clef eHealth 2017, SemEval 2014).

Availability and implementation
The Annotator+ has been successfully integrated into the SIFR BioPortal platform—an implementation of NCBO BioPortal for French biomedical terminologies and ontologies—to annotate English text. A Web user interface is available for testing and ontology selection (http://bioportal.lirmm.fr/ncbo_annotatorplus); however the Annotator+ is meant to be used through the Web service application programming interface (http://services.bioportal.lirmm.fr/ncbo_annotatorplus). The code is openly available, and we also provide a Docker packaging to enable easy local deployment to process sensitive (e.g. clinical) data in-house (https://github.com/sifrproject).

Supplementary information
Supplementary data are available at Bioinformatics online.
Hepatobiliary strongyloidiasis presenting as an ampullary lesion on esophagogastroduodenoscopy/endoscopic ultrasound
Authors: Ofori Emmanuel , Ramai Daryl , Khan Alisha , Xiao Philip , Reddy Madhavi , Shahzad Ghulamullah 
Published: January 2018

Abstract
Strongyloidiasis is an intestinal infection caused by the parasitic nematodes of the Strongyloides species, most commonly Strongyloides stercoralis. We report a case of a 66-year-old immigrant male from Haiti who presented with complaints of diarrhea and an unintentional 80-lb weight loss over the past 5 years. Stool examination was positive for strongyloidiasis. Following albendazole therapy, esophagogastroduodenoscopy (EGD) showed a unique ampullary lesion. Histopathology of the ampullary lesion showed reactive epithelium with Strongyloides larva. In addition, endoscopic ultrasound (EUS) detected a large pancreatic cyst. Both these findings were absent on EGD 5 years previously, prior to the onset of his symptoms. This paper documents a rare case of an ampullary lesion and pancreatic cyst secondary to hepatobiliary strongyloidiasis in a non-Human Immunodeficiency Virus (HIV) patient. We review the epidemiology, life cycle, clinical presentation and treatment of strongyloidiasis.
Density-independent and density-dependent factors affecting spatio-temporal dynamics of Atlantic cod (Gadus morhua) distribution in the Gulf of Maine
Authors: Li Zengguang , Ye Zhenjiang , Wan Rong , Tanaka Kisei R , Boenish Robert , Chen Yong 
Published: January 2018

Abstract
Due to strong spatial interplays between intraspecific interactions and environmental forcing, both density-dependent and density-independent processes can affect spatio-temporal dynamics of fish populations in a spatially explicit fashion. To this end, this study investigated the underlying mechanisms of spatio-temporal dynamics of Atlantic cod (Gadus morhua) in the Gulf of Maine (GoM). Based on the data from the Northeast Fisheries Science Center (NEFSC) bottom-trawl surveys in spring and fall from 1982 to 2013, empirical cumulative distribution function (ECDF) curves and geographic distribution indices were used to examine the species–environment and abundance–occupancy relationship, respectively. Then, a variable-coefficient generalized additive model was constructed to quantify the simultaneous effects of environmental variables and population size on the spatio-temporal dynamics of cod distribution. Area occupied remained relatively high through the late 1990s, but underwent a pronounced contraction into the western GoM (WGoM) for the reminder of the time-series. The model results suggest that the spatio-temporal dynamics of GoM cod have been driven by complex interactions of density-dependent and density-independent factors over the past three decades. Better knowledge of these dynamics can improve our understanding of the causality of abundance–occupancy and species–environment relationships and help to reduce error estimates for survey-based indices.
Prerupture Intracranial Aneurysm Morphology in Predicting Risk of Rupture: A Matched Case-Control Study
Authors: Skodvin Torbjørn Øygard , Evju Øyvind , Sorteberg Angelika , Isaksen Jørgen Gjernes 
Published: January 2018

Abstract

BACKGROUND
Maximal size and other morphological parameters of intracranial aneurysms (IAs) are used when deciding if an IA should be treated prophylactically. These parameters are derived from postrupture morphology. As time and rupture may alter the aneurysm geometry, possible morphological predictors of a rupture should be established in prerupture aneurysms.

OBJECTIVE
To identify morphological parameters of unruptured IAs associated with later rupture.

METHODS
Nationwide matched case-control study. Twelve IAs that later ruptured were matched 1:2 with 24 control IAs that remained unruptured during a median follow-up time of 4.5 (interquartile range, 3.7-8.2) yr. Morphological parameters were automatically measured on 3-dimensional models constructed from angiograms obtained at time of diagnosis. Cases and controls were matched by aneurysm location and size, patient age and sex, and the PHASES (population, hypertension, age, size of aneurysm, earlier subarachnoid hemorrhage from another aneurysm, and site of aneurysm) score did not differ between the 2 groups.

RESULTS
Only inflow angle was significantly different in cases vs controls in univariate analysis (P = .045), and remained significant in multivariable analysis. Maximal size correlated with size ratio in both cases and controls (P = .015 and <.001, respectively). However, maximal size and inflow angle were correlated in cases but not in controls (P = .004. and .87, respectively).

CONCLUSION
A straighter inflow angle may predispose an aneurysm to changes that further increase risk of rupture. Traditional parameters of aneurysm morphology may be of limited value in predicting IA rupture.
A Novel Single-Nucleotide Polymorphism Loop Mediated Isothermal Amplification Assay for Detection of Artemisinin-Resistant Plasmodium falciparum Malaria
Authors: Mohon Abu Naser , Menard Didier , Alam Mohammad Shafiul , Perera Kevin , Pillai Dylan R 
Published: January 2018

AbstractBackgroundArtemisinin-resistant malaria (ARM) remains a significant threat to malaria elimination. In the Greater Mekong subregion, the prevalence of ARM in certain regions has reached greater than 90%. Artemisinin-resistant malaria is clinically identified by delayed parasite clearance and has been associated with mutations in the propeller domain of the kelch 13 gene. C580Y is the most prevalent mutation. The detection of ARM currently relies on labor-intensive and time-consuming methods such as clinical phenotyping or in vitro susceptibility testing.MethodsWe developed a novel single-nucleotide polymorphism loop mediated isothermal amplification (SNP-LAMP) test method for the detection of the C580Y mutation using a novel primer design strategy.ResultsThe SNP-LAMP was 90.0% sensitive (95% confidence interval [CI], 66.9–98.3) and 91.9% specific (95% CI, 82.6–96.7) without knowledge of the parasite load and was 100% sensitive (95% CI, 79.9–100) and 97.3% specific (95% CI, 89.7–99.5) when the parasitemia was within the assay dynamic range. Tests with potential application near-to-patient such as SNP-LAMP may be deployed in low- and middle-income and developed countries.ConclusionsSingle-nucleotide polymorphism LAMP can serve as a surveillance tool and guide treatment algorithms for ARM in a clinically relevant time frame, prevent unnecessary use of additional drugs that may drive additional resistance, and avoid longer treatment regimens that cause toxicity for the patient.
Parallel Proximal Fixation in Rib-Based Growing Rod System
Authors: Heflin John , Welborn Michelle , Ramirez-Lluch Norman , Iriarte Ivan , El-Hawary Ron , Fedorak Graham T. , Smith John T. 
Published: January 2018

Study Design.
Retrospective case control.

Objective.
To report on differences in implant failure rates and complications requiring reoperation in children with early-onset scoliosis (EOS) treated with rib-based distraction utilizing four proximal fixation points in either a parallel or in-line configuration.

Summary of Background Data.
Proximal anchor failure continues to be a significant problem in growth-friendly surgery using rib-based distraction to treat children with EOS. Differences between parallel and in-line proximal anchor constructs have not been previously assessed.

Methods.
A multicenter registry was reviewed to identify children treated for EOS with rib-based distraction between 2011 and 2014 with a minimum of 2 years follow-up after implantation. Patients were divided into those with in-line and parallel proximal rib-cradle configurations, and only those with exactly four fixation points (two per side) were included. Charts were reviewed for demographic, clinical, and radiographic information.

Results.
A total of 56 patients were identified—31 with in-line constructs and 25 with parallel constructs. Follow-up in the in-line group was a mean of 4.06 years versus 3.16 in the parallel group (P = 0.001). Controlling for the different lengths of follow-up in the two groups there was a significantly higher rate of implant failure (P = 0.043) and requirement for nonroutine surgical intervention (P = 0.029) in the in-line group. There was a trend toward increased complications in the in-line group (P = 0.058).

Conclusion.
Failure of proximal fixation is the most common complication in management of EOS with rib-based distraction. This study identifies that when the number of proximal fixation points are matched, parallel constructs result in lower rates of implant failure and need for unplanned reoperation than in-line constructs. Although this study was limited to patients in whom the VEPTR device was employed, these principles are likely applicable to other rib-based distraction devices used to treat EOS.

Level of Evidence: 3
Tidemark Avulsions are a Predominant Form of Endplate Irregularity
Authors: Berg-Johansen Britta , Jain Deeptee , Liebenberg Ellen C. , Fields Aaron J. , Link Thomas M. , O’Neill Conor W. , Lotz Jeffrey C. 
Published: January 2018

Study Design.
Descriptive histologic and magnetic resonance imaging study of human cadaveric spines.

Objective.
To identify and characterize common endplate pathologies to form a histologic foundation for an etiology-based classification system.

Summary of Background Data.
Irregularities at the spinal disc-vertebra interface are associated with back pain and intervertebral disc herniation injuries. However, there is currently a lack of consensus regarding terminology for classification. This limits the potential for advancing understanding of back pain mechanisms, and prohibits meaningful comparisons for identifying priorities for prevention and treatment. Prior classification systems largely rely on observations from clinical imaging, which may miss subtle pathologic features.

Methods.
Fifteen cadaveric spines with moderate to severe disc degeneration were obtained and scanned with MRI in the sagittal plane using two-dimensional T1-weighted and T2-weighted fast spin-echo sequences. Eighty-nine lumbar and lower thoracic bone-disc-bone motion segments were extracted, fixed, sectioned, and stained for histologic evaluation. Focal endplate irregularities were identified and categorized based on features that inferred causation. The presence, type, and anatomic location were recorded. A classification system with three major categories of focal endplate irregularities was created.

Results.
Disc-vertebra avulsion and vertebral rim degeneration were more common than subchondral nodes: 50% of irregularities were classified as rim degeneration (75/150), 35% were classified as avulsions (52/150), and 15% were classified as nodes (23/150). Ninety percent of avulsions were subclassified as “tidemark avulsions,” a highly prevalent form of endplate irregularity in which the outer annulus separates from the vertebra at the tidemark. These tidemark avulsions have not been previously described, yet are visible on T2-weighted MRI as high-intensity regions.

Conclusion.
This study provides histologic basis for a system to classify focal endplate irregularities. Included is a previously unidentified but prevalent finding of tidemark avulsions, which are visible with both histology and magnetic resonance imaging. These observations will help clinicians better organize patients into meaningful groups to facilitate diagnosis, treatment, and clinical research.

Level of Evidence: 3
Cochlear Implant Surgery and the Risk of Falls in an Adult Population
Authors: Louza Julia , Klappert Caspar Leon , Ledderose Georg , Gürkov Robert , Krause Eike 
Published: January 2018

Objective:
To determine the effect of cochlear implant surgery on the balance and risk of falls in an adult patient population using a mobile posturograph.

Design:
Prospective clinical pilot study.

Setting:
Cochlear implant center at a tertiary referral hospital.

Subjects and Methods:
Twenty adult patients undergoing cochlear implant surgery were tested using a mobile posturograph (VertiGuard). The standard balancing deficit test, or the geriatric standard balancing deficit test protocol (for patients older than 60 yr), was performed both 1 day before and 3 to 5 days after surgery.

Outcome Measures:
The risk of falls (%) was calculated from the body sway both forward-to-backward and side-to-side in degrees per second.

Results:
The mean preoperative risk of falls in the whole study population was 51% (24–max. 86%) and was thus already higher than that in a normal healthy population (norm 0–40%). Comparison of the postoperative risk of falls to the preoperative risk for all 20 patients revealed a mean increased risk of falls of 1.25% after CI surgery. This is not a statistically significant increase. There was also no statistically significant increase when comparing the fall risk calculated using either the standard balancing deficit test protocol or the geriatric standard balancing deficit test protocol alone.

Conclusion:
Postural control in cochlear implant candidates is already decreased before surgery compared with a healthy population. However Comparison of pre- and postoperative body sway measurements did not reveal a significant increase in fall risk as a result of cochlea implant surgery. Therefore in this study population, cochlear implant surgery did not influence balance and risk of falls. Further testing with a larger study population would be necessary to determine the development of falls risk over time after cochlear implant surgery.