bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atropos: specific, sensitive, and speedy trimming of sequencing reads
Authors: Didion John P , Collins Francis S 
Published: January 2018

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leading-edge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves a four-fold increase in trimming accuracy and a decrease in execution time of ~50% (using 16 parallel execution threads). Furthermore, Atropos maintains high accuracy even when trimming simulated data with a high rate of error. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of most current-generation sequencing data sets.
Atropos is open source and free software written in Python and available at https://github.com/jdidion/atropos.
Identification of suitable reference genes for real-time quantitative PCR analysis of hydrogen peroxide-treated human umbilical vein endothelial cells
Authors: Li Tianyi , Diao Hongying , Zhao Lei , Xing Yue , Zhang Jichang , Liu Ning , Yan Youyou , Tian Xin , Sun Wei , Liu Bin 
Published: January 2018

Background. Oxidative stress could induce cell injury in vascular endothelial cells, which is the initial event in the development of atherosclerosis. Although quantitative real-time polymerase chain reaction (qRT-PCR) has been widely used in gene expression studies in oxidative stress injuries, using carefully validated reference genes has not cause sufficient attention in related researches. The objective of this study, therefore, was to select a set of stably expressed reference genes for use in qRT-PCR normalization in oxidative stress injuries in human umbilical vein endothelial cells (HUVECs) induced by hydrogen peroxide (H2O2).
Methods. HUVECs were treated with different concentrations of H2O2, geNorm and NormFinder software were conducted to evaluate the expression stabilities of 15 candidate reference genes. The optimal number of reference genes needed for qRT-PCR was determined using geNorm.
Results. Using geNorm analysis, we found that five stably expressed reference genes were sufficient for normalization in qRT-PCR analysis in HUVECs treated with H2O2. Genes with the most stable expression according to geNorm were U6 and TFRC, RPLP0, GAPDH and ACTB, and were ALAS1, TFRC, U6, GAPDH, and ACTB according to NormFinder.
Discussion. Taken together, our study demonstrated that the expression stability of reference genes may differ according to the statistical program used. U6, TFRC, RPLP0, GAPDH, and ACTB was the optimal set of reference genes for studies on gene expression with qRT-PCR assays in HUVECs under oxidative stress study.
Cryoelectrolysis - electrolytic processes in a frozen physiological saline medium
Authors: Lugnani Franco , Macchioro Matteo , Rubinsky Boris 
Published: January 2018

Background: Cryoelectrolysis is a new minimally invasive tissue ablation surgical technique that combines the processes of electrolysis and solid/liquid phase transformation (freezing).
Method: Performing a typical cryoelectrolytic ablation protocol in a tissue simulant made of physiological saline gel with a pH dye, we observed several new physical and electrochemical phenomena of relevance to tissue ablation.
Results: We found that electrolysis can occur simultaneously with phase transformation, at high subzero freezing temperatures, above the eutectic temperature of the frozen salt solution. Another interesting finding is that electro-osmotic flows affect the process of cryoelectrolysis at the anode and cathode, in different ways.
Discussion: The observations are consistent with a mechanism involving ionic movement through the concentrated saline solution channels between ice crystals, at subfreezing temperatures above the eutectic. The findings in this paper may become the scientific basis for designing future cryoelectrolytic ablation surgery protocols.
Cryoelectrolysis - electrolytic processes in a frozen physiological saline medium
Authors: Lugnani Franco , Macchioro Matteo , Rubinsky Boris 
Published: January 2018

Background: Cryoelectrolysis is a new minimally invasive tissue ablation surgical technique that combines the ablation techniques of electrolytic ablation with cryosurgery. The goal of this study is to examine the hypothesis that electrolysis can take place in a frozen aqueous saline solution.
Method: To examine the hypothesis we performed a cryoelectrolytic ablation protocol in which electrolysis and cryosurgery are delivered simultaneously in a tissue simulant made of physiological saline gel with a pH dye. We measured current flow, voltage and extents of freezing and pH dye staining.
Results: Using optical measurements and measurements of currents, we have shown that electrolysis can occur in frozen physiological saline, at high subzero freezing temperatures, above the eutectic temperature of the frozen salt solution. It was observed that electrolysis occurs when the tissue resides at high subzero temperatures during the freezing stage and essentially throughout the entire thawing stage. We also found that during thawing, the frozen lesion temperature raises rapidly to high subfreezing values and remains at those values throughout the thawing stage. Substantial electrolysis occurs during the thawing stage. Another interesting finding is that electro-osmotic flows affect the process of cryoelectrolysis at the anode and cathode, in different ways.
Discussion: The results showing that electrical current flow and electrolysis occur in frozen saline solutions imply a mechanism involving ionic movement in the fluid concentrated saline solution channels between ice crystals, at high subfreezing temperatures. Temperatures higher than the eutectic are required for the brine to be fluid. The particular pattern of temperature and electrical currents during the thawing stage of frozen tissue, can be explained by the large amounts of energy that must be removed at the outer edge of the frozen lesion because of the solid/liquid phase transformation on that interface.
Conclusion: Electrolysis can occur in a frozen domain at high subfreezing temperature, probably above the eutectic. It appears that the most effective period for delivering electrolytic currents in cryoelectrolysis is during the high subzero temperatures stage while freezing and immediately after cooling has stopped, throughout the thawing stage.
SNF: Synthesizing high performance NFV service chains
Authors: Katsikas Georgios P , Enguehard Marcel , Kuźniar Maciej , Maguire Jr. Gerald Q , Kostić Dejan 
Published: January 2018

In this paper we introduce SNF, a framework that synthesizes (S) network function (NF) service chains by eliminating redundant I/O and repeated elements, while consolidating stateful cross layer packet operations across the chain. SNF uses graph composition and set theory to determine traffic classes handled by a service chain composed of multiple elements. It then synthesizes each traffic class using a minimal set of new elements that apply single-read-single-write and early-discard operations.
Our SNF prototype takes a baseline state-of-the-art network functions virtualization (NFV) framework to the level of performance required for practical NFV service deployments. Software-based SNF realizes long (up to 10 NFs) and stateful service chains that achieve line-rate 40 Gbps throughput (up to 8.5x greater than the baseline NFV framework). Hardware-assisted SNF, using a commodity OpenFlow switch, shows that our approach scales at 40 Gbps for Internet Service Provider-level NFV deployments.
Are coupled file changes suggestions useful?
Authors: Ramadani Jasmin , Wagner Stefan 
Published: January 2018

Background. Software maintenance is an important activity in the process of software engineering where over time maintenance team members leave and new members join. The identification of files being changes together frequently has been proposed several times. Yet, existing studies about these file changes ignore the feedback from developers as well as the impact on the performance of maintenance and rely on the analysis findings and expert evaluation.
Methods. We conducted an experiment with the goal to investigate the usefulness of coupled file changes during maintenance tasks when developers are inexperienced in programming or when they are new on the project. Using data mining on software repositories we can identify files that changed most frequently together in the past. We extract coupled file changes from the Git repository of a Java software system and join them with corresponding attributes from the versioning and issue tracking system and the project documentation. We present a controlled experiment involving 36 student participants where we investigate if coupled file change suggestions influence the correctness of the task solutions and the time to complete them.
Results. The results show that coupled file change suggestions significantly increase the correctness of the solutions. However, there is only a small effect on the time to complete the tasks. We also derived a set of the most useful attributes based on the developers feedback.
Discussion. Coupled file changes and a limited number of the proposed attributes are useful for inexperienced developers working on maintenance tasks whereby although the developers using these suggestions solved more tasks, they still need time to organize and understand and implement this information.
SED-ML Web Tools: Generate, modify and export standard-compliant simulation studies
Authors: Bergmann Frank T , Nickerson David , Waltemath Dagmar , Scharm Martin 
Published: January 2018

The Simulation Experiment Description Markup Language (SED-ML) is a standardized format for exchanging simulation studies independently of software tools. We present the SED-ML Web Tools, a software that supports SED-ML Level 1 Version 2, including complex modifications and co-simulation of SBML and CellML models. This online application allows for creating, editing, simulating and validating SED-ML documents. It lowers the bar on working with SED-ML documents and helps users create valid simulation descriptions for models in CellML and SBML formats.
Availability and Implementation: sysbioapps.dyndns.org/SED-ML_Web_Tools.
Single exponential decay waveform; a synergistic combination of electroporation and electrolysis (E2) for tissue ablation
Authors: Klein Nina , Guenther Enric , Mikus Paul , Stehling Michael K , Rubinsky Boris 
Published: January 2018

Background: Electrolytic ablation and electroporation based ablation are minimally invasive, non-thermal surgical technologies that employ electrical currents and electric fields to ablate undesirable cells in a volume of tissue. In this study we explore the attributes of a new tissue ablation technology that simultaneously delivers a synergistic combination of electroporation and electrolysis (E2).
Method: A new device that delivers a controlled dose of electroporation field and electrolysis currents in the form of a single exponential decay waveform (EDW), was applied to the pig liver and the effect of various parameters on the extent of tissue ablation was examined with histology.
Results: Histological analysis shows that E2 delivered as EDW can produce tissue ablation in volumes of clinical significance, using electrical and temporal parameters which, if used in electroporation or electrolysis separately, cannot ablate the tissue
Discussion: The E2 combination has advantages over the three basic technologies of non-thermal ablation: electrolytic ablation, electrochemical ablation (reversible electroporation with injection of drugs) and irreversible electroporation. E2 ablates clinically relevant volumes of tissue in a shorter period of time than electrolysis and electroporation, without the need to inject drugs as in reversible electroporation or use paralyzing anesthesia as in irreversible electroporation.
A new correlation of the Cretaceous formations of the Western Interior of the United States, I: Santonian-Maastrichtian formations and dinosaur biostratigraphy
Authors: Fowler Denver W 
Published: January 2018

Late Cretaceous deposits of the North American Western Interior represent the best, if not only, opportunity to construct a high-resolution chronostratigraphic framework within which to conduct continental-scale geological and paleontological analyses. This is due to the serendipitous combination of large areas of outcrop, interfingering marine units with biostratigraphically informative fossils, and a consistent scattering of radiometric dates due to synorogenic volcanic activity. Accurate correlation is essential for testing a large number of current geological and paleobiological hypotheses; however, despite the large amount of data available, many published correlations suffer from inaccuracies or are simply based on outdated information.
Here I present a comprehensive high-resolution stratigraphic chart for terrestrial Late Cretaceous units of North America, combining published chronostratigraphic, lithostratigraphic, and biostratigraphic data. For the first time, nearly two hundred 40Ar / 39Ar radiometric dates are recalibrated to both current standard and decay constant pairings, correcting errors in previous recalibrations. Revisions to the stratigraphic placement of most units are slight, but important changes are made to the proposed correlations of the Aguja and Javelina Formations, Texas, and miscalculations in recently published analyses are corrected which in particular affects the relative age positions of the Belly River Group, Alberta; Judith River Group, Montana, Kaiparowits Formation, Utah, and Fruitland and Kirtland Formations, New Mexico.
This work represents the most extensive and accurate interbasinal correlation currently available for the North American Western Interior and should replace all previously published similar works and diagrams.
The stratigraphic ranges of selected dinosaur clades are plotted on the chronostratigraphic framework, typically forming stacks of short-duration species which do not overlap stratigraphically with preceding or succeeding forms. This is the expected pattern which is produced by an anagenetic mode of evolution, suggesting that true branching (speciation) events were rare and may have geographic significance. Purported north-south provinciality of dinosaurs is shown to be mostly an artifact of stratigraphic miscorrelation. Rapid stepwise acquisition of display characters in many dinosaur clades, in particular chasmosaurine ceratopsids, suggests that they may represent the highest resolution biostratigraphic markers to be used where radiometric dates are not available.
Revised geochronology, correlation, and dinosaur stratigraphic ranges of the Santonian-Maastrichtian (Late Cretaceous) formations of the Western Interior of North America
Authors: Fowler Denver W 
Published: January 2018

Interbasinal stratigraphic correlation provides the foundation for all consequent continental-scale geological and paleontological analyses. Correlation requires synthesis of lithostratigraphic, biostratigraphic and geochronologic data, and must be periodically updated to accord with advances in dating techniques, changing standards for radiometric dates, new stratigraphic concepts, hypotheses, fossil specimens, and field data. Outdated or incorrect correlation exposes geological and paleontological analyses to potential error.
The current work presents a high-resolution stratigraphic chart for terrestrial Late Cretaceous units of North America, combining published chronostratigraphic, lithostratigraphic, and biostratigraphic data. 40Ar / 39Ar radiometric dates are newly recalibrated to both current standard and decay constant pairings. Revisions to the stratigraphic placement of most units are slight, but important changes are made to the proposed correlations of the Aguja and Javelina Formations, Texas, and recalibration corrections in particular affect the relative age positions of the Belly River Group, Alberta; Judith River Formation, Montana; Kaiparowits Formation, Utah; and Fruitland and Kirtland formations, New Mexico.
The stratigraphic ranges of selected clades of dinosaur species are plotted on the chronostratigraphic framework, with some clades comprising short-duration species that do not overlap stratigraphically with preceding or succeeding forms. This is the expected pattern that is produced by an anagenetic mode of evolution, suggesting that true branching (speciation) events were rare and may have geographic significance. The recent hypothesis of intracontinental latitudinal provinciality of dinosaurs is shown to be affected by previous stratigraphic miscorrelation. Rapid stepwise acquisition of display characters in many dinosaur clades, in particular chasmosaurine ceratopsids, suggests that they may be useful for high resolution biostratigraphy.
Sorting things out - assessing effects of unequal specimen biomass on DNA metabarcoding
Authors: Elbrecht Vasco , Peinert Bianca , Leese Florian 
Published: January 2018

1) Environmental bulk samples often contain many taxa with biomass differences of several orders of magnitude. This can be problematic in DNA metabarcoding and metagenomic high throughput sequencing approaches, as large specimens contribute over proportionally much DNA template. Thus a few specimens of high biomass will dominate the dataset, potentially leading to smaller specimens remaining undetected. Sorting of samples and balancing the amounts of tissue used per size fraction should improve detection rates, but has not been systematically tested.
2) Here we tested the effects of size sorting on taxa detection using freshwater macroinvertebrates. Kick sampling was performed at two locations of a low-mountain stream in West Germany, specimens were morphologically identified and sorted into small, medium and large size classes (< 2.5x5, 5x10 and up to 10x20 mm). Tissue from the 3 size categories was extracted individually, and pooled to simulate bulk samples that were not sorted and samples which were sorted and then pooled proportionately by specimen size. DNA from all 5 extractions of both samples was amplified using 4 different freshwater primer sets for the COI gene and sequenced on a HiSeq Illumina sequencer.
3) Sorting taxa by size and pooling them proportionately according to their abundance lead to a more equal amplification compared to the processing of complete samples without sorting. The sorted samples recovered 30% more taxa than the unsorted samples, at the same sequencing depth. Our results imply that sequencing depth can be decreased ~ 5 fold when sorting the samples into three size classes.
4) Our results demonstrate that even a coarse size sorting can substantially improve detection rates. While high throughput sequencing will become more accessible and cheaper within the next years, sorting bulk samples by specimen biomass is a simple yet efficient method to reduce current sequencing costs.
Quantitative and correlation analysis of the DNA methylation and expression of DAPK in breast cancer
Authors: Zhu Youzhi , Li Shuiqin , Wang Qingshui , Chen Ling , Wu Kunlin , Huang Yide , Chen Xiangjin , Lin Yao 
Published: January 2018

Backgound. Death associated protein kinase 1 (DAPK) is an important tumor suppressor kinase involved in the regulation of multiple cellular activities such as apoptosis and autophagy. DNA methylation of DAPK gene was found in various types of cancers and often correlated with the clinicopathological characteristics. However, the mRNA and protein expression of DAPK in the same sample was rarely measured. Thus it was unclear if the correlation between DAPK gene methylation and clinicopathological parameters was due to the loss of DAPK expression.
Methods. In this study, the DNA methylation rate, mRNA and protein expression of DAPK was quantitatively detected in 15 pairs of breast cancer patient samples including tumor (T) and adjacent non-tumor (N) tissues. Results. The correlation between DNA methylation rate and mRNA expression, together with the correlation between mRNA and protein expression, was calculated. No correlation was observed between any levels using either the measurement value of each sample or the T/N ratio of each pair.
Discussion. These data suggested the DNA methylation status of DAPK did not correlate well with its mRNA or protein expression. Extra caution is needed when interpreting the DNA methylation data of DAPK gene in clinical studies.
Doctor safety in Australian after-hours house-call medical services: the use of chaperones and chauffeurs
Authors: Ifediora Chris Onyebuchi 
Published: January 2018

Objectives: The use of escorts (chauffeurs and chaperones) while on duty in after-hours-house-call (AHHC) is one key protective option available to doctors in the service and has been linked to low burnout and increased satisfaction in AHHC. This study aims to explore the patterns of engagement of escorts in Australian AHHC.
Method: A questionnaire-based, electronic survey of all 300 doctors involved in AHHC through the National Home Doctor Service (NHDS), Australia’s largest providers of the service.
Results: A total of 168 valid responses (56.0%) were received. 60.8% of the doctors engaged escorts. Of the doctors that engage chauffeurs, three-quarters do so “all or most times”, while only one-quarter engage chaperones to the same degree of frequency. Hiring escorts is very popular among Brisbane (91.7%) and Sydney-based (88.2%) practitioners, but is unpopular in the City of Gold Coast (26.1%). There were moderate patronages in Adelaide (52.9%) and Melbourne (46.4%).
Compared to females, males were more likely to drive themselves (OR 5.34; P=0.001; CI 2.08 to 13.74) and less likely to use chauffeurs (OR 0.19; p<0.001; CI 0.07 to 0.51). Doctors in legally recognized social unions (OR 0.24; p=0.03; CI 0.07 to 0.83) and those that have attained the postgraduate fellowships (OR 0.43; p=0.02; CI 0.21 to 0.87) were both less likely to work without escorts.
Conclusion: More needs to be done to increase the engagement of escorts by doctors involved in the Australian AHHC, particularly given their proven benefits in the service. Future studies may be needed to fully explore the real reasons behind the significant associations identified in this study.