bluuebunny/crossref_metadata_2025 huggingface dataset:
The effects of eye movements and alternative dual tasks on the vividness and emotionality of negative autobiographical memories: A meta-analysis of laboratory studies
Authors: Houben Sanne T. L. , Otgaar Henry , Roelofs Jeffrey , Merckelbach Harald , Muris Peter
Published: March 2020

Performing eye movements during memory retrieval is considered to be important for the therapeutic effect of eye movement desensitization and reprocessing (EMDR). We conducted a meta-analysis of laboratory studies that compared the effects of eye movements and/or alternative dual tasks (e.g., counting) on the vividness and emotionality of negative autobiographical memories with recall only (control) conditions. The databases PsycINFO and Web of Science were queried. Fifteen studies that involved 942 participants were included. Eye movements and alternative dual tasks produced similar vividness and emotionality decreases, with the impact on vividness being strong than that on emotionality. However, eye movements yielded a stronger overall vividness reduction than alternative dual tasks, although the associated effect size was small (Cohen’s d = .29). Because eye movements and alternative dual tasks produced comparable effects, one might conclude that both tasks are therapeutic equivalents. However, it should be acknowledged that only a limited number of laboratory studies were included in our meta-analysis, and the degree to which both procedures tax working memory was not independently established. Although our conclusion cannot be generalized to clinical practice, it does raise questions about the mode of action of EMDR.
Into the Prodrome: Diagnosis, Disadvantage, and Biomedical Ambiguity
Authors: Halpin Michael Allan
Published: March 2020

Within the field of neuroscience, a new illness stage called the “prodrome” is being characterized. The prodrome is a symptomatic period that precedes an official diagnosis. Huntington Disease (HD) is a neuropsychiatric disorder that has an extensively researched prodrome marked by psychiatric and cognitive symptoms. This paper provides a sociological investigation of the prodrome by analyzing 24 interviews with individuals with HD and 14 interviews with informal caregivers. I find that substantial disadvantages accompany the prodromal phase of HD, with the prodrome connected to: (1) inability to access healthcare, (2) inability to access health resources, (3) the depletion of personal resources, and (4) caregiver burden. Documentation of such disadvantages is important as prodromal phases are connected to a growing number of conditions. Study findings are discussed in relation to medicalization, as well as the tension between medical ambiguity and the organization of health institutions.
A comparative study of innovative percutaneous repair and open repair for acute Achilles tendon rupture: Innovative usage of intraoperative ultrasonography
Authors: Lee Jeong-Kil , Kang Chan , Hwang Deuk-Soo , Kang Dong-Hun , Lee Gi-Soo , Hwang Jung-Mo , Song Jae-Hwang , Lee Cheol-Won
Published: March 2020

Purpose:

There is no definitive consensus on the optimal treatment of Achilles tendon rupture. We comparatively analyzed the clinical outcomes of two types of repair surgeries in treating Achilles tendon rupture.

Methods:

This retrospective study included 12 patients of Achilles tendon rupture (group A) treated with ultrasound-guided percutaneous repair and 18 patients (group B) treated with open repair. Clinical evaluation was performed using the Arner–Lindholm scale, American Orthopedic Foot and Ankle Society (AOFAS) ankle–hindfoot score, Achilles Tendon Total Rupture score (ATRS), visual analog scale, time to single heel raise, bilateral calf circumferences, recovery of athletic ability, and other complications.

Results:

While the Arner–Lindholm scale, AOFAS ankle–hindfoot score, ATRS, time point when single heel raise was possible, differences in bilateral calf circumference, and recovery of athletic ability compared to pre-rupture level were not significantly different between the two groups (p = 0.999, 0.235, 0.357, 0.645, 0.497, and 0.881, respectively), overall and aesthetic satisfaction levels were higher in the group treated with percutaneous repair under ultrasonography guidance (p = 0.035 and 0.001, respectively). Overall, there were no cases involving sural nerve injury in either group.

Conclusion:

Innovative percutaneous repair provides not only similar clinical outcomes but also greater overall and aesthetic satisfaction levels of operative outcomes and minimal complications (i.e. sural nerve injury) compared to open repair surgeries. Therefore, percutaneous repair may be a useful technique in the treatment of Achilles tendon rupture.
Automated Tool for Health Utility Assessments: The Gambler II
Authors: Adejare Adeboye A. , Eckman Mark H.
Published: March 2020

Background. The Gambler II is a web-based utility assessment tool supporting visual analogue scale (VAS), standard gamble (SG), and time trade-off (TTO) utility assessments. It contains novel features, including an easy to use project development authoring tool and use of multimedia clips for health state descriptions. Objectives. Evaluate the usability and understandability of the patient-facing side of The Gambler. Investigate the feasibility of using The Gambler and evaluate its impact on patient knowledge regarding the relevant health states. Materials and Methods. We used The Gambler to assess utilities on a convenience sample of 55 users for common long-term complications of type 2 diabetes mellitus: diabetic neuropathy, diabetic retinopathy, and diabetic foot infection requiring transmetatarsal amputation. Using VAS, SG, and TTO, we collected metadata, such as time spent on each assessment and the entire assessment process. We evaluated usability with an adaptation of the System Usability Scale survey and understandability. We evaluated impact on knowledge gained through knowledge assessments about these complications before and after use of The Gambler. Results. Overall satisfaction with The Gambler was high, 4.02 on a 5-point scale. Usability rated highly at 84.93 on a normalized scale between 0 and 100. Knowledge scores increased significantly following use of The Gambler from pretest mean of 68% to posttest mean of 76% ( P < 0.01). Average time using the software: ∼7½ minutes. Conclusions. The Gambler is an easy to use and understand computer-based tool for utility assessment. It is feasible to use within clinical encounters to support shared decision making, and it has unique features that make it a powerful tool for investigators interested in research on health utilities.
Infrastructuring “data-driven” environmental governance in Louisiana’s coastal restoration plan
Authors: Nost Eric
Published: March 2020

Conservationists around the world advocate for “data-driven” environmental governance, expecting data infrastructures to make all relevant and actionable information readily available. But how exactly is data to be infrastructured and to what political effect? I show how putting together and maintaining environmental data for decision-making is not a straightforward technical task, but a practice shaped by and shaping politico-economic context. Drawing from the US state of Louisiana’s coastal restoration planning process, I detail two ways ecosystem modelers manage fiscal and institutional “frictions” to “infrastructuring” data as a resource for decision-making. First, these experts work with the data they have. They leverage, tweak, and maintain existing datasets and tools, spending time and money to gather additional data only to the extent it fits existing goals. The assumption is that these goals will continue to be important, but building coastal data infrastructure around current research needs, plans, and austerity arguably limits what can be said in and done with the future. Second, modelers acquire the data they made to need. Coastal communities have protested the state’s primary restoration tool: diversions of sediment from the Mississippi River. Planners reacted by relaxing institutional constraints and modelers brought together new data to highlight possible winners and losers from ecological restoration. Fishers and other coastal residents leveraged greater dissent in the planning process. Political ecologists show that technocentric environmental governance tends to foreclose dissent from hegemonic socioecological futures. I argue we can clarify the conditions in which this tends to happen by following how experts manage data frictions. As some conservationists and planners double down on driving with data in a “post-truth” world, I find that data’s politicizing effects stem from what is asked of it, not whether it is “big” or “drives.”
Enhanced thermal and electrical properties of epoxy/carbon fiber–silicon carbide composites
Authors: Kareem Aseel A
Published: March 2020

The silicon carbide/carbon fiber (SiC/CF) hybrid fillers were introduced to improve the electrical and thermal conductivities of the epoxy resin composites. Results of Fourier transform infrared spectroscopy revealed that the peaks at 3532 and 2850 cm−1 relate to carboxylic acid O–H stretching and aldehyde C–H stretching appearing deeper with an increased volume fraction of SiC. Scanning electron microscopic image shows a better interface bonding between the fiber and the matrix when the volume fraction of SiC particles are increased. As frequency increases from 102 Hz to 106 Hz, dielectric constants decrease slightly. Dissipation factor (tan δ) values keep low and almost constant from 102 Hz to 104 Hz, has a slight increase after 104 Hz, and obtain relaxation peaks approximately between 105 and 106 Hz. A sharp increase in dielectric constant and dissipation factors is observed in epoxy (Ep)/CF composites with 30 vol.% of SiC. The increase in electrical conductivity of composites may result from the increased chain ordering by annealing effect. The electrical conductivities of the Ep/CF composites are decreasing with the increasing volume fraction of SiC. It is attributed to the introduction of insulating SiC. The glass transition temperature ( T g) of the Ep/CF-30 vol.% SiC composite was 352 C, which was higher than other composites. The decomposition temperature at 5% weight loss, decomposition temperature at 10% weight loss, and maximum decomposition temperature of the Ep/CF-30 vol.% SiC composite were about 389.5°C, 410.7°C, and 591°C, respectively, and were higher than pure epoxy and other composites. A higher thermal conductivity of 1.86 W (m K)−1 could be achieved with 30 vol.% SiC/CF hybrid fillers, which is about nine times higher than that of native epoxy resin of 0.202 W (m.K)−1.
Targeted sequencing in DLBCL, molecular subtypes, and outcomes: a Haematological Malignancy Research Network report
Authors: Lacy Stuart E. , Barrans Sharon L. , Beer Philip A. , Painter Daniel , Smith Alexandra G. , Roman Eve , Cooke Susanna L. , Ruiz Camilo , Glover Paul , Van Hoppe Suzan J. L. , Webster Nichola , Campbell Peter J. , Tooze Reuben M. , Patmore Russell , Burton Cathy , Crouch Simon , Hodson Daniel J.
Published: March 2020

Based on the profile of genetic alterations occurring in tumor samples from selected diffuse large B-cell lymphoma (DLBCL) patients, 2 recent whole-exome sequencing studies proposed partially overlapping classification systems. Using clustering techniques applied to targeted sequencing data derived from a large unselected population-based patient cohort with full clinical follow-up (n = 928), we investigated whether molecular subtypes can be robustly identified using methods potentially applicable in routine clinical practice. DNA extracted from DLBCL tumors diagnosed in patients residing in a catchment population of ∼4 million (14 centers) were sequenced with a targeted 293-gene hematological-malignancy panel. Bernoulli mixture-model clustering was applied and the resulting subtypes analyzed in relation to their clinical characteristics and outcomes. Five molecular subtypes were resolved, termed MYD88, BCL2, SOCS1/SGK1, TET2/SGK1, and NOTCH2, along with an unclassified group. The subtypes characterized by genetic alterations of BCL2, NOTCH2, and MYD88 recapitulated recent studies showing good, intermediate, and poor prognosis, respectively. The SOCS1/SGK1 subtype showed biological overlap with primary mediastinal B-cell lymphoma and conferred excellent prognosis. Although not identified as a distinct cluster, NOTCH1 mutation was associated with poor prognosis. The impact of TP53 mutation varied with genomic subtypes, conferring no effect in the NOTCH2 subtype and poor prognosis in the MYD88 subtype. Our findings confirm the existence of molecular subtypes of DLBCL, providing evidence that genomic tests have prognostic significance in non-selected DLBCL patients. The identification of both good and poor risk subtypes in patients treated with R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone) clearly show the clinical value of the approach, confirming the need for a consensus classification.
YWHAE/14-3-3ε expression impacts the protein load, contributing to proteasome inhibitor sensitivity in multiple myeloma
Authors: Xu Yan , Fulciniti Mariateresa , Samur Mehmet K. , Ho Matthew , Deng Shuhui , Liu Lanting , Wen Kenneth , Yu Tengteng , Chyra Zuzana , Dereibal Sanika , Zhang Li , Yao Yao , Chakraborty Chandraditya , Morelli Eugenio , Li Na , Lopez Michael A. , Perini Tommaso , Mu Shidai , An Gang , Alonso Rafael , Bianchi Giada , Tai Yu-Tzu , Anderson Kenneth C. , Qiu Lugui , Munshi Nikhil C.
Published: March 2020

High protein load is a feature of multiple myeloma (MM), making the disease exquisitely sensitive to proteasome inhibitor (PIs). Despite the success of PIs in improving patient outcome, the majority of patients develop resistance leading to progressive disease; thus, the need to investigate the mechanisms driving the drug sensitivity vs resistance. With the well-recognized chaperone function of 14-3-3 proteins, we evaluated their role in affecting proteasome activity and sensitivity to PIs by correlating expression of individual 14-3-3 gene and their sensitivity to PIs (bortezomib and carfilzomib) across a large panel of MM cell lines. We observed a significant positive correlation between 14-3-3ε expression and PI response in addition to a role for 14-3-3ε in promoting translation initiation and protein synthesis in MM cells through binding and inhibition of the TSC1/TSC2 complex, as well as directly interacting with and promoting phosphorylation of mTORC1. 14-3-3ε depletion caused up to a 50% reduction in protein synthesis, including a decrease in the intracellular abundance and secretion of the light chains in MM cells, whereas 14-3-3ε overexpression or addback in knockout cells resulted in a marked upregulation of protein synthesis and protein load. Importantly, the correlation among 14-3-3ε expression, PI sensitivity, and protein load was observed in primary MM cells from 2 independent data sets, and its lower expression was associated with poor outcome in patients with MM receiving a bortezomib-based therapy. Altogether, these observations suggest that 14-3-3ε is a predictor of clinical outcome and may serve as a potential target to modulate PI sensitivity in MM.
Crucial role for lung iron level and regulation in the pathogenesis and severity of asthma
Authors: Ali Md. Khadem , Kim Richard Y. , Brown Alexandra C. , Mayall Jemma R. , Karim Rafia , Pinkerton James W. , Liu Gang , Martin Kristy L. , Starkey Malcolm R. , Pillar Amber L. , Donovan Chantal , Pathinayake Prabuddha S. , Carroll Olivia R. , Trinder Debbie , Tay Hock L. , Badi Yusef E. , Kermani Nazanin Z. , Guo Yi-Ke , Aryal Ritambhara , Mumby Sharon , Pavlidis Stelios , Adcock Ian M. , Weaver Jessica , Xenaki Dikaia , Oliver Brian G. , Holliday Elizabeth G. , Foster Paul S. , Wark Peter A. , Johnstone Daniel M. , Milward Elizabeth A. , Hansbro Philip M. , Horvat Jay C.
Published: March 2020

Accumulating evidence highlights links between iron regulation and respiratory disease. Here, we assessed the relationship between iron levels and regulatory responses in clinical and experimental asthma.

We show that cell-free iron levels are reduced in the bronchoalveolar lavage (BAL) supernatant of severe or mild–moderate asthma patients and correlate with lower forced expiratory volume in 1 s (FEV1). Conversely, iron-loaded cell numbers were increased in BAL in these patients and with lower FEV1/forced vital capacity (FVC) ratio. The airway tissue expression of the iron sequestration molecules divalent metal transporter 1 (DMT1) and transferrin receptor 1 (TFR1) are increased in asthma, withTFR1expression correlating with reduced lung function and increased Type-2 (T2) inflammatory responses in the airways. Furthermore, pulmonary iron levels are increased in a house dust mite (HDM)-induced model of experimental asthma in association with augmentedTfr1expression in airway tissue, similar to human disease. We show that macrophages are the predominant source of increased Tfr1 and Tfr1+macrophages have increasedIl13expression. We also show that increased iron levels induce increased pro-inflammatory cytokine and/or extracellular matrix (ECM) responses in human airway smooth muscle (ASM) cells and fibroblastsex vivoand induce key features of asthmain vivo, including airway hyper-responsiveness (AHR) and fibrosis, and T2 inflammatory responses.

Together these complementary clinical and experimental data highlight the importance of altered pulmonary iron levels and regulation in asthma, and the need for a greater focus on the role and potential therapeutic targeting of iron in the pathogenesis and severity of disease.
Energy efficiency trade-offs in small to large electric vehicles
Authors: Weiss Martin , Cloos Kira Christina , Helmers Eckard
Published: March 2020

Background

As electric kick scooters, three-wheelers, and passenger cars enter the streets, efficiency trade-offs across vehicle types gain practical relevance for consumers and policy makers. Here, we compile a comprehensive dataset of 428 electric vehicles, including seven vehicle types and information on certified and real-world energy consumption. Regression analysis is applied to quantify trade-offs between energy consumption and other vehicle attributes.

Results

Certified and real-world energy consumption of electric vehicles increase by 60% and 40%, respectively, with each doubling of vehicle mass, but only by 5% with each doubling of rated motor power. These findings hold roughly also for passenger cars whose energy consumption tends to increase 0.6 ± 0.1 kWh/100 km with each 100 kg of vehicle mass. Battery capacity and vehicle mass are closely related. A 10 kWh increase in battery capacity increases the mass of electric cars by 15 kg, their drive range by 40–50 km, and their energy consumption by 0.7–1.0 kWh/100 km. Mass-produced state-of-the-art electric passenger cars are 2.1 ± 0.8 kWh/100 km more efficient than first-generation vehicles, produced at small scale.

Conclusion

Efficiency trade-offs in electric vehicles differ from those in conventional cars—the latter showing a strong dependency of fuel consumption on rated engine power. Mass-related efficiency trade-offs in electric vehicles are large and could be tapped by stimulating mode shift from passenger cars to light electric road vehicles. Electric passenger cars still offer potentials for further efficiency improvements. These could be exploited through a dedicated energy label with battery capacity as utility parameter.
Fish biomarkers from a different perspective: evidence of adaptive strategy of Abramis brama (L.) to chemical stress
Authors: Tenji Dina , Micic Bojana , Sipos Sandor , Miljanovic Branko , Teodorovic Ivana , Kaisarevic Sonja
Published: March 2020

Background

A prerequisite for long-term survival of populations under multi-stress conditions is their capacity to set up efficient adaptive strategies. However, changes in the activity of molecular biomarkers have been for decades considered as early signals of the deterioration of the fish health and evidence of stress-related adverse biological effects. The aim of this study was to show that such changes actually represent adaptive response of fish to chemical stress. Gene expression and enzyme activity level in liver and brain of specimens from two populations of Abramis brama from contrasted habitats (nature reserve and urban) were examined. Selected parameters included biomarkers of general stress, antioxidative defence, xenobiotic metabolism, endocrine disruption, glucose homeostasis, iron homeostasis, and neurotoxicity.

Results

Exposure of A. brama population from urban area to chemical stress was confirmed by assessment of chronic toxic pressure at fish habitats using Toxic Unit approach. The most pronounced response to chemical stress is observed through the activation of antioxidative defence mechanisms in brain and liver at gene and enzyme activity level, high biotransformation capacity of liver, and activation of mechanisms that will meet energy demands and compensate for the metabolic costs of the response to toxicants (higher expression of genes related to glucose homeostasis in the exposed population). Higher hepatosomatic index in the exposed population implies liver hypertrophy due to increased functional load caused by pollution. Body condition factors indicate good overall condition of both fish populations and confirm high efficacy of mobilized adaptation mechanisms in the exposed population.

Conclusions

The study provided the first data on basal expression of a number of genes in A. brama, potentially valuable for biomonitoring studies in absence of clear pollution gradient and/or reference sites (conditions). The study highlights importance of newly identified roles of various genes and proteins, typically considered as biomarkers of effects, and shows that changes in these parameters do not necessarily indicate the deterioration of the fish health. Such changes should be considered as adaptive response to chemical stress, rather than direct proof of ecological impact of pollution in situ.
PESM: predicting the essentiality of miRNAs based on gradient boosting machines and sequences
Authors: Yan Cheng , Wu Fang-Xiang , Wang Jianxin , Duan Guihua
Published: March 2020

Background

MicroRNAs (miRNAs) are a kind of small noncoding RNA molecules that are direct posttranscriptional regulations of mRNA targets. Studies have indicated that miRNAs play key roles in complex diseases by taking part in many biological processes, such as cell growth, cell death and so on. Therefore, in order to improve the effectiveness of disease diagnosis and treatment, it is appealing to develop advanced computational methods for predicting the essentiality of miRNAs.

Result

In this study, we propose a method (PESM) to predict the miRNA essentiality based on gradient boosting machines and miRNA sequences. First, PESM extracts the sequence and structural features of miRNAs. Then it uses gradient boosting machines to predict the essentiality of miRNAs. We conduct the 5-fold cross-validation to assess the prediction performance of our method. The area under the receiver operating characteristic curve (AUC), F-measure and accuracy (ACC) are used as the metrics to evaluate the prediction performance. We also compare PESM with other three competing methods which include miES, Gaussian Naive Bayes and Support Vector Machine.

Conclusion

The results of experiments show that PESM achieves the better prediction performance (AUC: 0.9117, F-measure: 0.8572, ACC: 0.8516) than other three computing methods. In addition, the relative importance of all features also further shows that newly added features can be helpful to improve the prediction performance of methods.
LCQS: an efficient lossless compression tool of quality scores with random access functionality
Authors: Fu Jiabing , Ke Bixin , Dong Shoubin
Published: March 2020

Background

Advanced sequencing machines dramatically speed up the generation of genomic data, which makes the demand of efficient compression of sequencing data extremely urgent and significant. As the most difficult part of the standard sequencing data format FASTQ, compression of the quality score has become a conundrum in the development of FASTQ compression. Existing lossless compressors of quality scores mainly utilize specific patterns generated by specific sequencer and complex context modeling techniques to solve the problem of low compression ratio. However, the main drawbacks of these compressors are the problem of weak robustness which means unstable or even unavailable results of sequencing files and the problem of slow compression speed. Meanwhile, some compressors attempt to construct a fine-grained index structure to solve the problem of slow random access decompression speed. However, they solve the problem at the sacrifice of compression speed and at the expense of large index files, which makes them inefficient and impractical. Therefore, an efficient lossless compressor of quality scores with strong robustness, high compression ratio, fast compression and random access decompression speed is urgently needed and of great significance.

Results

In this paper, based on the idea of maximizing the use of hardware resources, LCQS, a lossless compression tool specialized for quality scores, was proposed. It consists of four sequential processing steps: partitioning, indexing, packing and parallelizing. Experimental results reveal that LCQS outperforms all the other state-of-the-art compressors on all criteria except for the compression speed on the dataset SRR1284073. Furthermore, LCQS presents strong robustness on all the test datasets, with its acceleration ratios of compression speed increasing by up to 29.1x, its file size reducing by up to 28.78%, and its random access decompression speed increasing by up to 2.1x. Additionally, LCQS also exhibits strong scalability. That is, the compression speed increases almost linearly as the size of input dataset increases.

Conclusion

The ability to handle all different kinds of quality scores and superiority in compression ratio and compression speed make LCQS a high-efficient and advanced lossless quality score compressor, along with its strength of fast random access decompression. Our tool LCQS can be downloaded from https://github.com/SCUT-CCNL/LCQSand freely available for non-commercial usage.
A deep learning-based framework for lung cancer survival analysis with biomarker interpretation
Authors: Cui Lei , Li Hansheng , Hui Wenli , Chen Sitong , Yang Lin , Kang Yuxin , Bo Qirong , Feng Jun
Published: March 2020

Background

Lung cancer is the leading cause of cancer-related deaths in both men and women in the United States, and it has a much lower five-year survival rate than many other cancers. Accurate survival analysis is urgently needed for better disease diagnosis and treatment management.

Results

In this work, we propose a survival analysis system that takes advantage of recently emerging deep learning techniques. The proposed system consists of three major components. 1) The first component is an end-to-end cellular feature learning module using a deep neural network with global average pooling. The learned cellular representations encode high-level biologically relevant information without requiring individual cell segmentation, which is aggregated into patient-level feature vectors by using a locality-constrained linear coding (LLC)-based bag of words (BoW) encoding algorithm. 2) The second component is a Cox proportional hazards model with an elastic net penalty for robust feature selection and survival analysis. 3) The third commponent is a biomarker interpretation module that can help localize the image regions that contribute to the survival model’s decision. Extensive experiments show that the proposed survival model has excellent predictive power for a public (i.e., The Cancer Genome Atlas) lung cancer dataset in terms of two commonly used metrics: log-rank test (p-value) of the Kaplan-Meier estimate and concordance index (c-index).

Conclusions

In this work, we have proposed a segmentation-free survival analysis system that takes advantage of the recently emerging deep learning framework and well-studied survival analysis methods such as the Cox proportional hazards model. In addition, we provide an approach to visualize the discovered biomarkers, which can serve as concrete evidence supporting the survival model’s decision.
RASflow: an RNA-Seq analysis workflow with Snakemake
Authors: Zhang Xiaokang , Jonassen Inge
Published: March 2020

Background

With the cost of DNA sequencing decreasing, increasing amounts of RNA-Seq data are being generated giving novel insight into gene expression and regulation. Prior to analysis of gene expression, the RNA-Seq data has to be processed through a number of steps resulting in a quantification of expression of each gene/transcript in each of the analyzed samples. A number of workflows are available to help researchers perform these steps on their own data, or on public data to take advantage of novel software or reference data in data re-analysis. However, many of the existing workflows are limited to specific types of studies. We therefore aimed to develop a maximally general workflow, applicable to a wide range of data and analysis approaches and at the same time support research on both model and non-model organisms. Furthermore, we aimed to make the workflow usable also for users with limited programming skills.

Results

Utilizing the workflow management system Snakemake and the package management system Conda, we have developed a modular, flexible and user-friendly RNA-Seq analysis workflow: RNA-Seq Analysis Snakemake Workflow (RASflow). Utilizing Snakemake and Conda alleviates challenges with library dependencies and version conflicts and also supports reproducibility. To be applicable for a wide variety of applications, RASflow supports the mapping of reads to both genomic and transcriptomic assemblies. RASflow has a broad range of potential users: it can be applied by researchers interested in any organism and since it requires no programming skills, it can be used by researchers with different backgrounds. The source code of RASflow is available on GitHub: https://github.com/zhxiaokang/RASflow.

Conclusions

RASflow is a simple and reliable RNA-Seq analysis workflow covering many use cases.
SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework
Authors: Lewinski Martin , Bramkamp Yannik , Köster Tino , Staiger Dorothee
Published: March 2020

Background

RNA-binding proteins interact with their target RNAs at specific sites. These binding sites can be determined genome-wide through individual nucleotide resolution crosslinking immunoprecipitation (iCLIP). Subsequently, the binding sites have to be visualized. So far, no visualization tool exists that is easily accessible but also supports restricted access so that data can be shared among collaborators.

Results

Here we present SEQing, a customizable interactive dashboard to visualize crosslink sites on target genes of RNA-binding proteins that have been obtained by iCLIP. Moreover, SEQing supports RNA-seq data that can be displayed in a different window tab. This allows, e.g. crossreferencing the iCLIP data with genes differentially expressed in mutants of the RBP and thus obtain some insights into a potential functional relevance of the binding sites. Additionally, detailed information on the target genes can be incorporated in another tab.

Conclusion

SEQing is written in Python3 and runs on Linux. The web-based access makes iCLIP data easily accessible, even with mobile devices. SEQing is customizable in many ways and has also the option to be secured by a password. The source code is available at https://github.com/malewins/SEQing.
Modeling methylation dynamics with simultaneous changes in CpG islands
Authors: Grosser Konrad , Metzler Dirk
Published: March 2020

Background

In vertebrate genomes, CpG sites can be clustered into CpG islands, and the amount of methylation in a CpG island can change due to gene regulation processes. Thus, single regulatory events can simultaneously change the methylation states of many CpG sites within a CpG island. This should be taken into account when quantifying the amount of change in methylation, for example in form of a branch length in a phylogeny of cell types.

Results

We propose a probabilistic model (the IWE-SSE model) of methylation dynamics that accounts for simultaneous methylation changes in multiple CpG sites belonging to the same CpG island. We further propose a Markov-chain Monte-Carlo (MCMC) method to fit this model to methylation data from cell type phylogenies and apply this method to available data from murine haematopoietic cells and from human cell lines. Combined with simulation studies, these analyses show that accounting for CpG island wide methylation changes has a strong effect on the inferred branch lengths and leads to a significantly better model fit for the methylation data from murine haematopoietic cells and human cell lines.

Conclusion

The MCMC based parameter estimation method for the IWE-SSE model in combination with our MCMC based inference method allows to quantify the amount of methylation changes at single CpG sites as well as on entire CpG islands. Accounting for changes affecting entire islands can lead to more accurate branch length estimation in the presence of simultaneous methylation change.
Correction to: Binding of Brucella protein, Bp26, to select extracellular matrix molecules
Authors: ElTahir Yasmin , Al-Araimi Amna , Nair Remya R. , Autio Kaija J. , Tu Hongmin , Leo Jack C. , Al-Marzooqi Waleed , Johnson Eugene H.
Published: March 2020

Following publication of the original article [1], an error was reported in the tagging of Eugene H. Johnson and Remya R. Nair in the author group.
Complex patterns of reticulate evolution in opportunistic weeds (Potentilla L., Rosaceae), as revealed by low-copy nuclear markers
Authors: Persson Nannie L. , Eriksson Torsten , Smedmark Jenny E. E.
Published: March 2020

Background

Most cinquefoils (Potentilla L., Rosaceae) are polyploids, ranging from tetraploid (4x) to dodecaploid (12x), diploids being a rare exception. Previous studies based on ribosomal and chloroplast data indicated that Norwegian cinquefoil (P. norvegica L.) has genetic material from two separate clades within Potentilla; the Argentea and the Ivesioid clades – and thus a possible history of hybridization and polyploidization (allopolyploidy). In order to trace the putative allopolyploid origin of the species, sequence data from low-copy, biparentally inherited, nuclear markers were used. Specimens covering the circumpolar distribution of P. norvegica and its two subspecies were included, along with the morphologically similar P. intermedia. Potentilla species of low ploidy level known to belong to other relevant clades were also included.

Results

Gene trees based on three low-copy nuclear markers, obtained by Bayesian Inference and Maximum Likelihood analyses, showed slightly different topologies. This is likely due to genomic reorganizations following genome duplication, but the gene trees were not in conflict with a species tree of presumably diploid taxa obtained by Multispecies Coalescent analysis. The results show that both P. norvegica and P. intermedia are allopolyploids with a shared evolutionary history involving at least four parental lineages, three from the Argentea clade and one from the Ivesioid clade.

Conclusions

This is the first time that reticulate evolution has been proven in the genus Potentilla, and shows the importance of continuing working with low-copy markers in order to properly resolve its evolutionary history. Several hybridization events between the Argentea and Ivesioid clades may have given rise to the species of Wolf’s grex Rivales. To better estimate when and where these hybridizations occurred, other Argentea, Ivesioid and Rivales species should be included in future studies.
Population structure of Apodemus flavicollis and comparison to Apodemus sylvaticus in northern Poland based on RAD-seq
Authors: Martin Cerezo Maria Luisa , Kucka Marek , Zub Karol , Chan Yingguang Frank , Bryk Jarosław
Published: March 2020

Background

Mice of the genus Apodemus are one the most common mammals in the Palaearctic region. Despite their broad range and long history of ecological observations, there are no whole-genome data available for Apodemus, hindering our ability to further exploit the genus in evolutionary and ecological genomics context.

Results

Here we present results from the double-digest restriction site-associated DNA sequencing (ddRAD-seq) on 72 individuals of A. flavicollis and 10 A. sylvaticus from four populations, sampled across 500 km distance in northern Poland. Our data present clear genetic divergence of the two species, with average p-distance, based on 21377 common loci, of 1.51% and a mutation rate of 0.0011 - 0.0019 substitutions per site per million years. We provide a catalogue of 117 highly divergent loci that enable genetic differentiation of the two species in Poland and to a large degree of 20 unrelated samples from several European countries and Tunisia. We also show evidence of admixture between the three A. flavicollis populations but demonstrate that they have negligible average population structure, with largest pairwise FST<0.086.

Conclusion

Our study demonstrates the feasibility of ddRAD-seq in Apodemus and provides the first insights into the population genomics of the species.
An exclusion mechanism is epistatic to an internal detoxification mechanism in aluminum resistance in Arabidopsis
Authors: Wang Yuqi , Yu Wancong , Cao Yu , Cai Yanfei , Lyi Sangbom M. , Wu Weiwei , Kang Yan , Liang Cuiyue , Liu Jiping
Published: March 2020

Background

InArabidopsis, the aluminum (Al) exclusion mechanism is mainly facilitated by ALMT1-mediated malate exudation and MATE-mediated citrate releases from the root. Recently, we have demonstrated that coordinated functioning between an ALMT1-mediated Al exclusion mechanism, via exudation of malate from the root tip, and a NIP1;2-facilitated internal detoxification mechanism, via removal of Al from the root cell wall and subsequent root-to-shoot Al translocation, plays critical roles in achieving overall Al resistance. However, the genetic relationship betweenALMT1andNIP1;2in these processes remained unclear.

Results

Through genetic and physiological analyses, we demonstrate that unlikeALMT1andMATE, which function independently and additively,ALMT1andNIP1;2show an epistatic relationship in Al resistance. These results indicate thatALMT1andNIP1;2function in the same biochemical pathway, whereasALMT1andMATEin different ones.

Conclusion

The establishment of the epistatic relationship and the coordinated functioning between the ALMT1 and NIP1;2-mediated exclusion and internal detoxification mechanisms are pivotal for achieving overall Al resistance in the non-accumulating Arabidopsis plant. We discuss and emphasize the indispensable roles of the root cell wall for the implementation of the Al exclusion mechanism and for the establishment of an epistatic relationship between the ALMT1-mediated exclusion mechanism and the NIP1;2-facilitated internal detoxification mechanism.
The role of mini-bronchoalveolar lavage fluid in the diagnosis of pulmonary tuberculosis in critically ill patients
Authors: Neves Cynthia Pessoa , Costa Allyson Guimarães , Safe Izabella Picinin , de Souza Brito Alexandra , Jesus Jaquelane Silva , Kritski Afranio Lineu , Lacerda Marcus Vinicius Guimarães , Viveiros Miguel , Cordeiro-Santos Marcelo
Published: March 2020

Background

The detection of Mycobacterium tuberculosis (MTB) in the intensive care unit (ICU) presents several challenges, mainly associated to the clinical state of the patient. The presence of HIV infection further aggravates this scenario, requiring a reliable collection method, with better performance in the microbiological/molecular techniques to be used. We evaluated the performance of two methods for sample collection, mini bronchoalveolar lavage (Mini-BAL) and endotracheal aspirate (ETA), for diagnosis of pulmonary tuberculosis (PTB) in critically ill patients.

Methods

This prospective study involved 26 HIV positive ICU internalized patients, with presumptive PTB who required mechanical ventilation. Two samples were obtained prospectively from 26 HIV ICU patients with presumptive PTB by Mini-BAL and ETA. The samples were processed for smear microscopy, Löwenstein-Jensen medium and the BACTEC Mycobacteria Growth Indicator Tube 960 system®. We define as confirmed PTB patients with positive MTB culture. Furthermore, all samples obtained through the Mini-BAL were analyzed by Xpert® MTB/RIF.

Results

Our results demonstrated that the respiratory samples obtained by Mini-BAL were able to increase MTB detection in critically ill patients with presumptive PTB. The Mini-BAL allowed 30% increased recovery and guaranteed enough sample volume for processing in all methods. In addition, the larger volume of the samples obtained with this technique enabled the Xpert® MTB/RIF molecular test for diagnosis of TB.

Conclusions

The Mini-BAL showed be an acceptable alternative to ETA in this population, since these critically ill and often-immunocompromised patients are more likely to develop complications related to invasive procedures.
Case reports of latent HBV hepatitis in patients after neurosurgical treatment for hypothalamic and pituitary tumors
Authors: Niizuma Kuniyasu , Ogawa Yoshikazu , Kogure Takayuki , Tominaga Teiji
Published: March 2020

Background

Hepatitis B virus (HBV) infection is a major public health problem worldwide. More than 2 billion people have been exposed to HBV, and about 257 million individuals are chronic carriers of HBV. HBV reactivation has been increasingly reported in HBV carriers who have undergone immunosuppression or chemotherapy, resulting in mortality. Treatment of hypothalamic/pituitary tumors in HBV carriers requires extensive care to avoid HBV reactivation as steroid therapy is required after surgery for hypothalamic/pituitary tumors.

Case presentation

This retrospective review identified 5 patients, who were HBV carriers positive for hepatitis B surface antigen among 1352 patients with surgically treated hypothalamic/pituitary tumor in Kohnan Hospital between February 2007 and April 2017. Transsphenoidal surgery was performed with particular attention to prevent damage to the pituitary gland, with delicate manipulation to minimize postoperative steroid coverage. All patients received nucleot(s)ide analogue to control HBV-DNA levels before the surgery. As a result, all patients had a good clinical course. Blood examinations found a transient increase of liver enzymes and HBV-DNA levels in all patients, which started to decrease within 2 weeks after surgery. No specific treatment other than nucleot(s)ide analogues was needed to maintain liver function, and all patients returned to their previous activities including reinstatement.

Conclusion

Initiation of nucleot(s)ide analogues administration prior to the surgery for hypothalamic/pituitary tumors can be an effective strategy for preventing reactivation in HBV carriers. Appropriate screening of the patient’s HBV phase, optimal timing of nucleot(s)ide analogues -administration, and administration period of nucleot(s)ide analogues need to be established.
A ruptured posterior communicating artery aneurysm presenting as tentorial and spinal isolated subdural hemorrhage: a case report and literature review
Authors: Al-Abdulwahhab Abdulrahman Hamad , Al-Sharydah Abdulaziz Mohammad , Al-Suhibani Sari Saleh , Almulhim Abdullah Salman , Al-Dhafeeri Obaied M. , Al-Jubran Saeed A.
Published: March 2020

Background

Ruptured intracranial aneurysms are often associated with subarachnoid or intraparenchymal hemorrhage. However, the prevalence of subdural hemorrhage post aneurysmal rupture is low and rarely reported in scientific studies. Here, we report an unusual case of a ruptured posterior communicating artery aneurysm resulting in an isolated subdural hematoma located in the tentorial and spinal canal without subarachnoid or intraparenchymal hemorrhage.

Case presentation

In this case, a 34-year-old woman with no history of trauma or coagulopathy was diagnosed with a subdural hematoma in the tentorium cerebellum tracing to the subdural space of the spinal column. Computed tomography angiography was used to identify the source of the bleeding, which revealed a ruptured left-sided posterior communicating artery saccular aneurysm. The aneurysm was clipped, and the hematoma was evacuated. The patient recovered without any neurological complications.

Conclusions

Our results suggest that a diagnosis of ruptured intracranial aneurysm should be considered in patients with nontraumatic subdural hematoma. Prompt diagnostic imaging and interventional diagnostic procedures are required to ensure proper management of these patients and to avoid unnecessary complications.
Healthcare professionals’ perceptions and experiences of using a cold cot following the loss of a baby: a qualitative study in maternity and neonatal units in the UK
Authors: Smith Paula , Vasileiou Konstantina , Jordan Abbie
Published: March 2020

Background

Best practice in perinatal bereavement care suggests offering parents the opportunity to spend time with their baby. Cold cots facilitate this purpose by reducing the deterioration of the body and evidence indicates their wide availability in maternity and neonatal units in the UK. This study aimed to examine healthcare professionals’ perceptions and experiences of using a cold cot following the loss of a baby.

Methods

A qualitative cross-sectional study was designed. In-depth, semi-structured interviews were conducted with 33 maternity and neonatal unit healthcare professionals who worked across three UK hospital settings. Data were analysed using inductive reflexive thematic analysis.

Results

Findings revealed that staff had predominantly positive views about, and experiences of, using a cold cot. The technology was highly valued because it facilitated parents to spend time with their baby and participants reported that it was generally easy to use and smoothly embedded into the clinical environment. Cold cots were deemed useful when mothers were medically unwell and needed time to recover, when parents struggled to say goodbye to their baby, wished to take the baby home, or wanted their baby to stay in the unit instead of going straight to the mortuary. The use of technology was further perceived to be relevant in scenarios of unexpected loss, post-mortem examination and with babies of late gestations or neonates. Despite staff expressing comfort with the delay of visual and olfactory body changes, the coldness of the baby’s body that was accelerated with the use of a cold cot was a major concern as it connoted and possibly exacerbated the reality of death.

Conclusions

Cold cots allow the materialisation of modern bereavement care practices that recognise the importance of continuing bonds with the deceased that is made possible through the creation of memories within an extremely restricted timeframe. Simultaneously, the body coldness concentrates the ambivalence toward an inherently paradoxical death, that of a baby. Training in perinatal bereavement care, including the use of cold cots, would help staff support bereaved parents whilst acknowledging dilemmas and managing contradictions encompassed in death at the time or near the time of birth.