bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA structural and physical properties reveal peculiarities in promoter sequences of the bacterium Escherichia coli K-12
Authors: Martinez Gustavo Sganzerla , de Ávila e Silva Scheila , Kumar Aditya , Pérez-Rueda Ernesto 
Published: July 2021

AbstractThe gene transcription of bacteria starts with a promoter sequence being recognized by a transcription factor found in the RNAP enzyme, this process is assisted through the conservation of nucleotides as well as other factors governing these intergenic regions. Faced with this, the coding of genetic information into physical aspects of the DNA such as enthalpy, stability, and base-pair stacking could suggest promoter activity as well as protrude differentiation of promoter and non-promoter data. In this work, a total of 3131 promoter sequences associated to six different sigma factors in the bacterium E. coli were converted into numeric attributes, a strong set of control sequences referring to a shuffled version of the original sequences as well as coding regions is provided. Then, the parameterized genetic information was normalized, exhaustively analyzed through statistical tests. The results suggest that strong signals in the promoter sequences match the binding site of transcription factor proteins, indicating that promoter activity is well represented by its conversion into physical attributes. Moreover, the features tested in this report conveyed significant variances between promoter and control data, enabling these features to be employed in bacterial promoter classification. The results produced here may aid in bacterial promoter recognition by providing a robust set of biological inferences.
Comparative spatial–temporal analysis and predictive modeling of climate change-induced malaria vectors’ invasion in new hotspots in Kenya
Authors: Kimuyu J. S. 
Published: July 2021

AbstractClimate change/variability is a major driving factor among others that contribute to the spread of suitable malaria vectors’ geographical extent. The current study employed comparative spatial–temporal analysis using bioclimatic envelope modeling to predict and quantify the possible surge of suitable malaria vectors’ habitats in new hotspots in Kenya. BIOCLIM and BIOCLIM True/False models were run with model data from HADCM3, CCCMA and SCIRO IPCC future climatic projections under A2a scenario. Prediction and projection of the malaria vectors’ prevalence and distribution were done for the whole country. Spatial–temporal models were generated for the baseline climate, and projections were done to depict how the vectors are likely to be distributed by the years 2020, 2050 and 2080 under the influence of climate change. The results showed that the highest suitable malaria vectors’ habitats by area was 227, 092 km2obtained when prediction was done with HADCM3 future climate by the year 2050. The least suitable habitats by area was 80, 060 km2which was predicted with CCCMA projection by the year 2050. Ecological niche prediction from HADCM3 and CSIRO showed a similar trend although at different magnitudes. The prediction results portrayed high likelihood of shift in some suitable habitats that could turn unsuitable, while new hotspots are likely to emerge. The BIOCLIM prediction with the three future climate models showed that the current endemic zones of the lake region and south coastal strip of the Indian Ocean will still remain suitable habitats but with a decline shift in spatial extent by the year 2020, then start to expand by the years 2050–2080. Predictions from HADCM3 by the year 2050 has shown possible wide spread of malaria spatial extents in counties like Narok, Kajiado, Kitui, Makueni, Machakos, Meru, Marsabit, Isiolo, Samburu, Baringo, West Pokot, Turkana and Mandera, while a few others of lower extent might have some emerging isolated hotspots. Laikipia County might become unsuitable habitat for malaria vectors by the year 2050, and the case may remain the same by the year 2080. The malaria burden is likely to shift from Laikipia to the neighboring counties of Baringo, Isiolo, Meru and Turkana. In conclusion, malaria vectors are likely to spread in new continuous and isolated hotspots with future likely increase in malaria prevalence hence possible epidemic upsurge by the year 2050. Consequently, evidence-based scientific research can be utilized to guide policy for sustainable development in the health agenda.
Demand and growth regimes in finance-dominated capitalism and the role of the macroeconomic policy regime: a post-Keynesian comparative study on France, Germany, Italy and Spain before and after the Great Financial Crisis and the Great Recession
Authors: Hein Eckhard , Martschin Judith 
Published: July 2021

AbstractWe contribute to the recent debates on demand and growth regimes in modern finance-dominated capitalism linking them to the post-Keynesian research on macroeconomic policy regimes. We examine the demand and growth regimes, as well as the macroeconomic policy regimes for the big four Eurozone countries, France, Germany, Italy and Spain, for the periods 2001–2009 and 2010–2019. First, our approach supports the usefulness of the identification of demand and growth regimes according to growth contributions of the main demand components and financial balances of the macroeconomic sectors. This allows for an understanding of the demand sources of growth, or stagnation, if there is a lack of demand, of how these sources are financed and of potential financial instabilities and fragilities. Second, when it comes to the macroeconomic policy drivers of demand and growth regimes, as well as their respective changes, we show that the exclusive focus on fiscal policies, as in the previous literature, is too limited and that it is the macroeconomic policy regime which matters here, i.e. the combination of monetary, fiscal and wage policies, as well as the open economy conditions.
Aerosol-based antimicrobial photoinactivation in the lungs: an action spectrum study
Authors: Treghini Chiara , Dell’Accio Alfonso , Fusi Franco , Romano Giovanni 
Published: July 2021

AbstractChronic lung infections are among the most diffused human infections, being often associated with multidrug-resistant bacteria. In this framework, the European project “Light4Lungs” aims at synthesizing and testing an inhalable light source to control lung infections by antimicrobial photoinactivation (aPDI), addressing endogenous photosensitizers only (porphyrins) in the representative case of S. aureus and P. aeruginosa. In the search for the best emission characteristics for the aerosolized light source, this work defines and calculates the photo-killing action spectrum for lung aPDI in the exemplary case of cystic fibrosis. This was obtained by applying a semi-theoretical modelling with Monte Carlo simulations, according to previously published methodology related to stomach infections and applied to the infected trachea, bronchi, bronchioles and alveoli. In each of these regions, the two low and high oxygen concentration cases were considered to account for the variability of in vivo conditions, together with the presence of endogenous porphyrins and other relevant absorbers/diffusers inside the illuminated biofilm/mucous layer. Furthermore, an a priori method to obtain the “best illumination wavelengths” was defined, starting from maximizing porphyrin and light absorption at any depth. The obtained action spectrum is peaked at 394 nm and mostly follows porphyrin extinction coefficient behavior. This is confirmed by the results from the best illumination wavelengths, which reinforces the robustness of our approach. These results can offer important indications for the synthesis of the aerosolized light source and definition of its most effective emission spectrum, suggesting a flexible platform to be considered in further applications.
BrcaSeg: A Deep Learning Approach for Tissue Quantification and Genomic Correlations of Histopathological Images
Authors: Lu Zixiao , Zhan Xiaohui , Wu Yi , Cheng Jun , Shao Wei , Ni Dong , Han Zhi , Zhang Jie , Feng Qianjin , Huang Kun 
Published: July 2021

Abstract
Epithelial and stromal tissues are components of the tumor microenvironment and play a major role in tumor initiation and progression. Distinguishing stroma from epithelial tissues is critically important for spatial characterization of the tumor microenvironment. Here, we propose BrcaSeg, an image analysis pipeline based on a convolutional neural network (CNN) model to classify epithelial and stromal regions in whole-slide hematoxylin and eosin (H&E) stained histopathological images. The CNN model is trained using well-annotated breast cancer tissue microarrays and validated with images from The Cancer Genome Atlas (TCGA) Program. BrcaSeg achieves a classification accuracy of 91.02%, which outperforms other state-of-the-art methods. Using this model, we generate pixel-level epithelial/stromal tissue maps for 1000 TCGA breast cancer slide images that are paired with gene expression data. We subsequently estimate the epithelial and stromal ratios and perform correlation analysis to model the relationship between gene expression and tissue ratios. Gene Ontology (GO) enrichment analyses of genes that are highly correlated with tissue ratios suggest that the same tissue is associated with similar biological processes in different breast cancer subtypes, whereas each subtype also has its own idiosyncratic biological processes governing the development of these tissues. Taken all together, our approach can lead to new insights in exploring relationships between image-based phenotypes and their underlying genomic events and biological processes for all types of solid tumors. BrcaSeg can be accessed at https://github.com/Serian1992/ImgBio.
i2dash: Creation of Flexible, Interactive, and Web-Based Dashboards for Visualization of Omics Data
Authors: Ustjanzew Arsenij , Preussner Jens , Bentsen Mette , Kuenne Carsten , Looso Carsten 
Published: July 2021

Abstract
Data visualization and interactive data exploration are important aspects of illustrating complex concepts and results from analyses of omics data. A suitable visualization has to be intuitive and accessible. Web-based dashboards have become popular tools for the arrangement, consolidation, and display of such visualizations. However, the combination of automated data processing pipelines handling omics data and dynamically generated, interactive dashboards is poorly solved. Here, we present i2dash, an R package intended to encapsulate functionality for the programmatic creation of customized dashboards. It supports interactive and responsive (linked) visualizations across a set of predefined graphical layouts. i2dash addresses the needs of data analysts/software developers for a tool that is compatible and attachable to any R-based analysis pipeline, thereby fostering the separation of data visualization on one hand and data analysis tasks on the other hand. In addition, the generic design of i2dash enables the development of modular extensions for specific needs. As a proof of principle, we provide an extension of i2dash optimized for single-cell RNA sequencing analysis, supporting the creation of dashboards for the visualization needs of such experiments. Equipped with these features, i2dash is suitable for extensive use in large-scale sequencing/bioinformatics facilities. Along this line, we provide i2dash as a containerized solution, enabling a straightforward large-scale deployment and sharing of dashboards using cloud services. i2dash is freely available via the R package archive CRAN (https://CRAN.R-project.org/package=i2dash).
scDPN for High-Throughput Single-Cell CNV Detection to Uncover Clonal Evolution During HCC Recurrence
Authors: Wu Liang , Jiang Miaomiao , Wang Yuzhou , Zhou Biaofeng , Sun Yunfan , Zhou Kaiqian , Xie Jiarui , Zhong Yu , Zhao Zhikun , Dean Michael , Hou Yong , Liu Shiping 
Published: July 2021

Abstract
Single-cell genomics provides substantial resources for dissecting cellular heterogeneity and cancer evolution. Unfortunately, classical DNA amplification-based methods have low throughput and introduce coverage bias during sample preamplification. We developed a single-cell DNA library preparation method without preamplification in nanolitre scale (scDPN) to address these issues. The method achieved a throughput of up to 1800 cells per run for copy number variation (CNV) detection. Also, our approach demonstrated a lower level of amplification bias and noise than the multiple displacement amplification (MDA) method and showed high sensitivity and accuracy for cell line and tumor tissue evaluation. We used this approach to profile the tumor clones in paired primary and relapsed tumor samples of hepatocellular carcinoma (HCC). We identified three clonal subpopulations with a multitude of aneuploid alterations across the genome. Furthermore, we observed that a minor clone of the primary tumor containing additional alterations in chromosomes 1q, 10q, and 14q developed into the dominant clone in the recurrent tumor, indicating clonal selection during recurrence in HCC. Overall, this approach provides a comprehensive and scalable solution to understand genome heterogeneity and evolution
Oxaliplatin, an Anticancer Agent, Causes Erectile Dysfunction in Rats due to Endothelial Dysfunction
Authors: Kataoka Tomoya , Mori Taiki , Suzuki Jun , Kawaki Yuto , Kito Yohei , Hotta Yuji , Kawade Yoshihiro , Maeda Yasuhiro , Kimura Kazunori 
Published: July 2021

ABSTRACT

Background
Chemotherapeutics, one of the standard treatment options for cancer worldwide, have various adverse effects, including erectile dysfunction (ED).

Aim
To investigate erectile function in an animal model after administration of the anticancer agent oxaliplatin (L-OHP).

Methods
Male Wistar/ST rats were divided into 2 groups: L-OHP rats (n = 21), which were intravenously administered L-OHP (4 mg/kg; twice a week for 4 weeks), and Control rats (n = 21), which were injected with the same volume of 5% glucose solution, using the same dosing schedule. At the end of the study period, erectile function was evaluated by measuring intracavernous pressure (ICP) and mean arterial pressure (MAP) after cavernous nerve stimulation (n = 9–10). Endothelial function was evaluated with an isometric tension study using corpus cavernosum strips (n = 11). Western blot analysis was used to assess neuronal nitric oxide (nNOS) and endothelial NO synthase (eNOS) protein levels (n = 7). Real-time quantitative polymerase chain reaction (qRT-PCR) was used to assess the expression of inflammation- and oxidative stress-related markers (nicotinamide adenine dinucleotide phosphate oxidase-1, p22phox, interleukin [IL]-6, and nuclear factor-kappa B) (n = 6). Statistical significance was determined using the Student’s t-test.

Outcomes
The L-OHP group had a significantly lower ICP:MAP ratio than the control group (P &lt; .05). Compared to the Control group, the L-OHP group exhibited significantly lower responses to ACh and eNOS protein levels and significantly higher inflammatory biomarker levels.

Clinical Translation
The results based on this animal model indicate that use of the anticancer agent L-OHP should be considered as a risk factor for ED occurring via reduction of NO bioavailability in humans; our results provide possible treatment strategies for maintaining the erectile function of cancer survivors.

Strengths and limitations
Our study showed that the anticancer agent L-OHP has the propensity to cause ED in rats. A major limitation of this study is the lack of an established cure for ED associated with L-OHP and the lack of clinical evidence.

CONCLUSIONS
L-OHP causes ED in rats via reduction of NO bioavailability caused by endothelial dysfunction.
Aggression-Related Sexual Fantasies: Prevalence Rates, Sex Differences, and Links with Personality, Attitudes, and Behavior
Authors: Bondü Rebecca , Birke Joseph B. 
Published: July 2021

ABSTRACT

Background
Aggression-related sexual fantasies (ASF) are considered an important risk factor for sexual aggression, but empirical knowledge is limited, in part because previous research has been based on predominantly male, North-American college samples, and limited numbers of questions.

Aim
The present study aimed to foster the knowledge about the frequency and correlates of ASF, while including a large sample of women and a broad range of ASF.

Method
A convenience sample of N = 664 participants from Germany including 508 (77%) women and 156 (23%) men with a median age of 25 (21–27) years answered an online questionnaire. Participants were mainly recruited via social networks (online and in person) and were mainly students. We examined the frequencies of (aggression-related) sexual fantasies and their expected factor structure (factors reflecting affective, experimental, masochistic, and aggression-related contents) via exploratory factor analysis. We investigated potential correlates (eg, psychopathic traits, attitudes towards sexual fantasies) as predictors of ASF using multiple regression analyses. Finally, we examined whether ASF would positively predict sexual aggression beyond other pertinent risk factors using multiple regression analysis.

Outcomes
The participants rated the frequency of a broad set of 56 aggression-related and other sexual fantasies, attitudes towards sexual fantasies, the Big Five (ie, broad personality dimensions including neuroticism and extraversion), sexual aggression, and other risk factors for sexual aggression.

RESULTS
All participants reported non-aggression-related sexual fantasies and 77% reported at least one ASF in their lives. Being male, frequent sexual fantasies, psychopathic traits, and negative attitudes towards sexual fantasies predicted more frequent ASF. ASF were the strongest predictor of sexual aggression beyond other risk factors, including general aggression, psychopathic traits, rape myth acceptance, and violent pornography consumption.

Clinical Translation
ASF may be an important risk factor for sexual aggression and should be more strongly considered in prevention and intervention efforts.

Strengths and Limitations
The strengths of the present study include using a large item pool and a large sample with a large proportion of women in order to examine ASF as a predictor of sexual aggression beyond important control variables. Its weaknesses include the reliance on cross-sectional data, that preclude causal inferences, and not continuously distinguishing between consensual and non-consensual acts.

CONCLUSION
ASF are a frequent phenomenon even in in the general population and among women and show strong associations with sexual aggression. Thus, they require more attention by research on sexual aggression and its prevention.
Neuro‐Fuzzy Kinematic Finite‐Fault Inversion: 1. Methodology
Authors: Kheirdast Navid , Ansari Anooshiravan , Custódio Susana 
Published: July 2021

AbstractKinematic finite‐fault source inversions aim at resolving the spatio‐temporal evolution of slip on a fault given ground motion recorded on the Earth's surface. This type of inverse problem is inherently ill posed due to two main factors. First, the number of model parameters is typically greater than the number of independent observed data. Second, small singular values are generated by the discretization of the physical rupture process and amplify the effect of noise in the inversion. As a result, one can find different slip distributions that fit the data equally well. This ill posedness can be mitigated by decreasing the number of model parameters, hence improving their relationship to the observed data. In this study, we propose a fuzzy function approximation approach to describe the spatial slip function. In particular, we use an Adaptive Network‐based Fuzzy Inference System (ANFIS) to find the most adequate discretization for the spatial variation of slip on the fault. The fuzzy basis functions and their respective amplitudes are optimized through hybrid learning. We solve this earthquake source problem in the frequency domain, searching for optimal spatial slip distribution independently for each frequency. The approximated frequency‐dependent spatial slip functions are then used to compute the forward relationship between slip on the fault and ground motion. The method is constrained through Tikhonov regularization, requiring a smooth spatial slip variation. We discuss how the number of model parameters can be decreased, while keeping the inversion stable and achieving an adequate resolution. The proposed inversion method is tested using the SIV1‐benchmark exercise.
The Impacts of Global Warming on Climate Zone Changes Over Asia Based on CMIP6 Projections
Authors: Kim Jeong‐Bae , Bae Deg‐Hyo 
Published: July 2021

AbstractIt is challenging to estimate how the regional climate will be shifted under future global warming. To reduce the potential risk of regional climate shift under future climates, examining the change in climate features over Asia is important, as approximately 60% of the world's population resides there. In this study, climate shifts are assessed over the Asian monsoon region under global mean temperature warming targets from 1.5°C to 5.0°C above preindustrial (PI) levels based on different shared socioeconomic pathway (SSP) scenarios. Global warming impacts the individual climate variables, and consequently, it impacts the regional climate features across the Asian region. Temperature change patterns are more dominant contributors to the spatial extent and magnitude of climate shifts than precipitation change patterns. Changes in regional climates show different behaviors according to the degree of global warming rather than the type of SSP scenario. Climate shifts are intensified under a higher level of global warming that is above the PI levels. The largest climate shifts in this region are shown under global warming of 5.0°C based on the SSP5‐8.5 scenario, especially in current polar climate zones. Future change patterns in individual climate zone can differ. Regions with tropical climates and arid climates are likely to be expanded, whereas some regions with warm temperate climates, cold climates, and polar climates are likely to shrink under global warming conditions. Therefore, this study supports the necessity of mitigating greenhouse gas (GHG) emissions and establishing an adaptation plan for future global warming conditions.
Constraining the Timespan of Fluvial Activity From the Intermittency of Sediment Transport on Earth and Mars
Authors: Hayden A. T. , Lamb M. P. , McElroy B. J. 
Published: July 2021

AbstractThe timespan recorded in deposits from fluvial activity is a key gap in our understanding of ancient environments on Earth and Mars. Because riverine sediment transport occurs under time‐variable water discharge, common models that represent sediment transport with a single bankfull discharge require an intermittency factor. For this reason, the ability to predict intermittency factor values based on environmental factors would improve estimates of time from fluvial deposits. To address this knowledge gap, we calculated intermittency factors from 201 modern rivers and six fans and deltas with depositional timespans of months to millions of years. Intermittency factors range from 0.0064–0.73; they are uncorrelated with averaging timescale, bed‐material grainsize, or climate aridity, but are larger in river catchments with greater rates of denudation relative to precipitation. Application to ancient fluvial systems on Mars indicates long‐lived depositional river systems for up to 104–106 years.