bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microcanonical thermostatistics of aggregation transition in a system with anisotropically interacting molecules
Authors: Trugilho L. F. , Rizzi L. G. 
Published: May 2020

Abstract
Microcanonical thermostatistics analysis has been introduced as an important method in the study of phase transitions observed in intrinsically small systems, such as folding transitions in proteins and surface adsorption transitions of polymeric chains. Here we consider a lattice model and apply microcanonical analysis to investigate the aggregation transition of a system with anisotropically interacting molecules. By performing multicanonical Monte Carlo simulations we are able to obtain free-energy profiles from where we extract physical quantities related to the aggregation transition such as its transition temperature, latent heat, and free-energy barriers. Our results confirms that the aggregation transition is a first-order type of transition and that it is related to the nucleation of molecules into elongated aggregates. Also, our analysis revealed an unexpected non-monotonic behavior for the free-energy barrier as a function of the anisotropic ratio ξ between strong and weak interactions of the molecules, indicating that the nucleation kinetics might be also influenced by ξ.
Denitrification hotspots in intertidal mixing zones linked to geologic heterogeneity
Authors: Heiss James W , Michael Holly A , Koneshloo Mohammad 
Published: May 2020

Abstract
The mixing between fresh and saline groundwater in beach aquifers promotes biogeochemical transformations that affect nutrient fluxes to the coastal ocean. We performed variable-density groundwater flow and reactive transport simulations with geostatistical representations of sedimentary structure to understand the influence of heterogeneity on groundwater dynamics and denitrification in intertidal mixing zones. Ensemble-averaged simulation results show that heterogeneity can enhance mixing between fresh and saline groundwater and increase residence time, resulting in up to 80% higher nitrate removal relative to equivalent effective homogeneous aquifer sediment. Denitrification hotspots form in high permeability structures where DOC and nitrate are readily supplied by convergent flow. The results provide a physical explanation for the formation of denitrification hotspots observed in beach aquifers and illustrate for the first time the influence of sediment heterogeneity on rates and spatial patterns of biogeochemical processes in intertidal aquifers that are critical mediators of land-sea solute fluxes along world coastlines.
Towards solving of the Illiteracy phenomenon for VEP-based brain-computer interfaces
Authors: Volosyak Ivan , Rezeika Aya , Benda Mihaly , Gembler Felix , Stawicki Piotr 
Published: May 2020

Abstract
Brain-Computer Interface (BCI) systems use brain activity as an input signal and enable communication without requiring bodily movement. This novel technology may help impaired patients and users with disabilities to communicate with their environment. Over the years, researchers investigated the performance of subjects in different BCI paradigms, stating that 15%–30% of BCI users are unable to reach proficiency in using a BCI system and therefore were labelled as BCI illiterates. Recent progress in the BCIs based on the visually evoked potentials (VEPs) necessitates re-considering of this term, as very often all subjects are able to use VEP-based BCI systems. This study examines correlations among BCI performance, personal preferences, and further demographic factors for three different modern visually evoked BCI paradigms: (1) the conventional Steady-State Visual Evoked Potentials (SSVEPs) based on visual stimuli flickering at specific constant frequencies (fVEP), (2) Steady-State motion Visual Evoked Potentials (SSmVEP), and (3) code-modulated Visual Evoked Potentials (cVEP). Demographic parameters, as well as handedness, vision correction, BCI experience, etc., have no significant effect on the performance of VEP-based BCI. Most subjects did not consider the flickering stimuli annoying, only 20 out of a total of 86 participants indicated a change in fatigue during the experiment. 83 subjects were able to successfully finish all spelling tasks with the fVEP speller, with a mean (SD) information transfer rate of 31.87 bit/min (9.83) and an accuracy of 95.28% (5.18), respectively. Compared to that, 80 subjects were able to successfully finish all spelling tasks using SSmVEP, with a mean information transfer rate of 26.44 bit/min (8.04) and an accuracy of 91.10% (6.01), respectively. Finally, all 86 subjects were able to successfully finish all spelling tasks with the cVEP speller, with a mean information transfer rate of 40.23 bit/min (7.63) and an accuracy of 97.83% (3.37).
Dark solitons embedded in a stable periodic pulse train emitted by a fiber ring laser
Authors: Huang Shen , Shao Guodong , Song Yufeng , Zhao Luming , Shen Deyuan , Tang Dingyuan 
Published: May 2020

Abstract
We report on the experimental observation of dark solitons embedded in a stable periodic pulse train emitted by a net normal dispersion cavity fiber laser. Our experimental result shows that in addition of forming in a continuous-wave background, a dark soliton could also be formed in a stable periodic pulse train background. Numerical simulations have well reproduced the experimental result. Moreover, numerical simulations also show that as a result of the periodic pulse train background the formed dark soliton could exhibit a dark pulse envelope that is much broader than its actual pulse width.
Dual decline in gait speed and cognition is associated with future dementia: evidence for a phenotype
Authors: Montero-Odasso Manuel , Speechley Mark , Muir-Hunter Susan W , Pieruccini-Faria Frederico , Sarquis-Adamson Yanina , Hachinski Vladimir , Bherer Louis , Borrie Michael , Wells Jennie , Garg Amit X , Tian Qu , Ferrucci Luigi , Bray Nick W , Cullen Stephanie , Mahon Joel , Titus Josh , Camicioli Richard ,   The Canadian Gait and Cognition Network
Published: May 2020

Abstract

Background
concurrent declines in gait speed and cognition have been associated with future dementia. However, the clinical profile of ‘dual decliners’, those with concomitant decline in both gait speed and cognition, has not been yet described. We aimed to describe the phenotype and the risk for incident dementia of those who present with dual decline in comparison with non-dual decliners.

Methods
prospective cohort of community-dwelling older adults free of dementia at baseline. We evaluated participants’ gait speed, cognition, medical status, functionality, incidence of adverse events and dementia, biannually over 7 years. Gait speed was assessed with a 6-m electronic walkway and global cognition using the MoCA test. We compared characteristics between dual decliners and non-dual decliners using t-test, chi-square and hierarchical regression models. We estimated incident dementia using Cox models.

Results
among 144 participants (mean age 74.23 ± 6.72 years, 54% women), 17% progressed to dementia. Dual decliners had a 3-fold risk (HR: 3.12, 95%CI: 1.23–7.93, P = 0.017) of progression to dementia compared with non-dual decliners. Dual decliners were significantly older with a higher prevalence of hypertension and dyslipidemia (P = 0.002). Hierarchical regression models show that age and sex alone explained 3% of the variation in the dual decliners group. Adding hypertension and dyslipidemia increased the explained variation by 8 and 10%, respectively. The risk of becoming a dual decliner was 4-fold higher if hypertension was present.

Conclusion
older adults with a concurrent decline in gait speed and cognition represent a group at the highest risk of progression to dementia. Older adults with dual decline have a distinct phenotype with a higher prevalence of hypertension, a treatable condition.
Differences in xylem development between Dutch and Japanese tomato (Solanum lycopersicum) correlate with cytokinin levels in hypocotyls
Authors: Qi Xiaohua , Takahashi Hirokazu , Kawasaki Yasushi , Ohta Yuya , Isozaki Masahide , Kojima Mikiko , Takebayashi Yumiko , Sakakibara Hitoshi , Imanishi Shunsuke , Chen Xuehao , Nakazono Mikio 
Published: May 2020

Abstract

Background and Aims
Dutch tomato cultivars tend to have a greater yield than Japanese cultivars even if they are grown under the same conditions. Factors contributing to the increased yield of the Dutch cultivars were a greater light use efficiency and greater leaf photosynthetic rate. On the other hand, the relationship between tomato yields and anatomical traits is still unclear. The aim of this study is to identify the anatomical traits related to the difference in yield between Dutch and Japanese cultivars.

Methods
Anatomical properties were compared during different growth stages of Dutch and Japanese tomatoes. Hormone profiles and related gene expression in hypocotyls of Dutch and Japanese cultivars were compared in the hypocotyls of 3- and 4-week-old plants.

Key results
Dutch cultivars have a more developed secondary xylem than Japanese cultivars, which would allow for greater transport of water, mineral nutrients and phytohormones to the shoots. The areas and ratios of the xylem in the hypocotyls of 3- to 6-week-old plants were larger in the Dutch cultivars. In reciprocal grafts of the Japanese and Dutch cultivars, xylem development at the scion and rootstock depended on the scion cultivar, suggesting that some factors in the scion are responsible for the difference in xylem development. The cytokinin content, especially the level of N6-(Δ 2-isopentenyl) adenine (iP)-type cytokinin, was higher in the Dutch cultivars. This result was supported by the greater expression of Sl-IPT3 (a cytokinin biosynthesis gene) and Sl-RR16/17 (a cytokinin-responsive gene) in the Dutch cultivars.

Conclusions
These results suggest that iP-type cytokinins, which are locally synthesized in the hypocotyl, contribute to xylem development. The greater xylem development in Dutch cultivars might contribute to the high yield of the tomato.
Automated inference of Boolean models from molecular interaction maps using CaSQ
Authors: Aghamiri Sara Sadat , Singh Vidisha , Naldi Aurélien , Helikar Tomáš , Soliman Sylvain , Niarakis Anna 
Published: May 2020

Abstract

Motivation
Molecular interaction maps have emerged as a meaningful way of representing biological mechanisms in a comprehensive and systematic manner. However, their static nature provides limited insights to the emerging behaviour of the described biological system under different conditions. Computational modelling provides the means to study dynamic properties through in silico simulations and perturbations. We aim to bridge the gap between static and dynamic representations of biological systems with CaSQ, a software tool that infers Boolean rules based on the topology and semantics of molecular interaction maps built with CellDesigner.

Results
We developed CaSQ by defining conversion rules and logical formulas for inferred Boolean models according to the topology and the annotations of the starting molecular interaction maps. We used CaSQ to produce executable files of existing molecular maps that differ in size, complexity and the use of Systems Biology Graphical Notation (SBGN) standards. We also compared, where possible, the manually built logical models corresponding to a molecular map to the ones inferred by CaSQ. The tool is able to process large and complex maps built with CellDesigner (either following SBGN standards or not) and produce Boolean models in a standard output format, Systems Biology Marked Up Language-qualitative (SBML-qual), that can be further analyzed using popular modelling tools. References, annotations and layout of the CellDesigner molecular map are retained in the obtained model, facilitating interoperability and model reusability.

Availability and implementation
The present tool is available online: https://lifeware.inria.fr/∼soliman/post/casq/ and distributed as a Python package under the GNU GPLv3 license. The code can be accessed here: https://gitlab.inria.fr/soliman/casq.

Supplementary information
Supplementary data are available at Bioinformatics online.
Factorized embeddings learns rich and biologically meaningful embedding spaces using factorized tensor decomposition
Authors: Trofimov Assya , Cohen Joseph Paul , Bengio Yoshua , Perreault Claude , Lemieux Sébastien 
Published: May 2020

Abstract

Motivation
The recent development of sequencing technologies revolutionized our understanding of the inner workings of the cell as well as the way disease is treated. A single RNA sequencing (RNA-Seq) experiment, however, measures tens of thousands of parameters simultaneously. While the results are information rich, data analysis provides a challenge. Dimensionality reduction methods help with this task by extracting patterns from the data by compressing it into compact vector representations.

Results
We present the factorized embeddings (FE) model, a self-supervised deep learning algorithm that learns simultaneously, by tensor factorization, gene and sample representation spaces. We ran the model on RNA-Seq data from two large-scale cohorts and observed that the sample representation captures information on single gene and global gene expression patterns. Moreover, we found that the gene representation space was organized such that tissue-specific genes, highly correlated genes as well as genes participating in the same GO terms were grouped. Finally, we compared the vector representation of samples learned by the FE model to other similar models on 49 regression tasks. We report that the representations trained with FE rank first or second in all of the tasks, surpassing, sometimes by a considerable margin, other representations.

Availability and implementation
A toy example in the form of a Jupyter Notebook as well as the code and trained embeddings for this project can be found at: https://github.com/TrofimovAssya/FactorizedEmbeddings.

Supplementary information
Supplementary data are available at Bioinformatics online.
Chemical–protein interaction extraction via Gaussian probability distribution and external biomedical knowledge
Authors: Sun Cong , Yang Zhihao , Su Leilei , Wang Lei , Zhang Yin , Lin Hongfei , Wang Jian 
Published: May 2020

Abstract

Motivation
The biomedical literature contains a wealth of chemical–protein interactions (CPIs). Automatically extracting CPIs described in biomedical literature is essential for drug discovery, precision medicine, as well as basic biomedical research. Most existing methods focus only on the sentence sequence to identify these CPIs. However, the local structure of sentences and external biomedical knowledge also contain valuable information. Effective use of such information may improve the performance of CPI extraction.

Results
In this article, we propose a novel neural network-based approach to improve CPI extraction. Specifically, the approach first employs BERT to generate high-quality contextual representations of the title sequence, instance sequence and knowledge sequence. Then, the Gaussian probability distribution is introduced to capture the local structure of the instance. Meanwhile, the attention mechanism is applied to fuse the title information and biomedical knowledge, respectively. Finally, the related representations are concatenated and fed into the softmax function to extract CPIs. We evaluate our proposed model on the CHEMPROT corpus. Our proposed model is superior in performance as compared with other state-of-the-art models. The experimental results show that the Gaussian probability distribution and external knowledge are complementary to each other. Integrating them can effectively improve the CPI extraction performance. Furthermore, the Gaussian probability distribution can effectively improve the extraction performance of sentences with overlapping relations in biomedical relation extraction tasks.

Availability and implementation
Data and code are available at https://github.com/CongSun-dlut/CPI_extraction.

Supplementary information
Supplementary data are available at Bioinformatics online.
Ventricular fibrillation mechanism and global fibrillatory organization are determined by gap junction coupling and fibrosis pattern
Authors: Handa Balvinder S , Li Xinyang , Baxan Nicoleta , Roney Caroline H , Shchendrygina Anastasia , Mansfield Catherine A , Jabbour Richard J , Pitcher David S , Chowdhury Rasheda A , Peters Nicholas S , Ng Fu Siong 
Published: May 2020

Abstract

Aims
Conflicting data exist supporting differing mechanisms for sustaining ventricular fibrillation (VF), ranging from disorganized multiple-wavelet activation to organized rotational activities (RAs). Abnormal gap junction (GJ) coupling and fibrosis are important in initiation and maintenance of VF. We investigated whether differing ventricular fibrosis patterns and the degree of GJ coupling affected the underlying VF mechanism.

Methods and results
Optical mapping of 65 Langendorff-perfused rat hearts was performed to study VF mechanisms in control hearts with acute GJ modulation, and separately in three differing chronic ventricular fibrosis models; compact fibrosis (CF), diffuse fibrosis (DiF), and patchy fibrosis (PF). VF dynamics were quantified with phase mapping and frequency dominance index (FDI) analysis, a power ratio of the highest amplitude dominant frequency in the cardiac frequency spectrum. Enhanced GJ coupling with rotigaptide (n = 10) progressively organized fibrillation in a concentration-dependent manner; increasing FDI (0 nM: 0.53 ± 0.04, 80 nM: 0.78 ± 0.03, P &lt; 0.001), increasing RA-sustained VF time (0 nM: 44 ± 6%, 80 nM: 94 ± 2%, P &lt; 0.001), and stabilized RAs (maximum rotations for an RA; 0 nM: 5.4 ± 0.5, 80 nM: 48.2 ± 12.3, P &lt; 0.001). GJ uncoupling with carbenoxolone progressively disorganized VF; the FDI decreased (0 µM: 0.60 ± 0.05, 50 µM: 0.17 ± 0.03, P &lt; 0.001) and RA-sustained VF time decreased (0 µM: 61 ± 9%, 50 µM: 3 ± 2%, P &lt; 0.001). In CF, VF activity was disorganized and the RA-sustained VF time was the lowest (CF: 27 ± 7% vs. PF: 75 ± 5%, P &lt; 0.001). Global fibrillatory organization measured by FDI was highest in PF (PF: 0.67 ± 0.05 vs. CF: 0.33 ± 0.03, P &lt; 0.001). PF harboured the longest duration and most spatially stable RAs (patchy: 1411 ± 266 ms vs. compact: 354 ± 38 ms, P &lt; 0.001). DiF (n = 11) exhibited an intermediately organized VF pattern, sustained by a combination of multiple-wavelets and short-lived RAs.

Conclusion
The degree of GJ coupling and pattern of fibrosis influences the mechanism sustaining VF. There is a continuous spectrum of organization in VF, ranging between globally organized fibrillation sustained by stable RAs and disorganized, possibly multiple-wavelet driven fibrillation with no RAs.
Exploring the Ecology and Indicator Value of Some Larvae of Odonata Genera in Colombia
Authors: Garzón-Salamanca Laura L , Rivera-Rondón Carlos A , Aristizabal Hernán , Forero Dimitri 
Published: May 2020

AbstractBioindication is a method to assess environmental conditions using indicator organisms. In Colombia, water quality evaluation is mostly performed following the Biological Monitoring Working Party/Colombia method (BMWP/Col), which uses aquatic macroinvertebrates at the taxonomic family level. Studies on potential bioindicators are important to produce comprehensive information on the requirements of macroinvertebrates and their value for water quality bioindication. We studied the larval ecology of several common genera of Odonata from Colombian freshwater ecosystems and assigned an indicator value to each genus. The physical and chemical water characteristics of 1,022 sites surveyed in Colombia from 2005 to 2016 were analyzed using a principal component analysis (PCA). The relationship between environmental conditions and Odonata genera found was studied using multiple logistic regressions between sample coordinates of the first three axes of the PCA and occurrence of the respective genus. We assigned an indicator value for each genus using the logistic regression and the water quality of samples. The highest indicator values were assigned to genera, which were mainly explained by the PCA axis associated with water quality, showed a high odds ratio to this axis, and were found in ecosystems with excellent water quality. The indicator values suggested for each taxon are, Brechmorhoga Kirby, 1894, 8; Macrothemis Hagen, 1868, 4; Micrathyria Kirby, 1889, 4 (Libellulidae); Progomphus Selys, 1854, 7 (Gomphidae); Acanthagrion Selys, 1876, 4; and Argia Rambur, 1842, 7 (Coenagrionidae). Differences in water quality preferences in genera of the same family suggest that higher taxonomic resolution may allow more detailed environmental assessments.
Symposium summary: Epigenetic inheritance—impact for biology and society 26–28 August 2019, Zurich, Switzerland
Authors: Lazar-Contes Irina , Roszkowski Martin , Tanwar Deepak K , Mansuy Isabelle M 
Published: May 2020

Abstract
The concept of epigenetic inheritance proposes a new and unconventional way to think about heredity in health and disease, at the interface between genetics and the environment. Epigenetic inheritance is a form of biological inheritance not encoded in the DNA sequence itself but mediated by epigenetic factors. Because epigenetic factors can be modulated by the environment, they can relay this information to the genome and modify its activity consequentially. If epigenetic changes induced by environmental exposure are present in the germline and persist in germ cells during development until conception, they have the potential to transfer the traces of ancestral exposure to the progeny.
This form of heredity relates to the extremely important question of nature versus nurture and how much of our own make-up is genetically or epigenetically determined, a question that remains largely unresolved. Because it questions the dominant dogma of genetics and brings a paradigm shift in sciences, it has to creating strong bridges between disciplines and provide solid causal evidence to be firmly established.
The second edition of a conference fully dedicated to epigenetic inheritance was held in August 2019 in Zurich, Switzerland. This symposium titled ‘Epigenetic inheritance: impact for biology and society’ (http://www.epigenetic-inheritance-zurich.ethz.ch), gathered experts in the field of epigenetic inheritance to discuss the concept and pertinent findings, exchange views and expertise about models and methods, and address challenges raised by this new discipline. The symposium offered a mix of invited lectures and short talks selected from abstracts, poster sessions and a workshop ‘Meet the experts: Q&A’. A tour of a local omics facility the Functional Genomics Center Zurich was also offered to interested participants. Additional comments and impressions were shared by attendees on Twitter #eisz19 during and after the symposium. This summary provides an overview of the different sessions and talks and describes the main findings presented.