bluuebunny/crossref_metadata_2025_split huggingface dataset:
SMILES-X: autonomous molecular compounds characterization for small datasets without descriptors
Authors: Lambard Guillaume , Gracheva Ekaterina 
Published: March 2020

Abstract
There is more and more evidence that machine learning can be successfully applied in materials science and related fields. However, datasets in these fields are often quite small (from tens to several thousands of samples). This means the most advanced machine learning techniques remain neglected, as they are considered to be applicable to big data only. Moreover, materials informatics methods often rely on human-engineered descriptors, that should be carefully chosen, or even created, to fit the physicochemical property that one intends to predict. In this article, we propose a new method that tackles both the issue of small datasets and the difficulty of developing task-specific descriptors. The SMILES-X is an autonomous pipeline for molecular compounds characterisation based on a {Embed-Encode-Attend-Predict} neural architecture with a data-specific Bayesian hyper-parameters optimisation. The only input to the architecture—the SMILES strings—are de-canonicalised in order to efficiently augment the data. One of the key features of the architecture is the attention mechanism, which enables the interpretation of output predictions without extra computational cost. The SMILES-X achieves state-of-the-art results in the inference of aqueous solubility (

RMSE

¯

test

≃
0.57
±
0.07

mols/L), hydration free energy (

RMSE

¯

test

≃
0.81
±
0.22

kcal/mol, which is ∼24.5% better than molecular dynamics simulations), and octanol/water distribution coefficient (

RMSE

¯

test

≃
0.59
±
0.02

for LogD at pH 7.4) of molecular compounds. The SMILES-X is intended to become an important asset in the toolkit of materials scientists and chemists. The source code for the SMILES-X is available at github.com/GLambard/SMILES-X.
Step by step evolution of Indeterminate Domain (IDD) transcriptional regulators: from algae to angiosperms
Authors: Prochetto Santiago , Reinheimer Renata 
Published: March 2020

AbstractIntroductionThe Indeterminate Domain (IDD) proteins are a plant-specific subclass of C2H2 Zinc Finger transcription factors. Some of these transcription factors play roles in diverse aspects of plant metabolism and development, but the function of most of IDD genes is unknown and the molecular evolution of the subfamily has not been explored in detail.MethodsIn this study, we mined available genome sequences of green plants (Viridiplantae) to reconstruct the phylogeny and then described the motifs/expression patterns of IDD genes.Key ResultsWe identified the complete set of IDD genes of 16 Streptophyta genomes. We found that IDD and its sister clade STOP arose by a duplication at the base of Streptophyta. Once on land, the IDD genes duplicated extensively, giving rise to at least ten lineages. Some of these lineages were lost in extant non-vascular plants and gymnosperms, but all of them were retained in angiosperms, duplicating profoundly in dicots and monocots and acquiring, at the same time, surprising heterogeneity in their C-terminal regions and expression patterns.ConclusionsIDDs were present in the last common ancestor of Streptophyta. On land, IDDs duplicated extensively, leading to ten lineages. Later, IDDs were recruited by angiosperms where they diversified greatly in number, C-terminal and expression patterns. Interestingly, such diversification occurred during the evolution of novel traits of the plant body. This study provides a solid framework of the orthology relationships of green land plant IDD transcription factors, thus increasing the accuracy of orthologue identification in model and non-model species and facilitating the identification of agronomically important genes related to plant metabolism and development.
Resolving single-cell heterogeneity from hundreds of thousands of cells through sequential hybrid clustering and NMF
Authors: Venkatasubramanian Meenakshi , Chetal Kashish , Schnell Daniel J , Atluri Gowtham , Salomonis Nathan 
Published: March 2020

Abstract

Motivation
The rapid proliferation of single-cell RNA-sequencing (scRNA-Seq) technologies has spurred the development of diverse computational approaches to detect transcriptionally coherent populations. While the complexity of the algorithms for detecting heterogeneity has increased, most require significant user-tuning, are heavily reliant on dimension reduction techniques and are not scalable to ultra-large datasets. We previously described a multi-step algorithm, Iterative Clustering and Guide-gene Selection (ICGS), which applies intra-gene correlation and hybrid clustering to uniquely resolve novel transcriptionally coherent cell populations from an intuitive graphical user interface.

Results
We describe a new iteration of ICGS that outperforms state-of-the-art scRNA-Seq detection workflows when applied to well-established benchmarks. This approach combines multiple complementary subtype detection methods (HOPACH, sparse non-negative matrix factorization, cluster ‘fitness’, support vector machine) to resolve rare and common cell-states, while minimizing differences due to donor or batch effects. Using data from multiple cell atlases, we show that the PageRank algorithm effectively downsamples ultra-large scRNA-Seq datasets, without losing extremely rare or transcriptionally similar yet distinct cell types and while recovering novel transcriptionally distinct cell populations. We believe this new approach holds tremendous promise in reproducibly resolving hidden cell populations in complex datasets.

Availability and implementation
ICGS2 is implemented in Python. The source code and documentation are available at http://altanalyze.org.

Supplementary information
Supplementary data are available at Bioinformatics online.
Brewery: deep learning and deeper profiles for the prediction of 1D protein structure annotations
Authors: Torrisi Mirko , Pollastri Gianluca 
Published: March 2020

Abstract

Motivation
Protein structural annotations (PSAs) are essential abstractions to deal with the prediction of protein structures. Many increasingly sophisticated PSAs have been devised in the last few decades. However, the need for annotations that are easy to compute, process and predict has not diminished. This is especially true for protein structures that are hardest to predict, such as novel folds.

Results
We propose Brewery, a suite of ab initio predictors of 1D PSAs. Brewery uses multiple sources of evolutionary information to achieve state-of-the-art predictions of secondary structure, structural motifs, relative solvent accessibility and contact density.

Availability and implementation
The web server, standalone program, Docker image and training sets of Brewery are available at http://distilldeep.ucd.ie/brewery/.

Contact
gianluca.pollastri@ucd.ie
Connected Carabids: Network Interactions and Their Impact on Biocontrol by Carabid Beetles
Authors: De Heij Stefanie E , Willenborg Christian J 
Published: March 2020

AbstractCarabid beetles can greatly contribute to biocontrol in agroecosystems, reducing both insect pests and weed seeds. However, insect foraging and feeding behavior can be highly dependent on the interaction network and spatial structure of the environment, which can make their biocontrol contributions variable. In the present article, we explore how the interaction network of carabids can affect their behavior and how spatial vegetation structure and specific agronomy practices can, in turn, affect the strength of interactions in their network. We suggest that research on carabid biocontrol should move toward an approach in which the network of interactions among pests, carabids, and other organisms within its spatial structure is evaluated, with equal focus on direct and indirect interactions, and provide examples of tools to do so. Overall, we believe this approach will improve our knowledge of carabid networks, help to elucidate the underlying mechanisms of biocontrol, and lay the foundation for future biocontrol strategies.
Mate Choice Behavior of Female Field Crickets Is Not Affected by Exposure to Heterospecific Calling Songs
Authors: Kuriwada Takashi , Kawasaki Rintaro , Kuwano Akifumi , Reddy Gadi V P 
Published: March 2020

AbstractMany animals produce acoustic signals to mark territories and attract mates. When different species produce acoustic signals simultaneously, the signals create a noisy environment, with potential acoustic interference between species. Theoretical studies suggest that such reproductive interference may have strong effects on species interaction. For example, the inferior resource competitor can survive if its disadvantage is counterbalanced by superiority in reproductive interference. Two field cricket species, Teleogryllus occipitalis (Audinet-Serville) (Orthoptera: Gryllidae) and Loxoblemmus equestris Saussure (Orthoptera: Gryllidae), cooccur in the same habitat. A previous study has shown that L. equestris is an inferior species to T. occipitalis in terms of resource competition. Therefore, we predicted that mate location and choice behavior of female T. occipitalis would be negatively affected by the acoustic signals of L. equestris and tested this with a series of playback experiments. The mate choice behavior of female T. occipitalis was not significantly affected by the calling song of L. equestris. Our results suggest that the acoustic interference does not explain the cooccurrence of the two species in the same habitat.
Multimodality imaging in cardiac amyloidosis: a primer for cardiologists
Authors: Jurcuţ Ruxandra , Onciul Sebastian , Adam Robert , Stan Claudiu , Coriu Daniel , Rapezzi Claudio , Popescu Bogdan A 
Published: March 2020

Abstract
Amyloidosis is a systemic infiltrative disease, in which unstable proteins misfold, form aggregates and amyloid fibrils which can deposit in various organs: heart, kidneys, liver, gastrointestinal tract, nervous system structures, lungs, or soft tissue. Cardiac amyloidosis (CA) diagnosis requires awareness, high level of clinical suspicion and expertise in integrating clinical, electrocardiographic, and multimodality imaging data. The overall scenario is complex and no single test emerges over the others, but different techniques are useful at various stages of the diagnostic workup. After a clinical suspicion of CA is raised by various non-imaging red-flags, eligible patients should undergo complete echocardiography and multiparametric cardiovascular magnetic resonance imaging. Even though the clinical suspicion of CA is confirmed by cardiac imaging, the accurate differentiation between the two most frequent and treatable amyloid types, i.e. light chain (AL) and transthyretin (ATTR) requires further work-up including phosphate scintigraphy. This article reviews the latest and essential data on multimodality imaging of patients with suspected or confirmed CA in a useful and practical manner for the general and imaging cardiologists.
Long-term dental stability after orthognathic surgery: a systematic review
Authors: Mulier Delphine , Gaitán Romero Lesly , Führer Alberto , Martin Catalina , Shujaat Sohaib , Shaheen Eman , Politis Constantinus , Jacobs Reinhilde 
Published: March 2020

Summary

Background
Long-term dental stability is one of the main objectives following combined orthodontic and orthognathic surgical treatment. It is influenced by multiple factors such as surgical, patient-related, and orthodontic aspects. While recent reviews mainly focus on short-term dental changes (0.5–2 years), longer follow-up dental stability remains hardly reviewed.

Objectives
The aim of this study was to evaluate long-term stability of dental and dentolabial changes following combined orthodontic and orthognathic surgical treatment with a minimum follow-up period of 5 years.

Search methods
A systematic search was conducted up to December 2019 using Pubmed, Embase, Web of Science, and Cochrane Central.

Selection criteria
Randomized controlled trials (RCTs), prospective and retrospective cohort studies, and case series with a minimum of 10 patients, which reported long-term dental stability following combined orthodontic and orthognathic treatment, were included.

Data collection and analysis
Long-term changes were assessed for overjet, overbite, maxillary, and mandibular incisors’ position and relationship of lip position to maxillary and mandibular incisors. Risk of bias was assessed according to the Cochrane Handbook.

Results
Following the screening of 3178 articles, 11 studies were included (2 RCT, 9 retrospective) with a postoperative follow-up period ranging from 5 to 15 years. A decrease in overjet was observed for patients with skeletal class III malocclusion, whereas overjet increased in class II patients at long-term follow-up. Overbite increased in class II patients, whereas class III showed variable results. The lower incisor position was more stable vertically than horizontally; the latter showing more outcome variability. Dentolabial changes corresponded to the normal ageing process and results were not clinically significant after long-term follow-up.

Conclusion
Current evidence suggests variability of dental and dentolabial stability in both skeletal class II and III patients. Further prospective studies are required to develop guidelines for long-term follow-up assessment using computer tomography or cone-beam computed tomography imaging, before final conclusions can be drawn.

Registration
The protocol for this systematic review (CRD42020133844) was registered in the International Prospective Register of Systematic Reviews (PROSPERO).
The origin of extracellular DNA in bacterial biofilm infectionsin vivo
Authors: Alhede Maria , Alhede Morten , Qvortrup Klaus , Kragh Kasper Nørskov , Jensen Peter Østrup , Stewart Philip Shook , Bjarnsholt Thomas 
Published: March 2020

ABSTRACTExtracellular DNA (eDNA) plays an important role in both the aggregation of bacteria and in the interaction of the resulting biofilms with polymorphonuclear leukocytes (PMNs) during an inflammatory response. Here, transmission electron and confocal scanning laser microscopy were used to examine the interaction between biofilms of Pseudomonas aeruginosa and PMNs in a murine implant model and in lung tissue from chronically infected cystic fibrosis patients. PNA FISH, DNA staining, labeling of PMN DNA with a thymidine analogue and immunohistochemistry were applied to localize bacteria, eDNA, PMN-derived eDNA, PMN-derived histone H3 (H3), neutrophil elastase (NE) and citrullinated H3 (citH3). Host-derived eDNA was observed surrounding bacterial biofilms but not within the biofilms. H3 localized to the lining of biofilms while NE was found throughout biofilms. CitH3, a marker for neutrophil extracellular traps (NETs) was detected only sporadically indicating that most host-derived eDNA in vivo was not a result of NETosis. Together these observations show that, in these in vivo biofilm infections with P. aeruginosa, the majority of eDNA is found external to the biofilm and derives from the host.
An update on the diversity, ecology and biogeography of the Saccharomyces genus
Authors: Alsammar Haya , Delneri Daniela 
Published: March 2020

ABSTRACT
Saccharomyces cerevisiae is the most extensively studied yeast and, over the last century, provided insights on the physiology, genetics, cellular biology and molecular mechanisms of eukaryotes. More recently, the increase in the discovery of wild strains, species and hybrids of the genus Saccharomyces has shifted the attention towards studies on genome evolution, ecology and biogeography, with the yeast becoming a model system for population genomic studies. The genus currently comprises eight species, some of clear industrial importance, while others are confined to natural environments, such as wild forests devoid from human domestication activities. To date, numerous studies showed that some Saccharomyces species form genetically diverged populations that are structured by geography, ecology or domestication activity and that the yeast species can also hybridize readily both in natural and domesticated environments. Much emphasis is now placed on the evolutionary process that drives phenotypic diversity between species, hybrids and populations to allow adaptation to different niches. Here, we provide an update of the biodiversity, ecology and population structure of the Saccharomyces species, and recapitulate the current knowledge on the natural history of Saccharomyces genus.
Comparative and Evolutionary Genomics of Isolates Provide Insight into the Pathoadaptation of Aeromonas
Authors: Talagrand-Reboul Emilie , Colston Sophie M , Graf Joerg , Lamy Brigitte , Jumas-Bilak Estelle 
Published: March 2020

Abstract
Aeromonads are ubiquitous aquatic bacteria that cause opportunistic infections in humans, but their pathogenesis remains poorly understood. A pathogenomic approach was undertaken to provide insights into the emergence and evolution of pathogenic traits in aeromonads. The genomes of 64 Aeromonas strains representative of the whole genus were analyzed to study the distribution, phylogeny, and synteny of the flanking sequences of 13 virulence-associated genes. The reconstructed evolutionary histories varied markedly depending on the gene analyzed and ranged from vertical evolution, which followed the core genome evolution (alt and colAh), to complex evolution, involving gene loss by insertion sequence-driven gene disruption, horizontal gene transfer, and paraphyly with some virulence genes associated with a phylogroup (aer, ser, and type 3 secretion system components) or no phylogroup (type 3 secretion system effectors, Ast, ExoA, and RtxA toxins). The general pathogenomic overview of aeromonads showed great complexity with diverse evolution modes and gene organization and uneven distribution of virulence genes in the genus; the results provided insights into aeromonad pathoadaptation or the ability of members of this group to emerge as pathogens. Finally, these findings suggest that aeromonad virulence-associated genes should be examined at the population level and that studies performed on type or model strains at the species level cannot be generalized to the whole species.
Epigenetic Modifications of GABAergic Interneurons Contribute to Deficits in Adult Hippocampus Neurogenesis and Depression-Like Behavior in Prenatally Stressed Mice
Authors: Zhong Haiquan , Rong Jing , Zhu Chunting , Liang Min , Li Yingchun , Zhou Rong 
Published: March 2020

Abstract

Background
Prenatal stress (PRS) is considered a risk factor for depressive disorder. Adult hippocampal neurogenesis is believed to play a role in the regulation of affective behaviors. GABAergic interneuron is a key modulator in adult hippocampal neurogenesis. Growing evidence indicates that PRS has adverse effects on adult hippocampal neurogenesis and DNA epigenetic modifications of the GABAergic system. The aim of this study was to investigate whether epigenetic GABAergic dysfunction participates in the negative impact of PRS on adult hippocampal neurogenesis and related emotional behaviors.

Methods
Behavioral tests were used to explore PRS-induced depression-like behaviors of adult female mice. Immunohistochemistry staining, real-time reverse transcription-polymerase chain reaction, western blot, and chromatin immunoprecipitation were employed to detect adult neurogenesis and epigenetic changes of the GABAergic system in the hippocampus of PRS mice.

Results
PRS mice developed a depression phenotype accompanied by the inhibited maturation of hippocampal newborn neurons. Compared with control mice, PRS mice showed decreased expression of glutamic acid decarboxylase 67 at the mRNA and protein levels. GABAA receptor agonist phenobarbital could rectify the decrease of 5-bromo-2-deoxyuridine/neuronal nuclei double-positive (BrdU+/NeuN+) cells in PRS mice. PRS mice also showed increased expression of DNA methyltransferase 1 and increased binding of DNA methyltransferase 1 to glutamic acid decarboxylase 67 promoter region. The treatment with DNA methyltransferase 1 inhibitor 5-aza-deoxycytidine restored the decrease of BrdU+/NeuN+ cells and depression-like behaviors in PRS mice via improving GABAergic system.

Conclusions
The present results indicate that epigenetic changes of the GABAergic system are responsible for adult hippocampus neurogenesis and depression-like behaviors in PRS mice.
Re-visioning International Studies: Innovation and Progress
Authors: Sandal Nukhet , Whitten-Woodring Jenifer 
Published: March 2020

Abstract
The 2019 theme for the International Studies Association's sixtieth annual convention was “Re-visioning International Studies: Innovation and Progress.” This theme challenged scholars to reflect on and overcome the methodological and theoretical differences that threaten to cloister international studies scholarship into silos. Communicating across these divides will not only facilitate progress in international studies scholarship but will also help to convey scholarly findings to policy circles and to have a positive impact on how local and global orders are constructed. The articles in this special issue identify opportunities to reenvision established theoretical and methodological assumptions, find common ground across different perspectives, and propose ways to incorporate and unify diverse approaches to international studies.
Mobile apps for real-world evidence in health care
Authors: Milne-Ives Madison , van Velthoven Michelle Helena , Meinert Edward 
Published: March 2020

Abstract
The use of real-world evidence for health care research and evaluation is growing. Mobile health apps have often-overlooked potential to contribute valuable real-world data that are not captured by other sources and could provide data that are more cost-effective and generalizable than can randomized controlled trials. However, there are several challenges that must be overcome to realize the potential value of patient-used mobile health app real-world data, including data quality, motivation for long-term use, privacy and security, methods of analysis, and standardization and integration. Addressing these challenges will increase the value of data from mobile health apps to inform real-world evidence and improve patient empowerment, clinical management, disease research, and treatment development.
Rapid response to COVID-19: health informatics support for outbreak management in an academic health system
Authors: Reeves J Jeffery , Hollandsworth Hannah M , Torriani Francesca J , Taplitz Randy , Abeles Shira , Tai-Seale Ming , Millen Marlene , Clay Brian J , Longhurst Christopher A 
Published: March 2020

Abstract

Objective
To describe the implementation of technological support important for optimizing clinical management of the COVID-19 pandemic.

Materials and Methods
Our health system has confirmed prior and current cases of COVID-19. An Incident Command Center was established early in the crisis and helped identify electronic health record (EHR)-based tools to support clinical care.

Results
We outline the design and implementation of EHR-based rapid screening processes, laboratory testing, clinical decision support, reporting tools, and patient-facing technology related to COVID-19.

Discussion
The EHR is a useful tool to enable rapid deployment of standardized processes. UC San Diego Health built multiple COVID-19-specific tools to support outbreak management, including scripted triaging, electronic check-in, standard ordering and documentation, secure messaging, real-time data analytics, and telemedicine capabilities. Challenges included the need to frequently adjust build to meet rapidly evolving requirements, communication, and adoption, and to coordinate the needs of multiple stakeholders while maintaining high-quality, prepandemic medical care.

Conclusion
The EHR is an essential tool in supporting the clinical needs of a health system managing the COVID-19 pandemic.