bluuebunny/crossref_metadata_2025_split huggingface dataset:
Network-based characterization of disease–disease relationships in terms of drugs and therapeutic targets
Authors: Iida Midori , Iwata Michio , Yamanishi Yoshihiro 
Published: May 2020

Abstract

Motivation
Disease states are distinguished from each other in terms of differing clinical phenotypes, but characteristic molecular features are often common to various diseases. Similarities between diseases can be explained by characteristic gene expression patterns. However, most disease–disease relationships remain uncharacterized.

Results
In this study, we proposed a novel approach for network-based characterization of disease–disease relationships in terms of drugs and therapeutic targets. We performed large-scale analyses of omics data and molecular interaction networks for 79 diseases, including adrenoleukodystrophy, leukaemia, Alzheimer's disease, asthma, atopic dermatitis, breast cancer, cystic fibrosis and inflammatory bowel disease. We quantified disease–disease similarities based on proximities of abnormally expressed genes in various molecular networks, and showed that similarities between diseases could be explained by characteristic molecular network topologies. Furthermore, we developed a kernel matrix regression algorithm to predict the commonalities of drugs and therapeutic targets among diseases. Our comprehensive prediction strategy indicated many new associations among phenotypically diverse diseases.

Supplementary information
Supplementary data are available at Bioinformatics online.
MinReact: a systematic approach for identifying minimal metabolic networks
Authors: Sambamoorthy Gayathri , Raman Karthik 
Published: May 2020

Abstract

Motivation
Genome-scale metabolic models are widely constructed and studied for understanding various design principles underlying metabolism, predominantly redundancy. Metabolic networks are highly redundant and it is possible to minimize the metabolic networks into smaller networks that retain the functionality of the original network.

Results
Here, we establish a new method, MinReact that systematically removes reactions from a given network to identify minimal reactome(s). We show that our method identifies smaller minimal reactomes than existing methods and also scales well to larger metabolic networks. Notably, our method exploits known aspects of network structure and redundancy to identify multiple minimal metabolic networks. We illustrate the utility of MinReact by identifying multiple minimal networks for 77 organisms from the BiGG database. We show that these multiple minimal reactomes arise due to the presence of compensatory reactions/pathways. We further employed MinReact for a case study to identify the minimal reactomes of different organisms in both glucose and xylose minimal environments. Identification of minimal reactomes of these different organisms elucidate that they exhibit varying levels of redundancy. A comparison of the minimal reactomes on glucose and xylose illustrates that the differences in the reactions required to sustain growth on either medium. Overall, our algorithm provides a rapid and reliable way to identify minimal subsets of reactions that are essential for survival, in a systematic manner.

Availability and implementation
Algorithm is available from https://github.com/RamanLab/MinReact.

Supplementary information
Supplementary data are available at Bioinformatics online.
A multimodal deep learning framework for predicting drug–drug interaction events
Authors: Deng Yifan , Xu Xinran , Qiu Yang , Xia Jingbo , Zhang Wen , Liu Shichao 
Published: May 2020

Abstract

Motivation
Drug–drug interactions (DDIs) are one of the major concerns in pharmaceutical research. Many machine learning based methods have been proposed for the DDI prediction, but most of them predict whether two drugs interact or not. The studies revealed that DDIs could cause different subsequent events, and predicting DDI-associated events is more useful for investigating the mechanism hidden behind the combined drug usage or adverse reactions.

Results
In this article, we collect DDIs from DrugBank database, and extract 65 categories of DDI events by dependency analysis and events trimming. We propose a multimodal deep learning framework named DDIMDL that combines diverse drug features with deep learning to build a model for predicting DDI-associated events. DDIMDL first constructs deep neural network (DNN)-based sub-models, respectively, using four types of drug features: chemical substructures, targets, enzymes and pathways, and then adopts a joint DNN framework to combine the sub-models to learn cross-modality representations of drug–drug pairs and predict DDI events. In computational experiments, DDIMDL produces high-accuracy performances and has high efficiency. Moreover, DDIMDL outperforms state-of-the-art DDI event prediction methods and baseline methods. Among all the features of drugs, the chemical substructures seem to be the most informative. With the combination of substructures, targets and enzymes, DDIMDL achieves an accuracy of 0.8852 and an area under the precision–recall curve of 0.9208.

Availability and implementation
The source code and data are available at https://github.com/YifanDengWHU/DDIMDL.

Supplementary information
Supplementary data are available at Bioinformatics online.
BioStructures.jl: read, write and manipulate macromolecular structures in Julia
Authors: Greener Joe G , Selvaraj Joel , Ward Ben J 
Published: May 2020

Abstract

Summary
Robust, flexible and fast software to read, write and manipulate macromolecular structures is a prerequisite for productively doing structural bioinformatics. We present BioStructures.jl, the first dedicated package in the Julia programming language for dealing with macromolecular structures and the Protein Data Bank. BioStructures.jl builds on the lessons learned with similar packages to provide a large feature set, a flexible object representation and high performance.

Availability and implementation
BioStructures.jl is freely available under the MIT license. Source code and documentation are available at https://github.com/BioJulia/BioStructures.jl. BioStructures.jl is compatible with Julia versions 0.6 and later and is system-independent.

Contact
j.greener@ucl.ac.uk
Disrupted Neural Synchrony Mediates the Relationship between White Matter Integrity and Cognitive Performance in Older Adults
Authors: Hinault T , Kraut M , Bakker A , Dagher A , Courtney S M 
Published: May 2020

Abstract
Our main goal was to determine the influence of white matter integrity on the dynamic coupling between brain regions and the individual variability of cognitive performance in older adults. Electroencephalography was recorded while participants performed a task specifically designed to engage working memory and inhibitory processes, and the associations among functional activity, structural integrity, and cognitive performance were assessed. We found that the association between white matter microstructural integrity and cognitive functioning with aging is mediated by time-varying alpha and gamma phase-locking value. Specifically, better preservation of the inferior fronto-occipital fasciculus in older individuals drives faster task-related modulations of alpha and gamma long-range phase-locking value between the inferior frontal gyrus and occipital lobe and lower local phase-amplitude coupling in occipital lobes, which in turn drives better cognitive control performance. Our results help delineate the role of individual variability of white matter microstructure in dynamic synchrony and cognitive performance during normal aging.
Olig2-Induced Semaphorin Expression Drives Corticospinal Axon Retraction After Spinal Cord Injury
Authors: Ueno Masaki , Nakamura Yuka , Nakagawa Hiroshi , Niehaus Jesse K , Maezawa Mari , Gu Zirong , Kumanogoh Atsushi , Takebayashi Hirohide , Lu Qing Richard , Takada Masahiko , Yoshida Yutaka 
Published: May 2020

Abstract
Axon regeneration is limited in the central nervous system, which hinders the reconstruction of functional circuits following spinal cord injury (SCI). Although various extrinsic molecules to repel axons following SCI have been identified, the role of semaphorins, a major class of axon guidance molecules, has not been thoroughly explored. Here we show that expression of semaphorins, including Sema5a and Sema6d, is elevated after SCI, and genetic deletion of either molecule or their receptors (neuropilin1 and plexinA1, respectively) suppresses axon retraction or dieback in injured corticospinal neurons. We further show that Olig2+ cells are essential for SCI-induced semaphorin expression, and that Olig2 binds to putative enhancer regions of the semaphorin genes. Finally, conditional deletion of Olig2 in the spinal cord reduces the expression of semaphorins, alleviating the axon retraction. These results demonstrate that semaphorins function as axon repellents following SCI, and reveal a novel transcriptional mechanism for controlling semaphorin levels around injured neurons to create zones hostile to axon regrowth.
Signet ring gastric and esophageal adenocarcinomas: characteristics and prognostic implications
Authors: Khan Niall , Donohoe Claire L , Phillips Alexander W , Griffin S Michael , Reynolds John V 
Published: May 2020

Summary
Controversy exists as to the relevance of the signet ring carcinoma (SRC) histological subtype of esophagogastric adenocarcinoma to long-term prognosis, with some studies reporting a worsened oncological outcome and others no clinically relevant impact. A retrospective analysis of outcomes of patients who underwent surgery with curative intent in two high-volume centers (2000–2015) was undertaken. Tumors were analyzed according to location (esophageal, junctional or gastric). Propensity score matching (PSM) analysis was used to match patients with signet ring histology to those without (195 SRC vs. 573 non-SRC), based on age, tumor location, use of neoadjuvant and adjuvant chemotherapy and pathological stage. A total of 2,500 patients with esophagogastric adenocarcinomas were treated, of whom 198 (7.9%) had signet ring histology. Signet ring tumors were more likely to have positive lymph nodes at pathological analysis (59% vs. 50%, P = 0.009). The 5-year survival rate for patients with early signet ring tumors (Stage 0/I/IIa) was 65% versus 85% for other early cancers (P &lt; 0.003). Patients with esophageal signet ring tumors had a particularly poor prognosis with 23% 2-year survival and none alive at 5 years. With PSM, overall survival (OS) was significantly poorer in the signet ring group (44.3 ± 8.6 vs. 59.8 ± 8.5 months, 5-year OS 41% vs. 50%, P = 0.027). Signet ring cells within esophagogastric adenocarcinoma are associated with a poorer prognosis. Genomic studies to identify the composition of such tumors as well as identify strategies to improve treatment for this subtype are warranted.
Practice patterns and adherence to clinical guidelines for diagnosis and management of eosinophilic esophagitis among gastroenterologists
Authors: Eluri Swathi , Iglesia Edward G A , Massaro Michael , Peery Anne F , Shaheen Nicholas J , Dellon Evan S 
Published: May 2020

Summary
Real-world practice patterns of eosinophilic esophagitis (EoE) among gastroenterologists are not well-described. The aim is to describe practice patterns of EoE diagnosis and management and assess concordance with consensus guidelines. We conducted a cross-sectional online survey of gastroenterologists in the USA using Qualtrics, which was dispersed through the North Carolina Society of Gastroenterology (NCSG) and the American College of Gastroenterology member listservs. A similar survey was sent to NCSG members in 2010 and responses were compared in a subanalysis. Of 240 respondents, 37% (n = 80) worked in an academic setting versus 63% (n = 138) community practice setting. Providers saw a median of 18 (interquartile range 2–100) EoE patients annually and 24% (n = 52) were ‘very familiar’ with EoE guidelines. A proton-pump inhibitor (PPI) trial was required by 37% of providers prior to EoE diagnosis. In total, 60% used a ≥15 eosinophils per high-power field cut point for diagnosis and 62% biopsied from the proximal and distal esophagus on initial exam. Only 12% (n = 28) followed EoE diagnosis guidelines. For first-line treatment, 7% used dietary therapy, 32% topical steroids, and 61% used PPIs; 67% used fluticasone as first-line steroid; 41% used maintenance steroid treatment in responders. In the NCSG cohort, a higher proportion in 2017 followed guideline diagnosis recommendations compared with 2010 (14% vs. 3%; P = 0.03) and a higher proportion used dietary therapy as first-line treatment (13% vs. 3%; P = 0.046). There is variability in EoE practice patterns for EoE management, with management differing markedly from consensus guidelines. Further education and guideline dissemination are needed to standardize practice.
The carbon sequestration potential of ‘analog’ forestry in Ecuador: an alternative strategy for reforestation of degraded pastures
Authors: Veintimilla Raúl Armando Ramos , MacFarlane David , Cooper Lauren 
Published: May 2020

Abstract
‘Analog’ forestry is a novel silvicultural approach for reforestation of degraded land that seeks to establish trees that are analogous in structure and ecological function to the original climax or subclimax vegetation of the region where they are planted. Analog forestry aims to strengthen rural communities, both socially and economically, with tree plantings of high biodiversity, which provide commercial products and resiliency, while avoiding agrochemicals and fossil fuels. The latter links this strategy to climate change mitigation and adaptation strategies, but there has been little analysis comparing the potential for above- and below-ground carbon storage in analog forests, as compared with more typical reforestation efforts via single-species plantations. We present the results of a study to estimate carbon sequestration levels, above- and below-ground, from an experimental analog forest system and a teak (Tectona grandis L.f.) plantation system, in comparison with a degraded pasture system. The study found that the analog and teak plantation forest systems stored higher quantities of total carbon (178 and 141 t C ha−1, respectively), when compared with a degraded pasture system (124 t C ha−1). However, the teak plantation had decreased soil carbon stocks, relative to the degraded pasture. The analog forest had the best balance of both above- and below-ground carbon stored over the 17-year study period and provided a more diverse array of timber and non-timber forest products when compared with the teak plantation. This suggests that analog forestry could be a viable social–ecological approach to carbon storage and reforestation in the study region and other places with large areas of degraded pasture and a good understanding of the structure and function of the original vegetation.
Childhood Friendship Experiences and Cognitive Functioning in Later Life: The Mediating Roles of Adult Social Disconnectedness and Adult Loneliness
Authors: Burr Jeffrey A , Han Sae Hwang , Peng Changmin 
Published: May 2020

AbstractBackground and ObjectivesThis study investigated the relationship between childhood friendships and cognitive functioning, as assessed with cognitive status and decline among adults aged 45 and older in China. We also examined the mediating effect of adult social disconnectedness and adult loneliness for this relationship.Research Design and MethodsThis study was based on 3 waves of data from the China Health and Retirement Longitudinal Study (CHARLS; 2011, 2013, 2015; N = 13,959). Cognitive functioning was assessed with episodic memory. Childhood friendship measures were taken from the 2014 life history module of the CHARLS. Two dimensions of adult social isolation, loneliness and social disconnectedness, were included as mediators. Latent growth curve modeling was utilized to test the associations between childhood friendships, adult social isolation, and cognitive functioning.ResultsAdverse childhood friendship experiences were found to be significantly associated with both lower initial cognitive status and the rate of decline in cognitive functioning. Our findings indicated that adult loneliness and social disconnectedness partly mediated the link between childhood friendship experiences and the initial level of cognitive functioning, but not cognitive decline later in life.Discussion and ImplicationsThe findings emphasized the enduring importance of childhood friendships for cognitive functioning later in life. Interventions that focus on improving social participation through fostering friendships in childhood may have long-term benefits for cognition later in life.
Reconciling elasticity tensor constraints from mineral physics and seismological observations: applications to the Earth’s inner core
Authors: Delbridge Brent G , Ishii Miaki 
Published: May 2020

SUMMARY
This study establishes the proper framework in which to compare seismic observations with mineral physics constraints for studies of the inner core by determining how the elements of the elasticity tensor are sampled by the normal modes of the Earth. The obtained mapping between the elements of the elasticity tensor and the seismic wave speeds shows that the choice of averaging scheme used to calculate isotropic properties is crucial to understand the composition of the inner core, especially for comparison with the shear wave speed such as that provided in PREM. For example, the appropriate shear wave speed calculated for an Fe-Ni-Si hcp alloy at inner-core conditions differs from the shear wave speed obtained by taking a Reuss average by as much as $27\, {\rm per\, cent}$. It is also shown for the first time that by combining the isotropic observations based upon normal-mode characteristic frequencies and anisotropic parameters from their splitting, the five independent elastic parameters (A, C, F, L and N) that fully describe a transversely isotropic inner core can be uniquely constrained. The elastic values based upon a variety of mode-splitting studies are reported, and the differences between models from various research groups are shown to be relatively small ($\lt 10\, {\rm per\, cent}$). Additionally, an analogous body-wave methodology is developed to approximately estimate the five independent elastic constants from observations of compressional wave traveltime anomalies. The body-wave observations are utilized to consider the depth dependence of inner-core anisotropy, in particular, the structure of the innermost inner core. Finally, we demonstrate that substantial errors may result when attempting to relate seismically observed P and S wave speeds from Debye velocities obtained through nuclear resonant inelastic X-ray scattering. The results of these experiments should be compared directly with the Debye velocity calculated from seismically constrained elastic constants. This manuscript provides a new set of formulae and values of seismic observations of the inner core that can be easily compared against mineral physics constraints for better understanding of the inner-core composition.
How images frame China's role in African development
Authors: Karavas George 
Published: May 2020

Abstract
Political leaders, policy-makers and academics routinely refer to development as an objective process of social change through the use of technical, value-free terms. Images of poverty and inequality are regularly presented as evidence of a world that exists ‘out there’ where development unfolds. This way of seeing reflects the value of scientific forms of knowledge but also sits in tension with the normative foundations of development that take European modernization and industrialization as the benchmark for comparison. The role images play in this process is often overlooked. This article argues that a dominant mode of visuality based on a Cartesian separation between subject and object, underpinning the ascendance of European hegemony and colonialism, aligns with the core premises of orthodox development discourse. An example of how visual representations of development matter is presented through images of Africa–China relations in western media sources. Using widely circulated images depicting China's impact on African development in western news media sources as an example of why visual politics matters for policy-making, the article examines how images play a role in legitimizing development planning by rendering associated forms of epistemological and structural violence ‘invisible to the viewer’.
Politics, policy-making and the presence of images of suffering children
Authors: Berents Helen 
Published: May 2020

Abstract
In 2017 Trump expressed pity for the ‘beautiful babies’ killed in a gas attack on Khan Shaykhun in Syria before launching airstrikes against President Assad's regime. Images of suffering children in world politics are often used as a synecdoche for a broader conflict or disaster. Injured, suffering, or dead; the ways in which images of children circulate in global public discourse must be critically examined to uncover the assumptions that operate in these environments. This article explores reactions to images of children by representatives and leaders of states to trace the interconnected affective and political dimensions of these images. In contrast to attending to the expected empathetic responses prompted by images of children, this article particularly focuses on when such images prompt bellicose foreign policy decision-making. In doing this, the article forwards a way of thinking about images as contentious affective objects in international relations. The ways in which images of children's bodies and suffering are strategically deployed by politicians deserves closer scrutiny to uncover the visual politics of childhood inherent in these moments of international politics and policy-making.
Misconceptions about Conception and Other Fallacies: Historical Bias in Reproductive Biology
Authors: Hayssen Virginia 
Published: May 2020

AbstractNatural selection (differential reproduction) is a major tenet of evolutionary theory. In mammals the success of reproduction is primarily controlled by females who provide the majority of offspring care via gestation and lactation. In some species, maternal care also extends post-weaning. This primacy of female reproduction in evolution has not quite crept into our understanding of organismal adaptations in anatomy, physiology, and behavior. This cultural legacy has left its mark and led to misconceptions in our understanding of reproductive biology that are especially prominent in the understanding of reproduction in the general public. Here, I give examples of such misconceptions. I focus on aspects of physiology (the “sperm race,” the “estrous cycle,” the “28-day” menstrual cycle, “sex” hormones, and meiosis) as well as aspects of terminology in morphology and behavior. The issues I raise are not new, but all remain embedded in the teaching of reproductive biology especially at the introductory level. For each issue, I examine the historical bias, the consequences of that bias, and, more importantly, ways to ameliorate that bias going forward.