bluuebunny/crossref_metadata_2025_split huggingface dataset:
V—Time and Subtle Pictures in the History of Philosophy
Authors: Thomas Emily 
Published: March 2020

AbstractFor centuries, philosophers of time have produced texts containing words and pictures. Although some historians study visual representations of time, I have not found any history of philosophy on pictures of time within texts. This paper argues that studying such pictures can be rewarding. I will make this case by studying pictures of time in the works of Leibniz, Arthur Eddington and C. D. Broad, and argue they play subtle roles. Further, I will argue that historians of philosophy more widely could benefit from paying more attention to pictures.
Recent advances in biomedical literature mining
Authors: Zhao Sendong , Su Chang , Lu Zhiyong , Wang Fei 
Published: March 2020

Abstract
The recent years have witnessed a rapid increase in the number of scientific articles in biomedical domain. These literature are mostly available and readily accessible in electronic format. The domain knowledge hidden in them is critical for biomedical research and applications, which makes biomedical literature mining (BLM) techniques highly demanding. Numerous efforts have been made on this topic from both biomedical informatics (BMI) and computer science (CS) communities. The BMI community focuses more on the concrete application problems and thus prefer more interpretable and descriptive methods, while the CS community chases more on superior performance and generalization ability, thus more sophisticated and universal models are developed. The goal of this paper is to provide a review of the recent advances in BLM from both communities and inspire new research directions.
QuartataWeb: Integrated Chemical–Protein-Pathway Mapping for Polypharmacology and Chemogenomics
Authors: Li Hongchun , Pei Fen , Taylor D Lansing , Bahar Ivet 
Published: March 2020

Abstract

Summary
QuartataWeb is a user-friendly server developed for polypharmacological and chemogenomics analyses. Users can easily obtain information on experimentally verified (known) and computationally predicted (new) interactions between 5494 drugs and 2807 human proteins in DrugBank, and between 315 514 chemicals and 9457 human proteins in the STITCH database. In addition, QuartataWeb links targets to KEGG pathways and GO annotations, completing the bridge from drugs/chemicals to function via protein targets and cellular pathways. It allows users to query a series of chemicals, drug combinations or multiple targets, to enable multi-drug, multi-target, multi-pathway analyses, toward facilitating the design of polypharmacological treatments for complex diseases.

Availability and implementation
QuartataWeb is freely accessible at http://quartata.csb.pitt.edu.

Supplementary information
Supplementary data are available at Bioinformatics online.
FUpred: detecting protein domains through deep-learning-based contact map prediction
Authors: Zheng Wei , Zhou Xiaogen , Wuyun Qiqige , Pearce Robin , Li Yang , Zhang Yang 
Published: March 2020

Abstract

Motivation
Protein domains are subunits that can fold and function independently. Correct domain boundary assignment is thus a critical step toward accurate protein structure and function analyses. There is, however, no efficient algorithm available for accurate domain prediction from sequence. The problem is particularly challenging for proteins with discontinuous domains, which consist of domain segments that are separated along the sequence.

Results
We developed a new algorithm, FUpred, which predicts protein domain boundaries utilizing contact maps created by deep residual neural networks coupled with coevolutionary precision matrices. The core idea of the algorithm is to retrieve domain boundary locations by maximizing the number of intra-domain contacts, while minimizing the number of inter-domain contacts from the contact maps. FUpred was tested on a large-scale dataset consisting of 2549 proteins and generated correct single- and multi-domain classifications with a Matthew’s correlation coefficient of 0.799, which was 19.1% (or 5.3%) higher than the best machine learning (or threading)-based method. For proteins with discontinuous domains, the domain boundary detection and normalized domain overlapping scores of FUpred were 0.788 and 0.521, respectively, which were 17.3% and 23.8% higher than the best control method. The results demonstrate a new avenue to accurately detect domain composition from sequence alone, especially for discontinuous, multi-domain proteins.

Availability and implementation
https://zhanglab.ccmb.med.umich.edu/FUpred.

Supplementary information
Supplementary data are available at Bioinformatics online.
Machine Learning Using Digitized Herbarium Specimens to Advance Phenological Research
Authors: Pearson Katelin D , Nelson Gil , Aronson Myla F J , Bonnet Pierre , Brenskelle Laura , Davis Charles C , Denny Ellen G , Ellwood Elizabeth R , Goëau Hervé , Heberling J Mason , Joly Alexis , Lorieul Titouan , Mazer Susan J , Meineke Emily K , Stucky Brian J , Sweeney Patrick , White Alexander E , Soltis Pamela S 
Published: March 2020

AbstractMachine learning (ML) has great potential to drive scientific discovery by harvesting data from images of herbarium specimens—preserved plant material curated in natural history collections—but ML techniques have only recently been applied to this rich resource. ML has particularly strong prospects for the study of plant phenological events such as growth and reproduction. As a major indicator of climate change, driver of ecological processes, and critical determinant of plant fitness, plant phenology is an important frontier for the application of ML techniques for science and society. In the present article, we describe a generalized, modular ML workflow for extracting phenological data from images of herbarium specimens, and we discuss the advantages, limitations, and potential future improvements of this workflow. Strategic research and investment in specimen-based ML methods, along with the aggregation of herbarium specimen data, may give rise to a better understanding of life on Earth.
In Their Own Words: Gregory Anderson
Authors: Verdier James M 
Published: March 2020

Abstract
In Their Own Words chronicles the stories of scientists who have made great contributions to their fields, particularly within the biological sciences. These short oral histories provide our readers a way to learn from and share their experiences. Each month, we will publish in the pages of BioScience and in our podcast, BioScience Talks (http://bioscienceaibs.libsyn.com), the results of these conversations. This oral history is with Gregory Anderson, who is with the Department of Ecology and Evolutionary Biology, at the University of Connecticut, Storrs. He previously served as president of the American Institute of Biological Sciences.
Note: Both the text and audio versions have been edited for clarity and length.
The mental health status of asylum seekers in middle- to high-income countries: a synthesis of current global evidence
Authors: Posselt Miriam , McIntyre Heather , Ngcanga Mtho , Lines Thomas , Procter Nicholas 
Published: March 2020

Abstract

Introduction
The last 5 years have witnessed a significant increase in the number of people fleeing their countries of origin and seeking refuge in host countries. By the end of 2018, there were 3.5 million asylum seekers awaiting outcomes on their applications, the majority of whom were hosted by middle- to high-income countries. This review aimed to identify and synthesize current knowledge regarding the mental health status of asylum seekers in middle- to high-income countries.

Sources of data
A search was conducted across various databases for research literature published within the last 5 years (2014–2019). The final review and synthesis included 25 articles.

Areas of agreement
Findings highlighted significant differences in the mental health status of asylum seekers compared to those with refugee status and permanent residence.

Areas of controversy
Guidelines from the World Health Organization and the United Nations High Commissioner for Refugees emphasize the need to understand and address mental health issues. Instead, there have been policy changes in many host countries regarding asylum applications, and the associated effects of these changes have been shown to negatively impact mental health.

Growing points
The synthesized findings from the present review provide information regarding the current mental health status of asylum seekers hosted by middle- to high-income countries. Areas of intervention and resource allocation were also identified.

Areas timely for developing research
Future research should consider the impact of large-scale, low-cost interventions to support the mental health of those seeking asylum.
Specificity and Diagnostic Utility of Cerebrospinal Fluid CXCL13 in Lyme Neuroborreliosis
Authors: Eckman Elizabeth A , Clausen Dana M , Herdt Aimee R , Pacheco-Quinto Javier , Halperin John J 
Published: March 2020

Abstract

Background
Demonstration of intrathecal production of Borrelia-specific antibodies (ITAb) is considered the most specific diagnostic marker of Lyme neuroborreliosis (LNB). Limitations include delayed detectability in early infection and continued presence long after successful treatment. Markers of active inflammation—increased cerebrospinal fluid (CSF) leukocytes, protein, and CXCL13—provide nonspecific markers of active infection. To assess the utility of CSF CXCL13, we measured its concentration in 132 patients with a broad spectrum of neuroinflammatory disorders, including LNB.

Methods
CSF CXCL13 was measured by immunoassay. Spearman rank correlation test was performed to explore its relationship to conventional markers of neuroinflammation and Borrelia-specific ITAb production.

Results
In non-LNB neuroinflammatory disorders, CSF CXCL13 elevation correlated with CSF immunoglobulin G (IgG) synthesis and leukocyte count. In LNB, CXCL13 concentration was far greater than expected from overall CSF IgG synthesis, and correlated with Borrelia-specific ITAb synthesis. Median CSF CXCL13 concentration in ITAb-positive LNB patients was &gt; 500 times greater than in any other group.

Conclusions
Intrathecal CXCL13 and IgG production are closely interrelated. CXCL13 is disproportionately increased in “definite LNB,” defined as having demonstrable Borrelia-specific ITAb, but not “probable LNB,” without ITAb. This disproportionate increase may help identify patients with very early infection or those with active vs treated LNB, or may help to differentiate ITAb-defined active LNB from other neuroinflammatory disorders. However, its reported specificity is closely related to the diagnostic requirement for ITAb. It may add little specificity to the demonstration of a pleocytosis or increased overall or specific IgG production in the CSF.
Performance Improvement Of Pre-trained Convolutional Neural Networks For Action Recognition
Authors: Ozcan Tayyip , Basturk Alper 
Published: March 2020

Abstract
Action recognition is a challenging task. Deep learning models have been investigated to solve this problem. Setting up a new neural network model is a crucial and time-consuming process. Alternatively, pre-trained convolutional neural network (CNN) models offer rapid modeling. The selection of the hyperparameters of CNNs is a challenging issue that heavily depends on user experience. The parameters of CNNs should be carefully selected to get effective results. For this purpose, the artificial bee colony (ABC) algorithm is used for tuning the parameters to get optimum results. The proposed method includes three main stages: the image preprocessing stage involves automatic cropping of the meaningful area within the images in the data set, the transfer learning stage includes experiments with six different pre-trained CNN models and the hyperparameter tuning stage using the ABC algorithm. Performance comparison of the pre-trained CNN models involving the use and nonuse of the ABC algorithm for the Stanford 40 data set is presented. The experiments show that the pre-trained CNN models with ABC are more successful than pre-trained CNN models without ABC. Additionally, to the best of our knowledge, the improved NASNet-Large CNN model with the ABC algorithm gives the best accuracy of 87.78% for the overall success rate-based performance metric.
The role of three-dimensional reconstructions in understanding the intersegmental plane: an anatomical study of segment 6
Authors: Sarsam Matthieu , Glorion Matthieu , de Wolf Julien , Cassiano Francesco , Puyo Philippe , Sage Edouard , Chapelier Alain 
Published: March 2020

Abstract

OBJECTIVES
The identification of the intersegmental plane during lung segmentectomies remains a practical difficulty, notably with minimally invasive approaches. The intraoperative techniques are based on demarcating either the bronchial or the vascular territories. The goal of this study was to evaluate the use of 3-dimensional reconstructions in understanding the intersegmental plane of segment 6.

METHODS
Between March and September 2018, Synapse 3-dimensional programme was used to carry out bilateral venous, arterial and bronchial segmentations of segment 6. All computed tomography (CT) scans were contrast-enhanced and of a high resolution (0.6 mm slices). The patients had normal results on respiratory function tests. The volumes obtained from each of the 3 modalities were then compared. The results are presented as mean and standard deviation and as median and interquartile ranges for lung volume measurements.

RESULTS
During the aforementioned period, 15 high-resolution chest CT scans were selected (8 men and 7 women). The median age was 70 years. In all of the studied segments (N = 30, 15 right S6 and 15 left S6), the segmental volume of the vein was greater than the segmental volumes of the bronchus and the artery. A significant difference was found between the segmental volumes obtained from the 3 modalities (P = 0.001). The segmental volume of the vein was significantly higher than the segmental volume of the bronchus (P &lt; 0.001) and the segmental volume of the artery (P &lt; 0.001). On the other hand, the segmental volume of the artery was significantly higher than the segmental volume of the bronchus (P = 0.01).

CONCLUSIONS
Within the limits of this study, the segmental venous volume of S6 was greater than the volumes of the segmental bronchial and arterial volumes. Thus, depending solely on bronchial techniques might lead to leaving a border zone in venous congestion.
Accumulation of Deleterious Mutations in Landlocked Threespine Stickleback Populations
Authors: Yoshida Kohta , Ravinet Mark , Makino Takashi , Toyoda Atsushi , Kokita Tomoyuki , Mori Seiichi , Kitano Jun 
Published: March 2020

AbstractColonization of new habitats often reduces population sizes and may result in the accumulation of deleterious mutations by genetic drift. Compared with the genomic basis for adaptation to new environments, genome-wide analysis of deleterious mutations in isolated populations remains limited. In the present study, we investigated the accumulation of deleterious mutations in five endangered freshwater populations of threespine stickleback (Gasterosteus aculeatus) in the central part of the mainland of Japan. Using whole-genome resequencing data, we first conducted phylogenomic analysis and confirmed at least two independent freshwater colonization events in the central mainland from ancestral marine ecotypes. Next, analyses of single nucleotide polymorphisms showed a substantial reduction of heterozygosity in freshwater populations compared with marine populations. Reduction in heterozygosity was more apparent at the center of each chromosome than the peripheries and on X chromosomes compared with autosomes. Third, bioinformatic analysis of deleterious mutations showed increased accumulation of putatively deleterious mutations in the landlocked freshwater populations compared with marine populations. For the majority of populations examined, the frequencies of putatively deleterious mutations were higher on X chromosomes than on autosomes. The interpopulation comparison indicated that the majority of putatively deleterious mutations may have accumulated independently. Thus, whole-genome resequencing of endangered populations can help to estimate the accumulation of deleterious mutations and inform us of which populations are the most severely endangered. Furthermore, analysis of variation among chromosomes can give insights into whether any particular chromosomes are likely to accumulate deleterious mutations.
Seismic repeaters linked to weak rock-mass creep in deep excavation mining
Authors: Kinscher J L , De Santis F , Poiata N , Bernard P , Palgunadi K H , Contrucci I 
Published: March 2020

SUMMARYSeismic repeaters are a phenomenon rarely observed in mining environments. In this study, we show that repeaters and associated aseismic slip can be the governing mechanism behind seismic triggering in response to excavation mining, providing new perspectives for rethinking and improving standard procedures for seismic rock burst hazard assessment and mining monitoring. Evidence comes from an extensive multiplet analysis on dense spatiotemporal microseismic event clusters (−2.5 &lt; Mw &lt; 1) that was recorded by a local microseismic network at the Lappberget orebody in the Garpenberg mine in Sweden at around 1 km depth. Analysis involved template matching, clustering, double-difference relocation, source parameter and mechanism estimation, as well as interevent time analysis. The results show that almost 80 per cent of the analysed events can be interpreted as seismic repeaters. Source mechanisms demonstrate systematic strike-slip faulting with a significant reverse faulting component, indicating that triggering of the repeaters is sensitive to increases in the horizontal compressive stresses. We suggest that seismic repeaters represent brittle frictional parts (asperity) of creeping, planar shaped, pre-exiting structures of several metres composed of weak rock-mass materials (e.g. talc) associated with strengthening friction behaviours. This repeater model and the here used definition of asperity thus slightly differs from its meaning in classical seismological models where repeating events are related to the locked fault patches along a creeping fault. In addition, we identified different asperity types for the different repeater families that we interpret as different friction properties. Some multiplet families represent rather a transitional case between multiplet and repeater occurrences that might imply a mixture of weakening and strengthening friction processes, that is, creep and brittle rupture along neighboured plane shaped anisotropies in a heterogeneous rock mass. The exact nature of asperities and seismic and aseismic coupling of the rock mass as well as the propagation mechanism of strain and stress associated with short-term (days to weeks) and long-term (months to years) post-blast creep remains uncertain and needs to be addressed by future investigations. The understanding of these processes is particularly important for assessing hazard of larger dynamic ruptures.
Non-Compensable Regulation versus Regulatory Expropriation: Are Climate Change Regulations Compensable?
Authors: Khachvani David 
Published: March 2020

Abstract
The global threat posed by climate change calls for increased governmental regulation in various fields of economic activity. New regulations, especially in the carbon-intensive industries, will likely interfere with economic interests and acquired rights of foreign investors. One of the main questions that investment treaty tribunals will have to answer in this context is whether, and to what extent, such regulations should be accompanied by compensation.
Investment treaty jurisprudence has yet to come up with comprehensive criteria for distinguishing compensable regulatory expropriation from non-compensable exercise of regulatory powers. This uncertainty is particularly evident from recent cases dealing with issues, such as plain packaging for tobacco, nuclear energy phase-out and solar energy tariffs. The absence of specific criteria causes concern among States, investors and other stakeholders, and contributes to the ongoing backlash against the investor–State dispute settlement system.
This article suggests drawing the borderline between non-compensable regulation and regulatory expropriation in reference to inherent limits of property rights that underlie foreign investments. Although the State owes compensation to an investor whose property rights are dispossessed by an increased regulation, it is uncontroversial that property rights are themselves limited by the rights of others. The precise limits change over time, in light of new circumstances and available scientific evidence. Prudent investors, especially those active in hazardous industries, assume the risk of such changes as part of their business risk. A regulation that does no more than to clarify the inherent limits of the investor’s rights in light of newly emerging circumstances does not constitute an interference with such rights and does not therefore qualify as expropriation. Under this approach, bona fide regulations that aim to tackle the emerging threats posed by climate change do not engender a right to compensation.
Disturbed Resting-State Whole-Brain Functional Connectivity of Striatal Subregions in Bulimia Nervosa
Authors: Wang Li , Bi Kun , Song Zhou , Zhang Zhe , Li Ke , Kong Qing-Mei , Li Xue-Ni , Lu Qing , Si Tian-Mei 
Published: March 2020

Abstract

Background
Disturbed self-regulation, taste reward, as well as somatosensory and visuospatial processes were thought to drive binge eating and purging behaviors that characterize bulimia nervosa. Although studies have implicated a central role of the striatum in these dysfunctions, there have been no direct investigations on striatal functional connectivity in bulimia nervosa from a network perspective.

Methods
We calculated the functional connectivity of striatal subregions based on the resting-state functional Magnetic Resonance Imaging data of 51 bulimia nervosa patients and 53 healthy women.

Results
Compared with the healthy women, bulimia nervosa patients showed increased positive functional connectivity in bilateral striatal nuclei and thalamus for nearly all of the striatal subregions, and increased negative functional connectivity in bilateral primary sensorimotor cortex and occipital areas for both ventral striatum and putamen subregions. Only for the putamen subregions, we observed reduced negative functional connectivity in the prefrontal (bilateral superior and middle frontal gyri) and parietal (right inferior parietal lobe and precuneus) areas. Several striatal connectivities with occipital and primary sensorimotor cortex significantly correlated with the severity of bulimia.

Conclusions
The findings indicate bulimia nervosa-related alterations in striatal functional connectivity with the dorsolateral prefrontal cortex supporting self-regulation, the subcortical striatum and thalamus involved in taste reward, as well as the visual occipital and sensorimotor regions mediating body image, which contribute to our understanding of neural circuitry of bulimia nervosa and encourage future therapeutic developments for bulimia nervosa by modulating striatal pathway.