bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring generative deep learning for omics data using log-linear models
Authors: Hess Moritz , Hackenberg Maren , Binder Harald 
Published: July 2020

Abstract

Motivation
Following many successful applications to image data, deep learning is now also increasingly considered for omics data. In particular, generative deep learning not only provides competitive prediction performance, but also allows for uncovering structure by generating synthetic samples. However, exploration and visualization is not as straightforward as with image applications.

Results
We demonstrate how log-linear models, fitted to the generated, synthetic data can be used to extract patterns from omics data, learned by deep generative techniques. Specifically, interactions between latent representations learned by the approaches and generated synthetic data are used to determine sets of joint patterns. Distances of patterns with respect to the distribution of latent representations are then visualized in low-dimensional coordinate systems, e.g. for monitoring training progress. This is illustrated with simulated data and subsequently with cortical single-cell gene expression data. Using different kinds of deep generative techniques, specifically variational autoencoders and deep Boltzmann machines, the proposed approach highlights how the techniques uncover underlying structure. It facilitates the real-world use of such generative deep learning techniques to gain biological insights from omics data.

Availability and implementation
The code for the approach as well as an accompanying Jupyter notebook, which illustrates the application of our approach, is available via the GitHub repository: https://github.com/ssehztirom/Exploring-generative-deep-learning-for-omics-data-by-using-log-linear-models.

Supplementary information
Supplementary data are available at Bioinformatics online.
The truth is in the detail: predators attack aposematic prey with less aggression than other prey types
Authors: Yamazaki Yuki , Pagani-Núñez Emilio , Sota Teiji , Barnett Craig R A 
Published: July 2020

AbstractAposematic organisms are often unprofitable to predators (e.g. because of defensive chemicals) which they advertise with a conspicuous signal (e.g. bright and conspicuous colour signals). Aposematism is thought to reduce predation of prey because the colour signal increases the ability of predators to learn, recognize and remember the prey’s defensive properties. The efficacy of aposematism has been extensively documented in laboratory studies, although its benefits seem to be harder to demonstrate in the field. In this study, we compared the levels of partial and overall predation among four prey types (undefended and cryptic, undefended and warning coloured, defended and cryptic, and aposematic prey). Overall, predation of warning coloured and defended (aposematic) prey was lower than the predation for cryptic and undefended prey; however, it was the same as predation of cryptic and defended prey. Moreover, aposematic prey had higher levels of partial predation (where prey was not wholly consumed by the predator) and lower attack intensities. This suggests that prey were being taste sampled, but also might be better able to survive attacks. Therefore, the benefits of aposematism may lie not only in reducing outright predation, but also in altering a predator’s post-attack behaviour, thus leading to greater escape opportunities and post-attack survival of prey. These results reinforce the importance of examining predation in more detail rather than simply examining attack rates.
Metabolic changes in mouse sperm during capacitation†
Authors: Balbach Melanie , Gervasi Maria Gracia , Hidalgo David Martin , Visconti Pablo E , Levin Lonny R , Buck Jochen 
Published: July 2020

AbstractMammalian sperm are stored in the epididymis in a dormant state. Upon ejaculation, they must immediately start producing sufficient energy to maintain motility and support capacitation. While this increased energy demand during capacitation is well established, it remains unclear how mouse sperm modify their metabolism to meet this need. We now show that capacitating mouse sperm enhance glucose uptake, identifying glucose uptake as a functional marker of capacitation. Using an extracellular flux analyzer, we show that glycolysis and oxidative phosphorylation increase during capacitation. Furthermore, this increase in oxidative phosphorylation is dependent on glycolysis, providing experimental evidence for a link between glycolysis and oxidative phosphorylation in mouse sperm.
Age- and sex-related features of atherosclerosis from coronary computed tomography angiography in patients prior to acute coronary syndrome: results from the ICONIC study
Authors: Conte Edoardo , Dwivedi Aeshita , Mushtaq Saima , Pontone Gianluca , Lin Fay Y , Hollenberg Emma J , Lee Sang-Eun , Bax Jeroen , Cademartiri Filippo , Chinnaiyan Kavitha , Chow Benjamin J W , Cury Ricardo C , Feuchtner Gudrun , Hadamitzky Martin , Kim Yong-Jin , Baggiano Andrea , Leipsic Jonathon , Maffei Erica , Marques Hugo , Plank Fabian , Raff Gilbert L , van Rosendael Alexander R , Villines Todd C , Weirich Harald G , Al’Aref Subhi J , Baskaran Lohendran , Cho Iksung , Danad Ibrahim , Han Donghee , Heo Ran , Lee Ji Hyun , Stuijfzand Wijnand J , Gransar Heidi , Lu Yao , Sung Ji Min , Park Hyung-Bok , Al-Mallah Mouaz H , de Araújo Gonçalves Pedro , Berman Daniel S , Budoff Matthew J , Samady Habib , Shaw Leslee J , Stone Peter H , Virmani Renu , Narula Jagat , Min James K , Chang Hyuk-Jae , Andreini Daniele 
Published: July 2020

Abstract

Aims
Although there is increasing evidence supporting coronary atherosclerosis evaluation by coronary computed tomography angiography (CCTA), no data are available on age and sex differences for quantitative plaque features. The aim of this study was to investigate sex and age differences in both qualitative and quantitative atherosclerotic features from CCTA prior to acute coronary syndrome (ACS).

Methods and results
Within the ICONIC study, in which 234 patients with subsequent ACS were propensity matched 1:1 with 234 non-event controls, our current subanalysis included only the ACS cases. Both qualitative and quantitative advance plaque analysis by CCTA were performed by a core laboratory. In 129 cases, culprit lesions identified by invasive coronary angiography at the time of ACS were co-registered to baseline CCTA precursor lesions. The study population was then divided into subgroups according to sex and age (&lt;65 vs. ≥ 65 years old) for analysis. Older patients had higher total plaque volume than younger patients. Within specific subtypes of plaque volume, however, only calcified plaque volume was higher in older patients (135.9 ± 163.7 vs. 63.8 ± 94.2 mm3, P &lt; 0.0001, respectively). Although no sex-related differences were recorded for calcified plaque volume, females had lower fibrous and fibrofatty plaque volume than males (Fibrofatty volume 29.6 ± 44.1 vs. 75.3 ± 98.6 mm3, P = 0.0001, respectively). No sex-related differences in the prevalence of qualitative high-risk plaque features were found, even after separate analyses considering age were performed.

Conclusion
Our data underline the importance of age- and sex-related differences in coronary atherosclerosis presentation, which should be considered during CCTA-based atherosclerosis quantification.
A theoretic approach to the mode of gut microbiome translocation in SIV-infected Asian macaques
Authors: Li Wendy , Ma Zhanshan (Sam) 
Published: July 2020

ABSTRACT
Human gut microbiome could translocate to other tissues, and the relocation triggered by HIV/SIV infection has received increasing attention. However, the underlying mode of this translocation, whether it is deterministic or random (passive) process, is not clear, not to mention quantitative estimation of the relocation probability and rates. Using multi-tissue microbiome datasets collected from SIV-infected macaques, originally reported by Klase et al. (2015), we apply Hubbell's unified neutral theory of biodiversity (UNTB) implemented by Harris et al. (2017) in the form of multi-site neutral (MSN) model to explore the translocation mode and rates of the gut microbiome. We found that (i) The translocation from gastrointestinal tract to tissues was driven by stochastic (neutral) forces as revealed by 100% neutrality-passing rates with MSN testing; (ii) The translocation probability from gastrointestinal tract to tissues is significantly larger than the baseline dispersal rates occurring within gastrointestinal tract (0.234 vs. 0.006 at the phylum level, P&lt; 0.001). (iii) Approximately, 23% of phyla and 55% of genera were migrated from gastrointestinal tract to the tissues (liver and mesenteric lymph nodes). Our findings offer the first interpretation of the microbial translocation mode from gastrointestinal tract to tissues, and the first estimates of the translocation probability and level.
IsXylella fastidiosaa serious threat to European forests?
Authors: Desprez-Loustau Marie-Laure , Balci Yilmaz , Cornara Daniele , Gonthier Paolo , Robin Cécile , Jacques Marie-Agnès 
Published: July 2020

AbstractThe recent emergence of Olive Quick Decline Syndrome in Italy, caused by Xylella fastidiosa, has drawn attention to the risks posed by this vector-borne bacterium to important crops in Europe (especially fruit trees and grapevine). Comparatively very little is known on actual and potential impacts of this pathogen in forests, in the native (North American) and introduced (European) regions, respectively. The present review aims to address important questions related to the threat posed by X. fastidiosa to European forests, such as the following: What are the symptoms, hosts and impact of bacterial leaf scorch caused by X. fastidiosa on trees in North America? Which forest tree species have been found infected in the introduction area in Europe? How does X. fastidiosa cause disease in susceptible hosts? Are there any X. fastidiosa genotypes (subspecies and sequence types) specifically associated with forest trees? How is X. fastidiosa transmitted? What are the known and potential vectors for forest trees? How does vector ecology affect disease? Is the distribution of X. fastidiosa, especially the strains associated with trees, restricted by climatic factors? Is disease risk for trees different in forest ecosystems as compared with urban settings? We conclude by pointing to important knowledge gaps related to all these questions and strongly advocate for more research about the Xylella-forest pathosystems, in both North America and Europe.
Age estimation of red snapper (Lutjanus campechanus) using FT-NIR spectroscopy: feasibility of application to production ageing for management
Authors: Passerotti Michelle S , Helser Thomas E , Benson Irina M , Barnett Beverly K , Ballenger Joseph C , Bubley Walter J , Reichert Marcel J M , Quattro Joseph M 
Published: July 2020

Abstract
Recent application of Fourier transform near infra-red spectroscopy (FT-NIRS) to predict age in fish otoliths has gained attention among fisheries managers as a potential alternative to costly production ageing of managed species. We assessed the age prediction capability of FT-NIRS scans in whole otoliths from red snapper, Lutjanus campechanus, collected from the US Gulf of Mexico and US Atlantic Ocean (South Atlantic). Otoliths were scanned with an FT-NIR spectrometer and resulting spectral signatures were regressed with traditionally estimated ages via partial least squares regression to produce calibration models, which were validated for predictive capability against test sets of otoliths. Calibration models successfully predicted age with R2 ranging 0.94–0.95, mean squared error ≤1.8 years, and bias &lt;0.02 years. Percent agreement between FT-NIRS and traditional ages was lower than within-reader agreement for traditional estimates, but average percent error was similar and Kolmogorov–Smirnov tests were not significantly different (p ≥ 0.06) between traditional and FT-NIRS predicted ages for optimal calibration models. Ages &gt;31 years were not well predicted, possibly due to light attenuation in the thickest otoliths. Our results suggest that FT-NIRS can improve efficiency in production ageing for fisheries management while maintaining data quality standards.
Boundary feedback control of an anti-stable wave equation
Authors: APKARIAN Pierre , NOLL Dominikus 
Published: July 2020

Abstract
We discuss boundary control of a wave equation with a non-linear anti-damping boundary condition. We design structured finite-dimensional $H_{\infty }$-output feedback controllers that stabilize the infinite-dimensional system exponentially in closed loop. The method is applied to control torsional vibrations in drilling systems with the goal to avoid slip-stick.
Characterization of a Unique γδ T-Cell Subset as a Specific Marker of Cytomegalovirus Infection Severity
Authors: Kaminski Hannah , Ménard Coline , El Hayani Bouchra , Adjibabi And-Nan , Marsères Gabriel , Courant Maxime , Zouine Atika , Pitard Vincent , Garrigue Isabelle , Burrel Sonia , Moreau Jean-François , Couzi Lionel , Visentin Jonathan , Merville Pierre , Déchanet-Merville Julie 
Published: July 2020

Abstract
Cytomegalovirus (CMV) is a major infectious cause of death and disease after transplantation. We have previously demonstrated that the tissue-associated adaptive Vδ2neg γδ T cells are key effectors responding to CMV and associated with recovery, contrasting with their innatelike circulating counterparts, the Vγ9posVδ2pos T cells that respond to phosphoantigens but not to CMV. A third Vγ9negVδ2pos subgroup with adaptive functions has been described in adults. In the current study, we demonstrate that these Vγ9negVδ2pos T cells are also components of the CMV immune response while presenting with distinct characteristics from Vδ2neg γδ T cells. In a cohort of kidney transplant recipients, CMV seropositivity was the unique clinical parameter associated with Vγ9negVδ2pos T-cell expansion and differentiation. Extensive phenotyping demonstrated their substantial cytotoxic potential and activation during acute CMV primary infection or reinfection. In vitro, Vγ9negVδ2pos T cells responded specifically to CMV-infected cells in a T-cell receptor–dependent manner and through strong interferon γ production. Finally, Vγ9negVδ2pos T cells were the only γδ T-cell subset in which expansion was tightly correlated with the severity of CMV disease. To conclude, our results identify a new player in the immune response against CMV and open interesting clinical perspectives for using Vγ9negVδ2pos T cells as an immune marker for CMV disease severity in immunocompromised patients.
Reviving the Principle of Non-Intervention in Cyberspace: The Path Forward
Authors: Moulin Thibault 
Published: July 2020

Abstract
The applicability of existing rules of international law (namely sovereignty or the prohibition to use force) is currently challenged in cyberspace. In contrast, the relevance of the non-intervention principle is accepted by states and raises less questions about the ‘territoriality’ or the ‘militarization’ of cyberspace. At first sight, it thus appears as a convenient source for the regulation of cyberthreats. However, the Nicaragua case also established a stringent test for a foreign interference to qualify as an unlawful intervention. First, it must bear ‘on matters in which each State is permitted, by the principle of State sovereignty to decide freely’ (ie the ‘domaine réservé’). Then, it must involve ‘methods of coercion in regard to such choices’. I contend that both criteria are maladjusted to address cyberthreats and must be reconceptualised. In fact, the domaine réservé describes domains where states are free from international rules. However, few domains, including electoral processes or main economic orientations, are totally isolated from international law. I thus argue that it must be reconceptualised into the so-called ‘domaine privilégié’. It consists of a domain with clear-cut contours, unaffected by the developments of international law, which encompasses the fundamental interests of a state and its population. Then, coercion describes situations where a state is compelled to act, or to refrain from acting, in a certain fashion. This traditional approach is also problematic, and I argue that coercion must be understood in terms of deprivation of control.
The Role of Bank Management in the EU Resolution Regime for NPLs
Authors: Kokkinis Andreas , Miglionico Andrea 
Published: July 2020

ABSTRACT
During the global financial crisis, the growth of non-performing loans (NPLs) was partly a consequence of lack of regulatory oversight and poor bank internal processes. NPLs require intrusive monitoring tools and effective corporate governance is crucial in dealing with the deterioration of loans; however, perverse incentives to delay their recognition leave the process at risk. The EU legislation has adopted a set of regulatory measures to resolve and restructure non-performing exposures. While existing literature approaches NPLs from a regulatory and accounting perspective, this article takes a distinctive corporate governance view in order to conceptualize the NPL problem. The strategies through which senior management and shareholder incentives may undermine regulatory objectives on NPL disclosure are identified and an evidence-based approach to reconsidering and settling these problems is advanced.
Genetic Diversity ofAnopheles coustani(Diptera: Culicidae) in Malaria Transmission Foci in Southern and Central Africa
Authors: Ciubotariu Ilinca I , Jones Christine M , Kobayashi Tamaki , Bobanga Thierry , Muleba Mbanga , Pringle Julia C , Stevenson Jennifer C , Carpi Giovanna , Norris Douglas E 
Published: July 2020

AbstractDespite ongoing malaria control efforts implemented throughout sub-Saharan Africa, malaria remains an enormous public health concern. Current interventions such as indoor residual spraying with insecticides and use of insecticide-treated bed nets are aimed at targeting the key malaria vectors that are primarily endophagic and endophilic. Anopheles coustani s.l., an understudied vector of malaria, is a species previously thought to exhibit mostly zoophilic behavior. Like many of these understudied species, An. coustani has greater anthropophilic tendencies than previously appreciated, is often both endophagic and exophagic, and carries Plasmodium falciparum sporozoites. The aim of this study was to explore genetic variation of An. coustani mosquitoes and the potential of this species to contribute to malaria parasite transmission in high transmission settings in Zambia and the Democratic Republic of the Congo (DRC). Morphologically identified An. coustani specimens that were trapped outdoors in these study sites were analyzed by PCR and sequencing for species identification and bloodmeal sources, and malaria parasite infection was determined by ELISA and qPCR. Fifty An. coustani s.s. specimens were confirmed by analysis of mitochondrial DNA cytochrome c oxidase subunit I (COI) and ribosomal internal transcribed spacer region 2 (ITS2). Maximum likelihood phylogenetic analysis of COI and ITS2 sequences revealed two distinct phylogenetic groups within this relatively small regional collection. Our findings indicate that both An. coustani groups have anthropophilic and exophagic habits and come into frequent contact with P. falciparum, suggesting that this potential alternative malaria vector might elude current vector control measures in northern Zambia and southern DRC.
Analysis of ciliary status via G-protein-coupled receptors localized on primary cilia
Authors: Kobayashi Yuki , Hamamoto Akie , Saito Yumiko 
Published: July 2020

AbstractG-protein-coupled receptors (GPCRs) comprise the largest and most diverse cell surface receptor family, with more than 800 known GPCRs identified in the human genome. Binding of an extracellular cue to a GPCR results in intracellular G protein activation, after which a sequence of events, can be amplified and optimized by selective binding partners and downstream effectors in spatially discrete cellular environments. Because GPCRs are widely expressed in the body, they help to regulate an incredible range of physiological processes from sensation to growth to hormone responses. Indeed, it is estimated that ∼ 30% of all clinically approved drugs act by binding to GPCRs. The primary cilium is a sensory organelle composed of a microtubule axoneme that extends from the basal body. The ciliary membrane is highly enriched in specific signaling components, allowing the primary cilium to efficiently convey signaling cascades in a highly ordered microenvironment. Recent data demonstrated that a limited number of non-olfactory GPCRs, including somatostatin receptor 3 and melanin-concentrating hormone receptor 1 (MCHR1), are selectively localized to cilia on several mammalian cell types including neuronal cells. Utilizing cilia-specific cell biological and molecular biological approaches, evidence has accumulated to support the biological importance of ciliary GPCR signaling followed by cilia structural changes. Thus, cilia are now considered a unique sensory platform for integration of GPCR signaling toward juxtaposed cytoplasmic structures. Herein, we review ciliary GPCRs and focus on a novel role of MCHR1 in ciliary length control that will impact ciliary signaling capacity and neuronal function.
The Reporting of Child Abuse and Neglect in Ireland in an International Context
Authors: Hanly Conor 
Published: July 2020

Abstract
Starting in the early 1990s, reports published over a quarter of a century detailed shocking levels of child abuse and child neglect in Ireland, along with failures by Church and State officials to take effective action. These revelations, supported by international research, made a compelling case for the introduction of some form of mandatory reporting. Yet until 2015, Ireland’s child protection system relied upon the discretion of those who suspected incidents of child abuse. The Children First Act 2015 introduced a new system of mandatory reporting that applies to professionals working in the health, education, childcare and law enforcement fields, a system that became active at the end of 2017. This article reviews the development of the reporting system in Ireland, and analyses the new obligations created by the 2015 Act. The article also analyses some initial figures for 2018, which show a substantial increase in the number of reports of child abuse and neglect made in that year. Additionally, the article argues for the insertion into the new system of some nuance in order that victim autonomy might be better respected.