bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Sickle Cell Disease Ontology: enabling universal sickle cell-based knowledge representation
Authors:   Sickle Cell Disease Ontology Working Group, Adekile Adekunle , Anie Kofi A , Hamda Cherif Ben , Brown Biobele , Bukini Daima , Campbell Andrew , Chaouch Melek , Chimusa Emile , Chunda-Liyoka Catherine , Dennis-Antwi Jemima , Derebail Vimal K , Flor-Park Miriam , Geard Amy , Ghedira Kais , Haendel Melissa , Hanchard Neil A , Hotchkiss Jade , Jonas Mario , Ibrahim Muntaser , Ingram Clair , Inusa Baba , Jimoh Adijat Ozohu , Jupp Simon , Kamga Karen , Kashim Zainab Abimbola , Knight-Madden Jennifer , Landouré Guida , Lopez-Sall Philomene , Makani Julie , Malasa Leonard , Masekoameng Tshepiso , Mazandu Gaston , Mnika Khuthala , Mulder Nicola , Munung Nchangwi Syntia , Munube Deogratias , Mwita Liberata , Nembaware Victoria , Nnodu Obiageli , Ofori-Acquah Solomon , Ohene-Frempong Kwaku , Osei-Akoto Alex , Paintsil Vivian , Panji Sumir , Rahimy Mohamed Cherif , Royal Charmaine , Sangeda Raphael Z , Tayo Bamidele , Tiouiri Ines , Tluway Furahini , Treadwell Marsha , Tshilolo Leon , Vasilevsky Nicole , Waiswa Kasadhakawo Musa , Wonkam Ambroise 
Published: September 2019

Abstract
Sickle cell disease (SCD) is one of the most common monogenic diseases in humans with multiple phenotypic expressions that can manifest as both acute and chronic complications. Although described more than a century ago, challenges in comprehensive disease management and collaborative research on this disease are compounded by the complex molecular and clinical phenotypes of SCD, environmental and psychosocial factors, limited therapeutic options and ambiguous terminology. This ambiguous terminology has hampered the integration and interoperability of existing SCD knowledge, and SCD research translation. The SCD Ontology (SCDO), which is a community-driven integrative and universal knowledge representation system for SCD, overcomes this issue by providing a controlled vocabulary developed by a group of experts in both SCD and ontology design. SCDO is the first and most comprehensive standardized human- and machine-readable resource that unambiguously represents terminology and concepts about SCD for researchers, patients and clinicians. It is built around the central concept ‘hemoglobinopathy’, allowing inclusion of non-SCD haemoglobinopathies, such as thalassaemias, which may interfere with or influence SCD phenotypic manifestations. This collaboratively developed ontology constitutes a comprehensive knowledge management system and standardized terminology of various SCD-related factors. The SCDO will promote interoperability of different research datasets, facilitate seamless data sharing and collaborations, including meta-analyses within the SCD community, and support the development and curation of data-basing and clinical informatics in SCD.
Cold Tolerance of Mountain Pine Beetle (Coleoptera: Curculionidae) Pupae
Authors: Bleiker K P , Smith G D 
Published: September 2019

Abstract
Determining the cold tolerance of mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae), is critical for assessing its long-term persistence and eruptive potential in its new habitat, as well as the risk of continued range expansion across Canada’s boreal forest. We used supercooling points (SCPs) and mortality assessments with exposure to different temperatures to determine the cold tolerance of pupae. Mountain pine beetle pupae cold tolerance did not increase with chilling and there was little change in the lethal temperature regardless of treatment or sample time. SCPs were reflective of expected mortality due to freezing: the lethal temperature for 50% mortality was –19.3°C and the mean SCP was –18.7°C. However, significant mortality occurred over time at much warmer temperatures (0 and –9°C), indicating that this life stage suffers significant prefreeze mortality. On the basis of our results, it is unlikely that pupae would be able to successfully overwinter in most regions in Canada. This study is part of a larger project aimed at producing a comprehensive assessment of the cold tolerance of all life stages of the mountain pine beetle to feed population models, climatic suitability indices, and spread assessments.
Seven principles for writing materials for English as a lingua franca
Authors: Kiczkowiak Marek 
Published: September 2019

Abstract
The unprecedented rise of English to become a global lingua franca has sparked a growing academic interest with numerous research publications on global Englishes, English as a lingua franca, and English as an international language. Although this research has led to numerous informative findings concerning pronunciation, pragmatics, and intercultural communicative skills, many course books still present English as if it was primarily used to communicate with ‘native speakers’. In addition, native speakerism, or the belief that ‘native speakers’ are not only better models but also better teachers of the language, is still widespread in ELT. As a result, this article aims to bridge the gap between the research and materials writing practice by suggesting seven research-based principles which can help materials writers not only write materials that are truly global and authentic, but also contribute to tackling native speakerism by addressing some of the discourses that support it.
Comparative Transcriptomics Provides Insights into Reticulate and Adaptive Evolution of a Butterfly Radiation
Authors: Zhang Wei , Leon-Ricardo Brian X , van Schooten Bas , Van Belleghem Steven M , Counterman Brian A , McMillan W Owen , Kronforst Marcus R , Papa Riccardo 
Published: September 2019

AbstractButterfly eyes are complex organs that are composed of a diversity of proteins and they play a central role in visual signaling and ultimately, speciation, and adaptation. Here, we utilized the whole eye transcriptome to obtain a more holistic view of the evolution of the butterfly eye while accounting for speciation events that co-occur with ancient hybridization. We sequenced and assembled transcriptomes from adult female eyes of eight species representing all major clades of the Heliconius genus and an additional outgroup species, Dryas iulia. We identified 4,042 orthologous genes shared across all transcriptome data sets and constructed a transcriptome-wide phylogeny, which revealed topological discordance with the mitochondrial phylogenetic tree in the Heliconius pupal mating clade. We then estimated introgression among lineages using additional genome data and found evidence for ancient hybridization leading to the common ancestor of Heliconius hortense and Heliconius clysonymus. We estimated the Ka/Ks ratio for each orthologous cluster and performed further tests to demonstrate genes showing evidence of adaptive protein evolution. Furthermore, we characterized patterns of expression for a subset of these positively selected orthologs using qRT-PCR. Taken together, we identified candidate eye genes that show signatures of adaptive molecular evolution and provide evidence of their expression divergence between species, tissues, and sexes. Our results demonstrate: 1) greater evolutionary changes in younger Heliconius lineages, that is, more positively selected genes in the cydno–melpomene–hecale group as opposed to the sara–hortense–erato group, and 2) suggest an ancient hybridization leading to speciation among Heliconius pupal-mating species.
Glucosylceramide synthase silencing combined with the receptor tyrosine kinase inhibitor axitinib as a new multimodal strategy for glioblastoma
Authors: Morais Catarina M , Cunha Pedro P , Melo Tânia , Cardoso Ana M , Domingues Pedro , Domingues M Rosário , Pedroso de Lima Maria C , Jurado Amália S 
Published: September 2019

Abstract
A great deal of evidence revealing that lipid metabolism is drastically altered during tumorigenesis has been accumulated. In this work, glucosylceramide synthase (GCS) was targeted, using RNA interference technology (siRNAs), in U87 and DBTRG human glioblastoma (GBM) cells, as in both cell types GCS showed to be overexpressed with respect to normal human astrocytes. The efficacy of a combined therapy to tackle GBM, allying GCS silencing to the new generation chemotherapeutics sunitinib and axitinib, or to the alkylating drugs etoposide and temozolomide, is evaluated here for the first time. With this purpose, studies addressing GBM cell viability and proliferation, cell cycle and apoptosis were performed, which revealed that combination of GCS silencing with axitinib treatment represents a promising therapeutic approach. The reduction of cell viability induced by this combined therapy is proposed to be mediated by excessive production of reactive oxygen species. This work, identifying GCS as a key molecular target to increase GBM susceptibility to a new generation chemotherapeutic, opens windows to the development of innovative strategies to halt GBM recurrence after surgical resection.
Abdominal Adipose Tissue Is Associated With Alterations in Tryptophan-Kynurenine Metabolism and Markers of Systemic Inflammation in People With Human Immunodeficiency Virus
Authors: Gelpi Marco , Ueland Per Magne , Trøseid Marius , Mocroft Amanda , Lebech Anne-Mette , Ullum Henrik , Midttun Øivind , Lundgren Jens , Nielsen Susanne D 
Published: September 2019

Abstract

Background
While both adipose tissue accumulation and tryptophan metabolism alterations are features of human immunodeficiency virus (HIV) infection, their interplay is unclear. We investigated associations between abdominal adipose tissue, alterations in kynurenine pathway of tryptophan metabolism, and systemic inflammation in people with HIV (PWH).

Methods
Eight hundred sixty-four PWH and 75 uninfected controls were included. Plasma samples were collected and analyzed for kynurenine metabolites, neopterin, high-sensitivity C-reactive protein (hs-CRP), and lipids. Regression models were used to test associations in PWH.

Results
PWH had higher kynurenine-to-tryptophan ratio than uninfected individuals (P < .001). In PWH, increase in waist-to-hip ratio was associated with higher kynurenine-to-tryptophan ratio (P = .009) and quinolinic-to-kynurenic acid ratio (P = .006) and lower kynurenic acid concentration (P = .019). Quinolinic-to-kynurenic acid ratio was associated with higher hs-CRP (P < .001) and neopterin concentrations (P < .001), while kynurenic acid was associated with lower hs-CRP (P = .025) and neopterin concentrations (P = .034).

Conclusions
In PWH, increase in abdominal adipose tissue was associated with increased quinolinic-to-kynurenic acid ratio, suggesting activation of proinflammatory pathway of kynurenine metabolism, with reduction of anti-inflammatory molecules and increase in systemic inflammation. Our results suggest dysregulation of kynurenine metabolism associated with abdominal fat accumulation to be a potential source of inflammation in HIV infection.
Keratin 8 Mutations Were Associated With Susceptibility to Chronic Hepatitis B and Related Progression
Authors: Ye Junzhao , Wu Yanqin , Li Minrui , Gong Xiaorong , Zhong Bihui 
Published: September 2019

Abstract

Background
Keratin 8 and 18 (K8/K18) are the exclusively expressed keratins intermediate filaments pair in hepatocytes that protect against liver injuries and viral infection. We aimed to explore the genetic link between keratin variants and chronic hepatitis B virus (CHB) infection in a large cohort from a high-epidemic area.

Methods
Genomic deoxyribonucleic acid was isolated from patients, and Sanger sequencing was applied to analyze variations in exon regions of K8/18. Biochemical and functional analysis of novel mutations was also performed.

Results
The 713 participants comprised 173 healthy controls and 540 patients, which covered chronic hepatitis (n = 174), decompensated cirrhosis (n = 192), and primary liver carcinoma (n = 174). The frequency of mutations in K8/18 was significantly higher among patients than among controls (8.15% vs 0.58%, P < .001). Significant differences were found between the chronic hepatitis subgroup and controls in multiple comparisons (6.32% vs 0.58%, P = .006). All 21 missense mutations (3.89%) were detected in the keratin 8 (K8), including 4 novel conserved missense variants (R469C, R469H, A447V, and K483T). Multivariate logistic regression analysis demonstrated a higher risk of acute-on-chronic liver failure (ACLF) and missense variants (odds ratio = 4.38, P = .035). Transfection of these variants caused keratin network disruption in vivo.

Conclusions
Novel K8 cytoskeleton-disrupting variants predispose toward ACLF in CHB.
Do Democracies Possess the Wisdom of Crowds? Decision Group Size, Regime Type, and Strategic Effectiveness
Authors: Blagden David 
Published: September 2019

Abstract
What is it about democracies—if anything—that enables them to avoid war with each other while navigating conflictual international politics in pursuit of their own interests? Recent research in International Studies Quarterly by Brad LeVeck and Neil Narang (2017) provides an elegant new answer to this longstanding question. Drawing on “wisdom of crowds” logic—the insight that a large-enough group of inexpert judges is more likely to average towards an accurate estimate of a continuous variable than a smaller group, even when the smaller group contains relevant experts—supported by experimental evidence, they suggest that democracies’ strategic advantages lie in their large, diverse decision-making communities. If such crowd wisdom equips democracies to accurately assess others’ capabilities and intentions, so the argument goes, then they should be better than alternative regime types at maximizing their own interests while still avoiding the bargaining failure that is resort to war. Unfortunately, however, the politics of democratic foreign policy-making compromise the crowd-wisdom mechanism. This response article thus elucidates key flaws in the argument that crowd wisdom underpins democratic peace, before progressing to explain how the crowd-wisdom insight nonetheless carries important implications—irrespective of regime type—for strategic effectiveness.
From germ cells to neonates: the beginning of life and the KEAP1–NRF2 system
Authors: Matsumaru Daisuke , Motohashi Hozumi 
Published: September 2019

Abstract
The Kelch-like ECH-associated protein 1(KEAP1)–NF-E2-related factor 2 (NRF2) system is one of the most studied environmental stress response systems. In the presence of oxidative and electrophilic insults, the thiols of cysteine residues in KEAP1 are modified, and subsequently stabilized NRF2 activates its target genes that are involved in detoxification and cytoprotection. A myriad of recent studies has revealed the broad range of contributions of the KEAP1–NRF2 system to physiological and pathological processes. However, its functions during gametic and embryonic development are still open for investigation. Although oxidative stress is harmful for embryos, Nrf2−/− mice do not show any apparent morphological abnormalities during development, probably because of the compensatory antioxidant functions of NF-E2-related factor 1 (NRF1). It can also be considered that the antioxidant system is essential for protecting germ cells during reproduction. The maturation processes of germ cells in both sexes are affected by Nrf2 mutation. Hence, in this review, we focus on the stress response system related to reproduction and embryonic development through the functions of the KEAP1–NRF2 system.
Genomic based analyses reveal unique mutational profiling and identify prognostic biomarker for overall survival in Chinese small-cell lung cancer
Authors: Wang Yu , Han Xiao , Wang Xingwen , Sheng Wei , Chen Zheng , Shu Weibin , Han Junqing , Zhao Songhui , Dai Yi , Wang Kai , Shi Weiwei , Yang Zhe 
Published: September 2019

Abstract

Objective
As an aggressive subtype of lung cancer, small-cell lung cancer (SCLC) presents a poor prognosis. Although molecular and clinical characteristics have been established for SCLC, limited investigation has been performed for predicting survival of SCLC patients.

Methods
Genomic alterations were profiled in Chinese SCLC patients (N = 37) using targeted sequencing. Clonal mutation burden (CMB) integrated the number of mutations with the clonal structure of the tumor. Specific pathways involving DNA damage repair (DDR) and cell cycle as well as CMB were studied as potential biomarkers for prognosis of SCLC.

Results
TP53 and RB1 gene mutations were the most common alterations (91.9% and 83.8%, respectively), followed by LRP1B, FAM135B, SPTA1, KMT2D, FAT1, and NOTCH3. Survival analysis revealed that mutation status of the DDR pathway was associated with worse OS in our cohort. Importantly, patients with higher CMB exhibited worse OS in our cohort and this observation was successfully validated in the cBioportal cohort. Moreover, multivariate analysis demonstrated CMB as a promising independent prognostic factor for OS in Chinese SCLC patients. Interestingly, patients with loss of function of RB1, validated by immunohistochemistry staining, appeared to have worse OS.

Conclusions
The mutational profiling of Chinese SCLC patients signified an ethnicity dependent component. CMB was firstly found to be associated with OS of Chinese SCLC patients and could be regarded as a prognostic marker for SCLC.
Grievances and Fears in Islamist Movements: Revisiting the Link between Exclusion, Insecurity, and Political Violence
Authors: Matesan Ioana Emy 
Published: September 2019

AbstractThis article examines how exclusionary policies and repressive measures affect the propensity of Islamist groups in nondemocratic settings to engage in violence. The central argument is that exclusion from electoral politics, from civil society, and from public discourse can increase political grievances, whereas symbolic threats to religious values spark sociocultural grievances; state violence and repression foster a sense of insecurity. The article proposes that Islamist groups are both principled and strategic actors, who may adopt violent rhetoric in response to political or sociocultural grievances, but who resort to violent tactics primarily out of a sense of insecurity. The quantitative examination of twenty-two Islamist groups from the Middle East confirms that exclusionary policies can spark violent rhetoric, whereas repression and threats to the physical integrity of a group increase the propensity toward violent behavior. However, when insecurity turns into disillusionment, groups can also move away from violence if they feel alienated from the public. The close investigation of the Muslim Brotherhood and al-Gama'a al-Islamiyya in Egypt shows that the response to repression depends on the length of the conflict, the level of fragmentation within an organization, and public opinion.
Improved supervised learning methods for EoR parameters reconstruction
Authors: Doussot Aristide , Eames Evan , Semelin Benoit 
Published: September 2019

ABSTRACT
Within the next few years, the Square Kilometre Array (SKA) or one of its pathfinders will hopefully detect the 21-cm signal fluctuations from the Epoch of Reionization (EoR). Then, the goal will be to accurately constrain the underlying astrophysical parameters. Currently, this is mainly done with Bayesian inference. Recently, neural networks have been trained to perform inverse modelling and, ideally, predict the maximum-likelihood values of the model parameters. We build on these by improving the accuracy of the predictions using several supervised learning methods: neural networks, kernel regressions, or ridge regressions. Based on a large training set of 21-cm power spectra, we compare the performances of these methods. When using a noise-free signal generated by the model itself as input, we improve on previous neural network accuracy by one order of magnitude and, using a local ridge kernel regression, we gain another factor of a few. We then reach an accuracy level on the reconstruction of the maximum-likelihood parameter values of a few per cents compared the 1σ confidence level due to SKA thermal noise (as estimated with Bayesian inference). For an input signal affected by an SKA-like thermal noise but constrained to yield the same maximum-likelihood parameter values as the noise-free signal, our neural network exhibits an error within half of the 1σ confidence level due to the SKA thermal noise. This accuracy improves to 10$\, {\rm per\, cent}$ of the 1σ level when using the local ridge kernel. We are thus reaching a performance level where supervised learning methods are a viable alternative to determine the maximum-likelihood parameters values.
Triggered star formation in a cometary atomic/molecular cloud in the Cep OB3 association
Authors: Marshall Brandon , Kerton C R 
Published: September 2019

ABSTRACT
We present a study of a small atomic/molecular cometary cloud associated with the infrared source IRAS 23153+6938. The cloud is located 70 pc from the massive O-type stars in the Cepheus OB3 association, and is very likely an excellent example of triggered star formation via radiation-driven implosion (RDI). The cloud was studied using $\rm{H\,\small{I}}$ and 12CO data from the Canadian Galactic Plane Survey (CGPS) and infrared observations from the Wide-field Infrared Survey Explorer (WISE) telescope. The molecular mass is approximately MH2 = 350 ± 45 M$\odot$, and we find that the single IRAS source is actually the centre of a small cluster of class I and class II young stellar objects (YSOs). To compare with theory, we make reasonable estimates for the cometary cloud’s initial conditions and find that the cloud is located within the correct theoretical phase space for RDI to occur. In addition, both the morphology of the cloud and the location of different YSO classes relative to the cloud match what would be expected for RDI. We conclude that RDI is the most likely explanation for star formation within the cloud, and we suggest that similar studies of molecular clouds associated with nearby OB associations may be able to identify comparable examples.
Power-law Sérsic profiles in hydrostatic stellar galaxy discs
Authors: Struck Curtis , Elmegreen Bruce G 
Published: September 2019

ABSTRACT
Previously, we showed that surface density profiles of the form of a power-law times a Sérsic function satisfy the hydrostatic Jeans equations, a variety of observational constraints, and the condition of a minimal radial entropy profile in two-dimensional galaxy discs with fixed power law, halo potentials. It was assumed that such density profiles are generated by star scattering by clumps, waves, or other inhomogeneities. Here, we generalize these models to self-gravitating discs. The cylindrically symmetric Poisson equation imposes strong constraints. Scattering processes favour smoothness, so the smoothest solutions, which minimize entropy gradients, are preferred. In the case of self-gravitating discs (e.g. inner discs), the gravity, surface density, and radial velocity dispersion in these smoothest models are all of the form 1/r times an exponential. When vertical balance is included, the vertical velocity dispersion squared has the same form as the surface density, and the scale height is constant. In combined self-gravitating plus halo gravity cases, the radial dispersion has an additional power-law term. None the less, the surface density profile has the same form at all radii, without breaks, satisfying the ‘disc–halo conspiracy’. The azimuthal velocity and velocity dispersions are smooth, though the former can have a distinct peak. In these models the vertical dispersion increases inwards, and scattering may mediate a transition to a secular bulge. If halo gravity dominates vertically in the outer disc, it flares. The models suggest a correlation between disc mass and radial scale length. The combination of smoothness, simplicity, ability to match generic observational features, and physical constraints is unique to these models.