bluuebunny/crossref_metadata_2025_split huggingface dataset:
Triaxially deformed freely precessing neutron stars: continuous electromagnetic and gravitational radiation
Authors: Gao Yong , Shao Lijing , Xu Rui , Sun Ling , Liu Chang , Xu Ren-Xin 
Published: August 2020

ABSTRACT
The shape of a neutron star (NS) is closely linked to its internal structure and the equation of state of supranuclear matters. A rapidly rotating, asymmetric NS in the Milky Way undergoes free precession, making it a potential source for multimessenger observation. The free precession could manifest in (i) the spectra of continuous gravitational waves (GWs) in the kilohertz (kHz) band for ground-based GW detectors, and (ii) the timing behaviour and pulse-profile characteristics if the NS is monitored as a pulsar with radio and/or X-ray telescopes. We extend previous work and investigate in great detail the free precession of a triaxially deformed NS with analytical and numerical approaches. In particular, its associated continuous GWs and pulse signals are derived. Explicit examples are illustrated for the continuous GWs, as well as timing residuals in both time and frequency domains. These results are ready to be used for future multimessenger observation of triaxially deformed freely precessing NSs, in order to extract scientific implication as much as possible.
Redshift inference from the combination of galaxy colours and clustering in a hierarchical Bayesian model – Application to realisticN-body simulations
Authors: Alarcon Alex , Sánchez Carles , Bernstein Gary M , Gaztañaga Enrique 
Published: August 2020

ABSTRACTPhotometric galaxy surveys constitute a powerful cosmological probe but rely on the accurate characterization of their redshift distributions using only broad-band imaging, and can be very sensitive to incomplete or biased priors used for redshift calibration. A hierarchical Bayesian model has recently been developed to estimate those from the robust combination of prior information, photometry of single galaxies, and the information contained in the galaxy clustering against a well-characterized tracer population. In this work, we extend the method so that it can be applied to real data, developing some necessary new extensions to it, especially in the treatment of galaxy clustering information, and we test it on realistic simulations. After marginalizing over the mapping between the clustering estimator and the actual density distribution of the sample galaxies, and using prior information from a small patch of the survey, we find the incorporation of clustering information with photo-z’s tightens the redshift posteriors and overcomes biases in the prior that mimic those happening in spectroscopic samples. The method presented here uses all the information at hand to reduce prior biases and incompleteness. Even in cases where we artificially bias the spectroscopic sample to induce a shift in mean redshift of $\Delta \bar{z} \approx 0.05,$ the final biases in the posterior are $\Delta \bar{z} \lesssim 0.003.$ This robustness to flaws in the redshift prior or training samples would constitute a milestone for the control of redshift systematic uncertainties in future weak lensing analyses.
Type Ia supernovae deflagration-to-detonation transition explosions powered by the Zel’dovich reactivity gradient mechanism
Authors: Brooker E , Plewa T , Fenn D 
Published: August 2020

ABSTRACT
Our aim in this work is to identify and explain the necessary conditions required for an energetic explosion of a Chandrasekhar-mass white dwarf. We construct and analyse weakly compressible turbulence models with nuclear burning effects for carbon/oxygen plasma at a density expected for the deflagration-to-detonation transition (DDT) to occur. We observe the formation of carbon deflagrations and transient carbon detonations at early times. As turbulence becomes increasingly inhomogeneous, sustained carbon detonations are initiated by the Zel’dovich reactivity gradient mechanism. The fuel is suitably preconditioned by the action of compressive turbulent modes with wavelength comparable to the size of resolved turbulent eddies; no acoustic wave is involved in this process. Oxygen detonations are initiated, aided either by reactivity gradients or by collisions of carbon detonations. The observed evolutionary time-scales are found to be sufficiently short for the above process to occur in the expanding, centrally ignited massive white dwarf. The inhomogeneous conditions produced prior to the DDT might be of consequence for the chemical composition of the outer ejecta regions of Type Ia supernovae from the single degenerate channel, and offer the potential for validation of the proposed model.
Experimental Evolution Reveals a Genetic Basis for Membrane-Associated Virus Release
Authors: Bou Juan-Vicente , Sanjuán Rafael 
Published: August 2020

Abstract
Many animal viruses replicate and are released from cells in close association to membranes. However, whether this is a passive process or is controlled by the virus remains poorly understood. Importantly, the genetic basis and evolvability of membrane-associated viral shedding have not been investigated. To address this, we performed a directed evolution experiment using coxsackievirus B3, a model enterovirus, in which we repeatedly selected the free-virion or the fast-sedimenting membrane-associated viral subpopulations. The virus responded to this selection regime by reproducibly fixing a series of mutations that altered the extent of membrane-associated viral shedding, as revealed by full-genome ultra-deep sequencing. Specifically, using site-directed mutagenesis, we showed that substitution N63H in the viral capsid protein VP3 reduced the ratio of membrane-associated to free viral particles by 2 orders of magnitude. These findings open new avenues for understanding the mechanisms and implications of membrane-associated viral transmission.
Distinct oligomeric structures of the YoeB–YefM complex provide insights into the conditional cooperativity of type II toxin–antitoxin system
Authors: Xue Lu , Yue Jian , Ke Jiyuan , Khan Muhammad Hidayatullah , Wen Wen , Sun Baolin , Zhu Zhongliang , Niu Liwen 
Published: August 2020

Abstract
YoeB–YefM, the widespread type II toxin–antitoxin (TA) module, binds to its own promoter to autoregulate its transcription: repress or induce transcription under normal or stress conditions, respectively. It remains unclear how YoeB–YefM regulates its transcription depending on the YoeB to YefM TA ratio. We find that YoeB–YefM complex from S.aureus exists as two distinct oligomeric assemblies: heterotetramer (YoeB–YefM2–YoeB) and heterohexamer (YoeB–YefM2–YefM2–YoeB) with low and high DNA-binding affinities, respectively. Structures of the heterotetramer alone and heterohexamer bound to promoter DNA reveals that YefM C-terminal domain undergoes disorder to order transition upon YoeB binding, which allosterically affects the conformation of N-terminal DNA-binding domain. At TA ratio of 1:2, unsaturated binding of YoeB to the C-terminal regions of YefM dimer forms an optimal heterohexamer for DNA binding, and two YefM dimers with N-terminal domains dock into the adjacent major grooves of DNA to specifically recognize the 5′-TTGTACAN6AGTACAA-3′ palindromic sequence, resulting in transcriptional repression. In contrast, at TA ratio of 1:1, binding of two additional YoeB molecules onto the heterohexamer induces the completely ordered conformation of YefM and disassembles the heterohexamer into two heterotetramers, which are unable to bind the promoter DNA optimally due to steric clashes, hence derepresses TA operon transcription.
MNDR v3.0: mammal ncRNA–disease repository with increased coverage and annotation
Authors: Ning Lin , Cui Tianyu , Zheng Boyang , Wang Nuo , Luo Jiaxin , Yang Beilei , Du Mengze , Cheng Jun , Dou Yiying , Wang Dong 
Published: August 2020

AbstractMany studies have indicated that non-coding RNA (ncRNA) dysfunction is closely related to numerous diseases. Recently, accumulated ncRNA–disease associations have made related databases insufficient to meet the demands of biomedical research. The constant updating of ncRNA–disease resources has become essential. Here, we have updated the mammal ncRNA–disease repository (MNDR, http://www.rna-society.org/mndr/) to version 3.0, containing more than one million entries, four-fold increment in data compared to the previous version. Experimental and predicted circRNA–disease associations have been integrated, increasing the number of categories of ncRNAs to five, and the number of mammalian species to 11. Moreover, ncRNA–disease related drug annotations and associations, as well as ncRNA subcellular localizations and interactions, were added. In addition, three ncRNA–disease (miRNA/lncRNA/circRNA) prediction tools were provided, and the website was also optimized, making it more practical and user-friendly. In summary, MNDR v3.0 will be a valuable resource for the investigation of disease mechanisms and clinical treatment strategies.
How mood tunes prediction: a neurophenomenological account of mood and its disturbance in major depression
Authors: Kiverstein Julian , Miller Mark , Rietveld Erik 
Published: August 2020

Abstract
In this article, we propose a neurophenomenological account of what moods are, and how they work. We draw upon phenomenology to show how mood attunes a person to a space of significant possibilities. Mood structures a person’s lived experience by fixing the kinds of significance the world can have for them in a given situation. We employ Karl Friston’s free-energy principle to show how this phenomenological concept of mood can be smoothly integrated with cognitive neuroscience. We will argue that mood is a consequence of acting in the world with the aim of minimizing expected free energy—a measure of uncertainty about the future consequences of actions. Moods summarize how the organism is faring overall in its predictive engagements, tuning the organism’s expectations about how it is likely to fare in the future. Agents that act to minimize expected free energy will have a feeling of how well or badly they are doing at maintaining grip on the multiple possibilities that matter to them. They will have what we will call a ‘feeling of grip’ that structures the possibilities they are ready to engage with over long time-scales, just as moods do.
Proceedings of the Comprehensive Oncology Network Evaluating Rare CNS Tumors (NCI-CONNECT) Adult Medulloblastoma Workshop
Authors: Penas-Prado Marta , Theeler Brett J , Cordeiro Brittany , Dunkel Ira J , Hau Peter , Mahajan Anita , Robinson Giles W , Willmarth Nicole , Aboud Orwa , Aldape Kenneth , Butman John A , Gajjar Amar , Kelly William , Rao Ganesh , Raygada Margarita , Siegel Christine , Romo Carlos G , Armstrong Terri S , Gilbert Mark R ,   NCI-CONNECT Adult Medulloblastoma Workshop, Penas-Prado Marta , Armstrong Terri S , Gilbert Mark R , Camphausen Kevin , Cordeiro Brittany , Dunkel Ira , Gajjar Amar , Galanis Eva , Hau Peter , Mahajan Anita , Penas-Prado Marta , Romo Carlos G , Wall Kathleen , Abdullaev Zied , Aldape Kenneth , Celiku Orieta , Chapman Lesley , Gilbert Mark R , Forsyth Peter , Jung Jinkyu , Leach Danielle , Nair Nishanth Ulhas , Kelly William , Rao Ganesh , Raygada Margarita , Robinson Giles , Schischlik Fiorella , Shih Helen , Siegel Christine , Theeler Brett J , Willmarth Nicole , Wu Jing , Aboud Orwa , Acquaye Alvina , Armstrong Terri S , Butman John A , Gonzalez Javier , Leeper Heather , Majd Nazanin , Oliver Kathy , Tsien Christina , Wen Patrick 
Published: August 2020

AbstractBackgroundMedulloblastoma (MB) is a rare brain tumor occurring more frequently in children in whom research has been primarily focused. Treatment recommendations in adults are mainly based on retrospective data and pediatric experience; however, molecular features and treatment tolerance differ between the 2 age groups. In adults, prognostic tools are suboptimal, late recurrences are typical, and long-term sequelae remain understudied. Treatment has not adapted to molecular classification advances; thus, the survival rate of adult MB has not improved.MethodsIn 2017, the National Cancer Institute (NCI) received support from the Cancer Moonshot℠ to address the challenges and unmet needs of adults with rare central nervous system tumors through NCI-CONNECT, a program that creates partnerships among patients, health care professionals, researchers, and advocacy organizations. On November 25, 2019, NCI-CONNECT convened leading clinicians and scientists in a workshop to review advances in research, share scientific insights, and discuss clinical challenges in adult MB.ResultsWorking groups identified unmet needs in clinical trial design, tissue acquisition and testing, tumor modeling, and measurement of clinical outcomes.ConclusionsParticipants identified opportunities for collaboration; discussed plans to create a working group of clinicians, researchers, and patient advocates; and developed specific action items to expedite progress in adult MB.
A Case of Steroid-Responsive, COVID-19 Immune Reconstitution Inflammatory Syndrome Following the Use of Granulocyte Colony-Stimulating Factor
Authors: Mertens Jonathan , Laghrib Yassine , Kenyon Chris 
Published: August 2020

AbstractWe present a case report of a 54-year-old male with metastasized nasopharyngeal carcinoma presenting to the hospital with dyspnea, anorexia and fever. Examination revealed chemotherapy-induced pancytopenia. The patient tested positive for SARSCoV-2, but respiratory complications were mild. The patient was treated with granulocyte-colony stimulating factor (G-CSF) leading to amelioration of the neutropenia. However, severe acute respiratory distress syndrome (ARDS) occurred, prompting the diagnosis of immune reconstitution inflammatory syndrome (IRIS). GCSF is currently investigated as additional therapy in ARDS, but this case report emphasizes that risks and benefits must be carefully assessed. To our knowledge, this is the first case report of IRIS-induced ARDS in a COVID-19 patient.
Oculoglandular Tularemia From Crushing an Engorged Tick
Authors: Lakos András , Nagy Gyöngyi , Kienle Zsuzsa 
Published: August 2020

Abstract
We report on an unusual case of oculoglandular tularemia acquired after crushing a tick removed from a dog. As a droplet sprayed into the patient’s eye the eyelids became inflamed, and on the fourth day, a high fever started. Prompt antibiotic treatment prevented serious complication.
Maize Defective Kernel605 Encodes a Canonical DYW-Type PPR Protein that Edits a Conserved Site of nad1 and Is Essential for Seed Nutritional Quality
Authors: Fan Kaijian , Peng Yixuan , Ren Zhenjing , Li Delin , Zhen Sihan , Hey Stefan , Cui Yu , Fu Junjie , Gu Riliang , Wang Jianhua , Wang Guoying , Li Li 
Published: August 2020

Abstract
Pentatricopeptide repeat (PPR) proteins involved in mitochondrial RNA cytidine (C)-to-uridine (U) editing mostly result in stagnant embryo and endosperm development upon loss of function. However, less is known about PPRs that are involved in farinaceous endosperm formation and maize quality. Here, we cloned a maize DYW-type PPR Defective Kernel605 (Dek605). Mutation of Dek605 delayed seed and seedling development. Mitochondrial transcript analysis of dek605 revealed that loss of DEK605 impaired C-to-U editing at the nad1-608 site and fails to alter Ser203 to Phe203 in NAD1 (dehydrogenase complex I), disrupting complex I assembly and reducing NADH dehydrogenase activity. Meanwhile, complexes III and IV in the cytochrome pathway, as well as AOX2 in the alternative respiratory pathway, are dramatically increased. Interestingly, the dek605 mutation resulted in opaque endosperm and increased levels of the free amino acids alanine, aspartic acid and phenylalanine. The down- and upregulated genes mainly involved in stress response-related and seed dormancy-related pathways, respectively, were observed after transcriptome analysis of dek605 at 12 d after pollination. Collectively, these results indicate that Dek605 specifically affects the single nad1-608 site and is required for normal seed development and resulted in nutritional quality relevant amino acid accumulation.
The Devils in the DALY: Prevailing Evaluative Assumptions
Authors: Solberg Carl Tollef , Sørheim Preben , Müller Karl Erik , Gamlund Espen , Norheim Ole Frithjof , Barra Mathias 
Published: August 2020

Abstract
In recent years, it has become commonplace among the Global Burden of Disease (GBD) study authors to regard the disability-adjusted life year (DALY) primarily as a descriptive health metric. During the first phase of the GBD (1990–1996), it was widely acknowledged that the DALY had built-in evaluative assumptions. However, from the publication of the 2010 GBD and onwards, two central evaluative practices—time discounting and age-weighting—have been omitted from the DALY model. After this substantial revision, the emerging view now appears to be that the DALY is primarily a descriptive measure. Our aim in this article is to argue that the DALY, despite changes, remains largely evaluative. Our analysis focuses on the understanding of the DALY by comparing the DALY as a measure of disease burden in the two most significant phases of GBD publications, from their beginning (1990–1996) to the most recent releases (2010–2017). We identify numerous assumptions underlying the DALY and group them as descriptive or evaluative. We conclude that while the DALY model arguably has become more descriptive, it remains, by necessity, largely evaluative.
Stressed but not Depressed: A Longitudinal Analysis of First-Generation College Students, Stress, and Depressive Symptoms
Authors: Wilbur Tabitha G 
Published: August 2020

Abstract
Using The National Longitudinal Study of Adolescent to Adult Health (Add Health), I examine stress exposure and depressive symptoms among first and continuing-generation college students before and during college. I find that first-generation college students experience more stressors during both adolescence and college attendance and higher levels of depressive symptoms during adolescence as compared to continuing-generation students. During college, however, first-generation students’ level of depressive symptoms is no different from their continuing-generation peers even before adjusting for stress exposure and adolescent depressive symptoms. The gap in symptoms closes because first-generation college students’ mental health improves while attending college, as they have significantly fewer depressive symptoms than they did during adolescence. Continuing-generation students, on the other hand, did not display a significant difference in their depressive symptoms between adolescence and college attendance. Possible explanations for these findings are discussed.
Hepatosplenic schistosomiasis, the ignored morbidity: experience from a referral hospital in Ethiopia
Authors: Abdela Seid Getahun , Hassen Nardos Girma , Hussien Foziya Mohammed , Yesuf Abdulaziz Mohammed , van Griensven Johan , van Henten Saskia 
Published: August 2020

Abstract

Background
Hepatosplenic schistosomiasis (HSS) is an important chronic complication of Schistosoma infection. However, its diagnosis and management are complicated due to lack of evidence and uniform guidance. In this study, we described the clinical profile and management of HSS in one of Ethiopia's referral hospitals.

Methods
A hospital-based, cross-sectional study was conducted using the medical records of patients diagnosed with HSS based on clinical symptoms and typical ultrasound findings observed at the gastroenterology clinic of Dessie referral hospital from September 2018 to December 2019.

Results
A total of 55 patient files were evaluated. Most patients (n=39; 70%) presented with upper gastrointestinal bleeding and severe anaemia. Nearly three-quarters of patients were admitted and 31 (56%) received a blood transfusion. Hepatitis B coinfection was documented in 11 patients (20%). Upper gastrointestinal endoscopy was performed in 31 patients (56%), in whom large oesophageal varices with red signs were the most common finding. Among patients who had endoscopy, band ligation was carried out in 21 cases (68%). Praziquantel was administered to 11 patients (20%).

Conclusion
HSS causes severe complications of portal hypertension, like variceal bleeding, which are currently not adequately treated. In addition to already existing preventive efforts, we advise control programmes to also address acute management and rehabilitation of these patients.
Efficient inference, potential, and limitations of site-specific substitution models
Authors: Puller Vadim , Sagulenko Pavel , Neher Richard A 
Published: August 2020

Abstract
Natural selection imposes a complex filter on which variants persist in a population resulting in evolutionary patterns that vary greatly along the genome. Some sites evolve close to neutrally, while others are highly conserved, allow only specific states, or only change in concert with other sites. On one hand, such constraints on sequence evolution can be to infer biological function, one the other hand they need to be accounted for in phylogenetic reconstruction. Phylogenetic models often account for this complexity by partitioning sites into a small number of discrete classes with different rates and/or state preferences. Appropriate model complexity is typically determined by model selection procedures. Here, we present an efficient algorithm to estimate more complex models that allow for different preferences at every site and explore the accuracy at which such models can be estimated from simulated data. Our iterative approximate maximum likelihood scheme uses information in the data efficiently and accurately estimates site-specific preferences from large data sets with moderately diverged sequences and known topology. However, the joint estimation of site-specific rates, and site-specific preferences, and phylogenetic branch length can suffer from identifiability problems, while ignoring variation in preferences across sites results in branch length underestimates. Site-specific preferences estimated from large HIV pol alignments show qualitative concordance with intra-host estimates of fitness costs. Analysis of these substitution models suggests near saturation of divergence after a few hundred years. Such saturation can explain the inability to infer deep divergence times of HIV and SIVs using molecular clock approaches and time-dependent rate estimates.