bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the vanishing orbital X-ray variability of the eclipsing binary millisecond pulsar 47 Tuc W
Authors: Hebbar P R , Heinke C O , Kandel D , Romani R W , Freire P C C 
Published: October 2020

ABSTRACT
Redback millisecond pulsars (MSPs) typically show pronounced orbital variability in their X-ray emission due to our changing view of the intrabinary shock (IBS) between the pulsar wind and stellar wind from the companion. Some redbacks (‘transitional’ MSPs) have shown dramatic changes in their multiwavelength properties, indicating a transition from a radio pulsar state to an accretion-powered state. The redback MSP 47 Tuc W showed clear X-ray orbital variability in the Chandra ACIS-S observations in 2002, which were not detectable in the longer Chandra HRC-S observations in 2005–06, suggesting that it might have undergone a state transition. However, the Chandra observations of 47 Tuc in 2014–15 show similar X-ray orbital variability as in 2002. We explain the different X-ray light curves from these epochs in terms of two components of the X-ray spectrum (soft X-rays from the pulsar versus harder X-rays from the IBS), and different sensitivities of the X-ray instruments observing in each epoch. However, when we use our best-fitting spectra with HRC response files to model the HRC light curve, we expect a more significant and shorter dip than that observed in the 2005–06 Chandra data. This suggests an intrinsic change in the IBS of the system. We use the icarus stellar modelling software, including calculations of heating by an IBS, to model the X-ray, optical, and UV light curves of 47 Tuc W. Our best-fitting parameters point towards a high-inclination system ($i \sim 60 \deg$), which is primarily heated by the pulsar radiation, with an IBS dominated by the companion wind momentum.
The relative orientation between the magnetic field and gas density structures in non-gravitating turbulent media
Authors: Körtgen Bastian , Soler Juan D 
Published: October 2020

ABSTRACT
Magnetic fields are a dynamically important agent for regulating structure formation in the interstellar medium. The study of the relative orientation between the local magnetic field and gas (column-) density gradient has become a powerful tool to analyse the magnetic field’s impact on the dense gas formation in the Galaxy. In this study, we perform numerical simulations of a non-gravitating, isothermal gas, where the turbulence is driven either solenoidally or compressively. We find that only simulations with an initially strong magnetic field (plasma-β &lt; 1) show a change in the preferential orientation between the magnetic field and isodensity contours, from mostly parallel at low densities to mostly perpendicular at higher densities. Hence, compressive turbulence alone is not capable of inducing the transition observed towards nearby molecular clouds. At the same high initial magnetization, we find that solenoidal modes produce a sharper transition in the relative orientation with increasing density than compressive modes. We further study the time evolution of the relative orientation and find that it remains unchanged by the turbulent forcing after one dynamical time-scale.
Mitogenomes Reveal Alternative Initiation Codons and Lineage-Specific Gene Order Conservation in Echinoderms
Authors: Quek Zheng Bin Randolph , Chang Jia Jin Marc , Ip Yin Cheong Aden , Chan Yong Kit Samuel , Huang Danwei 
Published: October 2020

AbstractThe mitochondrial genetic code is much more varied than the standard genetic code. The invertebrate mitochondrial code, for instance, comprises six initiation codons, including five alternative start codons. However, only two initiation codons are known in the echinoderm and flatworm mitochondrial code, the canonical ATG and alternative GTG. Here, we analyzed 23 Asteroidea mitogenomes, including ten newly sequenced species and unambiguously identified at least two other start codons, ATT and ATC, both of which also initiate translation of mitochondrial genes in other invertebrates. These findings underscore the diversity of the genetic code and expand upon the suite of initiation codons among echinoderms to avoid erroneous annotations. Our analyses have also uncovered the remarkable conservation of gene order among asteroids, echinoids, and holothuroids, with only an interchange between two gene positions in asteroids over ∼500 Ma of echinoderm evolution.
REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments
Authors: Mansi Luigi , Tangaro Marco Antonio , Lo Giudice Claudio , Flati Tiziano , Kopel Eli , Schaffer Amos Avraham , Castrignanò Tiziana , Chillemi Giovanni , Pesole Graziano , Picardi Ernesto 
Published: October 2020

Abstract
RNA editing is a relevant epitranscriptome phenomenon able to increase the transcriptome and proteome diversity of eukaryotic organisms. ADAR mediated RNA editing is widespread in humans in which millions of A-to-I changes modify thousands of primary transcripts. RNA editing has pivotal roles in the regulation of gene expression or modulation of the innate immune response or functioning of several neurotransmitter receptors. Massive transcriptome sequencing has fostered the research in this field. Nonetheless, different aspects of the RNA editing biology are still unknown and need to be elucidated. To support the study of A-to-I RNA editing we have updated our REDIportal catalogue raising its content to about 16 millions of events detected in 9642 human RNAseq samples from the GTEx project by using a dedicated pipeline based on the HPC version of the REDItools software. REDIportal now allows searches at sample level, provides overviews of RNA editing profiles per each RNAseq experiment, implements a Gene View module to look at individual events in their genic context and hosts the CLAIRE database. Starting from this novel version, REDIportal will start collecting non-human RNA editing changes for comparative genomics investigations. The database is freely available at http://srv00.recas.ba.infn.it/atlas/index.html.
DrugSpaceX: a large screenable and synthetically tractable database extending drug space
Authors: Yang Tianbiao , Li Zhaojun , Chen Yingjia , Feng Dan , Wang Guangchao , Fu Zunyun , Ding Xiaoyu , Tan Xiaoqin , Zhao Jihui , Luo Xiaomin , Chen Kaixian , Jiang Hualiang , Zheng Mingyue 
Published: October 2020

Abstract
One of the most prominent topics in drug discovery is efficient exploration of the vast drug-like chemical space to find synthesizable and novel chemical structures with desired biological properties. To address this challenge, we created the DrugSpaceX (https://drugspacex.simm.ac.cn/) database based on expert-defined transformations of approved drug molecules. The current version of DrugSpaceX contains &gt;100 million transformed chemical products for virtual screening, with outstanding characteristics in terms of structural novelty, diversity and large three-dimensional chemical space coverage. To illustrate its practical application in drug discovery, we used a case study of discoidin domain receptor 1 (DDR1), a kinase target implicated in fibrosis and other diseases, to show DrugSpaceX performing a quick search of initial hit compounds. Additionally, for ligand identification and optimization purposes, DrugSpaceX also provides several subsets for download, including a 10% diversity subset, an extended drug-like subset, a drug-like subset, a lead-like subset, and a fragment-like subset. In addition to chemical properties and transformation instructions, DrugSpaceX can locate the position of transformation, which will enable medicinal chemists to easily integrate strategy planning and protection design.
Missing the forest because of the trees: slower alternations during binocular rivalry are associated with lower levels of visual detail during ongoing thought
Authors: Ho Nerissa Siu Ping , Baker Daniel , Karapanagiotidis Theodoros , Seli Paul , Wang Hao Ting , Leech Robert , Bernhardt Boris , Margulies Daniel , Jefferies Elizabeth , Smallwood Jonathan 
Published: October 2020

Abstract
Conscious awareness of the world fluctuates, either through variation in how vividly we perceive the environment, or when our attentional focus shifts away from information in the external environment towards information that we generate via imagination. Our study combined individual differences in experience sampling, psychophysical reports of perception and neuroimaging descriptions of structural connectivity to better understand these changes in conscious awareness. In particular, we examined (i) whether aspects of ongoing thought—indexed via multi-dimensional experience sampling during a sustained attention task—are associated with the white matter fibre organization of the cortex as reflected by their relative degree of anisotropic diffusion and (ii) whether these neurocognitive descriptions of ongoing experience are related to a more constrained measure of visual consciousness through analysis of bistable perception during binocular rivalry. Individuals with greater fractional anisotropy in right hemisphere white matter regions involving the inferior fronto-occipital fasciculus, the superior longitudinal fasciculus and the cortico-spinal tract, described their ongoing thoughts as lacking external details. Subsequent analysis indicated that the combination of low fractional anisotropy in these right hemisphere regions, with reports of thoughts with high levels of external details, was associated with the shortest periods of dominance during binocular rivalry. Since variation in binocular rivalry reflects differences between bottom-up and top-down influences on vision, our study suggests that reports of ongoing thoughts with vivid external details may occur when conscious precedence is given to bottom-up representation of perceptual information.
Coherency and Constructions for Monoids
Authors: Dandan Yang , Gould Victoria , Hartmann Miklós , Ruškuc Nik , Zenab Rida-E 
Published: October 2020

AbstractA monoid S is right coherent if every finitely generated subact of every finitely presented right S-act is finitely presented. This is a finiteness condition, and we investigate whether or not it is preserved under some standard algebraic and semigroup theoretic constructions: subsemigroups, homomorphic images, direct products, Rees matrix semigroups, including Brandt semigroups, and Bruck–Reilly extensions. We also investigate the relationship with the property of being weakly right noetherian, which requires all right ideals of S to be finitely generated.
Flat ring epimorphisms and universal localizations of commutative rings
Authors: Angeleri Hügel Lidia , Marks Frederik , Št’ovíček Jan , Takahashi Ryo , Vitória Jorge 
Published: October 2020

Abstract
We study different types of localizations of a commutative noetherian ring. More precisely, we provide criteria to decide: (a) if a given flat ring epimorphism is a universal localization in the sense of Cohn and Schofield; and (b) when such universal localizations are classical rings of fractions. In order to find such criteria, we use the theory of support and we analyse the specialization closed subset associated to a flat ring epimorphism. In case the underlying ring is locally factorial or of Krull dimension one, we show that all flat ring epimorphisms are universal localizations. Moreover, it turns out that an answer to the question of when universal localizations are classical depends on the structure of the Picard group. We furthermore discuss the case of normal rings, for which the divisor class group plays an essential role to decide if a given flat ring epimorphism is a universal localization. Finally, we explore several (counter)examples which highlight the necessity of our assumptions.
Counting Algebraic Points in Expansions of O-Minimal Structures by a Dense Set
Authors: Eleftheriou Pantelis E 
Published: October 2020

Abstract
The Pila–Wilkie theorem states that if a set $X\subseteq \mathbb{R}^n$ is definable in an o-minimal structure $\mathcal{R}$ and contains ‘many’ rational points, then it contains an infinite semialgebraic set. In this paper, we extend this theorem to an expansion $\widetilde{\mathcal{R}}=\langle {\mathcal{R}}, P\rangle$ of ${\mathcal{R}}$ by a dense set P, which is either an elementary substructure of ${\mathcal{R}}$, or it is $\mathrm{dcl}$-independent, as follows. If X is definable in $\widetilde{\mathcal{R}}$ and contains many rational points, then it is dense in an infinite semialgebraic set. Moreover, it contains an infinite set which is ${\emptyset}$-definable in $\langle \overline{\mathbb{R}}, P\rangle$, where $\overline{\mathbb{R}}$ is the real field.
Along the way we introduce the notion of the ‘algebraic trace part’ $X^{{\, alg}}_t$ of any set $X\subseteq \mathbb{R}^n$, and we show that if X is definable in an o-minimal structure, then $X^{{\, alg}}_t$ coincides with the usual algebraic part of X.
Biomass partitioning and photosynthesis in the quest for nitrogen- use efficiency for citrus tree species
Authors: Dovis Veronica L , Erismann Norma M , Machado Eduardo C , Quaggio Jose A , Boaretto Rodrigo M , Mattos Júnior Dirceu 
Published: October 2020

Abstract
Optimizing the use of nitrogen (N) for food production is a major challenge in agricultural systems. The transformation of N into crop production results from intricate pathways, depending on plants, as well as the environment and fertilization regimes, which affect the N-use efficiency (NUE) of plants. In this context, lemon trees [Citrus limon (L.) Burm. f.] attain maximum harvest index at lower leaf N concentrations compared with sweet orange trees [Citrus sinensis (L.) Osbeck], and the processes governing these plant responses are not well known. The aim of this study was to understand how the higher NUE in lemons trees is constructed based on growth and biomass partitioning evaluation, as well as photochemical and biochemical characteristics of photosynthesis. To attain this goal, we evaluated growth, photosynthesis and biochemical characteristics in lemon and sweet orange trees under two different N levels over 14 months. We hypothesized that higher NUE in lemon trees is affected by plant capacity to grow with economy on nutrient resources. Furthermore, lemon trees could be more efficient in CO2 assimilation in non-limiting environmental conditions. We found that higher NUE in lemon trees was explained in part by the ability of trees to invest greater biomass in leaves instead of roots, even though this species exhibited lower relative recovery efficiency of N from the substrate than the sweet orange. We also found that lemon trees had a higher relative growth rate than sweet oranges, despite the fact that net CO2 assimilation and dark respiration were similar between the two species. As a consequence, we suggested that lemons could exhibit a lower biomass construction cost than oranges. Because lemon presented lower N concentration than sweet orange trees, the former exhibited better photosynthetic N-use efficiency (PNUE: 55–120 mmol CO2 g N−1 day−1) compared with the sweet orange (PNUE: 31–68 mmol CO2 g N−1 day−1). Lemon trees also exhibited a higher relative rate of electron transport per unit of chlorophyll (ETR/chlor: 350–850) compared with orange trees (ETR/chlor: 300–550) at both low and at high N supply. These characteristics were likely associated with transport facilitation of CO2 to the catalytic sites of plants. In fact, improved growth of lemon trees results from an array of events explained mostly by increase in leaf area and associated low construction cost despite N supply.
CENTRAL RETINAL VEIN OCCLUSION WITH SEVERE MACULAR EDEMA IN EARLY PREGNANCY
Authors: Pokroy Russell , Raskin Eyal , Masarwa Dua 
Published: October 2020

Purpose:
To report the clinical course and treatment outcomes of a patient with central retinal vein occlusion with severe macular edema in early pregnancy.

Methods:
Interventional case report.

Results:
A 39-year-old woman with gestational diabetes mellitus and a 15-pack year smoking history presented at 7 weeks gestation with decreased vision due to central retinal vein occlusion with marked macular edema. One month later, visual acuity had decreased to 20/400, and macular edema had worsened to a central subfield thickness of 1,432 μm. She was treated with a single intravitreal dexamethasone implant at 16 weeks gestation. She responded well with visual acuity improving to 20/40+ and complete resolution of macular edema. At 33 weeks gestation, the cystoid macular edema recurred, but the patient refused treatment. The cystoid macular edema spontaneously resolved 3 weeks postpartum but recurred 3 months later with visual acuity worsening to 20/50. This macular edema resolved completely after a single 1.25 mg bevacizumab injection. She required no further treatment, and 23 months later, her macula was dry with visual acuity of 20/25. Her baby was healthy.

Conclusion:
Although pregnancy seems to aggravate central retinal vein occlusion –associated macular edema, the visual loss may be reversible. Intravitreal steroid seems to be effective during pregnancy with no apparent systemic or fetal complications. Young patients with retinal vein occlusion and center-involving macular edema may stabilize with minimal treatment.
VITREOUS HEMORRHAGE IN TYPE 3 GAUCHER DISEASE: AN ANGIOGRAPHIC AND PATHOLOGIC ANALYSIS
Authors: Hua Hong-Uyen , Haghighi Arezu , Shillingford Nick , Lee Thomas C. , Nagiel Aaron 
Published: October 2020

Purpose:
To describe the case of a 12-year-old woman with vitreoretinal manifestations of Type 3 Gaucher disease.

Methods:
A retrospective case report including multimodal imaging and histologic examination of the vitreous.

Results:
A 12-year-old woman with a history of Gaucher disease Type 3 was referred to the ophthalmology service for evaluation of vitreous deposits in both eyes. Funduscopic examination was notable for white vitreous opacities in both eyes. Ultra-widefield fluorescein angiography demonstrated areas of blockage associated with the deposits and focal areas of leakage. Optical coherence tomography angiography showed shadow artifact without intrinsic flow at these sites. Three years after presentation, she developed a right hemorrhagic posterior vitreous detachment, requiring pars plana vitrectomy with scleral buckle. A vitreous sample was sent to pathology, which demonstrated Gaucher cells.

Conclusion:
Gaucher disease is a rare metabolic condition caused by an autosomal recessive deficiency of glucocerebrosidase. To the best of our knowledge, this is the first report of hemorrhagic posterior vitreous detachment in Type 3 Gaucher disease, including ultra-widefield imaging, optical coherence tomography angiography, and histopathology.
Structured Mentorship and the Nursing Clinical Ladder
Authors: Mijares Ann H. , Radovich Patricia 
Published: October 2020

When nursing turnover is greater than the national average, professional development of nursing staff increases job satisfaction and employment retention. One approach that can address the professional development is mentoring.

Purpose
The evidence-based practice (EBP) project's aim was to determine whether a short-term structured mentorship program led by a clinical nurse specialist increased work engagement among staff nurses within 8 to 10 weeks.

Description
The EBP project was implemented on 2 adult acute care inpatient units. Using Wagner's caring mentorship model, a mentorship program using the organization's clinical ladder criteria was established where nurses were able to participate and complete selected professional development activities based on personal interests and perceived strengths. The clinical nurse specialist provided guidance and advice based each participant's identified activity.

Outcome
Since the completion of the initial pilot, the organization has expanded the mentorship program to include mentorship of nursing leaders as well as staff on the clinical units. With this expansion, the organization has trained an additional 167 mentors and has a consistent 27% overall advancement of nurses on the clinical ladder. In addition, advanced practice registered nurses have implemented mentorship as part of their onboarding practice for advanced practice nursing.

Conclusion
The EBP project demonstrated that a mentorship program using an established clinical ladder can increase elements of work engagement and satisfaction with the mentor and program among hospital nursing staff. Sustaining and expanding the program can facilitate with increased nursing job satisfaction and employee retention.
The Value and Role of the Inpatient Rehabilitation Facility
Authors: Perret Danielle , Whyte John , Melvin John , Celnik Pablo , Knowlton Tiffany , Nguyen Benjamin , Roberts-Atwater Beverly , Wu Sam S. H. 
Published: October 2020

Abstract
Although healthcare is always changing, the inpatient rehabilitation facility has indispensable and enduring roles in patient care, medical education, and research. For patients with complex medical and functional limitations, inpatient rehabilitation facility–level care fosters recovery and community reintegration and plays a strategic role in optimizing healthcare transitions from acute and to postacute settings. It is an incomparable and distinct zone for interprofessional education: the healthcare system is dependent on the inpatient rehabilitation facility as the epicenter for instruction to healthcare professionals on how to care for patients with complex rehabilitation needs. As healthcare evolves, patients’ increasing medical complexity requires ongoing research focused on patients’ evolving healthcare needs. The inpatient rehabilitation facility alone offers the requisite infrastructure to support such discovery. In this Association of Academic Physiatrists Position Paper, we provide a fresh perspective on the value proposition of the inpatient rehabilitation facility and advocate for this unique clinical environment as a critical component of contemporary healthcare.
Sex Differences in the Impact of Childhood Socioeconomic Status on Immune Function
Authors: Gassen Jeffrey , White Jordon D. , Peterman Julia L. , Mengelkoch Summer , Leyva Randi P. Proffitt , Prokosch Marjorie L. , Eimerbrink Micah J. , Brice Kelly , Cheek Dennis J. , Boehm Gary W. , Hill Sarah E. 
Published: October 2020

AbstractWe examined relationships between multiple sources of early life stress and adult immune function in humans. Adult participants provided retrospective information about their childhood a) socioeconomic status, b) household unpredictability, and c) exposure to adverse experiences. Participants’ peripheral blood mononuclear cells were then isolated for use in functional assays: a) tumor cell lysis by natural killer cells, and b) phagocytosis of Escherichia coli bioparticles, and c) mitogen-induced leukocyte proliferation and cytokine release. In men, lower childhood socioeconomic status predicted decrements in immunological performance across functional assays, along with greater spontaneous cytokine release from PBMCs. These changes co-occurred with elevations in plasma testosterone levels. Similar effects were not observed for other sources of stress, nor were they found in women (with the exception of spontaneous cytokine release). These findings provide evidence that low childhood socioeconomic status has a lasting negative impact on multiple aspects of immune function, particularly in men.