bluuebunny/crossref_metadata_2025 huggingface dataset:
Bistable states and separation hysteresis in curved compression ramp flows
Authors: Hu Yan-Chao , Zhou Wen-Feng , Wang Gang , Yang Yan-Guang , Tang Zhi-Gong
Published: November 2020

The separation hysteresis of the boundary layer induced by the variation of the angle of attack (AOA) is observed and investigated numerically in curved compression ramp (CCR) flows. The occurrence of this new phenomenon is based on the bistable states of CCR flows even for the same free-stream and boundary conditions, indicating that the boundary layer’s state (attachment/separation) depends on its evolutionary history with AOA varying. Specifically, beginning with an attachment state, the boundary layer remains attached as AOA increases slowly and suddenly separates once AOA reaches a marginal angle αs. However, if we decrease AOA back from this angle, the boundary layer will not attach and remain separated until AOA reaches a small enough angle αa. The AOA extent [αa, αs] is called the dual-solution region. Three characteristic adverse pressure gradients (APGs), Isb, Icw, and Ib, are proposed to explain the existence of this dual-solution region, where Icw and Isb (Icw < Isb) are induced by the curved wall and the separation bubble, respectively, and Ib is the maximum APG that the boundary layer can resist. (i) When Ib > Isb, the flow must be attached, (ii) when Ib < Icw, the flow must be separated, and (iii) when Icw < Ib < Isb, both of these two states are theoretically possible. Since AOA-variation can make (i), (ii), and (iii) occur alternately, it could induce the separation hysteresis of CCR flows, which has been observed in this paper.
On framed simple purely real Hurwitz numbers
Authors: Kazarian M. E. , Lando S. K. , Natanzon S. M.
Published: November 2020

We study real Hurwitz numbers enumerating real meromorphic functions of a special kind, referred to as framed purely real functions. We deduce partial differential equations of cut-and-join type for the generating functions for these numbers. We also construct a topological field theory for them.
Adjoint

-classes on threefolds
Authors: Höring A.
Published: November 2020

We answer a question of Filip and Tosatti concerning a basepoint-free theorem for transcendental

-classes on compact Kähler threefolds.
Lattice of definability (of reducts) for integers with successor
Authors: Semenov A. L. , Soprunov S. F.
Published: November 2020

In this paper the lattice of definability for integers with a successor (the relation

) is described. The lattice, whose elements are also knows as reducts, consists of three (naturally described) infinite series of relations. The proof uses a version of the Svenonius theorem for structures of special form.
Dynamics and spectral stability of soliton-like structures in fluid-filled membrane tubes
Authors: Il’ichev A. T.
Published: November 2020

This survey presents results on the stability of elevation solitary waves in axisymmetric elastic membrane tubes filled with a fluid. The elastic tube material is characterized by an elastic potential (elastic energy) that depends non-linearly on the principal deformations and describes the compliant elastic media. Our survey uses a simple model of an inviscid incompressible fluid, which nevertheless makes it possible to trace the main regularities of the dynamics of solitary waves. One of these regularities is the spectral stability (linear stability in form) of these waves. The basic equations of the ‘axisymmetric tube – ideal fluid’ system are formulated, and the equations for the fluid are averaged over the cross-section of the tube, that is, a quasi-one-dimensional flow with waves whose length significantly exceeds the radius of the tube is considered. The spectral stability with respect to axisymmetric perturbations is studied by constructing the Evans function for the system of basic equations linearized around a solitary wave type solution. The Evans function depends only on the spectral parameter

, is analytic in the right-hand complex half-plane

, and its zeros in

coincide with unstable eigenvalues. The problems treated include stability of steady solitary waves in the absence of a fluid inside the tube (the case of constant internal pressure), together with the case of local inhomogeneity (thinning) of the tube wall, the presence of a steady fluid filling the tube (the case of zero mean flow) or a moving fluid (the case of non-zero mean flow), and also the problem of stability of travelling solitary waves propagating along the tube with non-zero speed.

Bibliography: 83 titles.
On Weyl multipliers of the rearranged trigonometric system
Authors: Karagulyan G. A.
Published: November 2020

We prove that the condition

is necessary for an increasing sequence of numbers

to be an almost everywhere unconditional convergence Weyl multiplier for the trigonometric system. This property was known long ago for Haar, Walsh, Franklin and some other classical orthogonal systems. The proof of this result is based on a new sharp logarithmic lower bound on

for the majorant operator related to the rearranged trigonometric system.

Bibliography: 32 titles.
Two centuries of monarch butterfly collections reveal contrasting effects of range expansion and migration loss on wing traits
Authors: Freedman Micah G. , Dingle Hugh , Strauss Sharon Y. , Ramírez Santiago R.
Published: November 2020

Significance

Monarch butterflies are famous for their seasonal migration in North America but have recently expanded around the globe. Using >6,000 monarchs collected over two centuries, we use the monarch’s recent global range expansion to test hypotheses about how dispersal traits evolve. Early monarch founders have large and elongated forewings, but postestablishment loss of migration repeatedly leads to smaller wings, a pattern detectable in both time series with historical specimens and experimentally reared monarchs. This research documents how migration-associated traits may be favored during range expansion but disfavored when species cease seasonal migration. Furthermore, it highlights the value of museum collections by combining historical specimens with experimental rearing to demonstrate contemporary evolution of migration-associated traits in natural monarch populations.
Government effectiveness and institutions as determinants of tropical cyclone mortality
Authors: Tennant Elizabeth , Gilmore Elisabeth A.
Published: November 2020

Significance

Tropical cyclone disasters frequently result in substantial loss of life. Institutional capacity and economic development are believed to play protective roles, but previous efforts have been unable to disentangle their relative effects. We establish empirically that stronger national and subnational institutions, independent of income, are associated with lower tropical cyclone mortality. This suggests that effective institutions play an important role in the success of disaster risk reduction strategies. Our approach of accounting for hazard intensity, population exposure, and socioeconomic conditions at high resolutions can be extended to other hazards and scales to further examine how institutions moderate risk.
Narrative structure of
A Song of Ice and Fire
creates a fictional world with realistic measures of social complexity
Authors: Gessey-Jones Thomas , Connaughton Colm , Dunbar Robin , Kenna Ralph , MacCarron Pádraig , O’Conchobhair Cathal , Yose Joseph
Published: November 2020

Significance

We use mathematical and statistical methods to probe how a sprawling, dynamic, complex narrative of massive scale achieved broad accessibility and acclaim without surrendering to the need for reductionist simplifications. Subtle narrational tricks such as how natural social networks are mirrored and how significant events are scheduled are unveiled. The narrative network matches evolved cognitive abilities to enable complex messages be conveyed in accessible ways while story time and discourse time are carefully distinguished in ways matching theories of narratology. This marriage of science and humanities opens avenues to comparative literary studies. It provides quantitative support, for example, for the widespread view that deaths appear to be randomly distributed throughout the narrative even though, in fact, they are not.
Daily mitochondrial dynamics in cone photoreceptors
Authors: Giarmarco Michelle M. , Brock Daniel C. , Robbings Brian M. , Cleghorn Whitney M. , Tsantilas Kristine A. , Kuch Kellie C. , Ge William , Rutter Kaitlyn M. , Parker Edward D. , Hurley James B. , Brockerhoff Susan E.
Published: November 2020

Significance

Mitochondria are organelles that make cellular energy. In the retina, mitochondrial health is important for photoreceptor cell function and normal vision. Photoreceptors need more energy at night, but it is unclear how their mitochondria adapt to changing energy demands. We investigated zebrafish cone photoreceptor mitochondria throughout the day. At night cone mitochondria are smaller, more numerous, and more metabolically active. Material from mitochondria is also released from photoreceptors during nighttime, forming stalks and networks outside of the cell. In daytime, photoreceptor mitochondria associate with ER and autophagosomes, organelles that mediate mitochondrial turnover. These daily changes to mitochondrial structure may help photoreceptors adapt to metabolic demands of daytime and nighttime.
Curtailing FGF19’s mitogenicity by suppressing its receptor dimerization ability
Authors: Niu Jianlou , Zhao Jing , Wu Jiamin , Qiao Guanting , Gu Junlian , Zhou Chuanren , Li Qi , Ying Lei , Wang Dezhong , Lin Huan , Li Xiaokun , Mohammadi Moosa , Huang Zhifeng
Published: November 2020

Significance

In this study, we posited that the metabolic and mitogenic activities of enterokine FGF19 are reflections of different thresholds of FGF19-induced FGF receptor (FGFR) dimerization. To test our hypothesis, we engineered three FGF19 variants that have progressively reduced FGFR dimerization capacity. We show that these variants have progressively reduced cell proliferative/tumorigenic activity but maintain FGF19
WT
-like metabolic activities. These observations substantiate our model in which FGF signaling specificity is regulated by different thresholds in FGF-induced FGFR dimer stability and longevity, and provide a simple stratagem to engineer safer agonists of FGF19—or indeed any other FGF—for the treatment of a range of metabolic diseases.
Akt3 induces oxidative stress and DNA damage by activating the NADPH oxidase via phosphorylation of p47
phox
Authors: Polytarchou Christos , Hatziapostolou Maria , Yau Tung On , Christodoulou Niki , Hinds Philip W. , Kottakis Filippos , Sanidas Ioannis , Tsichlis Philip N.
Published: November 2020

Significance

Although the three Akt isoforms share mechanisms of activation and exhibit overlaps in their downstream signaling pathways, significant differences are now being uncovered. Here, we show that among Akt isoforms, Akt3 preferably phosphorylates p47
phox
and activates NADPH oxidase, resulting in robust induction of reactive oxygen species (ROS). Akt3-induced ROS activate the DNA damage response and upregulate p53 expression. Consequently, the proliferation rate of Akt3-expressing cells is reduced, an effect reversed by p53 loss. In cancer, Akt3 expression correlates with the abundance of p53; however, tumors can adapt to high Akt3 activity by inactivating the DNA damage response. These findings reveal differences in the regulation of ROS by Akt isoforms, which may be exploited therapeutically for Akt3-driven cancers.
TREE1-EIN3–mediated transcriptional repression inhibits shoot growth in response to ethylene
Authors: Wang Likai , Ko Eun Esther , Tran Jaclyn , Qiao Hong
Published: November 2020

Significance

Ethylene is an important plant hormone that is essential for many physiological and developmental processes such as apical hook formation, shoot and root growth, root nodulation, flower senescence, abscission, and fruit ripening. Transcriptional activation in the ethylene response has been well studied. However, the transcriptional repression in the ethylene response remains unclear. Here, by combined approaches of data analysis, molecular biology, and genetics, we found that a transcriptional repressor TREE1 interacts with EIN3 to regulate transcriptional repression, leading to an inhibition of shoot growth in response to ethylene. Our work provides insight into how the transcriptional activator can be tuned to repress downstream gene expression in hormone signals.
Resonant Raman scattering of core–shell GaN/AlN nanowires
Authors: Cros A , Cristóbal A García , Hestroffer K , Daudin B , Wang J , Demangeot F , Péchou R
Published: November 2020

We have analyzed the electron–phonon coupling in GaN/AlN core–shell nanowires by means of Raman scattering excited at various wavelengths in the ultraviolet spectral range (335, 325 and 300 nm) and as a function of the AlN shell thickness. The detailed analysis of the multi-phonon spectra evidences important differences with excitation energy. Under 325 and 300 nm excitation the Raman process is mediated by the allowed A
1(LO) phonon mode, where the atoms vibrate along the NW axis. Considering its selection rules, this mode is easily accessible in backscattering along the wurtzite c axis. Interestingly, for 335 nm excitation the scattering process is instead mediated by the E
1(LO) phonon mode, where atoms vibrate in the c-plane and that is forbidden in this configuration. This change is ascribed to the band anticrossing caused by the uniaxial strain imposed by the AlN shell and the proximity, at this particular excitation energy, of real electronic transitions separated by the energy of the longitudinal optical phonon modes. The energy and character of the electronic bands can be tuned by varying the AlN shell thickness, a degree of freedom unique to core–shell nanowires. The interpretation of the experimental results is supported by calculations of the electronic transitions of GaN under uniaxial strain performed within the framework of a k · p model.
Enhanced higher temperature irreversibility field and critical current density in MgB2 wires with Dy2O3 additions
Authors: Yang Y , Sumption M D , Rindfleisch M , Tomsic M , Collings E W
Published: November 2020

Bulk samples of magnesium diboride (MgB2) doped with 0.5 wt% of the rare earth oxides (REOs) Nd2O3 and Dy2O3 (named B-ND and B-DY) prepared by standard powder processing, and wires of MgB2 doped with 0.5 wt% Dy2O3 (named W-DY) prepared by a commercial powder-in-tube processing were studied. Investigations included x-ray diffractometry, scanning- and transmission electron microscopy, magnetic measurement of superconducting transition temperature (T
c), magnetic and resistive measurements of upper critical field (B
c2) and irreversibility field (B
irr), as well as magnetic and transport measurements of critical current densities versus applied field (J
cm(B) and J
c(B), respectively). It was found that although the products of REO doping did not substitute into the MgB2 lattice, REO-based inclusions resided within grains and at grain boundaries. Curves of bulk pinning force density (F
p) versus reduced field (b = B/B
irr) showed that flux pinning was by predominantly by grain boundaries, not point defects. At all temperatures the F
p(b) of W-DY experienced enhancement by inclusion-induced grain boundary refinement but at higher temperatures F
p(b) was still further increased by a Dy2O3 additive-induced increase in B
irr of about 1 T at all temperatures up to 20 K (and beyond). It is noted that Dy2O3 increases B
irr and that it does so, not just at 4 K, but in the higher temperature regime. This important property, shared by a number of REOs and other oxides promises to extend the applications range of MgB2 conductors.
Stability of DC transport in HTS conductor with local critical current reduction
Authors: Gömöry Fedor , Šouc Ján
Published: November 2020

A common feature of commercially available conductors based on high-temperature superconducting compounds is the fluctuation of critical current along the length. Fortunately, the practice adopted by manufacturers nowadays is to supply the detailed I
c(x) data with the conductor. Compared to knowing just the average of critical current, this should also allow a much better prediction of the conductor performance. Statistical methods are suitable for this purpose in the case when the fluctuations are regular at the low end of critical current distribution. However, a different approach is necessary at the presence of ‘weak spots’ that drop out of any statistics. Because of the strong nonlinearity of the current–voltage curve, such a location could transform into a ‘hot spot’ at transporting direct current (DC), with an abrupt increase of temperature endangering the conductor operation. We present a set of analytical formulas including the prediction of the maximum DC that could be carried sustainably before the thermal runaway appears. It is necessary to know the cooling conditions as well as the properties of the conductor constituents and their architecture. A formula for the voltage appearing on a weak spot, and its dependence on the DC, is also proposed. For this purpose the result of previous theoretical work has been slightly modified after comparing it with numerical iterative computations and finite element modeling. We demonstrate that the derived model allows a powerful analysis of experimental data comprising an estimation of the weak spot parameters i.e. its critical current and the length of the defect zone.
Cognitive Fatigue Predicts Cognitive Failure in Multiple Sclerosis Patients and Healthy Controls: A Case-Control Study
Authors: Spiegelberg Nora , Breuer Svenja , Nielsen Jörn , Saliger Jochen , Montag Christian , Karbe Hans , Markett Sebastian
Published: November 2020

Objective

Fatigue and cognitive deficits are frequent symptoms of multiple sclerosis (MS). However, the exact nature of their co-occurrence is not fully understood. We sought to determine the impact of cognitive and physical fatigue on subjective cognitive deficits in MS patients and healthy controls.

Methods

Self-reports of fatigue (FSMC), depression (CES-D), cognitive deficits (CFQ), and personality traits (NEO-FFI, ANPS) among 30 MS inpatients and 30 healthy controls were analyzed using hierarchical regression models. The frequency of cognitive mistakes was used as the dependent variable and the extent of cognitive and physical fatigue as the independent variable.

Results

Cognitive fatigue was the only unique and significant predictor of cognitive mistakes in both groups, explaining 13.3% of additional variance in the MS group after correcting for age, mood, and physical fatigue. Physical fatigue had no significant impact on cognitive mistakes. While age had an impact on cognitive mistakes and depression in healthy controls, this association was not significant in MS patients. Depression was significantly correlated with cognitive mistakes and cognitive fatigue in MS patients.

Conclusions

The interplay of cognitive fatigue and subjective cognitive impairment can be generalized, with the exception of the variables of age and depression, which were shown to have differing impacts on cognitive mistakes in MS patients and healthy controls, respectively. Cognitive fatigue was linked to cognitive mistakes even after correcting for overlapping items in MS patients only. Future research should further investigate the link between cognitive fatigue and attention lapses in daily life by using various objective assessments.
Adaptive one-class Gaussian processes allow accurate prioritization of oncology drug targets
Authors: de Falco Antonio , Dezso Zoltan , Ceccarelli Francesco , Cerulo Luigi , Ciaramella Angelo , Ceccarelli Michele
Published: November 2020

Motivation

The cost of drug development has dramatically increased in the last decades, with the number new drugs approved per billion US dollars spent on R&D halving every year or less. The selection and prioritization of targets is one the most influential decisions in drug discovery. Here we present a Gaussian Process model for the prioritization of drug targets cast as a problem of learning with only positive and unlabeled examples.

Results

Since the absence of negative samples does not allow standard methods for automatic selection of hyperparameters, we propose a novel approach for hyperparameter selection of the kernel in One Class Gaussian Processes. We compare our methods with state-of-the-art approaches on benchmark datasets and then show its application to druggability prediction of oncology drugs. Our score reaches an AUC 0.90 on a set of clinical trial targets starting from a small training set of 102 validated oncology targets. Our score recovers the majority of known drug targets and can be used to identify novel set of proteins as drug target candidates.

Availability and implementation

The matrix of features for each protein is available at: https://bit.ly/3iLgZTa. Source code implemented in Python is freely available for download at https://github.com/AntonioDeFalco/Adaptive-OCGP.

Supplementary information

Supplementary data are available at Bioinformatics online.
Cultural Processes Shaping Stop-and-Check Practices and Interaction Dynamics in a Large Dutch City: Police Vulnerabilities, Thought Styles and Rituals
Authors: Brown Patrick , van Eijk Nathalie
Published: November 2020

Existing scholarship on police decision-making notes the importance of categories and ‘governing mentalities’ in shaping front-line discretionary practices. Much of this work explores categories of race and ethnicity. Important questions remain regarding how micro-level practices connect to organizational dynamics and why ethnic profiling endures despite attempts to counter such practices. Drawing on critical approaches to uncertainty and risk, not least Mary Douglas’s cultural theory, we analyse data drawn from an ethnographic study of police work in a large city in the Netherlands. Our analysis emphasizes the multiple lines of accountability that render officers vulnerable in different ways, officers’ combining of different rationalities of decision-making and the influence of everyday rituals that cultivate and reinforce particular organizational thought styles and discretionary practices.
Quantitative Polyunsaturated Fatty Acid Analysis of Chia Seed Oil by High-Performance Liquid Chromatography
Authors: Liu Bingbing , Yan Weidong
Published: November 2020

Alpha-linolenic acid (ALA) and linoleic acid (LA), abundant in chia seed oil, are useful polyunsaturated fatty acids (PUFA) with numerous health benefits. The objectives of the present study were to explore the optimum extraction condition of chia seed oil and the possibilities of direct analysis of ALA and LA in chia seed oil by reversed-phase high-performance liquid chromatography with ultraviolet detection (RP-HPLC-UV). The optimized chia seed oil extraction condition was set by the usage of Soxhlet extrator with hexane as a solvent, with the solvent to solid ratio of 8 and the extraction time of 8 h. Prior to HPLC-UV analysis, the oil was saponified in order to get the free fatty acids for detection. The results showed that the proposed HPLC-UV method allowed the quantification of ALA and LA in chia seed oil. The method was simple, rapid (within 18 min) and sensitive (limit of detection 0.006 mg/mL for ALA and 0.02 mg/mL for LA) and precise (RSD ≤ 2%). Thus, the proposed experimental designs were shown to offer considerable advantages over traditional derivatization approaches in the ALA and LA analyses.
Scottish Women’s Poetry: Introduction
Authors: Jones Carole , Mcculloch Fiona
Published: November 2020

This introduction to the Scottish Women’s Poetry special issue presents a brief overview of the current critical field, sets out the rationale behind the special issue as going some way to initiate a redressing of the critical neglect of twenty-first-century Scottish women poets, and addresses the significance of the terms of engagement before going on to introduce the essays. It argues for the special issue as a step toward encouraging greater critical engagement with Scottish women’s poetry and exploration of the diverse strands of practice in the field.
Left atrial mechanics for secondary prevention from embolic stroke of undetermined source
Authors: Sade Leyla Elif , Keskin Suzan , Can Ufuk , Çolak Ayşe , Yüce Deniz , Çiftçi Orçun , Özin Bülent , Müderrisoğlu Haldun
Published: November 2020

Aims 

Anticoagulation is not justified unless atrial fibrillation (AF) is detected in cryptogenic stroke (CS) patients. We sought to explore whether left atrial (LA) remodelling is associated with embolic stroke of undetermined source (ESUS).

Methods and results 

In this prospective study, we evaluated consecutively 186 patients in sinus rhythm who presented with an acute ischaemic stroke (embolic and non-embolic) and sex- and age-matched controls. We performed continuous electrocardiogram (ECG) monitoring to capture paroxysmal AF episodes as recommended by the guidelines. After 12 months of follow-up, continuous ECG monitoring was repeated in patients with undetected AF episodes. We quantified LA reservoir and contraction strain (LASr and LASct) by speckle-tracking, LA volumes by 3D echocardiography. Out of 186 patients, 149 were enrolled after comprehensive investigation for the source of ischaemic stroke and divided into other cause (OC) (n = 52) and CS (n = 97) groups. CS patients were also subdivided into AF (n = 39) and ESUS (n = 58) groups. Among CS patients, LA strain predicted AF independently from CHARGE-AF score and LA volume indices. ESUS group, despite no captured AF, had significantly worse LA metrics than OC and control groups. AF group had the worst LA metrics. Moreover, LASr predicted both CS (embolic stroke with and without AF) and ESUS (embolic stroke with no detected AF) independently from LAVImax and CHA2DS2-VASc score. LASr >26% yielded 86% sensitivity, 92% specificity, 92% positive, and 86% negative predictive values for the identification of ESUS (areas under curve: 0.915, P < 0.0001, 95% confidence interval: 0.86–0.97).

Conclusion 

Echocardiographic quantification of LA remodelling has great potential for secondary prevention from ESUS.
Correcting for experiment-specific variability in expression compendia can remove underlying signals
Authors: Lee Alexandra J , Park YoSon , Doing Georgia , Hogan Deborah A , Greene Casey S
Published: November 2020

Motivation

In the past two decades, scientists in different laboratories have assayed gene expression from millions of samples. These experiments can be combined into compendia and analyzed collectively to extract novel biological patterns. Technical variability, or "batch effects," may result from combining samples collected and processed at different times and in different settings. Such variability may distort our ability to extract true underlying biological patterns. As more integrative analysis methods arise and data collections get bigger, we must determine how technical variability affects our ability to detect desired patterns when many experiments are combined.

Objective

We sought to determine the extent to which an underlying signal was masked by technical variability by simulating compendia comprising data aggregated across multiple experiments.

Method

We developed a generative multi-layer neural network to simulate compendia of gene expression experiments from large-scale microbial and human datasets. We compared simulated compendia before and after introducing varying numbers of sources of undesired variability.

Results

The signal from a baseline compendium was obscured when the number of added sources of variability was small. Applying statistical correction methods rescued the underlying signal in these cases. However, as the number of sources of variability increased, it became easier to detect the original signal even without correction. In fact, statistical correction reduced our power to detect the underlying signal.

Conclusion

When combining a modest number of experiments, it is best to correct for experiment-specific noise. However, when many experiments are combined, statistical correction reduces our ability to extract underlying patterns.
New interpretation of the spreading evolution of the Knipovich Ridge derived from aeromagnetic data
Authors: Dumais M-A , Gernigon L , Olesen O , Johansen S E , Brönner M
Published: November 2020

Insights into the spreading evolution of the Knipovich Ridge and development of the Fram Strait are revealed from a recent aeromagnetic survey. As an ultraslow spreading ridge in an oblique system located between the Svalbard–Barents Sea and the Northeast Greenland rifted margins, the dynamics of the Knipovich Ridge opening has long been debated. Its 90° bend with the Mohns Ridge, rare in plate tectonics, affects the evolution of the Fram Strait and motivates the study of crustal deformation with this distinctive configuration. We identified magnetic isochrons on either side of the present-day Knipovich Ridge. These magnetic observations considerably reduce the mapped extent of the oceanic domain and question the present understanding of the conjugate rifted margins. Our analysis reveals a failed spreading system before a major spreading reorganization of the Fram Strait gateway around magnetic chron C6 (circa 20 Ma).
From 9 to 91: health promotion through the life-course—illuminating the inner child
Authors: Sjöblom Margareta , Jacobsson Lars , Öhrling Kerstin , Kostenius Catrine
Published: November 2020

A life-course perspective is according to the World Health Organization about increasing the effectiveness of health promotion interventions at all ages. This targets the needs of human beings throughout their life. Descriptions of the phenomenon of the inner child invite the possibility that it may be of help when promoting health throughout the life-course. The aim was to describe and understand schoolchildren’s, adults and older person’s experiences of childhood in connection to health and well-being in the present and through the life-course, illuminating the inner child. The research strategy used was a secondary analysis of the original transcribed data from three Swedish studies investigating new questions. In total, 53 individuals aged 9–91, 20 school children, 20 adults and 13 older persons were interviewed about childhood experiences. The schoolchildren were invited to create a drawing, and to narrate about it during the interview. The main question in the secondary analysis was ‘How do the participants’ narrations about childhood experiences illuminate the inner child, useful for health promotion through the life-course?’ The findings showed the importance of a secure atmosphere and trusting relationships, indicating that experiences during childhood can help us to adapt and pass along life lessons across generations. There were narratives about play as an activity where they learned to promote a healthy childhood, struggle for independence and learning how to be responsible when growing up. Dimensions of mental, social and existential well-being can be seen as examples of the inner child’s role in health promotion through the life-course.
Risk Factors for Cytomegalovirus Reactivation and Association With Outcomes in Critically Ill Adults With Sepsis: A Pooled Analysis of Prospective Studies
Authors: Imlay Hannah , Dasgupta Sayan , Boeckh Michael , Stapleton Renee D , Rubenfeld Gordon D , Chen Ying , Limaye Ajit P
Published: November 2020

We performed multivariable analysis of potential risk factors (including cytomegalovirus [CMV] reactivation) for clinical outcomes by day 28 (death or continued hospitalization, ventilator-free days, intensive care unit (ICU)-free days, hospital-free days) from pooled cohorts of 2 previous prospective studies of CMV-seropositive adults with sepsis. CMV reactivation at any level, >100 IU/mL, >1000 IU/mL, peak viral load, and area under the curve were independently associated with the clinical outcomes. We identified the potential effect size of CMV on outcomes that could be used as end points for future interventional trials of CMV prevention using antiviral prophylaxis in ICU patients with sepsis.
Can reproducibility be improved in clinical natural language processing? A study of 7 clinical NLP suites
Authors: Digan William , Névéol Aurélie , Neuraz Antoine , Wack Maxime , Baudoin David , Burgun Anita , Rance Bastien
Published: November 2020

Background

The increasing complexity of data streams and computational processes in modern clinical health information systems makes reproducibility challenging. Clinical natural language processing (NLP) pipelines are routinely leveraged for the secondary use of data. Workflow management systems (WMS) have been widely used in bioinformatics to handle the reproducibility bottleneck.

Objective

To evaluate if WMS and other bioinformatics practices could impact the reproducibility of clinical NLP frameworks.

Materials and Methods

Based on the literature across multiple researcho fields (NLP, bioinformatics and clinical informatics) we selected articles which (1) review reproducibility practices and (2) highlight a set of rules or guidelines to ensure tool or pipeline reproducibility. We aggregate insight from the literature to define reproducibility recommendations. Finally, we assess the compliance of 7 NLP frameworks to the recommendations.

Results

We identified 40 reproducibility features from 8 selected articles. Frameworks based on WMS match more than 50% of features (26 features for LAPPS Grid, 22 features for OpenMinted) compared to 18 features for current clinical NLP framework (cTakes, CLAMP) and 17 features for GATE, ScispaCy, and Textflows.

Discussion

34 recommendations are endorsed by at least 2 articles from our selection. Overall, 15 features were adopted by every NLP Framework. Nevertheless, frameworks based on WMS had a better compliance with the features.

Conclusion

NLP frameworks could benefit from lessons learned from the bioinformatics field (eg, public repositories of curated tools and workflows or use of containers for shareability) to enhance the reproducibility in a clinical setting.
Historicizing the Transpacific Settler Colonial Condition: Asian–Indigenous Relations in Shawn Wong’sHomebaseand Viet Thanh Nguyen’sThe Sympathizer
Authors: Gandhi Evyn Lê Espiritu
Published: November 2020

This article introduces the concept of a transpacific settler colonial condition, a term which captures the interconnected nature of Indigenous struggles against settler colonialism across the Americas, Asia, and the Pacific Islands, given shared histories of American empire and military violence. In order to historicize the transpacific settler colonial condition's coarticulation with Asian American political subjectivity, ever since the Asian American Movement of the Long Sixties, this article turns to two works of Asian American historical fiction: Shawn Wong's Homebase (1979), one of the first self-identified works of Asian American literature, and Viet Thanh Nguyen's The Sympathizer (2015), a contemporary best-selling novel. Both texts call attention to the interconnected nature of Indigenous sovereignty struggles across the continental United States, Guam, and Vietnam and grapple with the vexed positionality of Asian American subjects who at times uphold transpacific settler colonialism and at other times resist it. The article ends with a call for transpacific decolonization via a feminist refugee epistemology.
Intrinsicality and Entanglement
Authors: Wilhelm Isaac
Published: November 2020

I explore the relationship between a prominent analysis of intrinsic properties, due to Langton and Lewis, and the phenomenon of quantum entanglement. As I argue, the analysis faces a puzzle. The full analysis classifies certain properties of entangled particles as intrinsic. But when combined with an extremely plausible assumption about duplication, the main part of the analysis classifies those properties as non-intrinsic instead. I conclude that much of Lewis’s metaphysics is in trouble: Lewis based many of his metaphysical views—his thesis of Humean supervenience, for instance, and his account of recombination—on an analysis of intrinsicality which does not sit well with quantum phenomena.
On the evolution of a binary system with arbitrarily misaligned orbital and stellar angular momenta due to quasi-stationary tides
Authors: Ivanov P B , Papaloizou J C B
Published: November 2020

We consider the evolution of a binary system interacting due to tidal effects without restriction on the orientation of the orbital, and where significant, spin angular momenta, and orbital eccentricity. We work in the low tidal forcing frequency regime in the equilibrium tide approximation. Internal degrees of freedom are fully taken into account for one component, the primary. In the case of the companion the spin angular momentum is assumed small enough to be neglected but internal energy dissipation is allowed for as this can be significant for orbital circularization in the case of planetary companions. We obtain a set of equations governing the evolution of the orbit resulting from tidal effects. These depend on the masses and radii of the binary components, the form and orientation of the orbit, and for each involved component, the spin rate, the Coriolis force, the normalized rate of energy dissipation associated with the equilibrium tide due to radiative processes and viscosity, and the classical apsidal motion constant, k2. These depend on stellar parameters with no need of additional assumptions or a phenomenological approach as has been invoked in the past. They can be used to determine the evolution of systems with initial significant misalignment of spin and orbital angular momenta as hypothesized for systems containing Hot Jupiters. The inclusion of the Coriolis force may lead to evolution of the inclination between orbital and spin angular momenta and precession of the orbital plane which may have observational consequences.
Dynamic role of dust in formation of molecular clouds
Authors: Zhuravlev V V
Published: November 2020

Dust is the usual minor component of the interstellar medium. Its dynamic role in the contraction of the diffuse gas into molecular clouds is commonly assumed to be negligible because of the small mass fraction, f ≃ 0.01. However, as shown in this study, the collective motion of dust grains with respect to the gas may considerably contribute to the destabilization of the medium on scales λ ≲ λJ, where λJ is the Jeans length-scale. The linear perturbations of the uniform self-gravitating gas at rest are marginally stable at λ ≃ λJ, but as soon as the drift of grains is taken into account, they begin growing at a rate approximately equal to $(f \tau)^{1/3} t^{-1}_{\mathrm{ ff}}$, where τ is the stopping time of grains expressed in units of the free-fall time of the cloud, tff. The physical mechanism responsible for such a weak dependence of the growth rate on f is the resonance of heavy sound waves stopped by the self-gravity of gas with weak gravitational attraction caused by perturbations of the dust fraction. Once there is stationary subsonic bulk drift of the dust, the growing gas–dust perturbations at λ < λJ become waves propagating with the drift velocity projected on to the wavevector. Their growth has a resonant nature as well and the growth rate is substantially larger than that of the recently discovered resonant instability of gas–dust mixture in the absence of self-gravity. The new instabilities can facilitate gravitational contraction of cold interstellar gas into clouds and additionally produce dusty domains of sub-Jeans size at different stages of molecular cloud formation and evolution.
Visibility of black hole shadows in low-luminosity AGN
Authors: Bronzwaer Thomas , Davelaar Jordy , Younsi Ziri , Mościbrodzka Monika , Olivares Héctor , Mizuno Yosuke , Vos Jesse , Falcke Heino
Published: November 2020

Accreting black holes tend to display a characteristic dark central region called the black hole shadow, which depends only on space–time/observer geometry and which conveys information about the black hole’s mass and spin. Conversely, the observed central brightness depression, or image shadow, additionally depends on the morphology of the emission region. In this paper, we investigate the astrophysical requirements for observing a meaningful black hole shadow in GRMHD-based models of accreting black holes. In particular, we identify two processes by which the image shadow can differ from the black hole shadow: evacuation of the innermost region of the accretion flow, which can render the image shadow larger than the black hole shadow, and obscuration of the black hole shadow by optically thick regions of the accretion flow, which can render the image shadow smaller than the black hole shadow, or eliminate it altogether. We investigate in which models the image shadows of our models match their corresponding black hole shadows, and in which models the two deviate from each other. We find that, given a compact and optically thin emission region, our models allow for measurement of the black hole shadow size to an accuracy of 5 per cent. We show that these conditions are generally met for all MAD simulations we considered, as well as some of the SANE simulations.
A massive blow for ΛCDM – the high redshift, mass, and collision velocity of the interacting galaxy cluster El Gordo contradicts concordance cosmology
Authors: Asencio Elena , Banik Indranil , Kroupa Pavel
Published: November 2020

El Gordo (ACT-CL J0102-4915) is an extremely massive galaxy cluster (M200 ≈ 3 × 1015 M⊙) at redshift z = 0.87 composed of two subclusters with a mass ratio of 3.6 merging at speed Vinfall ≈ 2500 km s−1. Such a fast collision between individually rare massive clusters is unexpected in Lambda cold dark matter (ΛCDM) cosmology at such high z. However, this is required for non-cosmological hydrodynamical simulations of the merger to match its observed properties. Here, we determine the probability of finding a similar object in a ΛCDM context using the Jubilee simulation box with a side length of $6 \, h^{-1}$ Gpc. We search for galaxy cluster pairs that have turned around from the cosmic expansion with properties similar to El Gordo in terms of total mass, mass ratio, redshift, and collision velocity relative to virial velocity. We fit the distribution of pair total mass quite accurately, with the fits used in two methods to infer the probability of observing El Gordo in the surveyed region. The more conservative (and detailed) method involves considering the expected distribution of pairwise mass and redshift for analogue pairs with similar dimensionless parameters to El Gordo in the past light-cone of a z = 0 observer. Detecting one pair with its mass and redshift rules out ΛCDM cosmology at 6.16σ. We also use the results of Kraljic and Sarkar to show that the Bullet Cluster is in 2.78σ tension once the sky coverage of its discovery survey is accounted for. Using a χ2 approach, the combined tension can be estimated as 6.43σ. Both collisions arise naturally in a Milgromian dynamics (MOND) cosmology with light sterile neutrinos.
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation
Authors: Li Wenjun , O’Neill Kathleen R , Haft Daniel H , DiCuccio Michael , Chetvernin Vyacheslav , Badretdin Azat , Coulouris George , Chitsaz Farideh , Derbyshire Myra K , Durkin A Scott , Gonzales Noreen R , Gwadz Marc , Lanczycki Christopher J , Song James S , Thanki Narmada , Wang Jiyao , Yamashita Roxanne A , Yang Mingzhang , Zheng Chanjuan , Marchler-Bauer Aron , Thibaud-Nissen Françoise
Published: November 2020

The Reference Sequence (RefSeq) project at the National Center for Biotechnology Information (NCBI) contains nearly 200 000 bacterial and archaeal genomes and 150 million proteins with up-to-date annotation. Changes in the Prokaryotic Genome Annotation Pipeline (PGAP) since 2018 have resulted in a substantial reduction in spurious annotation. The hierarchical collection of protein family models (PFMs) used by PGAP as evidence for structural and functional annotation was expanded to over 35 000 protein profile hidden Markov models (HMMs), 12 300 BlastRules and 36 000 curated CDD architectures. As a result, >122 million or 79% of RefSeq proteins are now named based on a match to a curated PFM. Gene symbols, Enzyme Commission numbers or supporting publication attributes are available on over 40% of the PFMs and are inherited by the proteins and features they name, facilitating multi-genome analyses and connections to the literature. In adherence with the principles of FAIR (findable, accessible, interoperable, reusable), the PFMs are available in the Protein Family Models Entrez database to any user. Finally, the reference and representative genome set, a taxonomically diverse subset of RefSeq prokaryotic genomes, is now recalculated regularly and available for download and homology searches with BLAST. RefSeq is found at https://www.ncbi.nlm.nih.gov/refseq/.
Increasing incidence and improved survival in ANCA-associated vasculitis—a Danish nationwide study
Authors: Nelveg-Kristensen Karl Emil , Szpirt Wladimir , Carlson Nicholas , McClure Mark , Jayne David , Dieperink Hans , Gregersen Jon Waarst , Krarup Elizabeth , Ivarsen Per , Torp-Pedersen Christian , Egfjord Martin
Published: November 2020

Background

Anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) carries a high risk of morbidity and mortality, with outcomes modified by treatment and an incidence that may be increasing. We examined temporal changes in incidence and mortality during 2000–15 using nationwide healthcare registries.

Methods

Patients with incident AAV were identified using International Classification of Diseases Version 10 (ICD10) codes and grouped according to inclusion year (Period 1: 2000–04, Period 2: 2005–09, Period 3: 2010–15). Log link cumulative incidence regression adjusted for age, sex, renal function, cardiovascular disease, diabetes, hypertension and advanced disease severity were used to model survival.

Results

We identified 1631 patients (52% male), corresponding to an incidence of 18.5 persons/million/year (Period 1: 15.1, Period 2: 18.5, Period 3: 21.4). The slope of incident serologic ANCA testing was steeper than that of AAV (P = 0.002). Mean [standard deviation (SD)] age was 60.2 (16.7) years and mean (SD) follow-up was 6.8 (4.7) years. A total of 571 (35%) patients died (5-year mortality of 22.1%), with an absolute risk ratio (ARR) for Periods 2 and 3 compared with Period 1 of 0.80 [confidence interval (CI) 0.65–0.98, P = 0.031] and 0.39 (CI 0.31–0.50, P < 0.001). About 274 patients developed end-stage renal disease (ESRD) [16.8% (Period 1: 23.3%, Period 2: 17.6%, Period 3: 12.5%)], with ARR decreasing over time: Period 2 0.61 (CI 0.42–0.87, P = 0.007) and Period 3 0.57 (CI 0.39–0.83, P = 0.003). The overall risk of death associated with ESRD or chronic kidney disease was 1.74 (CI 1.29–2.37, P < 0.001) and 1.58 (CI 1.21–2.07, P < 0.001).

Conclusions

Incidence of ANCA testing and AAV diagnosis increased over the test period. Falls over time in mortality and ESRD risk may relate to earlier diagnosis and changes in treatment practice.