bluuebunny/crossref_metadata_2025 huggingface dataset:
Statistical Properties of X-Ray Flares from the Supergiant Fast X-Ray Transients
Authors: Zhang Wen-Long , Yi Shuang-Xi , Yang Yu-Peng , Qin Ying
Published: April 2022

Supergiant fast X-ray transients are a sub-class of high mass X-ray binaries, in which the compact object is a neutron star and it is accreting materials from its non-degenerate companion star. The sample of supergiant fast X-ray transients from XMM-Newton public observations have been intensively studied, and hence the corresponding parameters for identifying X-ray flares have been obtained by Sidoli et al., such as the rise time, the decay time, the duration time, the waiting time, the peak luminosity, the isotropic energy and the mean luminosity. In order to investigate the origin of the X-ray flares from the supergiant fast X-ray transients, we apply the cumulative distribution method with the power-law index

dN

(
x
)

/

dx
∝
(
x
+

x

0

)

−

α

x

to the target sample. We then find that the relevant parameters can be well described by the cumulative distribution with indices 1.0–1.9 for IGR J16418-4532, IGR J16328-4726 and IGR J18450-0435, respectively. This finding indicates that the X-ray flares are likely to be produced by the self-organizing critical process, one possible scenario may be due to reconnection in magnetized stellar wind blobs approaching into the magnetosphere of magnetized neutron star. Therefore, we suggest that the high mass X-ray binaries with similar X-ray flares likely belong to the self-organized criticality systems.
Thienoguanosine brightness in DNA duplexes is governed by the localization of its ππ* excitation in the lowest energy absorption band
Authors: Ciaco Stefano , Gavvala Krishna , Greiner Vanille , Mazzoleni Viola , Didier Pascal , Ruff Marc , Martinez-Fernandez Lara , Improta Roberto , Mély Yves
Published: April 2022

Thienoguanosine (thG) is an isomorphic fluorescent guanosine (G) surrogate, which almost perfectly mimics the natural G in DNA duplexes and may therefore be used to sensitively investigate for example protein-induced local conformational changes. To fully exploit the information given by the probe, we carefully re-investigated the thG spectroscopic properties in 12-bp duplexes, when the Set and Ring Associated (SRA) domain of UHRF1 flips its 5′ flanking methylcytosine (mC). The SRA-induced flipping of mC was found to strongly increase the fluorescence intensity of thG, but this increase was much larger when thG was flanked in 3′ by a C residue as compared to an A residue. Surprisingly, the quantum yield and fluorescence lifetime values of thG were nearly constant, regardless of the presence of SRA and the nature of the 3′ flanking residue, suggesting that the differences in fluorescence intensities might be related to changes in absorption properties. We evidenced that thG lowest energy absorption band in the duplexes can be deconvoluted into two bands peaking at ∼350 nm and ∼310 nm, respectively red-shifted and blue-shifted, compared to the spectrum of thG monomer. Using quantum mechanical calculations, we attributed the former to a nearly pure ππ* excitation localized on thG and the latter to excited states with charge transfer character. The amplitude of thG red-shifted band strongly increased when its 3′ flanking C residue was replaced by an A residue in the free duplex, or when its 5′ flanking mC residue was flipped by SRA. As only the species associated with the red-shifted band were found to be emissive, the highly unusual finding of this work is that the brightness of thG in free duplexes as well as its changes on SRA-induced mC flipping almost entirely depend on the relative population and/or absorption coefficient of the red-shifted absorbing species.
Simulation of Bragg coherent diffraction imaging
Authors: Mokhtar A H , Serban D , Newton M C
Published: April 2022

The arrangement of atoms within a crystal and information on deviations from the ideal lattice is encoded in the diffraction pattern obtained from an appropriately conducted Bragg coherent diffraction imaging (BCDI) experiment. A foreknowledge of how specific displacements of atoms within the unit cell alter the BCDI diffraction pattern and the subsequent real-space image is often useful for interpretation and can provide valuable insight for materials design. Here we report on an atomistic approach to efficiently simulate BCDI diffraction patterns by factorising and eliminating certain redundancies in the conventional approach. Our method is able to reduce the computation time by several orders of magnitude without compromising the recovered phase information and therefore enables feasible atomistic simulations on nanoscale crystals with arbitrary lattice distortions.
High-sensitivity pattern discovery in large, paired multiomic datasets
Authors: Ghazi Andrew R , Sucipto Kathleen , Rahnavard Ali , Franzosa Eric A , McIver Lauren J , Lloyd-Price Jason , Schwager Emma , Weingart George , Moon Yo Sup , Morgan Xochitl C , Waldron Levi , Huttenhower Curtis
Published: April 2022

Motivation

Modern biological screens yield enormous numbers of measurements, and identifying and interpreting statistically significant associations among features are essential. In experiments featuring multiple high-dimensional datasets collected from the same set of samples, it is useful to identify groups of associated features between the datasets in a way that provides high statistical power and false discovery rate (FDR) control.

Results

Here, we present a novel hierarchical framework, HAllA (Hierarchical All-against-All association testing), for structured association discovery between paired high-dimensional datasets. HAllA efficiently integrates hierarchical hypothesis testing with FDR correction to reveal significant linear and non-linear block-wise relationships among continuous and/or categorical data. We optimized and evaluated HAllA using heterogeneous synthetic datasets of known association structure, where HAllA outperformed all-against-all and other block-testing approaches across a range of common similarity measures. We then applied HAllA to a series of real-world multiomics datasets, revealing new associations between gene expression and host immune activity, the microbiome and host transcriptome, metabolomic profiling and human health phenotypes.

Availability and implementation

An open-source implementation of HAllA is freely available at http://huttenhower.sph.harvard.edu/halla along with documentation, demo datasets and a user group.

Supplementary information

Supplementary data are available at Bioinformatics online.
Attaining biochemical euthyroidism early after total thyroidectomy in Graves’ disease may lower long-term morbidity risk
Authors: Liu Xiaodong , Wong Carlos K H , Chan Wendy W L , Tang Eric H M , Woo Yu Cho , Liu Shirley Y W , Lam Cindy L K , Lang Brian H H
Published: April 2022

Background

The relationship between good early control of thyroid hormone levels after thyroidectomy for Graves’ disease (GD) and subsequent risks of mortality and morbidities is not well known. The aim of this study was to examine the association between thyroid hormone levels within a short interval after surgery and long-term mortality and morbidity risks from a population-based database.

Methods

Patients with GD who underwent complete/total thyroidectomy between 2006 and 2018 were selected from the Hong Kong Hospital Authority clinical management system. All patients were classified into three groups (euthyroidism, hypothyroidism, and hyperthyroidism) according to their thyroid hormone levels at 6, 12, and 24 months after surgery. Cox proportional hazards models were performed to compare the risks of all-cause mortality, cardiovascular disease (CVD), Graves’ ophthalmopathy, and cancer.

Results

Over a median follow-up of 68 months with 5709 person-years, 949 patients were included for analysis (euthyroidism, n = 540; hypothyroidism, n = 282; and hyperthyroidism, n = 127). The hypothyroidism group had an increased risk of CVD (HR = 4.20, 95 per cent c.i. 2.37 to 7.44, P < 0.001) and the hyperthyroidism group had an increased risk of cancer (HR = 2.14, 95 per cent c.i. 1.55 to 2.97, P < 0.001) compared with the euthyroidism group. Compared with patients obtaining euthyroidism both at 6 months and 12 months, the risk of cancer increased in patients who achieved euthyroidism at 6 months but had an abnormal thyroid status at 12 months (HR = 2.33, 95 per cent c.i. 1.51 to 3.61, P < 0.001) and in those who had abnormal thyroid status at 6 months but achieved euthyroidism at 12 months (HR = 2.52, 95 per cent c.i. 1.60 to 3.97, P < 0.001).

Conclusions

This study showed a higher risk of CVD in postsurgical hypothyroidism and a higher risk of cancer in hyperthyroidism compared with achieving euthyroidism early after thyroidectomy. Patients who were euthyroid at 6 months and 12 months had better outcomes than those achieving euthyroidism only at 6 months or 12 months. Attaining biochemical euthyroidism early after thyroidectomy should become a priority.
Risk factors associated with immune checkpoint inhibitor–induced acute kidney injury compared with other immune-related adverse events: a case–control study
Authors: Gérard Alexandre O , Barbosa Susana , Parassol Nadège , Andreani Marine , Merino Diane , Cremoni Marion , Laurain Audrey , Pinel Sylvine , Bourneau-Martin Delphine , Rocher Fanny , Esnault Vincent L M , Borchiellini Delphine , Sicard Antoine , Drici Milou-Daniel ,   French Network of Pharmacovigilance Centers
Published: April 2022

Background

Immune checkpoint inhibitors (ICIs) foster anti-cancer immune responses. Their efficacy comes at the cost of immune-related adverse events (IRAEs). The latter affects various organs, including kidneys, mostly as acute tubulointerstitial nephritis, the pathophysiology of which remains unclear. We conducted a multicentre case–control study to compare the characteristics of patients with renal IRAEs (ICI-AKI) with those of patients diagnosed with other IRAEs.

Methods

We queried the French pharmacovigilance database for all adverse events involving ICIs. Reports were classified as ICI-AKI or extrarenal IRAE. For each ICI-AKI report, four reports of extrarenal IRAEs were randomly included (control group, 4:1 ratio). Variables showing an association with a P < 0.05 were included as covariates in a multivariate analysis.

Results

Therefore, 167 ICI-AKI reports were compared with 668 extrarenal IRAEs. At least one concomitant extrarenal IRAE was mentioned in 44.3% of ICI-AKI reports. Patients with ICI-AKI were significantly older than patients with extrarenal IRAEs (69.1 versus 64.6 years; P = 0.0135), and chronic kidney disease was significantly more prevalent (12.0% versus 3.3%; P = 0.0125). Patients with ICI-AKI were significantly more likely to be treated with fluindione [adjusted odds ratio (OR) 6.53, 95% confidence interval (95% CI) 2.21–19.31; P = 0.0007], a non-steroidal anti-inflammatory drug (NSAID, OR 3.18, 95% CI 1.07–9.4; P = 0.0368) or a proton-pump inhibitor (PPI, OR 2.18, 95% CI 1.42–3.34; P = 0.0004).

Conclusion

This study is limited by a lack of data, preventing confirmation of numerous reports therefore not included in the analysis. We are unable to draw definite pathophysiological conclusions from our data. Nonetheless, we suggest that ICIs may be a ‘second-hit’ that precipitates acute kidney injury caused by another concomitant drug (fluindione, NSAID or PPI).
Response to acute vasodilator challenge and haemodynamic modifications after MitraClip in patients with functional mitral regurgitation and pulmonary hypertension
Authors: Mandurino-Mirizzi Alessandro , Munafò Andrea , Raineri Claudia , Magrini Giulia , Frassica Romina , Arzuffi Luca , Scelsi Laura , Turco Annalisa , Ferlini Marco , Gazzoli Fabrizio , Ferrario Maurizio , Ghio Stefano , Oltrona-Visconti Luigi , Crimi Gabriele
Published: April 2022

The effectiveness of transcatheter edge-to-edge repair (TEER) in patients with functional mitral regurgitation (FMR) and pulmonary hypertension (PH) is still debated and pre-procedural predictors of haemodynamic improvement after TEER in this setting are currently unknown. We investigated whether normalization of pulmonary artery wedge pressure (PAWP) in response to sodium nitroprusside (SNP) during baseline right heart catheterization might be predictive of a favourable haemodynamic response to MitraClip in patients with FMR and PH. Among 22 patients enrolled, 13 had a positive response to SNP (responders), nine were non-responders. At 6-months follow-up, responders showed a 33% reduction in PAWP and a 25% reduction in mean pulmonary artery pressure (PAP) (P = 0.002 and 0.004, respectively); no significant change occurred in non-responders. In patients with FMR and PH, pre-procedural vasodilator challenge with SNP may help define patients who may have haemodynamic improvement after TEER.
Percutaneous closure of a ‘whale tail’ left atrial appendage with a Watchman FLX device and pre-procedural FEops HEARTguide patient-specific computational simulation: a case report
Authors: Di Muro Francesca Maria , Stolcova Miroslava , Di Mario Carlo , Meucci Francesco
Published: April 2022

Background

Percutaneous left atrial appendage closure (LAAC) is an emerging alternative to oral anticoagulation for stroke prevention in atrial fibrillation (AF) in patients with AF, elevated stroke risk and contraindications to long-term anticoagulation treatment. Optimal pre-procedural planning is essential to ensure optimal procedural results.

Case summary

We report the case of a 62-year-old man with a history of right cerebellar haematoma referred for LAA closure. We describe the first use of FEops HEARTguide patient-specific computational simulation in the planning of LAAC with the Watchman Flex device (Boston Scientific, Marlborough, MA, USA) in an unusual ‘whale tail’-like LAA anatomy.

Discussion

Percutaneous left atrial appendage (LAA) closure is feasible in the majority of patients. However, certain LAA anatomies may pose substantial technical challenges. This case shows the crucial role of a pre-procedural assessment based on patient-specific computational simulations for LAA closure in difficult scenarios resulting in a more efficient procedure with the optimal result and good clinical outcomes.
Paradoxical sinus deceleration during dobutamine stress echocardiography: case series and review of the literature
Authors: Sulo Enxhela , Davidsen Einar Skulstad , Lønnebakken Mai Tone , Bleie Øyvind , Saeed Sahrai
Published: April 2022

Background

Dobutamine stress echocardiography is an established diagnostic modality for assessing myocardial ischaemia in patients with known or suspected coronary artery disease. Dobutamine infusion causes dose-dependent increase in heart rate and contractility. However, in some cases, it induces paradoxical sinus deceleration, whose underlying mechanism and clinical significance are not fully understood.

Case summary

We present episodes of paradoxical sinus deceleration observed during dobutamine stress echocardiography in six (four males and two females) patients and described its patterns of occurrence and clinical and echocardiographic characteristics.

Discussion

Paradoxical sinus deceleration occurred mostly at maximal dobutamine infusion was accompanied with a decline in blood pressure and resolved spontaneously following cessation of dobutamine infusion. Individuals experiencing paradoxical sinus deceleration had in common abnormal left ventricle geometry but differed with regard to age, sex, and cardiometabolic risk factors.
Impact of source and receiver distributions on imaging of dipping reflectors with passive reflection seismic interferometry
Authors: Beckel Ruth A , Juhlin Christopher
Published: April 2022

Passive reflection seismic interferometry (PRSI) facilitates imaging the subsurface structure using passive sources but according to the general theory, the target needs to be illuminated equally from all directions to obtain a kinematically correct result. In practice, this requirement is almost impossible to meet which can introduce artefacts into the PRSI results. Our study was motivated by an unsuccessful attempt to image a couple of known dipping reflectors by applying PRSI to a data set of local microearthquakes clustering around the glacially triggered Burträsk fault. Dipping reflectors are a special case since they introduce a directionality into the seismic-interferometry problem that makes the results especially sensitive to the source azimuths. To investigate which source distributions are favourable in such a case and to study the range of artefacts occurring, we analyse a number of acoustic and elastic synthetic data sets calculated using a simple model of a dipping fault. Our results show that the main contribution for imaging such a fault with PRSI comes from sources in the hangingwall whereas contributions from the footwall are often weak and kinematically incorrect. The type and position of the occurring artefacts depend upon both the source azimuth and the type of modelling. In the acoustic case, the main artefact is a gently dipping reflection caused by insufficient cancellation of the direct reflection at the fault. In the elastic case, the artefacts are dominated by a set of both gently and steeply dipping reflections related to P–S converted waves. These artefacts are present even for ideal illumination due to the use of source records containing both P- and S-wave contributions. During interpretation, it is essential to be able to distinguish between physically meaningful reflections and artefacts. We found that both acoustic and elastic artefacts stack best at lower than expected normal moveout velocities. If data quality is insufficient for velocity analysis, our results can serve as a reference point for the interpretation of dipping features in PRSI images.
Two-Dimensional Gross–Pitaevskii Equation With Space-Time White Noise
Authors: de Bouard Anne , Debussche Arnaud , Fukuizumi Reika
Published: April 2022

In this paper we consider the two-dimensional stochastic Gross–Pitaevskii equation, which is a model to describe Bose–Einstein condensation at positive temperature. The equation is a complex Ginzburg–Landau equation with a harmonic potential and an additive space-time white noise. We study the global well posedness of the model using an inhomogeneous Wick renormalization due to the potential and prove the existence of an invariant measure.
The effects of AGN feedback on the structural and dynamical properties of Milky Way-mass galaxies in cosmological simulations
Authors: Irodotou Dimitrios , Fragkoudi Francesca , Pakmor Ruediger , Grand Robert J J , Gadotti Dimitri A , Costa Tiago , Springel Volker , Gómez Facundo A , Marinacci Federico
Published: April 2022

Feedback from active galactic nuclei (AGNs) has become established as a fundamental process in the evolution of the most massive galaxies. Its impact on Milky Way (MW)-mass systems, however, remains comparatively unexplored. In this work, we use the auriga simulations to probe the impact of AGN feedback on the dynamical and structural properties of galaxies, focusing on the bar, bulge, and disc. We analyse three galaxies – two strongly and one unbarred/weakly barred – using three setups: (i) the fiducial auriga model, which includes both radio and quasar mode feedback, (ii) a setup with no radio mode, and (iii) one with neither the radio nor the quasar mode. When removing the radio mode, gas in the circumgalactic medium cools more efficiently and subsequently settles in an extended disc, with little effect on the inner disc. Contrary to previous studies, we find that although the removal of the quasar mode results in more massive central components, these are in the form of compact discs, rather than spheroidal bulges. Therefore, galaxies without quasar mode feedback are more baryon-dominated and thus prone to forming stronger and shorter bars, which reveals an anticorrelation between the ejective nature of AGN feedback and bar strength. Hence, we report that the effect of AGN feedback (i.e. ejective or preventive) can significantly alter the dynamical properties of MW-like galaxies. Therefore, the observed dynamical and structural properties of MW-mass galaxies can be used as additional constraints for calibrating the efficiency of AGN feedback models.
Clusters of galaxies up to z = 1.5 identified from photometric data of the Dark Energy Survey and unWISE
Authors: Wen Z L , Han J L
Published: April 2022

Using photometric data from the Dark Energy Survey and the Wide-field Infrared Survey Explorer, we estimate photometric redshifts for 105 million galaxies using the nearest-neighbour algorithm. From such a large data base, 151 244 clusters of galaxies are identified in the redshift range of 0.1 < z ≲ 1.5 based on the overdensity of the total stellar mass of galaxies within a given photometric redshift slice, among which 76 826 clusters are newly identified and 30 477 clusters have a redshift z > 1. We cross-match these clusters with those in the catalogues identified from the X-ray surveys and the Sunyaev–Zel’dovich (SZ) effect by the Planck, South Pole Telescope and Atacama Cosmology Telescope surveys, and get the redshifts for 45 X-ray clusters and 56 SZ clusters. More than 95 per cent SZ clusters in the sky region have counterparts in our catalogue. We find multiple optical clusters in the line of sight towards about 15 per cent of SZ clusters.
Transient behaviour of three SU UMa-type dwarf novae: AR Pic, QW Ser, and V521 Peg
Authors: Szegedi Hélène , Charles Philip A , Meintjes Pieter J , Odendaal Alida
Published: April 2022

Changes in the supercycle lengths of some SU UMa-type dwarf novae have been detected by other studies, and indicate that the mass transfer rates noticeably decrease over time. We investigated the supercycle lengths of three SU UMa-type dwarf novae: AR Pic, QW Ser, and V521 Peg, to determine if they have detectable changes in their supercycles. We present the results of optical spectroscopic and photometric observations of these sources. Our observations were conducted in 2016 and 2017 at the Boyden Observatory and the Sutherland station of the South African Astronomical Observatory. The quiescent results indicated that all three sources are typical SU UMa-type dwarf novae. We also present results of AR Pic and QW Ser in outburst and of V521 Peg during a precursor outburst and superoutburst. Light curves were supplemented by the Catalina Real-Time Transient Survey, the ASAS-3 and ASAS-SN archives, and the AAVSO International Database in order to investigate the long-term behaviour of these sources. Our results combined with catalogued properties for all short-period dwarf novae show a possible relationship between the supercycle time in SU UMa systems and their orbital periods, which is interpreted as the decline in the mass transfer rate as systems evolve towards and away from the ‘period minimum’. At the shortest orbital periods, SU UMa systems are almost indistinguishable from WZ Sge systems. However, we propose that the scaleheight between the secondary’s photosphere and L1 may be a factor that distinguish the SU UMa subclasses.
Rapidly alternating flux states of GX 339–4 during its 2021 outburst captured by Insight–HXMT
Authors: Liu Honghui , Jiang Jiachen , Zhang Zuobin , Bambi Cosimo , Ji Long , Kong Lingda , Zhang Shu
Published: April 2022

The low-mass X-ray binary GX 339–4 entered a new outburst in 2021. At the end of the hard to soft transition of this outburst, Insight–HXMT found that the source rapidly alternated between low flux and high flux states on a time-scale of hours. Two high flux states lasted only for a period comparable to the orbital period of the observatory. Time-resolved spectral analysis shows that the sudden changes of flux are confined in the hard X-ray band (>4 keV). The variable non-thermal emission, including the power-law continuum from the corona and the reflected emission from the inner accretion disc, is responsible for the observed variability. The strength of the disc thermal emission and the inner radius of the accretion disc are consistent between the two flux states. Assuming the lamppost geometry, our best-fitting disc reflection models suggest a very low corona height (within 3 Rg) and there is no evidence of significant variation in the corona geometry either. The observed rapidly alternating flux states suggest that the intrinsic power of the corona must change during the state transition. We discuss possible mechanisms for the observed sudden changes in the coronal power of GX 339–4.
Law as Performance
Authors: Stone Peters Julie
Published: April 2022

Tirades against legal theatrics are nearly as old as law itself, and yet so is the age-old claim that law must not merely be done, but “seen to be done.” Law as Performance traces the history of legal performance and spectatorship through the early modern period. Viewing law as the product not merely of edicts or doctrines but of expressive action, it investigates the performances that literally created law: in civic arenas, courtrooms, and judges’ chambers; on scaffolds; and in the streets. It examines the legal codes, learned treatises, trial reports, lawyers’ manuals, execution narratives, rhetoric books, images (and more) that confronted these performances, praising their virtues or denouncing their evils. In so doing, it recovers a long, rich, and largely overlooked tradition of jurisprudential thought about law as a performance practice. This tradition not only generated an elaborate poetics and politics of legal performance. It provided western jurisprudence with a set of constitutive norms that shaped the very identity of law. That identity emerged, in part, through an opposition: law stood for cool deliberation, by-the-book rules, and sovereign discipline; theatre stood for deceptive artifice, entertainment, histrionics, melodrama. And yet legal performance, even at its most theatrical, also appeared fundamental to law’s realization—a central mechanism for shaping legal subjects, key to persuasion, essential to deterrence, indispensable to law’s power—as it still does today.
DEPP: Deep Learning Enables Extending Species Trees using Single Genes
Authors: Jiang Yueyu , Balaban Metin , Zhu Qiyun , Mirarab Siavash
Published: April 2022

Placing new sequences onto reference phylogenies is increasingly used for analyzing environmental samples, especially microbiomes. Existing placement methods assume that query sequences have evolved under specific models directly on the reference phylogeny. For example, they assume single-gene data (e.g., 16S rRNA amplicons) have evolved under the GTR model on a gene tree. Placement, however, often has a more ambitious goal: extending a (genome-wide) species tree given data from individual genes without knowing the evolutionary model. Addressing this challenging problem requires new directions. Here, we introduce Deep-learning Enabled Phylogenetic Placement (DEPP), an algorithm that learns to extend species trees using single genes without prespecified models. In simulations and on real data, we show that DEPP can match the accuracy of model-based methods without any prior knowledge of the model. We also show that DEPP can update the multilocus microbial tree-of-life with single genes with high accuracy. We further demonstrate that DEPP can combine 16S and metagenomic data onto a single tree, enabling community structure analyses that take advantage of both sources of data. [Deep learning; gene tree discordance; metagenomics; microbiome analyses; neural networks; phylogenetic placement.]
Update on migraine management
Authors: Larkin Lisa
Published: April 2022

Migraine is a highly prevalent disorder in women associated with significant disability. Yet it remains underdiagnosed and undertreated. Recent advances in our understanding of the pathophysiology of migraine, including the role of calcitonin gene-related peptide, has led to the development of new targeted migraine therapies. It is important for all healthcare professionals caring for women to be familiar with the diagnostic criteria for migraine and for them to follow a stepwise approach to management of acute and chronic migraine that comprises biobehavioral and pharmacologic management, particularly the more recently approved therapies.
The Nuclear Proteins TP73 and CUL4A Confer Resistance to Cytarabine by Induction of Translesion DNA Synthesis via Mono-ubiquitination of PCNA
Authors: Rehberger Miriam , Schäfer Jonas A. , Krampitz Anna-Maria , Bretz Anne Catherine , Jost Lukas , Haferlach Torsten , Stiewe Thorsten , Neubauer Andreas
Published: April 2022

Resistance to cytarabine is a key problem in the treatment of acute myeloid leukemia (AML). To understand the molecular biology of resistance to cytarabine, a viability-based chemosensitizer screen was utilized. We screened synthetic lethal targets using 437 different small interfering RNAs (siRNAs) directed against factors involved in DNA repair mechanisms and cytarabine as the chemical compound. Three hits were identified: CUL4A, TP73, and RFC2. We show here that the ubiquitin ligase CULLIN 4A (CUL4A) and the tumor-suppressive transcription factor p73 contribute to drug resistance by modulating DNA damage response. P73 confers resistance to cytarabine therapy by transactivation of REV3L, encoding the catalytic subunit of translesion DNA polymerase ζ, and CUL4A probably by influencing proliferating cell nuclear antigen (PCNA) and the polymerase switch towards error-prone translesion DNA polymerases. Abrogation of the polymerase ζ by siRNA causes identical effects as siRNAs against CUL4A or TP73 and resensitizes cells towards cytarabine therapy in vitro. As CUL4A needs to be activated by neddylation to facilitate the degradation of several proteins including PCNA, we propose a novel explanation for the synergism between cytarabine and the neddylation inhibitor pevonedistat by inhibition of translesion synthesis. In keeping with this, in AML patients treated with cytarabine, we found high expression of CUL4A and TP73 to be associated with poor prognosis.
Cultural Competence and Cultural Humility: A Dialogue on Adopting a Multimodel Approach in Physical Therapist Education
Authors: Bangs Debra , Hayward Lorna M. , Donlan Pamela
Published: April 2022

Background and Purpose.

Integrating the concepts of cultural humility and cultural competence into physical therapy (PT) practice may reduce health care disparities and improve patient-centered care. Although several frameworks exist for teaching physical therapist students about cultural competence and cultural humility, discussion about which framework is comprehensive enough to capture the complexity of this topic is unresolved. The purpose of this position paper was to raise awareness in physical therapist and physical therapist assistant (PTA) education about existing frameworks of cultural competence and cultural humility and present a rationale for the inclusion of both in educational approaches.

Position and Rationale.

This article examines the concepts of cultural competence and cultural humility, explores the differences between these 2 concepts, and provides a rationale for integrating both theoretical constructs into PT and PTA education.

Discussion and Conclusion.

Cultural competence and cultural humility frameworks are evolving and so should faculty member approaches to teaching this content to PT students. Contemporary pedagogy requires a focused lens through which to prepare students for incorporating cultural awareness into clinical care to avoid potential cultural mismatches. Creating a new framework that synthesizes the principles of cultural competence and cultural humility may encourage more inclusivity. Cultural pedagogy has the potential to improve the patient experience and health outcomes by empowering students to provide care that is sensitive to important patient cultural differences.
Cell autonomous and non-autonomous consequences of deviations in translation machinery on organism growth and the connecting signalling pathways
Authors: Surya Agustian , Sarinay-Cenik Elif
Published: April 2022

Translation machinery is responsible for the production of cellular proteins; thus, cells devote the majority of their resources to ribosome biogenesis and protein synthesis. Single-copy loss of function in the translation machinery components results in rare ribosomopathy disorders, such as Diamond–Blackfan anaemia in humans and similar developmental defects in various model organisms. Somatic copy number alterations of translation machinery components are also observed in specific tumours. The organism-wide response to haploinsufficient loss-of-function mutations in ribosomal proteins or translation machinery components is complex: variations in translation machinery lead to reduced ribosome biogenesis, protein translation and altered protein homeostasis and cellular signalling pathways. Cells are affected both autonomously and non-autonomously by changes in translation machinery or ribosome biogenesis through cell–cell interactions and secreted hormones. We first briefly introduce the model organisms where mutants or knockdowns of protein synthesis and ribosome biogenesis are characterized. Next, we specifically describe observations in
Caenorhabditis elegans
and
Drosophila melanogaster
, where insufficient protein synthesis in a subset of cells triggers cell non-autonomous growth or apoptosis responses that affect nearby cells and tissues. We then cover the characterized signalling pathways that interact with ribosome biogenesis/protein synthesis machinery with an emphasis on their respective functions during organism development.
Cigarette smoke-induced oxidative stress activates NRF2 to mediate fibronectin disorganization in vascular formation
Authors: Xue Jinjiang , Liao Qiong , Luo Man , Hua Chenfeng , Zhao Junwei , Yu Gangfeng , Chen Xiangyu , Li Xueru , Zhang Xinchun , Ran Ruiguo , Lu Fanghui , Wang Yingxiong , Qiao Liangjun
Published: April 2022

Cigarette smoke significantly induces oxidative stress, resulting in cardiovascular disease. NRF2, a well-known antioxidative stress response factor, is generally considered to play protective roles in cardiovascular dysfunction triggered by oxidative stress. Interestingly, recent studies reported adverse effects of NRF2 on the cardiovascular system. These unfavourable pathogenic effects of NRF2 need to be further investigated. Our work shows that cigarette smoke extract (CSE)-induced oxidative stress disturbs fibronectin (FN) assembly during angiogenesis. Furthermore, this effect largely depends on hyperactive NRF2-STAT3 signalling, which consequently promotes abnormal FN deposition. Consistently, disruption of this pathway by inhibiting NRF2 or STAT3 prevents CSE-induced FN disorganization and vasculature disruption in human umbilical vein endothelial cells or zebrafish. Taken together, these findings demonstrate the cardiovascular dysfunction caused by CSE from a novel perspective that NRF2-dependent signalling engages in FN disorganization.
A mathematical model of network elastoplasticity
Authors: Kodama Hiroki , Yoshida Ken'ichi
Published: April 2022

We introduce a mathematical model, based on networks, for the elasticity and plasticity of materials. We define the tension tensor for a periodic graph in a Euclidean space, and we show that the tension tensor expresses elasticity under deformation. Plasticity is induced by local moves on a graph. The graph is described in terms of the weights of edges, and we discuss how these weights affect the plasticity.
High-temperature and high-pressure plastic phase of ice at the boundary of liquid water and ice VII
Authors: Prasad Dipak , Mitra Nilanjan
Published: April 2022

Simultaneous high-temperature and high-pressure studies reveal phase transformation of bulk liquid water to an ice-VII-like structure having an eight coordination. It was demonstrated through this numerical study that the observed high-temperature and high-pressure phase of water obtained upon shock compression and equilibration has high rotational diffusion and thereby the hydrogen dynamics of these crystal structures are significantly complex compared with ice VII. The current work provides new characterization methods for the numerically observed plastic crystal phase of ice at the boundary of the liquid water and ice VII phases in which the molecules have a defined lattice position but rotate freely. It is anticipated that the present work will provide important data and guide new theoretical and experimental investigations in the search for plastic crystal phases of water. The power spectra plots of bulk liquid water subjected to different temperature and pressure conditions have also been presented in this numerical study, demonstrating significant differences between these high-temperature and high-pressure shock-equilibrated phases and those of pure ice VII at 10 GPa and liquid water at ambient temperature and pressure, as well as at elevated pressures and temperatures.
Antibiofilm properties of Clitoria ternatea flower anthocyanin-rich fraction towards Pseudomonas aeruginosa
Authors: Jeyaraj Ethel Jeyaseela , Nathan Sheila , Lim Yau Yan , Choo Wee Sim
Published: April 2022

In Asia, Clitoria ternatea flowers are commonly used as a traditional medicinal herb and as a food colourant. Their bioactive compounds have anti-inflammatory, anti-microbial and anti-biofilm activities.

Pseudomonas aeruginosa

is one of the major pathogens that cause biofilm-associated infections resulting in an increase in antimicrobial resistance. Hence, the aim of this study was to investigate if the anti-biofilm properties of the anthocyanin-rich fraction of C. ternatea flowers were effective against

P. aeruginosa

. The effect of the anthocyanin-rich fraction of C. ternatea flowers on

P. aeruginosa

biofilms formed on a polystyrene surface was determined using the crystal violet assay and scanning electron microscopy (SEM). The anthocyanin-rich fraction reduced biofilm formation by four

P. aeruginosa

strains with a minimum biofilm inhibitory concentration value ranging between 0.625 and 5.0 mg ml−1. We further show that the biofilm-inhibiting activity of C. ternatea flowers is not due to the flavonols but is instead attributed to the anthocyanins, which had significant biofilm inhibitory activity (64.0±1.1 %) at 24 h in a time–response study. The anthocyanin-rich fraction also significantly reduced bacterial attachment on the polystyrene by 1.1 log c.f.u. cm−2 surface based on SEM analysis. Hence, anthocyanins from C. ternatea flowers have potential as an agent to decrease the risk of biofilm-associated infections.
A new chiral rare-earth organic framework constructed by tartaric acid: synthesis, structural, thermal investigations and optical properties
Authors: Belhouas Ratiba , Trifa Chahrazed , Bouacida Sofiane , Benmerad Belkacem , Souici Abdel Hafid , Boudaren Chaouki , Merazig Hocine
Published: April 2022

Hydrothermal reactions of rare-earth cerium with L-tartaric acid afford a new coordination polymer, namely, poly[[triaqua(μ4-L-tartrato)cerium(III)] chloride], {[Ce(C4H4O6)(H2O)3]Cl}
n
, (1). The structure was determined by single-crystal X-ray diffraction analysis and further characterized by IR and UV–Vis spectroscopy, powder X-ray diffraction and thermogravimetric analysis. Single-crystal X-ray diffraction analysis revealed that the compound is a new two-dimensional (2D) double-layered structure with one-dimensional left-handed helical chains. The different intermolecular interactions were confirmed using Hirshfeld surface analysis and molecular fingerprint plots. Molecular 2D fingerprint plots quantify the different interactions and highlight that H...H (24.8%), H...O/O...H (26.3%), Cl...H/H...Cl (19.6%), O...O (13.8%) and Ce...O/O...Ce (13.6%) interactions account for 99.8% of all contacts. Additionally, the photoluminescence properties of the compound were investigated in the solid state.
Zomato’s race to capture the foodtech market
Authors: Paluri Ratna Achuta , Jain Rishabh Upendra , Sankara Narayanan R.
Published: April 2022

Learning outcomes

This case allows students to critically analyse the business model of Zomato which is a multi-sided platform/in the foodtech industry. It helps students to critically analyse how firms enter into the global market to create value and maintain dominance over the local market (especially in a large market such as India). The case can also be used to introduce students to the business canvas model by analysing foodtech start-ups. The outcomes are as follows: to understand the Business Model Canvas as a tool to describe and analyse the foodtech business such as Zomato’s, based on its value proposition and the way it sells its services; to conduct a value chain analysis and analyse the business models adopted by foodtech companies; to understand how Zomato can aim at global value creation; and to design a clear growth strategy and evaluate Zomato’s options to internationalize or expand locally.

Case overview/synopsis

The year 2018 was an important year for Zomato as it geared up to chart new heights amidst the changing dynamics of the industry on one hand and a co-founder exiting the company on the other hand. Zomato was incepted in 2008 as a restaurant discovery platform offering users the ability to access restaurant menus and post online reviews. It provided a range of value-added services for both its restaurant partners and end customers. Its vertical integration enabled it to grow its revenues across its three lines of business, namely, dining out, delivery and sustainability. Zomato was an early internet start-up that expanded rapidly in the international markets. In the past ten years, the company both scaled and rolled back its operations with unique lessons learned in each market that paved its path for success both locally and globally. The domestic market was being dominated by a few large players sharing the market. Reports by market intelligence firms showed that Swiggy, the closest competitor was starting to dominate Zomato in India [1]. Deepinder, CEO, Zomato’s dilemma for adding value and increasing revenues by weighing options of whether the company should strengthen its presence in the domestic market, or, venture into foreign markets or serve both local and foreign markets.

Complexity academic level

This case is appropriate for postgraduate courses in Strategic Management or International Business.

Supplementary materials

Teaching notes are available for educators only.

Subject code

CSS 5: International Business.
Development of fashion recommendation system using collaborative deep learning
Authors: Lee Gwang Han , Kim Sungmin , Park Chang Kyu
Published: April 2022

Purpose

The purpose of this study is to solve the cold start problem caused by the lack of evaluation information about the products.

Design/methodology/approach

A recommendation system has been developed by using the image data of the clothing products, assuming that the user considers the visual characteristics importantly when purchasing fashion products. In order to evaluate the performance of the model developed in this study, it was compared with Random, Itempop, Matrix Factorization and Generalized Matrix Factorization models.

Findings

The newly developed model was able to cope with the cold start problem better than other models.

Social implications

A hybrid recommendation system has been developed that combines the existing recommendation system with deep learning to effectively recommend fashion products considering the user's taste.

Originality/value

This is the first research to improve the performance of fashion recommendation system using the deep learning model trained by the images of fashion products.
Assessment and appraisal of local governance on urban flood resilience in Bangkok Metropolitan Region: perspectives of SDGs 11 and 13
Authors: Pal Indrajit , Arboleda Jose Luis , Nitivattananon Vilas , Benjachat Nonthakarn
Published: April 2022

Purpose

The purpose of this study is to understand through the qualitative assessment, how the current strategy plans are geared toward reducing urban flood risks and achieving Sustainable Development Goals (SDGs) 11 and 13.

Design/methodology/approach

The Bangkok Metropolitan Region (BMR) plays a major role in Thailand’s economic development. Thus, when the 2011 Thailand flood disaster occurred, BMR suffered major economic and social losses, which impacted the rest of the country. This mega disaster prompted policymakers, the academe and other relevant stakeholders to reevaluate and amend the current urban flood risk reduction measures and governance. The present study attempts to evaluate and compare the post-2011 Thailand flood disaster strategy and master plans, policies and reports that directly and indirectly reduce urban flood risks in the provinces of BMR. Basing on SDGs 11 and 13 targets that impact urban flood risk and resilience, a set of criteria was developed to screen, score and asses the selected documents. A screening process of three levels are conducted to limit the documents to be reviewed, and subsequent content analysis for scoring also has been done.

Findings

The projected results indicate the need for improved and increased number of localized strategic plans and policies, which are more comprehensive and integrated as risk governance documents.

Research limitations/implications

Furthermore, it is projected that there is need to integrate measures to increase adaptive capacity for BMR.

Originality/value

This study is original, and methodology can be replicated for other urban areas for flood risks and resilience assessment.