bluuebunny/crossref_metadata_2025 huggingface dataset:
What Factors Influence the Final Outcome in Occipital Condyle Fractures?
Authors: Srinivasan U. S. , Sultan Al-Busaidi Ali , Mubarak Eltayeb Abdalla Ali
Published: August 2023

Introduction Diagnosis of occipital condyle fracture (OCF) following a trauma needs high awareness among the trauma surgeons.

Aim In our study, we attempt to discern if any factor or a combination of factors influences the final outcome following OCF.

Materials and Methods We prospectively analyzed the outcome in OCF patients admitted during 2017 to 2019 at our center. We had 14 patients with polytrauma with OCF. Among them two were lost for follow-up. So, 12 patients were followed up for 6 months after injury. The following 10 factors were analyzed—age, sex, injury, Glasgow Coma Scale, Injury Severity Score, spinal injury, associated injuries, blood pressure, medical conditions, and surgical intervention. Outcome was divided into good and poor outcomes. Chi-squared test was used. All these patients were treated conservatively for OCF for 3 months.

Results There was no significant factor, since p-value was greater than 0.05 for all variables. Only Injury Severity Score (0.091) was close to the significant p-value. Seven patients had severe head injuries and among them one died and four had the worst outcome. Among the five patients who had spinal injuries, only two had good outcomes.

Conclusion Our results indicate that the outcome following OCF is not determined by any single factor. Injury Severity Score comes close to determining the final outcome. This indicates that the overall patient management especially of associated injuries is the determining factor in the outcome in patients who had sustained OCF.
Challenging Management of an Acute Traumatic Carotid-Cavernous Fistula in a 2-Year-Old Child with Literature Review
Authors: Solis Frank , Macha Luis , Toledo Mauro , Gálvez Ricardo , Ecos Rosa
Published: August 2023

Traumatic carotid-cavernous fistula (TCCF) is a rare occurrence in the pediatric population. However, the neurological sequelae of TCCF are associated with higher morbidity and mortality in pediatric patients. We report the case of a 2-year-old child with TCCF treated at a public hospital in Peru. The etiology of the injury was due to a fall of approximately 5 meters. The diagnosis was made based on the clinical picture and neuroimaging findings. The initial proposed treatment was performed with the hope of preserving the parent artery; however, due to persistence of the TCCF, embolization of the parent artery with coils and embolizing substance was performed. A literature review of similar cases was performed and identified eight cases in children under 10 years of age. Endovascular management of an acute TCCF is a challenge due to the high morbidity and mortality during the acute phase and can be complicated when other traumatic injuries are present. Maintaining the parent artery is important; however, when this is not possible, trapping the parent artery may provide an alternate option when appropriate collaterals exist.
How has the Covid-19 pandemic affected wheelchair users? Time-series analysis of the number of railway passengers in Tokyo
Authors: Arai Yuko , Niwa Yukari , Kusakabe Takahiko , Honma Kentaro
Published: August 2023

The Coronavirus disease 2019 (COVID-19) has posed ‘new barriers’ to people with disabilities (PwDs) who have already experienced many barriers to using public transportation. However, there is limited quantitative knowledge of how PwDs have been affected by the COVID-19 pandemic. This study investigated the impact of the COVID-19 pandemic on the use of public transportation by PwDs over time. Specifically, we analysed time-series data on wheelchair rail passenger numbers and all rail passenger numbers in Tokyo from April 2012 to December 2021. The impact of COVID-19 was more accurately assessed by excluding seasonal variations in the time-series, and two key findings were obtained. First, the change point for the decline in the number of passengers owing to the COVID-19 pandemic was March 2020, one month earlier than the declaration of the state of emergency. Second, using the time-series model, the actual and estimated values were compared, and we found that wheelchair rail passenger numbers reduced by approximately 20 percentage points on average compared with all rail passengers. Wheelchair rail passengers were more severely affected by the COVID-19 pandemic than all rail passengers. Based on previous studies, these findings demonstrated that opportunities to participate in society were disproportionately reduced for PwDs during the COVID-19 pandemic. This study’s quantitative data and the resulting conclusions on wheelchair users are useful for inclusive planning for mitigating the pandemic’s impact by national administrations and public transport authorities.
Compartmentalizing Indigenous knowledge(s): binary framing and cognitive imperialism in social studies curriculum
Authors: Clarysse Liana Kibalenko
Published: August 2023

This qualitative analysis of the Social Studies curriculum for Grades 3 to 6 for the province of Ontario, Canada examines binary framing in curriculum as a mechanism of cognitive imperialism that compartmentalizes Indigenous knowledge(s). The following binaries are discussed: Positive/Negative; Conflict/Cooperation; and Us/Them in terms of the ways that they compartmentalize Indigenous knowledge(s) and reinforce cognitive imperialism. Themes for further research are noted including presumptions of neutrality that divorce power analysis from perspective-taking, the prioritizing of peaceful relations over redressing power imbalances and adding Indigenous-themed content to the curriculum is not enough. Recommendations for curriculum reform are indicated and decolonial justice education (DJE) is conceptualized for actionable steps towards answering the Calls to Action in the Truth and Reconciliation Commission of Canada (2015a, 2015b, 2015c).
Ion-acoustic instability of the cylindrical inhomogeneous helicon discharge plasma with rotating electrons
Authors: Mikhailenko V. V. , Lee H. J. , Mikhailenko V. S. , Azarenkov M. O.
Published: August 2023

The kinetic theory for the microinstabilities of a cylindrical plasma, produced by the cylindrical azimuthally symmetric (azimuthal mode number m0=0) helicon wave, based on the Vlasov–Poisson system of equations, is developed. The derived linear integral equation for the Fourier–Bessel transform of the electrostatic potential is the basic equation for the investigations of the parametric and the current-driven instabilities of the radially inhomogeneous cylindrical plasma in the radially inhomogeneous helicon wave. The short-wavelength solution of this equation for the electrostatic potential is derived in the form of the functional equation, which includes an infinite number of its satellites at a frequency separation equal to the helicon wave frequency. The analytical solution is derived for the high-frequency kinetic ion-acoustic instability of the cylindrical helicon plasma, driven by the coupled effect of the electron diamagnetic drift and of the steady azimuthal rotation of electrons relative to the ions with a radially inhomogeneous angular velocity.
On cyclic plasticity of nanostructured dual-phase CoCrFeNiAl high-entropy alloy: An atomistic study
Authors: Zhao Ziyu , Liu Jinxing
Published: August 2023

In this study, we have employed molecular dynamics simulations to examine plastic deformation mechanisms of a “supra-nanometer-sized dual-phase glass-crystal” (SNDP-GC) high-entropy alloy (HEA) composite under cyclic loadings. This composite is produced by embedding CoCrFeNi HEA crystalline grains into a softer CoCrFeNiAl2 HEA glass. Cyclic loadings of different amplitudes are applied on one polycrystalline CoCrFeNi sample and two SNDP-GC HEA samples mentioned above. For the polycrystalline sample, dislocation motion and grain boundary (GB)-mediated deformation control the plastic deformation process, and the sample loses its original structure after a few cycles of the set amplitude due to GB migration. However, for the two SNDP-GC samples, as the grain boundary is replaced by the metallic glass (MG) phase, the dominant plastic deformation mechanism has changed to concentrating shear transformation in the MG phase. Our results also show that structural stability is highly dependent on the MG phase thickness. For the sample with a thinner MG layer, MG cannot accommodate sufficient deformation—so voids are generated in it. However, for the sample with a thicker MG phase, MG can store adequate deformations, thus dislocation initiations in crystalline grains are reduced and void generation is prevented in the MG phase.
Incomplete localization for disordered chiral strips
Authors: Shapiro Jacob
Published: August 2023

We prove that a disordered analog of the Su–Schrieffer–Heeger model exhibits dynamical localization (i.e., the fractional moment condition) at all energies except possibly zero energy, which is singled out by chiral symmetry. Localization occurs at arbitrarily weak disorder, provided it is sufficiently random. If furthermore the hopping probability measures are properly tuned so that the zero energy Lyapunov spectrum does not contain zero, then the system exhibits localization also at that energy, which is of relevance for topological insulators. The method also applies to the usual Anderson model on the strip.
Design of Sturm global attractors 1: Meanders with three noses, and reversibility
Authors: Fiedler Bernold , Rocha Carlos
Published: August 2023

We systematically explore a simple class of global attractors, called Sturm due to nodal properties, for the semilinear scalar parabolic partial differential equation (PDE) ut=uxx+f(x,u,ux) on the unit interval 0<x<1, under Neumann boundary conditions. This models the interplay of reaction, advection, and diffusion. Our classification is based on the Sturm meanders, which arise from a shooting approach to the ordinary differential equation boundary value problem of equilibrium solutions ut=0. Specifically, we address meanders with only three “noses,” each of which is innermost to a nested family of upper or lower meander arcs. The Chafee–Infante paradigm, with cubic nonlinearity f=f(u), features just two noses. Our results on the gradient-like global PDE dynamics include a precise description of the connection graphs. The edges denote PDE heteroclinic orbits v1⇝v2 between equilibrium vertices v1,v2 of adjacent Morse index. The global attractor turns out to be a ball of dimension d, given as the closure of the unstable manifold Wu(O) of the unique equilibrium with maximal Morse index d. Surprisingly, for parabolic PDEs based on irreversible diffusion, the connection graph indicates time reversibility on the (d−1)-sphere boundary of the global attractor.
Physical insights from imaginary-time density–density correlation functions
Authors: Dornheim Tobias , Moldabekov Zhandos A. , Tolias Panagiotis , Böhme Maximilian , Vorberger Jan
Published: August 2023

An accurate theoretical description of the dynamic properties of correlated quantum many-body systems, such as the dynamic structure factor S(q, ω), is important in many fields. Unfortunately, highly accurate quantum Monte Carlo methods are usually restricted to the imaginary time domain, and the analytic continuation of the imaginary-time density–density correlation function F(q, τ) to real frequencies is a notoriously hard problem. Here, it is argued that often no such analytic continuation is required because by definition, F(q, τ) contains the same physical information as does S(q, ω), only represented unfamiliarly. Specifically, it is shown how one can directly extract key information such as the temperature or quasi-particle excitation energies from the τ domain, which is highly relevant for equation-of-state measurements of matter under extreme conditions [T. Dornheim et al., Nat. Commun. 13, 7911 (2022)]. As a practical example, ab initio path-integral Monte Carlo results for the uniform electron gas (UEG) are considered, and it is shown that even nontrivial processes such as the roton feature of the UEG at low density [T. Dornheim et al., Commun. Phys. 5, 304 (2022)] are manifested straightforwardly in F(q, τ). A comprehensive overview is given of various useful properties of F(q, τ) and how it relates to the usual dynamic structure factor. In fact, working directly in the τ domain is advantageous for many reasons and opens up multiple avenues for future applications.
Contribution of magnetized ions to dust vortex pattern formation
Authors: Nebbat E. , Annou R.
Published: August 2023

A time-dependent nonlinear model that describes the generation of vortex patterns of dust grains in a magnetized dusty plasma [Nebbat and Annou, Phys. Plasmas 17(9), 093702 (2010)] is revisited. The effect of the magnetic field on ions is investigated. Numerical results confirm the existence of a vortex low-density core surrounded by a high-density wall as well as dust density ripples, in agreement with experimental data.
Printable graphite-based thermoelectric foam for flexible thermoelectric devices
Authors: Duan Shengzhi , Wang Yifan , Wu Xiaowen , Wu Meihua , Wang Lianyi , Fang Minghao , Huang Zhaohui , Luo Ruiying
Published: August 2023

Flexible thermoelectric materials are primarily composed of organic thermoelectric materials, which suffer from issues such as instability and poor conductivity. To overcome these limitations, this study aims to develop a cost-effective thermoelectric material by utilizing graphite and hydroxypropyl methylcellulose as raw materials. Through a mechanical foaming process, a graphite-based foam with a porous structure is fabricated. The obtained foam exhibits a Seebeck coefficient of approximately 32 μV K−1 and a power factor of around 0.013 μW m−1 K2. Following an analysis of the microstructural morphology, the foam samples are subjected to compression treatment to convert the 3D foam into a porous film and thereby enhance the power generation efficiency of the thermoelectric material. Notably, the Seebeck coefficient of the compressed sample is 41 μV K−1, and its power factor is approximately 6.7 μW m−1 K2. Furthermore, owing to the high plasticity of the foam slurry prior to molding, it can be used to fabricate thermoelectric devices through printing techniques. By employing this approach, a thermoelectric device consisting of nine individual p-type graphite thermoelectric units is printed on the A4 paper. The device produces a temperature difference of 32 K and a thermoelectric potential of 10 mV on a 373 K heating plate. Since both the sample and the paper are flexible, the device can be folded to reduce its size, which broadens the range of potential applications of these thermoelectric materials.
Asymptotic analysis of contact line dynamics of spreading/retracting drops on spherical surfaces
Authors: Qin Jian
Published: August 2023

We investigate the spreading and retraction of a small sessile drop on a sphere governed by capillary and viscous forces. The lubrication equation established in spherical coordinates is solved analytically and numerically. The Navier slip model is adopted to overcome the singularity at the contact line. An asymptotic matching method is employed to study the contact line movement. The results show that the spreading process is always faster than the retraction process for a given drop volume. The position and speed of the contact line can be well-predicted using the asymptotic theory during the whole process of spreading and the late stage of retraction, while the theory becomes invalid at the early time of retraction because the macroscopic interface is significantly perturbed by the moving contact line.
ADAM17 targeting by human cytomegalovirus remodels the cell surface proteome to simultaneously regulate multiple immune pathways
Authors: Rubina Anzelika , Patel Mihil , Nightingale Katie , Potts Martin , Fielding Ceri A. , Kollnberger Simon , Lau Betty , Ladell Kristin , Miners Kelly L. , Nichols Jenna , Nobre Luis , Roberts Dawn , Trinca Terrence M. , Twohig Jason P. , Vlahava Virginia-Maria , Davison Andrew J. , Price David A. , Tomasec Peter , Wilkinson Gavin W. G. , Weekes Michael P. , Stanton Richard J. , Wang Eddie C. Y.
Published: August 2023

Human cytomegalovirus (HCMV) is a major human pathogen whose life-long persistence is enabled by its remarkable capacity to systematically subvert host immune defenses. In exploring the finding that HCMV infection up-regulates tumor necrosis factor receptor 2 (TNFR2), a ligand for the pro-inflammatory antiviral cytokine TNFα, we found that the underlying mechanism was due to targeting of the protease, A Disintegrin And Metalloproteinase 17 (ADAM17). ADAM17 is the prototype ‘sheddase’, a family of proteases that cleaves other membrane-bound proteins to release biologically active ectodomains into the supernatant. HCMV impaired ADAM17 surface expression through the action of two virally-encoded proteins in its U
L
/
b’
region, UL148 and UL148D. Proteomic plasma membrane profiling of cells infected with an HCMV double-deletion mutant for UL148 and UL148D with restored ADAM17 expression, combined with ADAM17 functional blockade, showed that HCMV stabilized the surface expression of 114 proteins (
P
< 0.05) in an ADAM17-dependent fashion. These included reported substrates of ADAM17 with established immunological functions such as TNFR2 and jagged1, but also numerous unreported host and viral targets, such as nectin1, UL8, and UL144. Regulation of TNFα-induced cytokine responses and NK inhibition during HCMV infection were dependent on this impairment of ADAM17. We therefore identify a viral immunoregulatory mechanism in which targeting a single sheddase enables broad regulation of multiple critical surface receptors, revealing a paradigm for viral-encoded immunomodulation.
Density and magnetic field strength dependence of radio pulses induced by energetic air showers
Authors: Ammerman-Yebra Juan , Alvarez-Muñiz Jaime , Zas Enrique
Published: August 2023

We have studied the effect of changing the density and magnetic field strength in the coherent pulses that are emitted as energetic showers develop in the atmosphere. For this purpose we have developed an extension of ZHS, a program to calculate coherent radio pulses from electromagnetic showers in homogeneous media, to account for the Lorentz force due to a magnetic field. This makes it possible to perform quite realistic simulations of radio pulses from air showers in a medium similar to the atmosphere but without variations of density with altitude. The effects of independently changing the density, the refractive index and the magnetic field strength are studied in the frequency domain for observers in the Cherenkov direction at far distances from the shower. This approach is particularly enlightening providing an explanation of the spectral behavior of the induced electric field in terms of shower development parameters. More importantly, it clearly displays the complex scaling properties of the pulses as density and magnetic field strength are varied. The usually assumed linear behavior of electric field amplitude with magnetic field strength is shown to hold up to a given magnetic field strength at which the extra time delays due to the deflection in the magnetic field break it. Scaling properties of the pulses are obtained as the density of air decreases relative to sea level. A remarkably accurate scaling law is obtained that relates the spectra of pulses obtained when reducing the density and increasing the magnetic field.
Generation of structure light in probe absorption spectrum via microwave-driven Y-type atomic system
Authors: Saeed Muhammad , Abbas Muqaddar
Published: August 2023

Behavior of structure light is investigated by monitoring probe absorption using a microwave-driven Y-type atomic media configuration. The system under consideration is driven by one of the control vortex beams as well as an extra non-vortex control beam to ensure electromagnetically induced transparency. The significant aspect in the generation of structured light is the azimuthal phase-dependent modification for probe absorption. Further intensity distribution for absorption spectra is examined for simultaneously evaluating both the control vortex beams. We also go through the radial distribution of intensity for various orbital angular momentum values. Different modes of structural beams may be distinguished using the suggested approach. Our research gives us a way for rapidly transferring vortex wavefronts from control field to probe absorption profile. This could be useful in quantum information processing.
Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data
Authors: Cho Hunyong , Qu Yixiang , Liu Chuwen , Tang Boyang , Lyu Ruiqi , Lin Bridget M , Roach Jeffrey , Azcarate-Peril M Andrea , Aguiar Ribeiro Apoena , Love Michael I , Divaris Kimon , Wu Di
Published: August 2023

Understanding the function of the human microbiome is important but the development of statistical methods specifically for the microbial gene expression (i.e. metatranscriptomics) is in its infancy. Many currently employed differential expression analysis methods have been designed for different data types and have not been evaluated in metatranscriptomics settings. To address this gap, we undertook a comprehensive evaluation and benchmarking of 10 differential analysis methods for metatranscriptomics data. We used a combination of real and simulated data to evaluate performance (i.e. type I error, false discovery rate and sensitivity) of the following methods: log-normal (LN), logistic-beta (LB), MAST, DESeq2, metagenomeSeq, ANCOM-BC, LEfSe, ALDEx2, Kruskal–Wallis and two-part Kruskal–Wallis. The simulation was informed by supragingival biofilm microbiome data from 300 preschool-age children enrolled in a study of childhood dental disease (early childhood caries, ECC), whereas validations were sought in two additional datasets from the ECC study and an inflammatory bowel disease study. The LB test showed the highest sensitivity in both small and large samples and reasonably controlled type I error. Contrarily, MAST was hampered by inflated type I error. Upon application of the LN and LB tests in the ECC study, we found that genes C8PHV7 and C8PEV7, harbored by the lactate-producing Campylobacter gracilis, had the strongest association with childhood dental disease. This comprehensive model evaluation offers practical guidance for selection of appropriate methods for rigorous analyses of differential expression in metatranscriptomics. Selection of an optimal method increases the possibility of detecting true signals while minimizing the chance of claiming false ones.
A Bayesian model for genomic prediction using metabolic networks
Authors: Onogi Akio
Published: August 2023

Motivation

Genomic prediction is now an essential technique in breeding and medicine, and it is interesting to see how omics data can be used to improve prediction accuracy. Precedent work proposed a metabolic network-based method in biomass prediction of Arabidopsis; however, the method consists of multiple steps that possibly degrade prediction accuracy.

Results

We proposed a Bayesian model that integrates all steps and jointly infers all fluxes of reactions related to biomass production. The proposed model showed higher accuracies than methods compared both in simulated and real data. The findings support the previous excellent idea that metabolic network information can be used for prediction.

Availability and implementation

All R and stan scripts to reproduce the results of this study are available at https://github.com/Onogi/MetabolicModeling.
BEENE: deep learning-based nonlinear embedding improves batch effect estimation
Authors: Rahman Md Ashiqur , Tutul Abdullah Aman , Sharmin Mahfuza , Bayzid Md Shamsuzzoha
Published: August 2023

Motivation

Analyzing large-scale single-cell transcriptomic datasets generated using different technologies is challenging due to the presence of batch-specific systematic variations known as batch effects. Since biological and technological differences are often interspersed, detecting and accounting for batch effects in RNA-seq datasets are critical for effective data integration and interpretation. Low-dimensional embeddings, such as principal component analysis (PCA) are widely used in visual inspection and estimation of batch effects. Linear dimensionality reduction methods like PCA are effective in assessing the presence of batch effects, especially when batch effects exhibit linear patterns. However, batch effects are inherently complex and existing linear dimensionality reduction methods could be inadequate and imprecise in the presence of sophisticated nonlinear batch effects.

Results

We present Batch Effect Estimation using Nonlinear Embedding (BEENE), a deep nonlinear auto-encoder network which is specially tailored to generate an alternative lower dimensional embedding suitable for both linear and nonlinear batch effects. BEENE simultaneously learns the batch and biological variables from RNA-seq data, resulting in an embedding that is more robust and sensitive than PCA embedding in terms of detecting and quantifying batch effects. BEENE was assessed on a collection of carefully controlled simulated datasets as well as biological datasets, including two technical replicates of mouse embryogenesis cells, peripheral blood mononuclear cells from three largely different experiments and five studies of pancreatic islet cells.

Availability and implementation

BEENE is freely available as an open source project at https://github.com/ashiq24/BEENE.
Defining the cellular complexity of the zebrafish bipotential gonad
Authors: Kossack Michelle E , Tian Lucy , Bowie Kealyn , Plavicki Jessica S
Published: August 2023

Zebrafish are routinely used to model reproductive development, function, and disease, yet we still lack a clear understanding of the fundamental steps that occur during early bipotential gonad development, including when endothelial cells, pericytes, and macrophage arrive at the bipotential gonad to support gonad growth and differentiation. Here, we use a combination of transgenic reporters and single-cell sequencing analyses to define the arrival of different critical cell types to the larval zebrafish gonad. We determined that blood initially reaches the gonad via a vessel formed from the swim bladder artery, which we have termed the gonadal artery. We find that vascular and lymphatic development occurs concurrently in the bipotential zebrafish gonad and our data suggest that similar to what has been observed in developing zebrafish embryos, lymphatic endothelial cells in the gonad may be derived from vascular endothelial cells. We mined preexisting sequencing datasets to determine whether ovarian pericytes had unique gene expression signatures. We identified 215 genes that were uniquely expressed in ovarian pericytes, but not expressed in larval pericytes. Similar to what has been shown in the mouse ovary, our data suggest that pdgfrb+ pericytes may support the migration of endothelial tip cells during ovarian angiogenesis. Using a macrophage-driven photoconvertible protein, we found that macrophage established a nascent resident population as early as 12 dpf and can be observed removing cellular material during gonadal differentiation. This foundational information demonstrates that the early bipotential gonad contains complex cellular interactions, which likely shape the health and function of the mature gonad.
Neural, physiological and behavioural correlates of empathy for pain in Tourette syndrome
Authors: Weiblen Ronja , Robert Carina , Petereit Pauline , Heldmann Marcus , Münte Thomas F , Münchau Alexander , Müller-Vahl Kirsten , Krämer Ulrike M
Published: August 2023

Persons with Tourette syndrome show altered social behaviours, such as echophenomena and increased personal distress in emotional situations. These symptoms may reflect an overactive mirror neuron system, causing both increased automatic imitation and a stronger tendency to share others’ emotions. To test this, we measured the individual level of echophenomena with a video protocol and experimentally induced empathy for pain in 21 participants with Tourette syndrome and 25 matched controls. In the empathy for pain paradigm, pictures of hands and feet in painful or neutral situations were presented, while we measured participants’ EEG and skin conductance response. Changes in somatosensory mu suppression during the observation of the pictures and pain ratings were compared between groups, and correlations were calculated with the occurrence of echophenomena, self-reported empathy and clinical measures. Our Tourette syndrome sample showed significantly more echophenomena than controls, but the groups showed no behavioural differences in empathic abilities. However, controls, but not patients with Tourette syndrome, showed the predicted increased mu suppression when watching painful compared to neutral actions. While echophenomena were present in all persons with Tourette syndrome, the hypothesis of an overactive mirror neuron system in Tourette syndrome could not be substantiated. On the contrary, the Tourette syndrome group showed a noticeable lack of mu attenuation in response to pain stimuli. In conclusion, we found a first hint of altered processing of others’ emotional states in a brain region associated with the mirror neuron system.
Digital fingerprinting for identifying malicious collusive groups on Twitter
Authors: Ikwu Ruth , Giommoni Luca , Javed Amir , Burnap Pete , Williams Matthew
Published: August 2023

Propagation of malicious code on online social networks (OSNs) is often a coordinated effort by collusive groups of malicious actors hiding behind multiple online identities (or digital personas). Increased interaction in OSN has made them reliable for the efficient orchestration of cyberattacks such as phishing click bait and drive-by downloads. URL shortening enables obfuscation of such links to malicious websites and massive interaction with such embedded malicious links in OSN guarantees maximum reach. These malicious links lure users to malicious endpoints where attackers can exploit system vulnerabilities. Identifying the organized groups colluding to spread malware is non-trivial owing to the fluidity and anonymity of criminal digital personas on OSN. This paper proposes a methodology for identifying such organized groups of criminal actors working together to spread malicious links on OSN. Our approach focuses on understanding malicious users as ‘digital criminal personas’ and characteristics of their online existence. We first identify those users engaged in propagating malicious links on OSN platforms, and further develop a methodology to create a digital fingerprint for each malicious OSN account/digital persona. We create similarity clusters of malicious actors based on these unique digital fingerprints to establish ‘collusive’ behaviour. We evaluate the ability of a cluster-based approach on OSN digital fingerprinting to identify collusive behaviour in OSN by estimating within-cluster similarity measures and testing it on a ground-truth dataset of five known colluding groups on Twitter. Our results show that our digital fingerprints can identify 90% of cyber personas engaged in collusive behaviour and 75% of collusion in a given sample set.
MineProt: a stand-alone server for structural proteome curation
Authors: Zhu Yunchi , Tong Chengda , Zhao Zuohan , Lu Zuhong
Published: August 2023

AlphaFold-like systems are rapidly expanding the scale of proteome structuring, and MineProt provides an effective solution for custom curation of these novel high-throughput data. It enables researchers to build their own server in simple steps, run almost out-of-the-box scripts to annotate and curate their proteins, analyze their data via a user-friendly online interface, and utilize plugins to extend the functionality of server. It is expected to support researcher productivity and facilitate data sharing in the new era of structural proteomics.

Database URL MineProt is open-source software available at https://github.com/huiwenke/MineProt.
Modulation of macrophages by biophysical cues in health and beyond
Authors: Wilson Heather M
Published: August 2023

Macrophages play a key role in tissue development and homeostasis, innate immune defence against microbes or tumours, and restoring homeostasis through tissue regeneration following infection or injury. The ability to adopt such diverse functions is due to their heterogeneous nature, which is driven largely by their developmental origin and their response to signals they encounter from the microenvironment. The most well-characterized signals driving macrophage phenotype and function are biochemical and metabolic. However, the way macrophages sense and respond to their extracellular biophysical environment is becoming increasingly recognized in the field of mechano-immunology. These biophysical cues can be signals from tissue components, such as the composition and charge of extracellular matrix or topography, elasticity, and stiffness of the tissue surrounding cells; and mechanical forces such as shear stress or stretch. Macrophages are important in determining whether a disease resolves or becomes chronic. Ageing and diseases such as cancer or fibrotic disorders are associated with significant changes in the tissue biophysical environment, and this provides signals that integrate with those from biochemical and metabolic stimuli to ultimately dictate the overall function of macrophages. This review provides a brief overview of macrophage polarization, followed by a selection of commonly recognized physiological and applied biophysical stimuli impacting macrophage activity, and the potential signalling mechanisms driving downstream responses. The effects of biophysical cues on macrophages’ function in homeostasis and disease and the associated clinical implications are also highlighted.
Comparing clinical outcomes of peroral endoscopic myotomy for achalasia between Eastern and Western countries: a systematic review and meta-analysis
Authors: Zhang Han , Pu Xinxin , Huang Shu , Xia Huifang , Zou Kang , Zeng Xinyi , Jiang Jiao , Ren Wensen , Peng Yan , Lü Muhan , Tang Xiaowei
Published: August 2023

Peroral endoscopic myotomy (POEM) has revolutionized the therapeutic strategy for achalasia with promising results. We conducted this meta-analysis to compare clinical outcomes between Eastern and Western countries. A comprehensive literature search was conducted in PubMed, EMBASE, Web of Science and Cochrane Library databases to query for studies that assessed the efficacy of POEM for achalasia. All articles published from inception to December 31, 2021 were included. The primary outcome was the pooled clinical success rate. The secondary outcomes included the pooled technical success rate, incidence of adverse events, procedure time and hospital stay. Eighteen Eastern studies involving 5962 patients and 11 Western studies involving 1651 patients were included. The pooled clinical success rate and technical success rate for POEM was equal in the Eastern studies compared to Western studies. The pooled incidence of procedure adverse events for POEM was a little lower in the Eastern studies compared to Western studies (6.6% vs. 8.7%). Similarly, the incidence of reflux-related adverse events was lower in Eastern studies than that in Western studies. The pooled procedure time of POEM was shorter in Eastern studies compared to Western studies (61 minutes vs. 80 minutes), while the length of hospital stay was longer in Eastern studies compared to Western studies (5.8 days vs. 2.4 days). Overall, Eastern countries have the similar POEM outcomes compared to Western countries. However, Eastern countries still need to do more to reduce the length of hospital stay.
The effect of aging on short- and long-term results after esophagectomy: an international multicenter retrospective analysis
Authors: Mengardo Valentina , Weindelmayer Jacopo , Ceccherini Giovanni , Wilkinson Michelle , de Manzoni Giovanni , Allum William , Giacopuzzi Simone
Published: August 2023

The optimal treatment for esophageal cancer in elderly patients is still debated and data on postoperative results are limited. This retrospective international study aims to clarify the impact of age on clinical and oncological outcomes after esophagectomy. All patients that underwent esophagectomy for cancer between 2007 and 2016 at two European high-volume Centers have been included in the study. Patients were divided into three groups according to their age: young-age group (YAG) (18–69), middle-age group (70–74) and old-age group (>74). Primary outcome was 5-year overall survival (OS), while secondary outcomes considered were 5-year disease free survival and disease related survival, 90-day morbidity and mortality, readmission rate and radicality. A total of 575 patients were included. No differences emerged in terms of morbidity and length of stay, while mortality increased with aging from 2% in YAG to 4.8% in old-aged (P = 0.003). Old-age patients had less neoadjuvant treatment (P < 0.001), a less aggressive mediastinal lymphadenectomy and presented a more advanced pathological stage. As expected, OS decreased significantly for older patients compared with the other two age groups (P = 0.044) but, on the other hand, disease free and disease related survival were comparable between the groups. Age itself should not be considered a contraindication to esophagectomy. Although in patients older than 75 years postoperative mortality is significantly increased, esophagectomy could be still an option in selected patients, favoring the use of minimally invasive techniques and enhanced recovery protocols.
Late gadolinium enhancement distribution patterns in non-ischaemic dilated cardiomyopathy: genotype–phenotype correlation
Authors: de Frutos Fernando , Ochoa Juan Pablo , Fernández Ana Isabel , Gallego-Delgado María , Navarro-Peñalver Marina , Casas Guillem , Basurte María Teresa , Larrañaga-Moreira José María , Mogollón María Victoria , Robles-Mezcua Ainhoa , García-Granja Pablo Elpidio , Climent Vicente , Palomino-Doza Julián , García-Álvarez Ana , Brion María , Brugada Ramón , Jiménez-Jáimez Juan , Bayes-Genis Antoni , Ripoll-Vera Tomas , Peña-Peña María Luisa , Rodríguez-Palomares José F , Gonzalez-Carrillo Josefa , Villacorta Eduardo , Espinosa Maria Angeles , Garcia-Pavia Pablo , Mirelis Jesus G
Published: August 2023

Aims

Late gadolinium enhancement (LGE) is frequently found in patients with dilated cardiomyopathy (DCM); there is little information about its frequency and distribution pattern according to the underlying genetic substrate. We sought to describe LGE patterns according to genotypes and to analyse the risk of major ventricular arrhythmias (MVA) according to patterns.

Methods and results

Cardiac magnetic resonance findings and LGE distribution according to genetics were performed in a cohort of 600 DCM patients followed at 20 Spanish centres. After exclusion of individuals with multiple causative gene variants or with variants in infrequent DCM-causing genes, 577 patients (34% females, mean age 53.5 years, left ventricular ejection fraction 36.9 ± 13.9%) conformed to the final cohort. A causative genetic variant was identified in 219 (38%) patients, and 147 (25.5%) had LGE. Significant differences were found comparing LGE patterns between genes (P < 0.001). LGE was absent or rare in patients with variants in TNNT2, RBM20, and MYH7 (0, 5, and 20%, respectively). Patients with variants in DMD, DSP, and FLNC showed a predominance of LGE subepicardial patterns (50, 41, and 18%, respectively), whereas patients with variants in TTN, BAG3, LMNA, and MYBPC3 showed unspecific LGE patterns. The genetic yield differed according to LGE patterns. Patients with subepicardial, lineal midwall, transmural, and right ventricular insertion points or with combinations of LGE patterns showed an increased risk of MVA compared with patients without LGE.

Conclusion

LGE patterns in DCM have a specific distribution according to the affected gene. Certain LGE patterns are associated with an increased risk of MVA and with an increased yield of genetic testing.
Gene-echocardiography: refining genotype–phenotype correlations in hypertrophic cardiomyopathy
Authors: Zhou Nianwei , Weng Haobo , Zhao Weipeng , Tang Lu , Ge Zhendan , Tian Fangyan , Meng Fangmin , Pan Cuizhen , Shu Xianhong
Published: August 2023

Aims

This study aims to clarify the association between hypertrophic patterns and genetic variants in hypertrophic cardiomyopathy (HCM) patients, contributing to the advancement of personalized management strategies for HCM.

Methods and results

A comprehensive evaluation of genetic mutations was conducted in 392 HCM-affected families using Whole Exome Sequencing. Concurrently, relevant echocardiographic data from these individuals were collected. Our study revealed an increased susceptibility to enhanced septal and interventricular septal thickness in HCM patients harbouring gene mutations compared with those without. Mid-septal hypertrophy was found to be associated predominantly with myosin binding protein C3 (MYBPC3) variants, while a higher septum-to-posterior wall ratio correlated with myosin heavy chain 7 (MYH7) variants. Mutations in MYH7, MYBPC3, and other sarcomeric or myofilament genes (troponin I3 [TNNI3], tropomyosin 1 [TPM1], and troponin T2 [TNNT2]) showed a relationship with increased hypertrophy in the anterior wall, interventricular septum, and lateral wall of the left ventricle. In contrast, alpha kinase 3 (ALPK3)-associated hypertrophy chiefly presented in the apical region, while hypertrophy related to titin (TTN) and obscurin (OBSCN) mutations exhibited a uniform distribution across the myocardium. Hypertrophic patterns varied with the type and category of gene mutations, offering valuable diagnostic insights.

Conclusion

Our findings underscore a strong link between hypertrophic patterns and genetic variants in HCM, providing a foundation for more accurate genetic testing and personalized management of HCM patients. The novel concept of ‘gene-echocardiography’ may enhance the precision and efficiency of genetic counselling and testing in HCM.
Bioinformatic platforms for clinical stratification of natural history of atherosclerotic cardiovascular diseases
Authors: Benincasa Giuditta , Suades Rosa , Padró Teresa , Badimon Lina , Napoli Claudio
Published: August 2023

Although bioinformatic methods gained a lot of attention in the latest years, their use in real-world studies for primary and secondary prevention of atherosclerotic cardiovascular diseases (ASCVD) is still lacking. Bioinformatic resources have been applied to thousands of individuals from the Framingham Heart Study as well as health care-associated biobanks such as the UK Biobank, the Million Veteran Program, and the CARDIoGRAMplusC4D Consortium and randomized controlled trials (i.e. ODYSSEY, FOURIER, ASPREE, and PREDIMED). These studies contributed to the development of polygenic risk scores (PRS), which emerged as novel potent genetic-oriented tools, able to calculate the individual risk of ASCVD and to predict the individual response to therapies such as statins and proprotein convertase subtilisin/kexin type 9 inhibitor. ASCVD are the first cause of death around the world including coronary heart disease (CHD), peripheral artery disease, and stroke. To achieve the goal of precision medicine and personalized therapy, advanced bioinformatic platforms are set to link clinically useful indices to heterogeneous molecular data, mainly epigenomics, transcriptomics, metabolomics, and proteomics. The DIANA study found that differential methylation of ABCA1, TCF7, PDGFA, and PRKCZ significantly discriminated patients with acute coronary syndrome from healthy subjects and their expression levels positively associated with CK-MB serum concentrations. The ARIC Study revealed several plasma proteins, acting or not in lipid metabolism, with a potential role in determining the different pleiotropic effects of statins in each subject. The implementation of molecular high-throughput studies and bioinformatic techniques into traditional cardiovascular risk prediction scores is emerging as a more accurate practice to stratify patients earlier in life and to favour timely and tailored risk reduction strategies. Of note, radiogenomics aims to combine imaging features extracted for instance by coronary computed tomography angiography and molecular biomarkers to create CHD diagnostic algorithms useful to characterize atherosclerotic lesions and myocardial abnormalities. The current view is that such platforms could be of clinical value for prevention, risk stratification, and treatment of ASCVD.
Decreased liver-to-spleen ratio in low-dose computed tomography as a biomarker of fatty liver disease reflects risk for myocardial ischaemia
Authors: Hokkanen A , Hämäläinen H , Laitinen T M , Laitinen T P
Published: August 2023

Aims

A strong association between fatty liver disease (FLD) and coronary artery disease is consistently reported. Our aim was to evaluate whether FLD diagnosed using low-dose non-contrast computed tomography (LDCT), as a by-product of myocardial perfusion imaging (MPI), is associated with myocardial ischaemia or left ventricular function parameters.

Methods and results

We analysed 742 patients who had undergone MPI using single photon emission computed tomography (SPECT) and LDCT. A liver-to-spleen ratio (in Hounsfield units) of <1 was defined as FLD. Myocardial ischaemia was defined as a summed difference score (SDS) ≥3. Left ventricular size and systolic function were assessed from the electrocardiogram-gated SPECT. FLD patients were younger (63 vs. 68 years) and had a higher body mass index (34.6 vs. 29.0 kg/m2) and a higher SDS (2.65 vs. 1.63), P < 0.001 for all. Independently of several possible confounding factors including traditional risk factors, patients with FLD had a 1.70-fold risk of ischaemia (95% confidence interval 1.11–2.58, P = 0.014). Left ventricular end-diastolic volume (109 vs. 109 mL) and ejection fraction (61 vs. 61%) were comparable in those with and without FLD (non-significant for both).

Conclusions

With the help of LDCT, it is possible to identify FLD, which is associated with an increased risk of myocardial ischaemia. Therefore, evaluation of FLD from LDCT is recommended along with MPI.
First report of the wattle rust pathogen, Uromycladium acaciae (Raveneliaceae, Pucciniales) in Ethiopia
Authors: Pham Nam Q , Wingfield Michael J , Marincowitz Seonju , Tanga Agena A , Tiki Kumela R , Kassie Weldesenbet B , Hurley Brett P , Germishuizen Ilaria , Lawson Simon A , Healey Madaline A , Wondafrash Mesfin
Published: August 2023

Australian Acacia species are among the most important trees planted for wood and pulp production in several African countries, including Ethiopia. In 2020, symptoms of a serious shoot and leaf rust disease were observed on black wattle (Acacia mearnsii De Wild.) trees across the three main wattle growing regions of Ethiopia. The aim of this study was to describe the disease and identify its causal agent based on morphological characteristics as well as DNA sequence data for the ITS and LSU regions of ribosomal DNA. Here we report for the first time, the presence of the wattle rust pathogen, Uromycladium acaciae, in Ethiopia.