bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparing two different types of stochastic parametrization in geophysical flow
Authors: Holm D. D. , Pan W. , Woodfield J. M.
Published: November 2024

This paper investigates the effects of stochastic variations in bathymetry on the solutions of the thermal quasi-geostrophic (TQG) equations. These stochastic perturbations generate a variety of different types of ensemble spread in the solution behavior whilst also preserving the deterministic Lie–Poisson structure and Casimir conservation laws. We numerically compare the solution sensitivity to another type of structure-preserving stochastic perturbation where instead of bathymetry, the velocity is stochastically perturbed.
Synergistic optimization on Seebeck coefficient and electrical conductivity in 2H-MoS2 enabled by progressively evolved stacking faults under high pressure and high temperature
Authors: Wang Dianzhen , Zou Jing , You Cun , Ge Yufei , Wang Xinglin , Liang Xiao , Zhou Qiang , Tao Qiang , Chen Yanli , Zhu Pinwen , Cui Tian
Published: November 2024

In thermoelectricity, the stacking faults (SFs) have been investigated mainly in phonon transport but rarely in carrier transport. For the layered thermoelectric materials, the layered nature makes them prone to SFs, especially under high pressure because of the induced shear stress between grains. Herein, we take the typical layered 2H-MoS2 as an example to investigate the effect of high-pressure in situ-induced SFs on the thermoelectric transport properties under high pressure and high temperature. It was found that a continuous transition of P-N-P type conductive behavior with increasing pressure was observed in the sign of Seebeck coefficient, finally leading to a not weakened Seebeck coefficient. Furthermore, the in situ-induced SFs enhanced the interlayer interaction and provided transport channels for carriers across the interlayers to boost the electrical conductivity to ∼11 100 S m−1 at 5.5 GPa, 1110 K. Consequently, combined with intrinsic ultralow thermal conductivity of MoS2, a maximum ZT value of 0.191 was obtained at 5.5 GPa, 1110 K, comparable to those doped/composited MoS2. This conduction-type transition induced synergistic optimization on Seebeck coefficient and electrical conductivity could be ascribed to that SFs, which had a progressive evolution process for stabilization with rising pressure, in which some associated defects might be induced, and the band structure could be modified for regulating the carrier distributions and the density of states around the Fermi level. This study provided profound insights of regulating conduction type via dynamically modulating the lattice defects for designing a high-efficiency TE device.
The size dependence of flexoelectricity at nanocracks
Authors: Hao Yihan , Xu Mengkang , Tian Xinpeng , Deng Qian
Published: November 2024

The flexoelectric effect is an electro-mechanical coupling between strain gradients and the electric polarization, and it is especially significant for nanoscale structures. Since the strain gradient scales up with the decrease in the sample's feature size, the flexoelectric effect is size dependent. Due to the stress concentration, large strain gradients can be found at the crack tip and result in significant flexoelectric effect. However, for micro- or nanoscale cracks, it is still not clear how the flexoelectric effect changes with the size of cracks. In practice, the crack tip has finite radius. So, in addition to the crack length, the crack tip radius is also one of the geometric parameters describing the size of nanocracks. In this work, using our collocation mixed finite element method (CMFEM), we study the size dependence of flexoelectricity around nanocracks through these two parameters. Numerical simulation results indicate that stronger flexoelectric field can be formed around the tip of cracks with either larger crack length or smaller tip radius. We also analyze the interplay of the crack length and the tip radius and show how the crack tip flexoelectric field varies when both of these two parameters are changing.
Physics-informed data-driven reconstruction of turbulent wall-bounded flows from planar measurements
Authors: Hora Gurpreet S. , Gentine Pierre , Momen Mostafa , Giometto Marco G.
Published: November 2024

Obtaining accurate and dense three-dimensional estimates of turbulent wall-bounded flows is notoriously challenging, and this limitation negatively impacts geophysical and engineering applications, such as weather forecasting, climate predictions, air quality monitoring, and flow control. This study introduces a physics-informed variational autoencoder model that reconstructs realizable three-dimensional turbulent velocity fields from two-dimensional planar measurements thereof. Physics knowledge is introduced as soft and hard constraints in the loss term and network architecture, respectively, to enhance model robustness and leverage inductive biases alongside observational ones. The performance of the proposed framework is examined in a turbulent open-channel flow application at friction Reynolds number Reτ=250. The model excels in precisely reconstructing the dynamic flow patterns at any given time and location, including turbulent coherent structures, while also providing accurate time- and spatially-averaged flow statistics. The model outperforms state-of-the-art classical approaches for flow reconstruction such as the linear stochastic estimation method. Physical constraints provide a modest but discernible improvement in the prediction of small-scale flow structures and maintain better consistency with the fundamental equations governing the system when compared to a purely data-driven approach.
Forced convection heat transfer control for cylinder via closed-loop continuous goal-oriented reinforcement learning
Authors: Liu Yangwei , Wang Feitong , Zhao Shihang , Tang Yumeng
Published: November 2024

Forced convection heat transfer control offers considerable engineering value. This study focuses on a two-dimensional rapid temperature control problem in a heat exchange system, where a cylindrical heat source is immersed in a narrow cavity. First, a closed-loop continuous deep reinforcement learning (DRL) framework based on the deep deterministic policy gradient (DDPG) algorithm is developed. This framework swiftly achieves the target temperature with a temperature variance of 0.0116, which is only 5.7% of discrete frameworks. Particle tracking technology is used to analyze the evolution of flow and heat transfer under different control strategies. Due to the broader action space for exploration, continuous algorithms inherently excel in addressing delicate control issues. Furthermore, to address the deficiency that traditional DRL-based active flow control (AFC) frameworks require retraining with each goal changes and cost substantial computational resources to develop strategies for varied goals, the goal information is directly embedded into the agent, and the hindsight experience replay (HER) is employed to improve the training stability and sample efficiency. Then, a closed-loop continuous goal-oriented reinforcement learning (GoRL) framework based on the HER-DDPG algorithm is first proposed to perform real-time rapid temperature transition control and address multiple goals without retraining. Generalization tests show the proposed GoRL framework accomplishes multi-goal tasks with a temperature variance of 0.0121, which is only 5.8% of discrete frameworks, and consumes merely 11% of the computational resources compared with frameworks without goal-oriented capability. The GoRL framework greatly enhances the ability of AFC systems to handle multiple targets and time-varying goals.
Fast modulation of a long-wave infrared laser based on the two-photon absorption of CO2
Authors: Xie Zhenzhen , Li Zhiyong , Zhu Ziren , Liu Yu , Wang Hai , Wang Ziming , Ning Fangjin , Li Hui , Wang Zhaoxiang , Hu Liemao , Ke Changjun , Zheng Yijun , Zhao Wanli , Tan Rongqing
Published: November 2024

In this work, we report a long-wave infrared (LWIR) modulator based on the two-photon absorption of CO2 gas. The effect of gas pressure and laser power on the modulation under different wavelengths is discussed. A maximum modulation depth of 21.5% with a rise time (full time) less than 20 ns for a 9.36 μm laser was achieved. The gaseous modulator, which adopts a 2.75 μm laser as the pumping source, is capable of converting the pulse characteristics of the pump light into the modulation of the long-wave infrared light. It demonstrates promising potential for applications in the rapid optical modulation of LWIR lasers.
Passive radiative cooling: Not such an off-the-wall idea
Authors: Miller Johanna L.
Published: November 2024

A growing class of materials can cool horizontal surfaces to below the ambient temperature with no power input. Now there’s a material that works on vertical surfaces too.
Adjective + noun collocations in L2 spoken English
Authors: Gablasova Dana , Brezina Vaclav
Published: November 2024

This study explores the development of L2 phraseological knowledge, focusing on the relationship between L2
proficiency and the use of adjective-noun combinations from the perspective of collocation density and association strength. While
a growing body of evidence suggests that more advanced L2 production tends to be characterised by (i) a greater collocation
density and (ii) more strongly associated collocations, several studies did not find this trend. The present study draws on the
British Council-Lancaster Aptis Corpus and data from four proficiency levels (A2-C of the CEFR) to test a
hypothesis about the direction of collocation development in order to contribute to a systematic advancement of knowledge about
the development of productive L2 collocation use. The study replicates some of the key findings from previous research, confirming
that these trends are generalisable to different samples of L2 speakers and across different modes of communication.
Evolution of structural, magnetic and transport properties of 3d-5d based double perovskites Nd2–xSrxCoIrO6
Authors: Datta Raktim , Mondal Suman , Mondal Suchanda , Kalyan Pradhan Suman , Majumdar Subham , Kumar De Subodh
Published: November 2024

The evolution of the structural, magnetic and transport properties of the intermediate compounds Nd

2
−
x

Sr
x
CoIrO6 with x = 0.2, 0.4, 0.6, 1 and 1.5 have been studied to establish important roles of sizes and oxidation states of cations on various phases. The replacement of Nd3+ by Sr2+ primarily influences the oxidation states of Co (Co2+

→

Co3+) and Ir (Ir4+

→

Ir5+) ions to maintain the charge neutrality in the entire system. The Sr dopants give rise to an increasing Co/Ir antisite disorder (ASD) to accommodate the variation of charge state and ionic radius of Co and Ir. The nature of magnetic interaction induced by Sr changes from being a ferrimagnetic (FIM) to a more dominant antiferromagnetic. The suppression of the second magnetic transition below 30 K in samples for x

>

0.2 is entirely due to dilution of the Nd–Nd magnetic interaction. The combined effects of ASD and mixed oxidation state of Co and Ir ions generate various types of magnetic exchange pathways and create competitive magnetic interactions to stabilize a particular magnetic ground state. In the middle compound NdSrCoIrO6, a Griffith like phase in the temperature region 65–150 K and exchange bias field of 658 Oe at 2.3 K under a cooling field of 50 kOe has been observed. The compounds show an insulating kind of behaviour, and with hole doping the value of room temperature resistivity drastically decreases. The nature of conduction is found to follow three dimensional Mott’s variable range hopping process.
Investigation of performance-enhanced GaN-based E-mode p-channel MOSFET with pre-ohmic-annealing treatment
Authors: Su Huake , Zhang Tao , Xu Shengrui , Tao Hongchang , Wang Yibo , Gao Yuan , Hao Yue , Zhang Jincheng
Published: November 2024

Pre-ohmic-annealing (POA) treatment of P-GaN/AlN/AlGaN epitaxy under N2 atmosphere was demonstrated to effectively achieve good p-type ohmic contact as well as decreased epitaxy sheet resistance. Ohmic contact resistance (R
c) extracted by transfer length method reduced from 38 to 23 Ω·mm with alleviated contact barrier height from 0.55 to 0.51 eV after POA treatment. X-ray photoelectron spectroscopy and Hall measurement confirmed that POA treatment was able to reduce surface state density and improve the hole concentration of p-GaN. Due to the decreased R
c and improved two-dimensional hole gas (2DHG) density, an outstanding-performance GaN E-mode p-channel MOSFET was successfully realized.
The Asymptotic Geometry of 𝐺₂-Monopoles
Authors: Fadel Daniel , Nagy Ákos , Oliveira Goncalo
Published: November 2024

This article investigates the asymptotics of

G

2

\mathrm {G}_2

-monopoles.

First, we prove that when the underlying

G

2

\mathrm {G}_2

-manifold is nonparabolic (i.e. admits a positive Green’s function), finite intermediate energy monopoles with bounded curvature have finite mass. The second main result restricts to the case when the underlying

G

2

\mathrm {G}_2

-manifold is asymptotically conical. In this situation, we deduce sharp decay estimates and that the connection converges, along the end, to a pseudo-Hermitian–Yang–Mills connection over the asymptotic cone.

Finally, our last result exhibits a Fredholm setup describing the moduli space of finite intermediate energy monopoles on an asymptotically conical

G

2

\mathrm {G}_2

-manifold.
Early Christianity in Roman Legal Measures
Authors: Janssen K P S
Published: November 2024

The fourth chapter in this study is focused on the legal treatment of early Christianity.It opens by discussing the different schools of thought on the legal basis for trials against Christians, as well as the debate about the date of separation between Christian and Jewish communities. The chapter argues that legal interactions with Christians usually took the shape of cognitio procedures, and that negotiations between governors, the local population, and (sometimes) the emperor therefore played an important role in determining both whether accusations against Christians would be accepted and what the exact character of the proceedings would be. It also suggests that this process of negotiation serves to explain why charges of ‘being Christian’ are so frequently accompanied by accusations of criminal or otherwise disruptive behaviour, and argues that the traditional distinction between the nomen ipsum and flagitia cohaerentia nomini introduced by Pliny the Younger cannot be said to have been clearly made in legal practice. Indeed, legal measures against Christians were much more diverse than has often been assumed: they could vary significantly in scope, outcome, and character, and our sources strongly suggest that no coherent policy, let alone centralized persecutions or even well-established precedents, emerged during the period under discussion.
A Victorian Childhood and Early Adulthood
Authors: Whitehouse Deja
Published: November 2024

This chapter begins with a general overview of the education options available for young middle-class women in late nineteenth-century England, citing reports from the Taunton and Bryce Education Commissions and other contemporary sources. Although new schools offering academic subjects for girls had been established, many parents preferred their daughters to learn accomplishments, such as music and drawing, designed to attract a suitable husband. These were taught either by governesses and private tutors or in small establishments run by lady proprietors. Harris’s own childhood and education are explored and comparisons drawn with those of her female esoteric contemporaries. The chapter concludes with an analysis of Harris’s life as a young woman prior to her marriage to Percy Harris.
Crowley’s Magical Pupil
Authors: Whitehouse Deja
Published: November 2024

This chapter examines Harris’s esoteric and spiritual development during her involvement with Crowley. She became his magical pupil, not only to support her work on the Tarot designs, but also as a member of Crowley’s magical orders, the Ordo Templi Orientis (O.T.O.) and A⸫A⸫ Consideration is given to her previous occult knowledge and the direction her studies took under Crowley’s tutelage. Her membership of a Masonic lodge enabled her to affiliate to the O.T.O. at an equivalent level. In addition she was initiated into the A⸫A⸫, and her progression through the various degrees of the order is analysed in detail. In particular, Harris’s relationship with the god Mercury and the impact it had on various aspects of her life are explored. The chapter concludes with an assessment of Harris’s commitment to Crowley and Thelema.
Traumatic Brain Injury and Risk of Incident Dementia: Forensic Applications of Current Research
Authors: Clem Matthew A , LoBue Christian , Schaffert Jeff , Cullum C Munro
Published: November 2024

Objective

Traumatic Brain Injury (TBI) has been identified as a risk factor for later developing neurodegenerative disorders, and there has been significant attention on this association in forensic settings. As a result, forensic neuropsychologists are frequently asked to comment on risk for dementia after an alleged TBI in litigation and criminal cases. This article provides an evidence-based foundation to aid forensic practice by synthesizing comprehensive information pertaining to: (i) the role of the neuropsychologist in TBI-related litigation, (ii) the complexities associated with identifying TBIs in forensic cases, (iii) the science of TBI in relation to incident dementia, and (iv) current scientific evidence for chronic traumatic encephalopathy.

Results

Developing a neurodegenerative disorder after TBI is the exception rather than the rule. Prevalence rates suggest that only a small subset (< 5%) of individuals with moderate-to-severe TBI, and even fewer (< 1%) with mild TBI (mTBI), appear to develop certain neurodegenerative diseases, and the characteristics that place some at risk remain unclear. The literature is mixed in terms of identifying a relationship between mTBI and later-in-life dementia risk. Also, the quality of positive evidence for risk of dementia after mTBI is weak and mostly consists of observational studies characterized by methodological limitations.

Conclusions

Methods used to establish the likely occurrence of a TBI in a forensic context are typically more extensive than those used in a routine clinical evaluation. Research methodology to define TBI is often even more rudimentary and inconsistent. Applying clinical research results of TBI and dementia outcomes to forensic cases at an individual level carries significant limitations. Estimating the contribution of remote head hits or concussion in a causal manner to dementia is a challenge forensic experts sometimes face, yet at present, the task is impossible beyond correlations and speculation.
Forensic Neuropsychology Goes from Nowhere to Almost Everywhere: Lessons Learned During Decades of Practice
Authors: Sweet Jerry J
Published: November 2024

Objective

To provide a narrative overview of the development of forensic neuropsychology (FN) in the last 40-plus years.

Methods

Personal history description, highlighted by key data-based publications.

Results

Anecdotal and relevant data-based findings converge to present a perspective of a wealth of FN resources currently available to the well-documented growing numbers of practitioners.

Conclusion

The de facto subspecialty of FN is now a visible and prominent part of the landscape of clinical neuropsychology.
Diagnosed and Nondisclosed Concussions Among Young Athletes With ADHD
Authors: Schmitt Ara J , Matta Michael , Bretzin Abigail C , Benno Maria Tina , Franklin Kirstin , Beidler Erica
Published: November 2024

Objective

Within a sample of young athletes with attention-deficit/hyperactivity disorder (ADHD), to explore the frequency of disclosed and nondisclosed concussions, identify reasons the youth did not report a suspected concussion, and learn the frequency that the youth still practiced or played in a game after a suspected concussion.

Method

Cross-sectional surveys were completed by 448 youth athletes (ages 8–14 years) and a corresponding parent (or caregiver). As part of larger respective surveys, questions regarding ADHD status and concussion history were asked of the youth and parents. Data regarding 40 youth with ADHD were available for analyses. Due to the low frequency of concussive injuries within the total sample, descriptive statistics and qualitative techniques were used to contextualize the data.

Results

The youth with ADHD were not more likely to experience at least one diagnosed concussion or nondisclosed concussion as compared to non-ADHD controls. Three of 40 youth athletes with ADHD (8%) had been diagnosed with a concussion, whereas 5 (13%) self-reported a nondisclosed concussion. Not wanting to lose playing time and not wanting to miss a game were the two most endorsed reasons for concussion nondisclosure.

Conclusions

More research is needed to understand the present results considering other research that puts similarly aged athletes with ADHD at greater risk for concussion. Education for youth with ADHD might help reduce the number of nondisclosed concussions that have a more complex recovery trajectory in this population.
No evidence for phenotypic condition-dependent ejaculate allocation in response to sperm competition in a seed beetle
Authors: Wyber Blake W , Tomkins Joseph L , Simmons Leigh W
Published: November 2024

Sperm competition is known to favor the evolution of male traits that confer an advantage in gaining fertilizations when females mate multiply. Ejaculate production can be costly and the strategic allocation of sperm in relation to the sperm competition environment is a taxonomically widespread phenomenon. However, variation among males in their ability to adjust ejaculate allocation has rarely been explored. Here, we manipulated the phenotypic condition of male seed beetles, Callosobruchus maculatus, via larval diet quality and measured ejaculate allocation across varying levels of sperm competition manipulated using olfactory cues. Furthermore, we asked how strategic ejaculation was impacted by previous ejaculation. We found no variation in ejaculate allocation in response to experimentally manipulated cues to sperm competition. Ejaculate allocation was reduced by a male’s previous mating history but was unaffected by the larval diets on which males were reared. We suggest that either male seed beetles are unable to adjust ejaculate size to the immediate competitive environment, or that sperm displacement strategies employed by males favor maximal investment at all mating events, especially when unmated females are infrequently encountered. As our study is one of few to examine condition dependence in strategic ejaculation, emphasis should be placed on future studies investigating this possibility across a wider range of taxa and animal mating systems.
SeqLengthPlot v2.0: an all-in-one, easy-to-use tool for visualizing and retrieving sequence lengths from FASTA files
Authors: Domínguez-Pérez Dany , Agüero-Chapin Guillermin , Leone Serena , Modica Maria Vittoria
Published: November 2024

Motivation

Accurate sequence length profiling is essential in bioinformatics, particularly in genomics and proteomics. Existing tools like SeqKit and the Trinity toolkit provide basic sequence statistics but often fall short in offering comprehensive analytics and plotting options. For instance, SeqKit is a very complete and fast tool for sequence analysis, delivering useful metrics (e.g. number of sequences, average, minimum, and maximum lengths) and can return sequences either shorter or longer (but not both at once) for a given length. Similarly, Trinity's Perl-based scripts provide detailed contig length distributions (e.g. N50, median, and average lengths) but do not include the total number of sequences or offer graphical representations of the data.

Results

Given that key sequence analysis tasks are often distributed across multiple tools, we introduce SeqLengthPlot v2.0, an all-in-one, easy-to-use Python-based tool. Through a simple command-line interface, this straightforward tool enables users to split input FASTA files (nucleotide and protein) into two distinct files based on a customizable sequence length cutoff. It also automatically retrieves the resulting FASTA files, generates length distribution plots, and provides comprehensive statistical summaries.

Availability and implementation

SeqLengthPlot_v2.0.2 can be accessed at https://github.com/danydguezperez/SeqLengthPlot/releases/tag/v2.0.2.
Micro-DeMix: a mixture beta-multinomial model for investigating the heterogeneity of the stool microbiome compositions
Authors: Liu Ruoqian , Wang Yue , Cheng Dan
Published: November 2024

Motivation

Extensive research has uncovered the critical role of the human gut microbiome in various aspects of health, including metabolism, nutrition, physiology, and immune function. Fecal microbiota is often used as a proxy for understanding the gut microbiome, but it represents an aggregate view, overlooking spatial variations across different gastrointestinal (GI) locations. Emerging studies with spatial microbiome data collected from specific GI regions offer a unique opportunity to better understand the spatial composition of the stool microbiome.

Results

We introduce Micro-DeMix, a mixture beta-multinomial model that deconvolutes the fecal microbiome at the compositional level by integrating stool samples with spatial microbiome data. Micro-DeMix facilitates the comparison of microbial compositions across different GI regions within the stool microbiome through a hypothesis-testing framework. We demonstrate the effectiveness and efficiency of Micro-DeMix using multiple simulated datasets and the inflammatory bowel disease data from the NIH Integrative Human Microbiome Project.

Availability and implementation

The R package is available at https://github.com/liuruoqian/MicroDemix.
DrugRepPT: a deep pretraining and fine-tuning framework for drug repositioning based on drug’s expression perturbation and treatment effectiveness
Authors: Fan Shuyue , Yang Kuo , Lu Kezhi , Dong Xin , Li Xianan , Zhu Qiang , Li Shao , Zeng Jianyang , Zhou Xuezhong
Published: November 2024

Motivation

Drug repositioning (DR), identifying novel indications for approved drugs, is a cost-effective strategy in drug discovery. Despite numerous proposed DR models, integrating network-based features, differential gene expression, and chemical structures for high-performance DR remains challenging.

Results

We propose a comprehensive deep pretraining and fine-tuning framework for DR, termed DrugRepPT. Initially, we design a graph pretraining module employing model-augmented contrastive learning on a vast drug–disease heterogeneous graph to capture nuanced interactions and expression perturbations after intervention. Subsequently, we introduce a fine-tuning module leveraging a graph residual-like convolution network to elucidate intricate interactions between diseases and drugs. Moreover, a Bayesian multiloss approach is introduced to balance the existence and effectiveness of drug treatment effectively. Extensive experiments showcase the efficacy of our framework, with DrugRepPT exhibiting remarkable performance improvements compared to SOTA (state of the arts) baseline methods (improvement 106.13% on Hit@1 and 54.45% on mean reciprocal rank). The reliability of predicted results is further validated through two case studies, i.e. gastritis and fatty liver, via literature validation, network medicine analysis, and docking screening.

Availability and implementation

The code and results are available at https://github.com/2020MEAI/DrugRepPT.
Gene count estimation with pytximport enables reproducible analysis of bulk RNA sequencing data in Python
Authors: Kuehl Malte , Wong Milagros N , Wanner Nicola , Bonn Stefan , Puelles Victor G
Published: November 2024

Transcript quantification tools efficiently map bulk RNA sequencing (RNA-seq) reads to reference transcriptomes. However, their output consists of transcript count estimates that are subject to multiple biases and cannot be readily used with existing differential gene expression analysis tools in Python.

Here we present pytximport, a Python implementation of the tximport R package that supports a variety of input formats, different modes of bias correction, inferential replicates, gene-level summarization of transcript counts, transcript-level exports, transcript-to-gene mapping generation, and optional filtering of transcripts by biotype. pytximport is part of the scverse ecosystem of open-source Python software packages for omics analyses and includes both a Python as well as a command-line interface.

With pytximport, we propose a bulk RNA-seq analysis workflow based on Bioconda and scverse ecosystem packages, ensuring reproducible analyses through Snakemake rules. We apply this pipeline to a publicly available RNA-seq dataset, demonstrating how pytximport enables the creation of Python-centric workflows capable of providing insights into transcriptomic alterations.

Availability and implementation

pytximport is licensed under the GNU General Public License version 3. The source code is available at https://github.com/complextissue/pytximport and via Zenodo with DOI: 10.5281/zenodo.13907917. A related Snakemake workflow is available through GitHub at https://github.com/complextissue/snakemake-bulk-rna-seq-workflow and Zenodo with DOI: 10.5281/zenodo.12713811. Documentation and a vignette for new users are available at: https://pytximport.readthedocs.io.
Drug survival and safety of biosimilars for treating psoriasis compared with originator adalimumab: a multinational cohort study
Authors: Phan Duc Binh , Jourdain Hugo , Descalzo-Gallego Miguel Angel , González-Quesada Alicia , Zureik Mahmoud , Rivera-Díaz Raquel , Sahuquillo-Torralba Antonio , Lunt Mark , Garcia-Doval Ignacio , Sbidian Emilie , Warren Richard B , Yiu Zenas Z N
Published: November 2024

Background

The lack of evidence from routine clinical settings has limited the widespread adoption of adalimumab biosimilars for the treatment of psoriasis.

Objectives

To compare the drug survival and safety of adalimumab biosimilars with Humira® in psoriasis.

Methods

We conducted a prevalent new-user cohort study using data from the French National Health Data System (SNDS), the British Association of Dermatologists Biologics and Immunomodulators Register (BADBIR) and the Spanish Registry of Systemic Therapy in Psoriasis (BIOBADADERM). Adalimumab-naïve patients initiating adalimumab biosimilars (new users) were compared with Humira new users. Patients switching from Humira to biosimilars (switchers) were compared with those who continued Humira treatment. Patients were matched 1 : 1 based on previous adalimumab exposure time to create equal-sized cohorts of biosimilar and Humira users. Co-primary outcomes included drug discontinuation and serious adverse events (SAEs). Hazard ratios (HRs) were calculated using Cox proportional hazard models. Meta-analyses using random-effect models were performed to combine results from the three databases.

Results

In total, 7387 biosimilar new users and 3654 switchers were matched and compared with Humira users. No differences in all-cause discontinuation were found between biosimilar and Humira new users [HR 0.99, 95% confidence interval (CI) 0.94–1.04]. Switching from Humira to biosimilars was associated with a higher discontinuation rate than remaining on Humira (HR 1.35, 95% CI 1.19–1.52). Similar results were observed for discontinuation due to ineffectiveness or adverse events. Risks of SAEs were similar between biosimilar new users and Humira new users [incidence rate ratio (IRR) 0.91, 95% CI 0.80–1.05] or between switchers and continuous Humira users (IRR 0.92, 95% CI 0.83–1.01).

Conclusions

Adalimumab biosimilars can be considered viable alternatives to Humira for new patients, with comparable effectiveness and safety. However, owing to the higher likelihood of discontinuation, patients who switch from Humira to biosimilars may require closer monitoring and support.
Inpatient dermatology referrals: what is the burden? A retrospective review of 14 years of dermatology inpatient referrals
Authors: Cnudde Marie-Julie A M , Thomas Charles , Aldridge Christian
Published: November 2024

Background

The lack of dermatological knowledge by nondermatologists is exposed by the increasing number of requests made for inpatient dermatological consultations. Patients have been commenced on inappropriate treatment because of poor dermatology training.

Objectives

To determine the burden and accuracy of inpatient dermatology referrals.

Methods

A retrospective cohort study using paper inpatient dermatology referrals from one health board (Cwm Taf Morgannwg University Health Board, Wales, UK) between June 2007 and July 2021. Data analysis included timing of referrals, referring specialty, diagnosis and treatment. Descriptive statistics, using Excel, were used for analyses.

Results

The average number of referrals per year was 106 (range 79–166). The most frequent day of referral was Monday (26%). Most referrals were from medical teams (73%).

Differential diagnosis was suggested by the referring team in 59% of referrals. In only 29% of referrals did the dermatology team agree with the differential diagnosis. There was a discrepancy in the correctness of diagnosis in all categories; however, paediatricians were most likely to offer a correct differential (44%). In 44% of referrals, treatment was commenced by the referring team, most commonly antibiotics.

Conclusions

There is an extra burden on dermatology teams to cover inpatients. Our figures highlight two important issues. Firstly, the need for better dermatological education in medical schools to improve diagnostic accuracy and management of conditions. Secondly, the need for an inpatient dermatology service to review inpatient referrals and advise in the diagnosis and management of dermatology cases on the wards and to protect the service from being uncoupled from the main hospital.
Successful lanadelumab dose spacing in type I hereditary angio-oedema
Authors: Teixeira João , Flor Duarte , Xará Joana , Gonçalo Margarida
Published: November 2024

Type I hereditary angio-oedema (HAE) is a rare autosomal dominant disorder characterized by recurrent bradykinin-mediated angio-oedema affecting the skin, respiratory system and gastrointestinal tract. Lanadelumab, a monoclonal antibody targeting plasma kallikrein to reduce bradykinin production, has shown efficacy in long-term prophylaxis (LTP) for patients aged 2 years and above, with a recommended dose of 300 mg biweekly. We present two cases of patients with type I HAE, poorly controlled with traditional LTP therapies, demonstrating complete response and extended attack-free intervals with lanadelumab, suggesting that administration intervals beyond 4 weeks may be feasible, improving patient quality of life and healthcare cost-effectiveness.
Three-dimensional stereophotogrammetry: an effective tool for detecting disease progression in lupus erythematosus panniculitis
Authors: Hashemi Kimberly B , Ortiz-López Laura I , Santiago-Soltero Karla M , Nguyen Tyler T , Castillo Rochelle L , Dedeoglu Fatma , Ganske Ingrid M , Shaw Katharina S , Vleugels Ruth Ann
Published: November 2024

Lupus erythematosus panniculitis (LEP) is a rare variant of chronic cutaneous lupus erythematosus that commonly affects the face, upper arms, thighs and buttocks. It is distinguished by its potential to cause irreversible scarring, lipoatrophy and disfigurement. Even in patients with a known diagnosis of LEP, monitoring for ongoing disease activity can be challenging as overlying erythema and evolving subcutaneous nodularity and/or atrophy can be subtle. To our knowledge, we report the first case of a patient with facial LEP monitored longitudinally using three-dimensional stereophotogrammetry.
Mobile subcutaneous tumour on the trapezius
Authors: Konisky Hailey , Villanueva-Siles Esperanza , Kobets Kseniya
Published: November 2024

This is a dermatopathology case for learners to test their knowledge of the pathology of subcutaneous nodules and tumours.
Gray values and noise behavior of cone-beam computed tomography machines—an in vitro study
Authors: Oliveira-Santos Nicolly , Gaêta-Araujo Hugo , Spin-Neto Rubens , Dagassan-Berndt Dorothea , Bornstein Michael M , Oliveira Matheus L , Haiter-Neto Francisco , Freitas Deborah Q , Schulze Ralf
Published: November 2024

Objectives

To systematically evaluate the mean gray values (MGVs) and noise provided by bone and soft tissue equivalent materials and air imaged with varied acquisition parameters in 9 cone-beam computed tomography (CBCT) machines.

Methods

The DIN6868-161 phantom, composed of bone and soft tissue equivalent material and air gap, was scanned in 9 CBCT machines. Tube current (mA) and tube voltage (kV), field of view (FOV) size, and rotation angle were varied over the possible range. The effect of the acquisition parameters on the MGV and contrast-to-noise indicator (CNI) was analyzed by Kruskal Wallis and Dunn-Bonferroni tests for each machine independently (α = 0.05).

Results

Tube current did not influence MGV in most machines. Viso G7 and Veraview X800 presented a decrease in the MGV for increasing kV. For ProMax 3D Max and X1, the kV did not affect the MGV. For the majority of machines, MGV decreased with increasing FOV height. In general, the rotation angle did not affect the MGV. In addition, CNI was lower with lower radiation and large FOV and did not change from 80 kV in all machines.

Conclusions

The MGV and noise provided by the tested phantom vary largely among machines. The MGV is mainly influenced by the FOV size, especially for bone equivalent radiodensity. For most machines, when the acquisition parameters affect the MGV, the MGV decrease with the increase in the acquisition parameters.
Carotid calcifications in panoramic radiographs can predict vascular risk
Authors: Garoff Maria , Ahlqvist Jan , Levring Jäghagen Eva , Wester Per , Johansson Elias
Published: November 2024

Objectives

Carotid artery calcification (CAC) is occasionally detected in panoramic radiographs (PRs). Bilateral vessel-outlining (BVO) CACs are independent risk markers for future vascular events and have been associated with large plaque area. If accounting for plaque area, BVO CACs may no longer be an independent risk marker for vascular events. The aim of this study was to explore the association between BVO CACs and vascular events and its relationship with carotid ultrasound plaque area.

Methods

In this cohort study we prospectively included 212 consecutive participants with CACs detected in PR that were performed to plan and evaluate odontologic treatment. Of these 212, 43 (20%) had BVO CACs. Plaque area was assessed with ultrasound at baseline. Primary outcome was major adverse cardiovascular events (MACEs) during follow-up.

Results

Vessel-outlining CAC was associated with larger plaque area on the same side (P = .03) and BVO CACs were associated with larger total plaque area (both sides summed) than other CAC features (P = .004). Mean follow-up was 7.0 years and 72 (34%) participants had more than 1 MACE. In bivariable analyses, both BVO CACs (HR 2.5, P < .001) and total plaque area (HR 1.8 per cm2, P = .008) were associated with MACE. When entering BVO CACs, plaque area and other relevant co-variates in a multivariable model, BVO CACs were virtually unchanged (HR 2.4, P = .001), but total plaque area was no longer significant (HR 1.0, P = .92).

Conclusion

Present results support the contention that BVO CACs are a stronger predictor for future vascular events than carotid ultrasound plaque area.
A case report of verapamil toxicity leading to haemodynamic compromise in obstructive hypertrophic cardiomyopathy
Authors: Gau Jonathan W , Rader Florian , Mody Behram , Lee Andy Y
Published: November 2024

Background

Hypertrophic cardiomyopathy (HCM) is an inherited condition characterized by left ventricular (LV) hypertrophy unexplained by increased afterload, often with concomitant outflow tract obstruction. Verapamil is commonly used to treat symptomatic patients. However, its potential for adverse effects should be recognized.

Case summary

This report provides a case of cardiogenic shock in HCM, where a patient presented with chief complaint of fatigue and shortness of breath with an acute decline in LV systolic function on echocardiogram. His symptoms were attributed to verapamil toxicity following a recent increase in dosage. He achieved rapid symptom relief after holding his home medications, in addition to conservative management.

Discussion

This case report aims to elucidate the potential for multiple adverse effects involved with verapamil use in patients with obstructive HCM.
Anonymize or synthesize? Privacy-preserving methods for heart failure score analytics
Authors: Johann Tim I , Otte Karen , Prasser Fabian , Dieterich Christoph
Published: November 2024

Aims

Data availability remains a critical challenge in modern, data-driven medical research. Due to the sensitive nature of patient health records, they are rightfully subject to stringent privacy protection measures. One way to overcome these restrictions is to preserve patient privacy by using anonymization and synthetization strategies. In this work, we investigate the effectiveness of these methods for protecting patient privacy using real-world cardiology health records.

Methods and results

We implemented anonymization and synthetization techniques for a structure data set, which was collected during the HiGHmed Use Case Cardiology study. We employed the data anonymization tool ARX and the data synthetization framework ASyH individually and in combination. We evaluated the utility and shortcomings of the different approaches by statistical analyses and privacy risk assessments. Data utility was assessed by computing two heart failure risk scores on the protected data sets. We observed only minimal deviations to scores from the original data set. Additionally, we performed a re-identification risk analysis and found only minor residual risks for common types of privacy threats.

Conclusion

We could demonstrate that anonymization and synthetization methods protect privacy while retaining data utility for heart failure risk assessment. Both approaches and a combination thereof introduce only minimal deviations from the original data set over all features. While data synthesis techniques produce any number of new records, data anonymization techniques offer more formal privacy guarantees. Consequently, data synthesis on anonymized data further enhances privacy protection with little impacting data utility. We share all generated data sets with the scientific community through a use and access agreement.
Treatment with PCSK9 monoclonal antibodies is associated with discontinuation of oral lipid lowering therapy
Authors: Engebretsen Ingrid , Ødegaard Kristina Malene , Halvorsen Sigrun , Bugge Christoffer , Kristiansen Ivar Sønbø , Støvring Henrik , Munkhaugen John
Published: November 2024

Aims

Proprotein convertase subtilisin/kexin type 9 monoclonal antibodies (PCSK9 mAbs) are recommended for high-risk patients if the low-density lipoprotein cholesterol targets are not achieved with statins and ezetimibe. We studied persistence and adherence to (i) PCSK9 mAbs and (ii) statins and ezetimibe in a nationwide cohort of incident PCSK9 mAb users.

Methods and results

Information on all PCSK9 mAb users ≤80 years from 2015 through 2023 were extracted from the Norwegian Drug Registry. Discontinuation was defined as a gap in treatment ≥180 days and ≥90 days. Adherence was measured as the proportion of days covered during the initial year of PCSK9 mAb therapy. We analysed adherence of statins and ezetimibe before and after PCSK9 mAb initiation. Of 4784 patients initiating PCSK9 mAbs, the median age was 63 years, 41% were female, 61% had atherosclerotic disease, and 34% had familial hypercholesterolaemia. Within 3 years after initiation, 17% experienced a PCSK9 mAb treatment gap exceeding 180 days. In the 12-month period preceding PCSK9 mAb initiation, 74% dispensed statins whereas 67% dispensed ezetimibe. These numbers were reduced to 35% for statins and 42% for ezetimibe during the 12-month period after PCSK9 mAb initiation. Atherosclerotic disease, using ≥3 statins previously, and older age were significantly associated with discontinuation of statins and ezetimibe.

Conclusion

In this high-risk cohort of incident PCSK9 mAb users, more than 1 out of 2 stopped taking statin treatment whereas 40% discontinued ezetimibe. There is a major potential for improving adherence to oral LLD treatment following initiation of PCSK9 mAb.
Association between warfarin use and thromboembolic events in patients post-Fontan operation: propensity-score overlap weighting analyses
Authors: Maki Wakana , Aso Shotaro , Inuzuka Ryo , Matsui Hiroki , Fushimi Kiyohide , Yasunaga Hideo
Published: November 2024

OBJECTIVES

The appropriate antithrombotic regimen after a Fontan operation is yet to be elucidated. Hence, this study aimed to compare the incidence of thromboembolic events in patients with and without receiving warfarin for thromboprophylaxis in a large post-Fontan population.

METHODS

This retrospective cohort study used data from the Diagnosis Procedure Combination database in Japan between April 2011 and March 2022. We identified all patients who underwent a Fontan operation and excluded those who were born before 2010, died during the hospitalization or received mechanical heart replacement. Propensity score overlap weighting was performed between patients discharged with warfarin (with or without aspirin) and the control group (only aspirin or neither aspirin nor warfarin). Cox and Fine-Gray hazards models compared thromboembolic and bleeding events.

RESULTS

We identified 2007 eligible patients, including 1670 warfarin users and 337 non-users. The mean follow-up duration was 2.1 years. The crude proportions of thromboembolic events were 3.0% and 3.0% and those of bleeding events were 0.4% and 0.3% in the warfarin and control groups, respectively. There was no significant difference in thromboembolic events between the groups (sub-distribution hazard ratio: 0.77; 95% confidence interval 0.39–1.51; P = 0.45) or bleeding events (sub-distribution hazard ratio: 0.78; 95% confidence interval 0.09–7.03; P = 0.83).

CONCLUSIONS

Warfarin use at discharge after a Fontan operation may not be necessary for thromboembolism prophylaxis in paediatric patients, based on large-scale real-world data, with a mean postoperative follow-up duration of 2.1 years. There is room for further studies to reconsider routine warfarin use in patients post-Fontan operation.