bluuebunny/crossref_metadata_2025 huggingface dataset:
Cardiac arrhythmia in individuals with steroid sulfatase deficiency (X-linked ichthyosis): candidate anatomical and biochemical pathways
Authors: Wren Georgina H. , Davies William
Published: April 2024

Circulating steroids, including sex hormones, can affect cardiac development and function. In mammals, steroid sulfatase (STS) is the enzyme solely responsible for cleaving sulfate groups from various steroid molecules, thereby altering their activity and water solubility. Recent studies have indicated that Xp22.31 genetic deletions encompassing STS (associated with the rare dermatological condition X-linked ichthyosis), and common variants within the STS gene, are associated with a markedly elevated risk of cardiac arrhythmias, notably atrial fibrillation/flutter. Here, we consider emerging basic science and clinical findings which implicate structural heart abnormalities (notably septal defects) as a mediator of this heightened risk, and propose candidate cellular and biochemical mechanisms. Finally, we consider how the biological link between STS activity and heart structure/function might be investigated further and the clinical implications of work in this area.
Quantifying Dosage in Self-Managed Speech-Language Therapy: Exploring Components of Cumulative Intervention Intensity in a Real-World Mobile Health Data Set
Authors: Cordella Claire , Kiran Swathi
Published: April 2024

Purpose:

Cumulative Intervention Intensity (CII) is a proposed framework for conceptualizing and calculating dose that has been used to quantify intensity of speech-language therapy (SLT) in highly controlled laboratory studies and clinical trials. However, it is unknown whether CII can be applied to characterize the practice patterns of patients undertaking at-home, self-managed SLT. The current study leverages real-world mobile health data to investigate the applicability of CII parameters to self-managed SLT, including the interrelationships between individual CII parameters and their utility for identifying naturally occurring subgroups of patient users.

Method:

Anonymized data from 2,223 poststroke survivors who used the Constant Therapy application were analyzed. Four quantitative CII parameters—dose, session frequency, session duration, and total intervention duration—were calculated per user over a 3-month analysis period using raw session-level data. We conducted correlation analyses at the level of the individual and group to examine the degree of relatedness between each of the CII parameters. CII parameter measures were additionally used as inputs to a k-mean clustering analysis to identify practice pattern subgroups.

Results:

Results demonstrate the feasibility of calculating components of CII based on available usage statistics from a commercial app for self-managed SLT. Specifically, results suggest that, although CII parameters are related, session frequency offers complementary and nonoverlapping information (cf. dose, session duration, total intervention duration) about dosage. Clustering results show that practice patterns can be broadly differentiated according to the (a) amount and (b) frequency of practice.

Conclusions:

The calculation of CII may provide both users and clinicians with a fuller picture of at-home, self-managed practice habits than looking at any one dosage component alone. The study represents a first step toward more comprehensive and theoretically grounded dose reporting for self-managed SLT.

Supplemental Material:

https://doi.org/10.23641/asha.25511191
Person-Centered Stories on the Main Stage in Intervention: Case Examples From the My Story Project, Aphasia! This Is Our World, and Aphasia-Friendly Reading
Authors: O'Bryan Erin L. , Strong Katie A.
Published: April 2024

Purpose:

Researchers working in the Life Participation Approach to Aphasia (LPAA) framework are beginning to recognize the value of supportive co-constructed storytelling for people with aphasia. Supported storytelling facilitates identity reconstruction that is part of rehabilitation as defined in the LPAA and the Living with Aphasia: Framework for Outcome Measurement. This clinical focus article reviews the therapeutic value of using co-constructed storytelling in clinical practice and describes how this was done in the My Story Project, Aphasia! This Is Our World, and Aphasia-Friendly Reading. These projects used co-constructed storytelling in intervention with people with aphasia in university and support group settings. Three case examples are presented, including sample therapy goals and documentation. Co-constructed person-centered storytelling has been used in clinical projects and has been shown to have immense value in rehabilitation for improving quality of life for people with aphasia.

Conclusions:

Co-constructed stories can provide a powerful opportunity for targeting life participation, identity, and environmental factors, while simultaneously targeting language. Clinicians are encouraged to consider incorporating the use of co-constructed person-centered storytelling in clinical practice. Guidance is offered for preparing for storytelling intervention sessions and documenting these sessions as billable, skilled services.
The ALPINE-ALMA [CII] survey: Dust emission effective radius up to 3 kpc in the early Universe
Authors: Pozzi F. , Calura F. , D’Amato Q. , Gavarente M. , Bethermin M. , Boquien M. , Casasola V. , Cimatti A. , Cochrane R. , Dessauges-Zavadsky M. , Enia A. , Esposito F. , Faisst A. L. , Gilli R. , Ginolfi M. , Gobat R. , Gruppioni C. , Hayward C. C. , Ibar E. , Koekemoer A. M. , Lemaux B. C. , Magdis G. E. , Molina J. , Romano M. , Talia M. , Vallini L. , Vergani D. , Zamorani G.
Published: April 2024

Aims. Measurements of the size of dust continuum emission are an important tool for constraining the spatial extent of star formation, and hence the buildup of stellar mass. Compact dust emission has generally been observed at cosmic noon (z ∼ 2 − 3). However, at earlier epochs, toward the end of the reionization (z ∼ 4 − 6), only the sizes of a handful of infrared (IR) bright galaxies have been measured. In this work, we derive the dust emission sizes of main-sequence (MS) galaxies at z ∼ 5 from the ALPINE survey.

Methods. We measured the dust effective radius, re, FIR, in the uv-plane in Band 7 of ALMA for seven ALPINE galaxies with resolved emission and we compared it with rest-frame ultraviolet (UV) and [CII]158 μm measurements. We studied the re, FIR − LIR scaling relation by considering our dust size measurements and all the data in the literature at z ∼ 4 − 6. Finally, we compared our size measurements with predictions from simulations.

Results. The dust emission in the selected ALPINE galaxies is rather extended (re, FIR ∼ 1.5 − 3 kpc), similar to [CII]158 μm but a factor of ∼2 larger than the rest-frame UV emission. Putting together all the measurements at z ∼ 5, spanning two decades in luminosity from LIR ∼ 1011 L⊙ to LIR ∼ 1013 L⊙, the data highlight a steeply increasing trend of the re, FIR − LIR relation at LIR < 1012 L⊙, followed by a downturn and a decreasing trend at brighter luminosities. Finally, simulations that extend up to the stellar masses of the ALPINE galaxies considered in the present work predict a subset of galaxies (∼25% at 1010 M⊙ < M⋆ < 1011 M⊙) with sizes as large as those measured.
Interstellar meteors from the tidal disruption of rocky planets on eccentric orbits around M dwarfs
Authors: Loeb Abraham , MacLeod Morgan
Published: April 2024

Context. Low-mass stars appear to frequently host planetary systems. When these rocky planets develop high eccentricities as a result of secular torques or dynamical scatterings, they occasionally pass close to the host star. In these close passages, the planets can be tidally disrupted, and sheared into bound and unbound debris tails. To suffer such a disruption, the stellar density must be higher than the planetary density.

Aims. This condition is met for the most common star and planet systems, M dwarf stars hosting rocky planets. We describe the dynamics of a tidal disruption, and estimate the typical velocities of unbound ejecta.

Methods. We simulate the gas dynamics of a planetary tidal disruption, and show that disruptions preserve the layered structure of a rocky body, with the outermost layers flung into interstellar space with the highest velocities.

Results. We compare these properties to those of the candidate interstellar meteoroid CNEOS-2014-01-08 (IM1). IM1's approximately 60 km s−1 excess speed relative to the local standard of rest is naturally reproduced by the unbound debris of the disruption of an Earth-like planet around an M dwarf star. We suggest that such an encounter might explain the interstellar kinematics of IM1, and its unusual composition, especially if it originated in the fastest-expelled crust of a differentiated rocky planet. Finally, we estimate that the disruption of ~10 M⊕ reservoirs of rocky planets per M dwarf are needed to reproduce the inferred rate of IM1-like objects.
How does the power structure affect the acquisition price and inventory decisions in the reverse supply chain
Authors: Sun Hong , Li Yan
Published: April 2024

With growing concerns about environmental sustainability, reverse supply chains play a crucial role in recycling, remanufacturing, and reducing waste. Investigating the power structure’s impact on decisions related to acquisition prices and inventory management can provide insights into the integration of sustainable practices. This study analyzes a reverse supply chain with a supplier and a remanufacturer, in which the supplier provides the remanufacturer with sorted used cores. We investigate the acquisition pricing and inventory decisions under different power structures (supplierled Stackelberg model, remanufacturer-led Stackelberg model) through game theory analysis. We first establish the centralized model to explore optimal acquisition decisions and profit of the total system. Then we evaluate the acquisition quantity, wholesale prices, the profit of supplier and remanufacturer in the supplier-led model and in the remanufacturer-led model. Finally, the impact of power structure on the performance of supplier and remanufacturer are explored by numerical analysis, as well as the supply chain system. Our significant findings show that (i) the total profit of the supplier-led and remanufacturer-led reverse supply chain are less than the centralized model due to the double marginalization; (ii) the remanufacturer-led reverse supply chain is superior to the supplier-led model reverse supply chain; (iii) the selected grades in the supplier-led model is proved the same as that in the remanufacturer-led model, which could not been affected by the wholesale price; (iv) the greater the inventory risk (the uncertainty in demand), the greater the profit share for the remanufacturer (supplier) in the supplier-led (remanufacturer-led) model.
Persistent Left SVC Draining to Right Atrium through Common Channel with Suprahepatic IVC: A Rare Finding
Authors: Bhardwaj Akshit , Kushwaha Dinesh Singh , Prabhakar Ankit , Sharma Pankaj
Published: April 2024

The knowledge of different anatomic venous variants of central vessels is essential to improve the safety of procedures like central venous access and tunneled central catheter (TCC) placement. Persistent left superior vena cava (PLSVC) is an uncommon variant seen in 0.5 to 2% of common population, in 80 to 90% of which PLSVC commonly drains into the right atrium (RA) via the coronary sinus. We describe a rare case of PLSVC draining into RA through common channel with suprahepatic inferior vena cava, encountered while placing TCC into left internal jugular vein. This report highlights the radiological findings and the implications of this anatomic anomaly.
The impact of perceived environmental corporate social responsibility on idea generation and idea implementation
Authors: Yu Li , Wu Weiwei
Published: April 2024

Scholars have already made a few outcomes regarding the effect of environmental corporate social responsibility (ECSR) on employees’ workplace behaviors. However, research on how perceived ECSR influences employee innovation remains largely unexplored. Drawing from the social identity theory (SIT) and stakeholder theory, this research fills this gap by examining: (a) the influence of perceived ECSR on idea generation (IG). (b) the influence of perceived ECSR on idea implementation (II). (c) the moderating effects of psychological capital (PsyCap) on these relationships. Using data on 348 employees from Chinese firms, the results demonstrate that perceived ECSR effectively fosters IG and II, yet when PsyCap is high, the positive influence of perceived ECSR is stronger. Our findings offer new insights for understanding the role of ECSR perception in the employee innovation domain by revealing that perceived ECSR can generate IG and promote II, and delimiting their boundaries from a psychological perspective. In addition, our findings make several practical implications for firms to cultivate their employees’ ECSR perception and improve employees’ IG and II to achieve sustainable development.
Head-on collision of compressed plasma jets shows promise for high-gain laser fusion
Authors: Ikenson Ben
Published: April 2024

Creating high-density plasmas for the double cone ignition scheme
Direct imprint of optical skyrmions in azopolymers as photoinduced relief structures
Authors: Tamura Rihito , Kumar Praveen , Rao A. Srinivasa , Tsuda Kazuki , Getzlaff Fanny , Miyamoto Katsuhiko , Litchinitser Natalia M. , Omatsu Takashige
Published: April 2024

Skyrmions, topologically stable configurations of a three-component vector field with sophisticated textures, have been considered in many contexts, including atomic physics, Bose–Einstein condensates, liquid crystals, and magnetic materials. Although optical counterparts of skyrmions have extensively been studied theoretically and recently demonstrated in the laboratory experiments, their experimental mapping is challenging due to the fine, three-dimensional, and complicated structure of their polarization distributions. Here, we propose and demonstrate a straightforward mapping of the polarization textures of optical Néel-, Bloch-, and anti-skyrmions based on the radiation pressure and direct imprinting of the skyrmion textures on azopolymers. These results not only elucidate the exotic interaction that occurs between topologically protected quasiparticles of light and matter but also provide a simple approach for generation and characterization of optical skyrmions, based on a dual-path polarization shaping configuration with a single spatial light modulator, and their measurements based on the radiation pressure.
Harnessing nonlinear conductive characteristic of TiO2/HfO2 memristor crossbar for implementing parallel vector–matrix multiplication
Authors: Wei Wei , Wang Cong , Pan Chen , Yangdong Xing-Jian , Yang Zai-Zheng , Yang Yuekun , Cheng Bin , Liang Shi-Jun , Miao Feng
Published: April 2024

Memristor crossbar arrays are expected to achieve highly energy-efficient neuromorphic computing via implementing parallel vector–matrix multiplication (VMM) in situ. The similarities between memristors and neural synapses offer opportunities for realizing hardware-based brain-inspired computing, such as spike neural networks. However, the nonlinear I–V characteristics of the memristors limit the implementation of parallel VMM on passive memristor crossbar arrays. In our work, we propose to utilize differential conductance as a synaptic weight to implement linear VMM operations on a passive memristor array in parallel. We fabricated a TiO2/HfO2 memristor crossbar array, in which differential-conductance-based synaptic weight exhibits plasticity, nonvolatility, multi-states, and tunable ON/OFF ratio. The noise-dependent accuracy performance of VMM operations based on the proposed approach was evaluated, offering an optimization guideline. Furthermore, we demonstrated a spike neural network circuit capable of processing small spiking signals through the differential-conductance-based synapses. The experimental results showcase effective space-coded and time-coded spike pattern recognition. Importantly, our work opens up new possibilities for the development of passive memristor arrays, leading to increased energy and area efficiency in brain-inspired chips.
The length and spacing of river tributaries
Authors: Robinson Michael J. , Scheingross Joel S.
Published: April 2024

River networks are composed of a mainstem and tributaries. These tributaries dissect landscapes, regulate water and habitat availability, and transport sediment and nutrients. Despite the importance of tributaries, we currently lack theory and data describing whether and how tributary length and spacing varies within watersheds, thereby limiting our ability to accurately describe river network geometry. We address this knowledge gap by analyzing 4,696 tributaries across six landscapes with varying climate, tectonic setting, and lithology. Our results show that both tributary length and spacing systematically increase with downstream distance along the mainstem river, following a power-law scaling. This power-law scaling can be modulated by basin shape, with tributaries becoming shorter and, in some cases, more closely spaced as basin elongate. Furthermore, the power-law scaling may break down in cases where river networks have been disturbed by pervasive faulting, raising the possibility that the scaling we observe is not unique to all branching networks, and instead may be universal across undisturbed fluvial networks. These findings can be used to improve predictions of river network geometry and potentially to distinguish fluvial river networks from other branching networks.
The Unity of Movement
Authors: Tsz-Ming Lee Tommy
Published: April 2024

Displacement (of linguistic expressions) is a ubiquitous phenomenon in natural language. In the generative tradition, displacement is modelled in terms of transformation, or more precisely, movement, which establishes dependencies among syntactic constituents in a phrase structure. This book probes the question regarding to what extent movement theories can be unified. Specifically, I address issues surrounding the debate of the distinction between head movement and phrasal movement over the past few decades. The distinction presupposes that structural complexity of the moving element is correlated with its movement properties. The goal of this book is to show that this is an unwarranted assumption. Based on a number of case studies on verb displacement phenomena in Cantonese, I attempt a unified theory of movement by abandoning the head/phrase distinction in movement theories. These case studies converge on the conclusion that the phrase structure status of syntactic constituents bears a minimal role in theorizing displacement phenomena in natural language. This volume represents a minimalist pursuit of a unified theory of movement.
Modulation effect of focusing mirror on beam propagation through anisotropic turbulence
Authors: Yu Zhou , Wang Wenhai , Zhou Xu , Liu Chengzhao , Hu Zhengda , Zhu Yun
Published: April 2024

In this study, we modulated the Bessel-Gaussian (BG) beam using a focusing mirror to enhance the performance of wireless optical communication (WOC) while considering the angles between turbulence cells and the transmitted direction when beams propagate through anisotropic atmospheric turbulence along a slant path. Numerical results reveal that when the BG beam is modulated by a focusing mirror with a focusing length of 1 km, the detection probability of orbital angular momentum (OAM) is increased by 9.06% compared with the unmodulated BG beam when the OAM quantum number is 1. Simultaneously, this modulation method effectively reduces the bit error rate and enhances the channel capacity in OAM-based WOC. Furthermore, we observed that the smaller the OAM number, the better the effect of the modulation. Through our analysis, we identified that the most significant distortions in OAM mode propagation occur at the exponential parameter approximately

3.1

in the modified von Karman spectrum. Moreover, we demonstrated that the effects of the anisotropic tilt angle can not be negligible for beams through a slant path. Therefore, the modulation of the focusing mirror, in combination with a well-designed propagation direction that takes appropriate angles into account, can significantly improve the overall quality and performance of optical communication systems.
Investigation of structural, electrical, and magnetic variations of Ni-Zn-Co ferrites by substituting rare earth Ho3+ for high-frequency applications
Authors: Routray Krutika L , Saha Sunirmal
Published: April 2024

The investigation of structural, magnetic, and electrical properties of Ni0.6Zn0.3Co0.1HoxFe2−xO4 (NZCHF, 0 ≤ x ≤ 0.2) ferrites, synthesized through the sol–gel autocombustion method, has been undertaken. The refined x-ray diffraction (XRD) analysis was performed for XRD data analysis using Fullprof Suite software and it confirmed a single-phase cubic spinel structure, with the determination of crystallite size, refinement parameters and lattice constants. The bulk density of the samples consistently remained lower than the x-ray density, with densities increasing proportionally to the enhancement of Ho concentration. FTIR analysis corroborated the presence of metal-oxygen bonds within the ferrite possessing a spinel cubic structure. 57Fe Mossbauer spectroscopy showed that the hyperfine magnetic field of tetrahedral (A) and octahedral (B) sites decreased with the substitution of Ho3+ ions that preferentially occupy the B site. The impedance analyzer and vibrating sample magnetometer (VSM) were utilized to measure the real and imaginary parts of the complex permeability and magnetic properties of the samples, respectively. Complex impedance plots were scrutinized to discern the contributions of grain and grain boundary resistances, providing insights into the electrical behavior of the ferrite samples. Furthermore, the introduction of Ho concentration led to alterations in other key properties of the ferrites, including coercivity (H

c
), retentivity (M

r
), anisotropy constant (K), and magnetic moment (μ

B
).The impact of the rare-earth content on the magnetic features of the prepared NiZnCo ferrite microspheres was investigated by analyzing magnetic-hysteresis (M-H) loops, which showed soft ferrimagnetism. Concurrently, the dielectric constant and dielectric loss tangent of the studied samples exhibited a decrease with the rise in Ho3+ concentration. The expected reduction in tan loss in the prepared samples is attributed to the increase in ac resistivity associated with the higher Ho3+ content.
Real-time observation of soliton pulsation and explosion in an Yb-doped fiber laser
Authors: Fu Mingzhu , Wang Xude , Fan Yuhan , Lu Mengxiang , Li Kaixin , Li Suwen
Published: April 2024

Nonlinear dissipative systems support pulsating solutions and exhibit many interesting dynamic behaviors. Here, we report various soliton pulsations and explosions in an all-normal dispersion ytterbium-doped fiber laser by utilizing the dispersive Fourier transform technique. By the different soliton dynamics, these phenomena can be classified into single-soliton pulsation and explosion, dual-soliton synchronous and asynchronous pulsation, as well as dual-soliton asynchronous explosion. Solitons exhibit identical periodic fluctuations in the synchronous pulsation while showing the anti-phase behavior in asynchronous pulsation. The dual-soliton asynchronous pulsation might be related to the periodic modulation of the polarization state of solitons. As for the dual-soliton asynchronous explosion, it can be regarded as the asynchronously triggered transient solitons containing periodic explosion through the gain-mediated soliton interactions. These findings may provide new insights into complex dynamics in the field of ultrafast lasers.
Domestic and international aviation emission inventories for the UNFCCC parties
Authors: Klenner Jan , Muri Helene , Strømman Anders H
Published: April 2024

Global aviation emissions have been growing despite international efforts to limit climate change. Quantifying the status quo of domestic and international aviation emissions is necessary for establishing an understanding of current emissions and their mitigation. Yet, a majority of the United Nations framework convention on climate change (UNFCCC)-ratifying parties have infrequently disclosed aviation emissions within the international framework, if at all. Here, we present a set of national aviation emission and fuel burn inventories for these 197 individual parties, as calculated by the high-resolution aviation transport emissions assessment model (AviTeam) model. In addition to CO2 emissions, the AviTeam model calculates pollutant emissions, including NOx, SOx, unburnt hydrocarbons, black carbon, and organic carbon. Emission inventories are created in aggregated and gridded format and rely on Automatic Dependent Surveillance–Broadcast combined with schedule data. The cumulative global fuel burn is estimated at 291 Tg for the year 2019. This corresponds to CO2 emissions of 920 Tg, with 306 Tg originating from domestic aviation. We present emissions from 151 countries that have yet to report their emissions for 2019, which sum to 417 TgCO2. The improved availability of national emissions data facilitated by this inventory could support mitigation efforts in developed and developing countries and shows that such tools could bolster sector reporting to the UNFCCC.
Quantum Davidson algorithm for excited states
Authors: Tkachenko Nikolay V , Cincio Lukasz , Boldyrev Alexander I , Tretiak Sergei , Dub Pavel A , Zhang Yu
Published: April 2024

Excited state properties play a pivotal role in various chemical and physical phenomena, such as charge separation and light emission. However, the primary focus of most existing quantum algorithms has been the ground state, as seen in quantum phase estimation and the variational quantum eigensolver (VQE). Although VQE-type methods have been extended to explore excited states, these methods grapple with optimization challenges. In contrast, the quantum Krylov subspace (QKS) method has been introduced to address both ground and excited states, positioning itself as a cost-effective alternative to quantum phase estimation. However, conventional QKS methodologies depend on a pre-generated subspace through real or imaginary-time evolutions. This subspace is inherently expansive and can be plagued with issues like slow convergence or numerical instabilities, often leading to relatively deep circuits. Our research presents an economic QKS algorithm, which we term the quantum Davidson (QDavidson) algorithm. This innovation hinges on the iterative expansion of the Krylov subspace and the incorporation of a pre-conditioner within the Davidson framework. By using the residues of eigenstates to expand the Krylov subspace, we manage to formulate a compact subspace that aligns closely with the exact solutions. This iterative subspace expansion paves the way for a more rapid convergence in comparison to other QKS techniques, such as the quantum Lanczos. Using quantum simulators, we employ the novel QDavidson algorithm to delve into the excited state properties of various systems, spanning from the Heisenberg spin model to real molecules. Compared to the existing QKS methods, the QDavidson algorithm not only converges swiftly but also demands a significantly shallower circuit. This efficiency establishes the QDavidson method as a pragmatic tool for elucidating both ground and excited state properties on quantum computing platforms.
High-brightness green InP-based QLEDs enabled by in-situ passivating core surface with zinc myristate
Authors: Cheng Yuanbin , Li Qian , Chen Mengyuan , Chen Fei , Wu Zhenghui , Shen Huaibin
Published: April 2024

The performance of red InP and blue ZnTeSe-based quantum dots (QDs) and corresponding QD light emitting diodes (QLEDs) has already been improved significantly, whose external quantum efficiencies (EQEs) and luminances have exceeded 20% and 80 000 cd m−2, respectively. However, the inferior performance of the green InP-based device hinders the commercialization of full-color Cd-free QLED technology. The ease of oxidation of the highly reactive InP cores leads to high non-radiative recombination and poor photoluminescence quantum yield (PL QY) of the InP-based core/shell QDs, limiting the performance of the relevant QLEDs. Here, we proposed a fluoride-free synthesis strategy to in-situ passivate the InP cores, in which zinc myristate reacted with phosphine dangling bonds to form Zn–P protective layer and protect InP cores from the water and oxygen in the environment. The resultant InP/ZnSe/ZnS core/shell QDs demonstrated a high PL QY of 91%. The corresponding green-emitting electroluminescence devices exhibited a maximum EQE of 12.74%, along with a luminance of over 175 000 cd m−2 and a long T50@100 cd m−2 lifetime of over 20 000 h.
Littlewood and Duffin–Schaeffer-Type Problems in Diophantine Approximation
Authors: Chow Sam , Technau Niclas
Published: April 2024

Gallagher’s theorem describes the multiplicative diophantine approximation rate of a typical vector. We establish a fully inhomogeneous version of Gallagher’s theorem, a diophantine fibre refinement, and a sharp and unexpected threshold for Liouville fibres. Along the way, we prove an inhomogeneous version of the Duffin–Schaeffer conjecture for a class of nonmonotonic approximation functions.
Adapting beyond borders: Insights from the 19th Student Council Symposium (SCS2023), the first hybrid ISCB Student Council global event
Authors: Al Sium Syed Muktadir , Torrejón Estefania , Chowdhury Sanjana Fatema , Ahmed Rubaiat , Jain Aakriti , Treccani Mirko , Veschetti Laura , Riaz Arsalan , Eranti Pradeep , Olguín-Orellana Gabriel J
Published: April 2024

The 19th ISCB Student Council Symposium (SCS2023) organized by ISCB-SC adopted a hybrid format for the first time, allowing participants to engage in-person in Lyon, France, and virtually via an interactive online platform. The symposium prioritized inclusivity, featuring on-site sessions, poster presentations, and social activities for in-person attendees, while virtual participants accessed live sessions, interactive Q&A, and a virtual exhibit hall. Attendee statistics revealed a global reach, with Europe as the major contributor. SCS2023’s success in bridging in-person and virtual experiences sets a precedent for future events in Computational Biology and Bioinformatics.

Availability and Implementation

The details of the symposium, speaker information, schedules, and accepted abstracts, are available in the program booklet (https://doi.org/10.5281/zenodo.8173977). For organizers interested in adopting a similar hybrid model, it would be beneficial to have access to details regarding the online platform used, the types of sessions offered, and the challenges faced. Future iterations of SCS can address these aspects to further enhance accessibility and inclusivity.
Extending BioMASS to construct mathematical models from external knowledge
Authors: Arakane Kiwamu , Imoto Hiroaki , Ormersbach Fabian , Okada Mariko
Published: April 2024

Motivation

Mechanistic modeling based on ordinary differential equations has led to numerous findings in systems biology by integrating prior knowledge and experimental data. However, the manual curation of knowledge necessary when constructing models poses a bottleneck. As the speed of knowledge accumulation continues to grow, there is a demand for a scalable means of constructing executable models.

Results

We previously introduced BioMASS—an open-source, Python-based framework–to construct, simulate, and analyze mechanistic models of signaling networks. With one of its features, Text2Model, BioMASS allows users to define models in a natural language-like format, thereby facilitating the construction of large-scale models. We demonstrate that Text2Model can serve as a tool for integrating external knowledge for mathematical modeling by generating Text2Model files from a pathway database or through the use of a large language model, and simulating its dynamics through BioMASS. Our findings reveal the tool's capabilities to encourage exploration from prior knowledge and pave the way for a fully data-driven approach to constructing mathematical models.

Availability and implementation

The code and documentation for BioMASS are available at https://github.com/biomass-dev/biomass and https://biomass-core.readthedocs.io, respectively. The code used in this article are available at https://github.com/okadalabipr/text2model-from-knowledge.
Adjusting for covariates and assessing modeling fitness in machine learning using MUVR2
Authors: Yan Yingxiao , Schillemans Tessa , Skantze Viktor , Brunius Carl
Published: April 2024

Motivation

Machine learning (ML) methods are frequently used in Omics research to examine associations between molecular data and for example exposures and health conditions. ML is also used for feature selection to facilitate biological interpretation. Our previous MUVR algorithm was shown to generate predictions and variable selections at state-of-the-art performance. However, a general framework for assessing modeling fitness is still lacking. In addition, enabling to adjust for covariates is a highly desired, but largely lacking trait in ML. We aimed to address these issues in the new MUVR2 framework.

Results

The MUVR2 algorithm was developed to include the regularized regression framework elastic net in addition to partial least squares and random forest modeling. Compared with other cross-validation strategies, MUVR2 consistently showed state-of-the-art performance, including variable selection, while minimizing overfitting. Testing on simulated and real-world data, we also showed that MUVR2 allows for the adjustment for covariates using elastic net modeling, but not using partial least squares or random forest.

Availability and implementation

Algorithms, data, scripts, and a tutorial are open source under GPL-3 license and available in the MUVR2 R package at https://github.com/MetaboComp/MUVR2.
phylaGAN: data augmentation through conditional GANs and autoencoders for improving disease prediction accuracy using microbiome data
Authors: Sharma Divya , Lou Wendy , Xu Wei
Published: April 2024

Motivation

Research is improving our understanding of how the microbiome interacts with the human body and its impact on human health. Existing machine learning methods have shown great potential in discriminating healthy from diseased microbiome states. However, Machine Learning based prediction using microbiome data has challenges such as, small sample size, imbalance between cases and controls and high cost of collecting large number of samples. To address these challenges, we propose a deep learning framework phylaGAN to augment the existing datasets with generated microbiome data using a combination of conditional generative adversarial network (C-GAN) and autoencoder. Conditional generative adversarial networks train two models against each other to compute larger simulated datasets that are representative of the original dataset. Autoencoder maps the original and the generated samples onto a common subspace to make the prediction more accurate.

Results

Extensive evaluation and predictive analysis was conducted on two datasets, T2D study and Cirrhosis study showing an improvement in mean AUC using data augmentation by 11% and 5% respectively. External validation on a cohort classifying between obese and lean subjects, with a smaller sample size provided an improvement in mean AUC close to 32% when augmented through phylaGAN as compared to using the original cohort. Our findings not only indicate that the generative adversarial networks can create samples that mimic the original data across various diversity metrics, but also highlight the potential of enhancing disease prediction through machine learning models trained on synthetic data.

Availability and implementation

https://github.com/divya031090/phylaGAN.
Pacybara: accurate long-read sequencing for barcoded mutagenized allelic libraries
Authors: Weile Jochen , Ferra Gabrielle , Boyle Gabriel , Pendyala Sriram , Amorosi Clara , Yeh Chiann-Ling , Cote Atina G , Kishore Nishka , Tabet Daniel , van Loggerenberg Warren , Rayhan Ashyad , Fowler Douglas M , Dunham Maitreya J , Roth Frederick P
Published: April 2024

Motivation

Long-read sequencing technologies, an attractive solution for many applications, often suffer from higher error rates. Alignment of multiple reads can improve base-calling accuracy, but some applications, e.g. sequencing mutagenized libraries where multiple distinct clones differ by one or few variants, require the use of barcodes or unique molecular identifiers. Unfortunately, sequencing errors can interfere with correct barcode identification, and a given barcode sequence may be linked to multiple independent clones within a given library.

Results

Here we focus on the target application of sequencing mutagenized libraries in the context of multiplexed assays of variant effects (MAVEs). MAVEs are increasingly used to create comprehensive genotype-phenotype maps that can aid clinical variant interpretation. Many MAVE methods use long-read sequencing of barcoded mutant libraries for accurate association of barcode with genotype. Existing long-read sequencing pipelines do not account for inaccurate sequencing or nonunique barcodes. Here, we describe Pacybara, which handles these issues by clustering long reads based on the similarities of (error-prone) barcodes while also detecting barcodes that have been associated with multiple genotypes. Pacybara also detects recombinant (chimeric) clones and reduces false positive indel calls. In three example applications, we show that Pacybara identifies and correctly resolves these issues.

Availability and implementation

Pacybara, freely available at https://github.com/rothlab/pacybara, is implemented using R, Python, and bash for Linux. It runs on GNU/Linux HPC clusters via Slurm, PBS, or GridEngine schedulers. A single-machine simplex version is also available.
How to explore a new environment: exploratory tactics of the black rat (Rattus rattus)
Authors: Štolhoferová Iveta , Rudolfová Veronika , Skalíková Hana , Vobrubová Barbora , Frynta Daniel
Published: April 2024

The black rat (Rattus rattus) is a unique model for studying exploratory tactics due to its enormous colonizing potential. Considerable behavioral variability and consistent interindividual differences might help populations inhabit new environments and persist there even under intense pressure. Additionally, the affinity of the black rat for climbing might be another advantage, widening their potential niche. In this study, we describe the exploratory tactics of the black rats when introduced to a novel environment. In the first experiment, we tested 12 rats and calculated repeatability of their behaviors across 12 sessions of an enriched open-field test. We concluded that climbing is a highly repeatable behavior that serves as an important source of interindividual variability. In the second experiment, we tested 24 black rats in a unique L-shaped arena. Each rat was tested twice. We found that the majority of rats distributed their activity evenly, exploring each part of the apparatus for a similar amount of time, thus maximizing their chances of finding resources. Nevertheless, these “even” explorers still greatly differed in their level of activity, orderliness and affinity for climbing, generating large variability. In contrast, the minority of rats concentrated their activity only on a section of the new environment and were therefore characterized as selective explorers. Overall, we concluded that a combination of such exploratory tactics as well as a bias for even explorers enables black rats to quickly colonize new environments and persist there even under unfavorable conditions.
Distinct communities under the snow: describing characteristics of subnivium arthropod communities
Authors: Ziadeh Christopher P , Ziadeh Shayleigh B , Aflague Breanne H , Townley Mark A , Ayres Matthew P , Contosta Alexandra R , Garnas Jeff R
Published: April 2024

Arthropods are active during the winter in temperate regions. Many use the seasonal snowpack as a buffer against harsh ambient conditions and are active in a refugium known as the subnivium. While the use of the subnivium by arthropods is well established, far less is known about subnivium community composition, abundance, biomass, and diversity and how these characteristics compare with the community in the summer. Understanding subnivium communities is especially important given the observed and anticipated changes in snowpack depth and duration due to the changing climate. We compared subnivium arthropod communities with those active during the summer using pitfall trapping in northern New Hampshire. We found that compositions of ground-active arthropod communities in the subnivium differed from those in the summer. The subnivium arthropod community featured moderate levels of richness and other measures of diversity that tended to be lower than the summer community. More strikingly, the subnivium community was much lower in overall abundance and biomass. Interestingly, some arthropods were dominant in the subnivium but either rare or absent in summer collections. These putative “subnivium specialists” included the spider Cicurina brevis (Emerton 1890) (Araneae: Hahniidae) and 3 rove beetles (Coleoptera: Staphylinidae): Arpedium cribratum Fauvel, 1878, Lesteva pallipes LeConte, 1863, and Porrhodites inflatus (Hatch, 1957). This study provides a detailed account of the subnivium arthropod community, establishes baseline information on arthropod communities in temperate forests of northeastern North America, and explores the idea of subnivium specialist taxa that are highly active in winter and might be especially vulnerable to climate change.
Ceramides: a potential cardiovascular biomarker in young adult childhood cancer survivors?
Authors: Broberg Olof , Weismann Constance G , Øra Ingrid , Wiebe Thomas , Laaksonen Reijo , Liuba Petru
Published: April 2024

Aims

The aim of this study was to investigate circulating ceramides involved in cardiovascular disease (CVD) in young adult childhood cancer survivors (CCS) and their correlations to previously reported adverse cardiovascular changes in this cohort.

Methods and results

Fifty-seven CCS and 53 healthy controls (age 20–30 years) were studied. Plasma long-chain ceramides, known to be cardiotoxic (C16:0, C18:0, C24:0, and C24:1), were analysed by mass spectrometry. The coronary event risk test 2 (CERT2) score was calculated from the ceramide data. Cardiac and carotid artery ultrasound data and lipid data available from previous studies of this cohort were used to study partial correlations with ceramide and CERT2 score data. All four analysed ceramides were elevated in CCS compared with controls (P ≤ 0.012). The greatest difference was noted for C18:0, which was 33% higher in CCS compared with controls adjusted for sex, age, and body mass index (BMI) (P < 0.001). The CERT2 score was higher in CCS compared with controls (P < 0.001). In the CCS group, 35% had a high to very high CERT2 score (7–12) when compared with 9% in the control group (P < 0.001). The CCS subgroup with a CERT2 score ≥ 7 had higher heart rate, systolic blood pressure, and higher levels of apolipoprotein B compared with CCS with a CERT2 score < 6 (P ≤ 0.011). When adjusted for age, sex, and BMI, CERT2 score was significantly correlated with arterial stiffness, growth hormone, and cranial radiotherapy (P < 0.044).

Conclusion

Ceramides could be important biomarkers in understanding the pathophysiology of CVD and in predicting CVD disease risk in young adult CCS.
Borrowing Constraints and Demand for Remedial Education: Evidence from Tanzania
Authors: Burchardi Konrad , de Quidt Jonathan , Gulesci Selim , Sulaiman Munshi
Published: April 2024

We use a cash transfer to relax households’ borrowing constraints, then elicit their willingness to pay for a remedial education programme offering tutoring and life skills training. Lottery losers were willing to pay 3,300 Tanzanian Shillings for the programme, which is 7% of per capita monthly expenditures. For those identified at baseline as able to borrow, willingness to pay increases by 3% upon winning a lottery prize of 3,200 Tanzanian Shillings. For those unable to borrow, willingness to pay increases by 27% upon winning the lottery. We conclude that borrowing constraints limit access to educational programmes, and may increase inequality of educational attainment.
Extended septal myectomy versus alcohol septal ablation: clinical results at a national referral centre
Authors: de Villarreal-Soto Juan Esteban , Oteo-Domínguez Juan Francisco , Martínez-López Daniel , Ríos-Rosado Elsa Carolina , Vera-Puente Beatriz , Olivo-Soto Jean Carlo , Arízaga-Arce Fernando , García-Pavía Pablo , Ospina Mosquera Víctor Manuel , Villar García Susana , García Suárez Jessica , Cavero Miguel Ángel , Martín-López Carlos Esteban , Forteza-Gil Alberto
Published: April 2024

OBJECTIVES

Extended septal myectomy and alcohol septal ablation are 2 invasive treatments for hypertrophic obstructive cardiomyopathy. Our goal was to compare which of these techniques achieved a higher reduction in gradients, improvement in New York Heart Association (NYHA) functional class and reduction in medical treatment.

METHODS

It is a single-centre observational and retrospective analysis. We used multivariable regression analyses to assess the association of ablation/myectomy with different outcomes. The odds ratio or coefficient along with the 95% confidence interval was estimated according to the group and adjusted for the corresponding preprocedural variables and EuroSCORE II.

RESULTS

A total of 78 patients underwent septal myectomy, and 25 patients underwent alcohol septal ablation. Basal and Valsalva gradients after myectomy were reduced to a higher degree in comparison to ablation: 21.0 mmHg [P < 0.001, 95% confidence interval -30.7; -11.3], and 34.3 mmHg (P < 0.001, -49.1; -19.5) respectively. Those patients who received a myectomy had a lower probability of having moderate mitral regurgitation (odds ratio = 0.18, P = 0.054). Patients after septal myectomy were more likely to be NYHA functional class I (80.4%), whereas patients after ablation were more likely to be NYHA functional class III (48%). Both groups continued with beta-blocker therapy, but disopyramide could be discontinued after the myectomy in more cases (20%–36% vs 59%–1.3%; P < 0.001), and there was a tendency to discontinue calcium channel blockers (48%–16% vs 15.4–3.8%; P = 0.054).

CONCLUSIONS

After adjustment using preprocedural gradients and EuroSCORE II, myectomy achieves greater reduction in left ventricular outflow tract gradients compared to septal ablation.
Derived Equivalence for Elliptic K3 Surfaces and Jacobians
Authors: Meinsma Reinder , Shinder Evgeny
Published: April 2024

We present a detailed study of elliptic fibrations on Fourier-Mukai partners of K3 surfaces, which we call derived elliptic structures. We fully classify derived elliptic structures in terms of Hodge-theoretic data, similar to the Derived Torelli Theorem that describes Fourier-Mukai partners. In Picard rank two, derived elliptic structures are fully determined by the Lagrangian subgroups of the discriminant group. As a consequence, we prove that for a large class of Picard rank 2 elliptic K3 surfaces all Fourier-Mukai partners are Jacobians, and we partially extend this result to non-closed fields. We also show that there exist elliptic K3 surfaces with Fourier-Mukai partners, which are not Jacobians of the original K3 surface. This gives a negative answer to a question raised by Hassett and Tschinkel.