bluuebunny/crossref_metadata_2025_split huggingface dataset:
Equivalent lossy redwood circuits for high-frequency piezoelectric array elements
Authors: Reskal Hayat , Bybi Abdelmajid , Boujenoui Anouar , Elmaimouni Lahoucine 
Published: January 2025

Abstract
Ultrasonic transducer arrays in medical imaging are typically composed of multiple piezoelectric elements. This research focuses on modeling high-frequency piezoelectric slender bars, along with their front and back matching layers, using 1D and 2D Redwood equivalent circuits. The entire ultrasonic transducer under examination includes an active piezoelectric component (Motorola 3203HD), two front acoustic matching layers (ML#107 and ML#103), and a backing material designed for absorption. The novelty of this work consists in proposing an accurate Lossy 2D Redwood model that accounts for various dissipations, including piezoelectric, dielectric, and mechanical losses, as well as the thickness and width modes and the coupling between them. Additionally, when building our lossy transmission lines, the frequency change of the acoustic attenuation is taken into account. The proposed 2D model is implemented in LTspice software to analyze the effects of the front and back matching layers on the transducer’s electromechanical performance, specifically its electrical impedance. The simulation results align well with existing literature, confirming the validity of the proposed approach. The advantages of the proposed model are its ease of use, simplicity, and, most importantly, its shorter computation time when compared to the numerical models that are frequently used in the literature. The proposed Lossy 2D Redwood model is anticipated to prove useful for modeling comprehensive transducer arrays and analyzing crosstalk phenomena, which will be explored in future work.
Performance and emission characteristics of domestic LPG gas burners with hydrogen integration
Authors: Pillai Sidharth K , Rajpara Parag , Subramonia Pillai Madhushankar , Khan M M , Kolhe P S , Balusamy Saravanan 
Published: January 2025

Abstract
Domestic gas burners are a significant source of indoor air pollution and contribute substantially to household energy consumption. While transitioning to carbon-free fuels, such as hydrogen, presents considerable safety challenges, blending hydrogen with conventional fuels can improve combustion efficiency and reduce emissions. However, factors like the differences in the Wobbe index, loading height, power input, and fuel blending complicate understanding the aerated burner performance. This is particularly relevant for large establishments like restaurants and canteens, where hydrogen blending can have a notable impact. This study evaluates four burner designs—commercial (A), straight holes (B), slots (C), and swirl (D)—across thermal inputs (0.8–1.6 kW), with a focus on the swirl burner using hydrogen blends (0%, 34%, and 52% by volume) and varying loading heights (5 mm, 10 mm, and 15 mm). Straight hole (B) and swirl (D) burners were 3D-printed using stainless steel metal powder, while the slot (C) burner was machined. Key performance metrics such as flame behavior, thermal efficiency, pressure drop, and CO emissions were analyzed. Improving primary aeration by reducing flow resistance and enhancing secondary aeration through swirl action resulted in better flame-load interaction and minimized heat loss. The slot burner (C) achieved a thermal efficiency of 63.5%, while the swirl burner (D) reached 65% efficiency at a 10 mm height. The swirl burner maintained high efficiency with up to 52% hydrogen by volume across a wide range of operational conditions, with some exceptions. Additionally, the use of hydrogen eliminated soot emissions. Optimal performance occurred at a 10 mm loading height, with stable efficiency and lower emissions across various power inputs and hydrogen blends. The complex interactions between primary aeration, secondary mixing, and flame-load dynamics during hydrogen blending require thorough evaluation before incorporating hydrogen into aerated LPG burners.
Impact of Synchronized Radiofrequency and High-intensity Facial Electrical Stimulation on Facial Muscles and the Superficial Fascial System in the Midface
Authors: Frank Konstantin , Kaye Kai O , Casabona Gabriela , Glaue Emily , Zeng Rui , Lim Ting Song , Brebant Vanessa , Prantl Lukas , Moellhoff Nicholas , Cotofana Sebastian 
Published: January 2025

Abstract

Background
Midfacial aging involves skeletal changes, muscle weakening, and fat redistribution, resulting in volume loss, skin sagging, and deepened nasolabial folds. High-intensity facial electrical stimulation (HIFES) combined with radiofrequency (RF) is a novel noninvasive method for addressing these changes by enhancing muscle mass and remodeling subcutaneous tissue.

Objectives
The goal of this study was to assess the efficacy of HIFES and synchronized RF in improving midfacial aesthetics, specifically muscle thickness, skin displacement, and facial volume.

Methods
This prospective, nonrandomized study included 37 participants who underwent 4 HIFES and RF treatments over 24 weeks. Assessments at baseline, 4, 16, and 24 weeks were performed with ultrasound imaging, electromyography (EMG), 3-dimensional surface imaging, and the Modified Fitzpatrick Wrinkle Scale. A related porcine study evaluated the treatment's histological effects.

Results
Zygomaticus major muscle thickness increased from 2.06 mm to 2.80 mm, with a 39.3% rise in EMG signal strength, indicating improved muscle function. Skin displacement analysis revealed horizontal (0.90 mm) and vertical (1.01 mm) shifts, particularly laterally. Midface volume increased by 1.43 cm³ at 24 weeks. The porcine study confirmed increased muscle fiber size, myonucleus count, and mass density, aligning with human results.

Conclusions
HIFES and synchronized RF treatments significantly improved muscle thickness, skin displacement, and facial volume, effectively rejuvenating the midface. These clinical findings, supported by histological evidence, suggest a promising noninvasive approach for facial rejuvenation. Further randomized studies are needed to confirm these results and assess long-term effects.

Level of Evidence: 4 (Therapeutic)
DrugAssist: a large language model for molecule optimization
Authors: Ye Geyan , Cai Xibao , Lai Houtim , Wang Xing , Huang Junhong , Wang Longyue , Liu Wei , Zeng Xiangxiang 
Published: January 2025

Abstract
Recently, the impressive performance of large language models (LLMs) on a wide range of tasks has attracted an increasing number of attempts to apply LLMs in drug discovery. However, molecule optimization, a critical task in the drug discovery pipeline, is currently an area that has seen little involvement from LLMs. Most of existing approaches focus solely on capturing the underlying patterns in chemical structures provided by the data, without taking advantage of expert feedback. These non-interactive approaches overlook the fact that the drug discovery process is actually one that requires the integration of expert experience and iterative refinement. To address this gap, we propose DrugAssist, an interactive molecule optimization model which performs optimization through human–machine dialogue by leveraging LLM’s strong interactivity and generalizability. DrugAssist has achieved leading results in both single and multiple property optimization, simultaneously showcasing immense potential in transferability and iterative optimization. In addition, we publicly release a large instruction-based dataset called ‘MolOpt-Instructions’ for fine-tuning language models on molecule optimization tasks. We have made our code and data publicly available at https://github.com/blazerye/DrugAssist, which we hope to pave the way for future research in LLMs’ application for drug discovery.
Fast and exact gap-affine partial order alignment with POASTA
Authors: van Dijk Lucas R , Manson Abigail L , Earl Ashlee M , Garimella Kiran V , Abeel Thomas 
Published: January 2025

Abstract

Motivation
Partial order alignment is a widely used method for computing multiple sequence alignments, with applications in genome assembly and pangenomics, among many others. Current algorithms to compute the optimal, gap-affine partial order alignment do not scale well to larger graphs and sequences. While heuristic approaches exist, they do not guarantee optimal alignment and sacrifice alignment accuracy.

Results
We present POASTA, a new optimal algorithm for partial order alignment that exploits long stretches of matching sequence between the graph and a query. We benchmarked POASTA against the state-of-the-art on several diverse bacterial gene datasets and demonstrated an average speed-up of 4.1× and up to 9.8×, using less memory. POASTA’s memory scaling characteristics enabled the construction of much larger POA graphs than previously possible, as demonstrated by megabase-length alignments of 342 Mycobacterium tuberculosis sequences.

Availability and implementation
POASTA is available on Github at https://github.com/broadinstitute/poasta.
The interleukin-6 signal transducer receptor subunit is required for optimal in vitro bovine embryo development
Authors: Speckhart Savannah L , Pollock Abigayle B , Alward Kayla J , Farrell Kayla , Oliver Mary A , Lee Kiho , Biase Fernando H , Ealy Alan D 
Published: January 2025

Abstract
This work explored whether bovine embryo development relies on signaling from the interleukin-6 (IL6) cytokine family. This was accomplished by interrupting IL6 signal transducer (IL6ST), the common beta-subunit receptor used by the IL6 family. One series of studies cultured in vitro–produced embryos with SC144, a pharmacological IL6ST inhibitor. Providing the inhibitor at a concentration that partially diminished IL6ST signaling reduced development to the 16-cell and blastocyst stages and reduced inner-cell-mass cell numbers. Inhibitor concentrations that completely blocked IL6ST signaling prevented blastocyst development. Another series of studies used CRISPR-Cas9 to disrupt IL6ST. Two electroporation approaches were used to introduce guide RNAs and Cas9 protein into one-cell in vitro–produced embryos. Editing efficiency was ≥82%. Targeting IL6ST did not affect cleavage but reduced development to the 16-cell and blastocyst stages. A reduction in inner-cell-mass cell numbers was detected, and disorganization of the inner cell mass was observed in approximately one-half of the IL6ST-targeted blastocysts. These observations indicate that embryo-derived IL6 family members that signal through IL6ST are needed to support normal in vitro bovine embryo development. These signals are needed by the 16-cell stage and for inner-cell-mass cell development at the blastocyst stage. There is also evidence that these signals support the overall cellular organization of the blastocyst.
Cochlear implantation in adults with acquired single-sided deafness improves cortical processing and comprehension of speech presented to the non-implanted ears: a longitudinal EEG study
Authors: Chen Ya-Ping , Neff Patrick , Leske Sabine , Wong Daniel D E , Peter Nicole , Obleser Jonas , Kleinjung Tobias , Dimitrijevic Andrew , Dalal Sarang S , Weisz Nathan 
Published: January 2025

Abstract
Former studies have established that individuals with a cochlear implant (CI) for treating single-sided deafness experience improved speech processing after implantation. However, it is not clear how each ear contributes separately to improve speech perception over time at the behavioural and neural level. In this longitudinal EEG study with four different time points, we measured neural activity in response to various temporally and spectrally degraded spoken words presented monaurally to the CI and non-CI ears (5 left and 5 right ears) in 10 single-sided CI users and 10 age- and sex-matched individuals with normal hearing. Subjective comprehension ratings for each word were also recorded. Data from single-sided CI participants were collected pre-CI implantation, and at 3, 6 and 12 months after implantation. We conducted a time-resolved representational similarity analysis on the EEG data to quantify whether and how neural patterns became more similar to those of normal hearing individuals. At 6 months after implantation, the speech comprehension ratings for the degraded words improved in both ears. Notably, the improvement was more pronounced for the non-CI ears than the CI ears. Furthermore, the enhancement in the non-CI ears was paralleled by increased similarity to neural representational patterns of the normal hearing control group. The maximum of this effect coincided with peak decoding accuracy for spoken-word comprehension (600–1200 ms after stimulus onset). The present data demonstrate that cortical processing gradually normalizes within months after CI implantation for speech presented to the non-CI ear. CI enables the deaf ear to provide afferent input, which, according to our results, complements the input of the non-CI ear, gradually improving its function. These novel findings underscore the feasibility of tracking neural recovery after auditory input restoration using advanced multivariate analysis methods, such as representational similarity analysis.
Organoids in skin wound healing
Authors: Wang Zitong , Zhao Feng , Lang Hongxin , Ren Haiyue , Zhang Qiqi , Huang Xing , He Cai , Xu Chengcheng , Tan Chiyu , Ma Jiajie , Duan Shu , Wang Zhe 
Published: January 2025

Abstract
Stem cells (SCs) can self-replicate and differentiate into multiple lineages. Organoids, 3D cultures derived from SCs, can replicate the spatial structure and physiological characteristics of organs in vitro. Skin organoids can effectively simulate the physiological structure and function of skin tissue, reliably restoring the natural skin ecology in various in vitro environments. Skin organoids have been employed extensively in skin development and pathology research, offering valuable insights for drug screening. Moreover, they play crucial roles in skin regeneration and tissue repair. This in-depth review explores the construction and applications of skin organoids in wound healing, with a focus on their construction process, including skin appendage integration, and significant advancements in wound-healing research.
Clinical predictors of disease severity in oral lichen planus
Authors: P Unnikrishnan Sreedevi , Boggon Janice , Mclaughlin Bernice , Cruickshank Maggie E , Abu-Eid Rasha , Hijazi Karolin 
Published: January 2025

Abstract

Background
The limited understanding of factors influencing the disease progression of oral lichen planus (OLP) poses challenges in delivering effective and personalised treatment for this condition, known to increase the risk of oral cancer and adversely impact patient quality of life.

Objective
This study aimed to systematically identify clinical predictors of disease severity in OLP patients.

Methods
This cross-sectional and single-site prospective study was conducted between December 2021 and February 2024 in the Departments of Oral Medicine and Oral & Maxillofacial Surgery, Aberdeen Royal Infirmary. Patients presenting with OLP aged 18 years or older diagnosed using Van der Meij and Van der Waal criteria were eligible to the study. Out of a total of 270 eligible OLP patients presenting consecutively to the outpatient clinics during the study period, 89 patients agreed to participate and were enrolled into the study. Participants demographic and relevant clinical data, namely medical history, smoking status, alcohol consumption, perceived stress levels, oral hygiene status and haematologic and biochemical parameters, including full blood count, haematinics, vitamin D were recorded. The outcome measure was OLP disease severity measured as the Oral Disease Severity Score (ODSS), Gingival ODSS and Reticular/hyperkeratotic, Erosive/erythematous, Ulcerative (REU scoring system).

Results
A total of 89 participants were recruited into the study. The median [IQRs] age of the study population was 66 [58 to 73] years, and 65 (73%) patients were females. The median total ODSS score was 10 (range: 0-44). After adjustment for confounding factors, patients with lichen planus affecting skin or other mucosal sites had a 5.76-unit higher OLP severity score (B=5.76, 95% CI=.74-10.78, P=.025) than those without extraoral involvement as measured by ODSS. Patients with insufficient vitamin D exhibited 5.49-unit increase in disease severity (B = 5.49, 95% CI = 1.13-9.84, P= 0.014) compared to those with adequate vitamin D levels.

Conclusions
This study identified the importance of cutaneous and/or genital lichen planus in phenotyping OLP disease severity. We also highlight the role of vitamin D as a significant predictor of disease severity of OLP, suggesting the importance of adequate vitamin D levels in lichen planus.
Single-crystal-to-single-crystal transformation based on ionophore-like transport
Authors: Ito Mizuki , Manabe Jun , Inoue Katsuya , Hirao Takehiro , Haino Takeharu , Akutagawa Tomoyuki , Takahashi Kiyonori , Nakamura Takayoshi , Nishihara Sadafumi 
Published: January 2025

Abstract
We have already reported that Li2([18]crown-6)3[Ni(dmit)2]2(H2O)4 crystals, which have an ion channel structure, can be reversibly converted to Ca([18]crown-6)[Ni(dmit)2]2(H2O)3 crystals by ion exchange while maintaining their single-crystal state. In this process, inorganic ions as well as crown ethers traverse in and out of the crystal. In this study, [18]crown-6-d4, a partially deuterated [18]crown-6, was used to investigate the behavior of inorganic ions and crown ethers during ion exchange and found that Li+-[18]crown-6 supramolecules could act as ionophores in the crystal.
Development of a Reference Standard to Assign Bacterial Versus Viral Infection Etiology Using an All-inclusive Methodology for Comparison of Novel Diagnostic Tool Performance
Authors: Allen Coburn , Deanehan J Kate , Dotan Yaniv , Eisenberg Matthew A , Fine Andrew M , Isenberg Jonathan , Kane Ann , Kirshner Dani , Lyons Todd W , Maor Yasmin , Neuberger Ami , Ostermayer Daniel G , Paz Sharona , Scheuerman Oded , Shiber Shachaf , Statler Victoria A , Stein Michal , Yakubov Renata , Yanai Shirly , Navon Roy , Kellerman Lior , Gottlieb Tanya M , Eden Eran 
Published: January 2025

Abstract

Background
Diagnostic test evaluation requires a reference standard. We describe an approach for creating a reference standard for acute infection using unrestricted adjudication and apply it to compare biomarker tools.

Methods
Adults and children with suspected acute infection enrolled in three prospective studies at emergency departments and urgent cares were included. Adjudicators, blinded to C-reactive protein, procalcitonin, and MeMed BV (MMBV), labeled each case (bacterial/viral/non-infectious/indeterminate). Initial adjudication involved 3 adjudicators. Reference standard cohorts were defined: Microbiologically confirmed (3/3 adjudicators concur with high confidence and a concordant microbiological finding), unanimous (3/3 adjudicators concur with high confidence), suspected (3/3 adjudicators concur with high/moderate confidence or 2/3 adjudicators concur with high confidence), and all-inclusive (remaining unlabeled cases were reviewed by up to 7 additional adjudicators until reaching a leading label).

Results
Among 1016 patients, 156 difficult-to-diagnose cases required over 3 adjudicators. The area under the receiver operating characteristic curve in the microbiologically confirmed (n = 427), unanimous (n = 565), suspected (n = 860), and all-inclusive (n = 1016) cohorts for MMBV were 0.98 (95% confidence interval .94–1.00), 0.98 (.95–1.00), 0.95 (.92–.98) and 0.90 (.87–.93), respectively, and for procalcitonin were 0.69 (.57–.81), 0.77 (.68–.86), 0.74 (.68–.80) and 0.70 (.65–.75), respectively. A delta in performance between MMBV and procalcitonin was maintained across the different cohorts.

Conclusions
Creating a reference standard that includes difficult-to-diagnose cases demands an approach to addressing diagnostic uncertainty in acute infections. Tool performance depends on the reference standard applied and decreases as the difficulty to diagnose increases, highlighting the importance of using the same reference standard when comparing tools.
Low-Pass Whole Genome Sequencing of Cell-Free DNA from Cerebrospinal Fluid: A Focus on Pediatric Central Nervous System Tumors
Authors: O’Halloran Katrina , Christodoulou Eirini , Paulson Vera A , Cole Bonnie L , Margol Ashley S , Biegel Jaclyn A , Leary Sarah E S , Lockwood Christina M , Crotty Erin E 
Published: January 2025

Abstract

Background
Cell-free DNA (cfDNA) technology has allowed for cerebrospinal fluid (CSF), a previously underutilized biofluid, to be analyzed in new ways. The interrogation of CSF-derived cfDNA is giving rise to novel molecular insights, particularly in pediatric central nervous system (CNS) tumors, where invasive tumor tissue acquisition may be challenging. Contemporary disease monitoring is currently restricted to radiographic surveillance by magnetic resonance imaging and CSF cytology to directly detect abnormal cells and cell clusters. Alternatively, cfDNA is often present in the CSF from pediatric patients with both malignant and nonmalignant CNS tumors and can be accessed by minimally invasive lumbar puncture and other CSF-liberating procedures, offering a promising alternative for longitudinal molecular disease analysis and surveillance.

Content
This review explores the use of low-pass whole genome sequencing (LP-WGS) to analyze cfDNA from the CSF of pediatric patients with CNS tumors. This platform is uniquely poised for the detection of tumors harboring copy number variants, which are prevalent in this population. The utility and sensitivity of LP-WGS as a clinical tool is explored and discussed in the context of alternative CSF liquid biopsy interrogation modalities, including nanopore sequencing and methylation array.

Summary
Analysis of CSF-derived cfDNA by LP-WGS has broad diagnostic, prognostic, and clinical implications for pediatric patients with CNS tumors. Careful interpretation of LP-WGS results may aid in therapeutic targeting of pediatric CNS tumors and may provide insight into tumor heterogeneity and evolution over time, without the need for invasive and potentially risky tissue sampling.