bluuebunny/crossref_metadata_2025 huggingface dataset:
Tuning of electronic, optical and lipophilic behaviours of adamantane through various substitutions
Authors: R Aravindhan , Hu Jianping , Momeen M Ummal
Published: January 2025

Successive tuning of electronic, optical and lipophilic characteristics of adamantane molecules are obtained by various halogen substitutions at bridgehead and bridge positions of adamantane. In accordance with this, surface passivated halo adamantanes and dodecahalo adamantanes exhibit impressive tuning of transport properties. In all molecular complexes, electrophilicity and molecular polarizability show progressive growth from fluorine to iodine whereas vertical excitation energies of molecules also follow the same trend. Prominent sigma holes are observed on the outer lobe of bromine and iodine in most of the cases. High hydrophobicity and lipophilicity of the adamantane has a prominent application in medicinal chemistry as a lipophilic bullet for a drug. Through halogen substitution this is more significant in both electropositive and electronegative binding sites exhibited by the anisotropic charge distribution of the halogen.
Experimental investigation of CF8 stainless steel impeller quality using PLA-based fused deposition modeling-assisted investment casting
Authors: Shah Margi , Patel Dhiren , Pande Sarang , Abidi Mustufa Haider , Alasim Fahad
Published: January 2025

The conventional Investment Casting (IC) process is extensively used for manufacturing parts with intricate shapes and complex geometries. However, its drawbacks include long cycle times and costly tooling, making it ideal for mass production but inefficient for frequent design changes, small batch production, or customized products. To address these challenges, a novel hybrid method known as Fused Deposition Modeling Assisted Investment Casting (FDMAIC) has been developed. In FDMAIC, the wax pattern is replaced by an FDM-printed pattern, while all other steps follow the conventional IC process. In this study, a semi-open impeller for a centrifugal pump was produced using FDMAIC, with Polylactic Acid (PLA) as the pattern material and CF8 for casting. Dimensional accuracy and surface roughness, key indicators of quality, were evaluated at both the printing and casting stages. Critical dimensions such as outer and inner diameters, shroud and blade thicknesses, and total height were measured, along with surface roughness at the shroud and blade surfaces. In the final cast, maximum dimensional deviation was observed in Outer diameter(−2.408 mm), and minimum dimensional deviation was observed in total height(−0.169 mm). The surface roughness values obtained at the shroud and blade surface of the final cast were 4.64 μm 6.67 μm, respectively. Microstructure and hardness testing were also performed on the FDMAIC impeller to validate the process. The results provide detailed insights into the feasibility of FDMAIC and suggest areas for further improvement.
Preparation and flame retardancy of an Al2O3 infiltration layer on polycarbonate surface
Authors: Ren Shibo , Xu Jianlin , Niu Lei , Yang Penghui
Published: January 2025

In this study, the surface flame retardancy of polycarbonate (PC) was improved and the impact of flame retardants on the substrate were minimized by pre-mixing Al2O3 particles with dichloromethane, an infiltration promoter, to form a suspension, and then treating PC with the suspension to form an Al2O3 infiltration layer. For this layer, its structure and composition were characterized, its flame retardancy was evaluated, and its flame retardancy mechanism was investigated. The characterization results confirmed that an Al2O3 infiltration layer was successfully prepared on the PC surface under the aid of dichloromethane and that the involvement of dichloromethane induced certain microscopic pores and voids in the PC, with some dichloromethane remaining within the surface infiltration layer. The surface Al2O3 infiltration layer mainly served as a condensed-phase flame retardant. The infiltration layer prepared using a suspension with a dichloromethane-to-Al2O3 mass ratio of 24:1 not only exhibited a good overall performance but also achieved the best improvement in the PC flame retardancy, such as an increase in the vertical burning rating from HB to V-0, as well as the LOI increased from 24 to 31.3, and a 35% reduction in the peak heat release rate compared to those of pure PC.
Cultural and creative industries development on cities: a perspective from urban innovation ecosystems
Authors: Dong Yue , Zhang Qingfeng
Published: January 2025

As an emerging economic form, the cultural and creative industries (CCI) have gradually become a key force in driving urban economic transformation and enhancing urban competitiveness. In the knowledge economy, the CCI are producers of cultural content and vital sources of innovative resources. This study explores CCI’s role within urban innovation ecosystems and their impact on cities. The research employs a combination of theoretical model construction and empirical analysis. It begins with a literature review and theoretical analysis to construct a relationship model between the CCI and urban innovation ecosystems, as well as a hypothetical model of the impact of the CCI on cities. An online survey was conducted to collect data, and the results validate the models’ effectiveness. The findings indicate that the CCI significantly promotes urban development. They directly drive the economic transformation and upgrading of cities and indirectly foster sustainable urban development by optimizing the innovation environment and enhancing the vitality of innovation entities. The CCI plays a crucial role in urban innovation ecosystems, enhancing urban innovation capacity and competitiveness through interactions. The system reveals the pathways through which the CCI functions within urban innovation ecosystems and offers corresponding development recommendations. It provides theoretical support and practical references for promoting the synergy between the CCI and urban development.
GPM-based analysis of vertical structure of typical precipitation during 2020 extra-long Meiyu season in Northern Zhejiang
Authors: Du Shuang , Wu Bin , Yin Hao , Shen Yian
Published: January 2025

The Meiyu season during 2020 in China was an extra-long flood season, in particular, the northern region of Zhejiang experienced long duration of precipitation and frequent heavy rainfall processes. In this study, we selected three typical precipitation cases during 2020 ultra-long Meiyu season, using dual frequency spaceborne radar data (GPM DPR) revealed the characteristics of precipitation macro-micro vertical structure characteristics at different life cycle. In the development stage, the large-value area of particle diameter (≥ 2 mm) between the height of 5 km and ground level corresponds to heavy rain zone, while a lower particle number density for the same particle size results in temporarily reduced precipitation efficiency. In the maturity stage, large-scale water condensate particles remain between the height of 5 and 6 km, and cloud anvil structures are identifiable in radar reflectivity factor profiles. In the dissipation stage, with the weakness of the dynamic weather conditions, the height of the radar echo and particle distribution shifts closer to the surface layer. Further analysis of the effect of water condensate particles on surface rainfall intensity shows that the changes from development to maturity and dissipation stages in convective precipitation are primarily determined by the hydrometeor particle concentration during the Meiyu season. For stratiform precipitation, it is more closely related to particle concentration parameters. Even when particle concentration and size are high, the absence of strong dynamic mechanisms to trigger latent heat release means raindrops do not continue to grow, resulting in minimal precipitation.
Development of Eco-friendly CQDs/TiO2 nanocomposite for enhanced photocatalytic degradation of methyl orange dye
Authors: Prabhakaran Prasanna Kumar , Balu Surendar , Sridharan Gokul , Ganapathy Dhanraj , Sundramoorthy Ashok K
Published: January 2025

This research explores the photocatalytic degradation of methyl orange (MO) dye using a novel TiO2/biowaste-derived carbon quantum dots (CQDs) composite under visible light. The TiO2, biowaste-derived CQDs, and TiO2/CQDs composite were synthesized via a hydrothermal method and characterized using UV-visible spectroscopy (UV–vis), Fourier-transform infrared spectroscopy (FTIR), x-ray diffraction (XRD), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). TEM analysis revealed a uniform distribution of CQDs within the TiO2 matrix, confirming the successful integration of CQDs into the nanocomposite structure. The incorporation of CQDs significantly reduced the band gap of the composite, enhancing its photocatalytic activity under visible light. Photocatalytic experiments, conducted with a 300 W Xe lamp as the light source, utilized a 20 mg catalyst dosage for a 15 ppm MO solution. The TiO2/CQDs composite demonstrated an outstanding degradation efficiency of 85% within 130 min, following a pseudo-first-order kinetic model with a rate constant of k = 0.01353 min−1. In comparison, pure TiO2 and CQDs achieved degradation efficiencies of 61% and 19%, respectively, under the same conditions. These findings underline the potential of TiO2/biowaste-derived CQDs composites as a sustainable, eco-friendly approach for wastewater treatment and environmental remediation through visible-light-driven photocatalysis.
Methodology for designing low-cost robots with parallel kinematics
Authors: Dimitrova Reneta , Nikolov Stiliyan , Tsolov Stanislav , Dimitrov Slav
Published: January 2025

In this paper, a methodology for the design of low-cost robots with parallel kinematics is proposed, involving ten stages. The methodology offers an alternative to the classic methods used in the design of robots with parallel kinematics, taking into account the capabilities of modern CAD/CAE systems, which is of particular importance due to the limited financial resources for designing and manufacturing low-cost robots with parallel kinematics. The main classical methods used in the design of robots with parallel kinematics are described, at the individual stages of the proposed methodology and the possibilities for accelerated solving of the relevant tasks with the use of CAD/CAE systems. Recommendations are given for the methods and means used at each of the proposed stages. The proposed methodology can serve as a basis for defining the main steps performed when designing robots with parallel kinematics. The developed methodology has been tested for the design of a low-cost robot with parallel kinematics, with a positioning accuracy of ± 0.1 mm. The results of the application of the proposed methodology have been analyzed.
Equivalent lossy redwood circuits for high-frequency piezoelectric array elements
Authors: Reskal Hayat , Bybi Abdelmajid , Boujenoui Anouar , Elmaimouni Lahoucine
Published: January 2025

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

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

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

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

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

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

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

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

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

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

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

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.

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.
Mate-Pair Sequencing Enables Identification and Delineation of Balanced and Unbalanced Structural Variants in Prenatal Cytogenomic Diagnostics
Authors: Qian Jicheng , Wang Huilin , Liang Hailei , Zheng Yuting , Yu Mingyang , Tse Wing Ting , Kwan Angel Hoi Wan , Wong Lo , Wong Natalie Kwun Long , Wah Isabella Yi Man , Lau So Ling , Hui Shuk Yi Annie , Chau Matthew Hoi Kin , Chen Xiaoyan , Zhang Rui , Poon Liona C , Leung Tak Yeung , Liu Pengfei , Choy Kwong Wai , Dong Zirui
Published: January 2025

Background

Mate-pair sequencing detects both balanced and unbalanced structural variants (SVs) and simultaneously informs in relation to both genomic location and orientation of SVs for enhanced variant classification and clinical interpretation, while chromosomal microarray analysis (CMA) only reports deletion/duplication. Herein, we evaluated its diagnostic utility in a prospective back-to-back prenatal comparative study with CMA.

Methods

From October 2021 to September 2023, 426 fetuses with ultrasound anomalies were prospectively recruited for mate-pair sequencing and CMA in parallel for prenatal genetic diagnosis. Balanced/unbalanced SVs and regions with absence of heterozygosity (AOH) were detected and classified independently, and comparisons were made between mate-pair sequencing and CMA to assess concordance. In addition, novel SVs were investigated for potential RNA perturbations using cultured cells, whenever available.

Results

Mate-pair sequencing and CMA successfully yielded results for all 426 fetuses without the need for cell culturing. In addition, mate-pair sequencing identified 19 cases with aneuploidies, 16 cases with pathogenic simple deletions/duplications, and 5 cases with pathogenic translocations/insertions, providing a 25% incremental diagnostic yield compared to CMA (9.4%, 40/426 vs 7.6%, 32/426). Furthermore, by identifying the location and orientation of SVs, mate-pair sequencing improved the variant interpretation and/or follow-up approach for 40.0% (12) of the 30 cases with likely clinically significant deletions/duplications reported by CMA. Lastly, both platforms reported 3 cases (3/426) with multiple regions of AOH likely attributable to parental consanguinity.

Conclusions

Mate-pair sequencing detects additional balanced/unbalanced SVs and improves variant interpretation in comparison to CMA, indicating its potential to serve as a comprehensive prenatal cytogenomic diagnostic method.
Innovations in Short-Read Sequencing Technologies and Their Applications to Clinical Genomics
Authors: Polonis Katarzyna , Blommel Joseph H , Hughes Andrew E O , Spencer David , Thompson Joseph A , Schroeder Molly C
Published: January 2025

Background

Massively parallel sequencing (MPS) of nucleic acids has been a transformative technology for basic and applied genomic science, increasing efficiencies and decreasing costs to enable studies of unprecedented scope and impact. In clinical settings, these technological and scientific advances have led to the development of tests that are increasingly fast, comprehensive, and more frequently employed. Practitioners of genomic medicine have applied these tools across clinical settings, including diagnosis of inherited disorders and cancers and infectious disease detection and surveillance. In recent years, the commercial marketplace for MPS sequencers and reagents has been dominated by a few companies. The growing demand for sequencing has led to the recent emergence of several new sequencing platforms with techniques that may provide alternatives or improvements to existing workflows or allow the adoption of sequencing workflows in new settings. Clinical genomics laboratories will evaluate these platforms from a unique perspective, focusing on how technological advancements can improve patient care.

Content

This review describes short-read sequencing platforms provided by Illumina, Element Biosciences, MGI, PacBio, Singular Genomics, Thermo Fisher Scientific, and Ultima Genomics. This review discusses their innovative approaches, principles, workflows, and applications.

This review aims to inform laboratory geneticists, clinicians, and researchers about emerging short-read technologies and their applications in clinical genomics. By highlighting their principles and potential contributions, we aim to assist laboratories in selecting suitable solutions for their sequencing needs considering key factors such as applications, throughput, and integration with existing laboratory workflows.
Detection of Clinically Relevant Monogenic Copy-Number Variants by a Comprehensive Genome-Wide Microarray with Exonic Coverage
Authors: Chau Matthew Hoi Kin , Anderson Stephanie A , Song Rodger , Cooper Lance , Ward Patricia A , Yuan Bo , Shaw Chad , Stankiewicz Paweł , Cheung Sau Wai , Vossaert Liesbeth , Wang Yue , Owen Nichole M , Smith Janice , Bacino Carlos A , Schulze Katharina V , Bi Weimin
Published: January 2025

Background

Disease-causing copy-number variants (CNVs) often encompass contiguous genes and can be detected using chromosomal microarray analysis (CMA). Conversely, CNVs affecting single disease-causing genes have historically been challenging to detect due to their small sizes.

Methods

A custom comprehensive CMA (Baylor College of Medicine - BCM v11.2) containing 400k probes and featuring exonic coverage for >4200 known or candidate disease-causing genes was utilized for the detection of CNVs at single-exon resolution. CMA results across a consecutive clinical cohort of more than 13 000 patients referred for genetic investigation at Baylor Genetics were examined. The genomic characteristics of CNVs impacting single protein-coding genes were investigated.

Results

Pathogenic or likely pathogenic (P/LP) CNVs (n = 190) affecting single protein-coding genes were detected in 188 patients, accounting for 9.9% (188/1894) of patients with P/LP CMA findings. The P/LP monogenic CNVs accounted for 9.2% (190/2058) of all P/LP nuclear CNVs detected by CMA. A total of 57.9% (110/190) of P/LP monogenic CNVs were smaller than 50 kb in size. Single exons were affected by 26.3% (50/190) of P/LP monogenic CNVs while 13.2% (25/190) affected 2 exons. CNVs were detected across 107 unique genes associated with predominantly autosomal dominant (AD) and X-linked (XL) conditions but also contributed to autosomal recessive (AR) conditions.

Conclusions

CMA with exon-targeted coverage of disease-associated genes facilitated the detection of small CNVs affecting single protein-coding genes, adding substantial clinical sensitivity to comprehensive CNV investigation. This approach resolved monogenic CNVs associated with autosomal and X-linked monogenic etiologies and yielded multiple significant findings. Monogenic CNVs represent an underrecognized subset of disease-causing alleles for Mendelian disorders.
Integrative Assessment of Total and Intact HIV-1 Reservoir by a 5-Region Multiplexed Rainbow DNA Digital PCR Assay
Authors: Delporte Mareva , Lambrechts Laurens , Blomme Evy E , van Snippenberg Willem , Rutsaert Sofie , Verschoore Maxime , De Smet Evelien , Noppe Ytse , De Langhe Nele , De Scheerder Marie-Angélique , Gerlo Sarah , Vandekerckhove Linos , Trypsteen Wim
Published: January 2025

Background

Persistent latent reservoirs of intact HIV-1 proviruses, capable of rebounding despite suppressive antiretroviral therapy (ART), hinder efforts towards an HIV-1 cure. Hence, assays specifically quantifying intact proviruses are crucial to assess the impact of curative interventions. Two recent assays have been utilized in clinical trials: intact proviral DNA assay (IPDA) and quadruplex quantitative PCR (Q4PCR). While IPDA is more sensitive due to amplifying short fragments, it may overestimate intact fractions by relying only on quantification of 2 proviral regions. Q4PCR samples 4 proviral regions, yet is sequencing-based, favoring amplification of shorter, hence non-intact, proviral sequences.

Methods

Leveraging digital PCR (dPCR) advancements, we developed the “Rainbow” 5-plex proviral HIV-1 DNA assay. This first-in-its-kind assay was evaluated using standard materials and samples from 83 people living with HIV-1, enabling simultaneous quantification of both total and intact HIV-1 DNA levels. HIV proviral unique molecular identifier (UMI)-mediated long-read sequencing (HIV-PULSE) was used to validate the specificity of the Rainbow HIV-1 DNA assay.

Results

The Rainbow assay proved equally sensitive but more specific than IPDA and is not subjected to bias against full-length proviruses, enabling high-throughput quantification of total and intact reservoir size. The near full-length sequences allowed validation of the Rainbow specificity and the design of personalized Rainbow primer/probe sets, which enabled the detection of intact HIV-1 DNA.

Conclusions

This innovation offers potential for targeted evaluation and monitoring of potential rebound-competent reservoirs, contributing to HIV-1 management and cure strategies. ClinicalTrials.gov Registration Numbers: NCT04553081, NCT04305665.
Inferring the Demographic History of Aye-Ayes (Daubentonia madagascariensis) from High-Quality, Whole-Genome, Population-Level Data
Authors: Terbot John W , Soni Vivak , Versoza Cyril J , Pfeifer Susanne P , Jensen Jeffrey D
Published: January 2025

The nocturnal aye-aye, Daubentonia madagascariensis, is one of the most elusive lemurs on the island of Madagascar. The timing of its activity and arboreal lifestyle has generally made it difficult to obtain accurate assessments of population size using traditional census methods. Therefore, alternative estimates provided by population genetic inference are essential for yielding much needed information for conservation measures and for enabling ecological and evolutionary studies of this species. Here, we utilize genomic data from 17 individuals—including 5 newly sequenced, high-coverage genomes—to estimate this history. Essential to this estimation are recently published annotations of the aye-aye genome which allow for variation at putatively neutral genomic regions to be included in the estimation procedures, and regions subject to selective constraints, or in linkage to such sites, to be excluded owing to the biasing effects of selection on demographic inference. By comparing a variety of demographic estimation tools to develop a well-supported model of population history, we find strong support for two demes, separating northern Madagascar from the rest of the island. Additionally, we find that the aye-aye has experienced two severe reductions in population size. The first occurred rapidly, ∼3,000 to 5,000 years ago, and likely corresponded with the arrival of humans to Madagascar. The second occurred over the past few decades and is likely related to substantial habitat loss, suggesting that the species is still undergoing population decline and remains at great risk for extinction.
Squirt flow in a tight sandstone: an interlaboratory study
Authors: Ógúnsàmi Abdulwaheed R , Jackson Ian , Pimienta Lucas , Fortin Jérôme
Published: January 2025

In the spirit of interlaboratory benchmarking of related techniques, we have re-examined the seismic-frequency mechanical properties of a low-porosity Wilkeson sandstone specimen tested in axial stress oscillation under water-saturated conditions by Pimienta et al. The same specimen has been newly tested at periods of 1–1000 s under dry and argon-, water- and glycerine-saturated conditions by torsional and flexural oscillation methods, allowing direct measurement of the shear modulus G and Young's modulus E and associated strain-energy dissipations. The results show a steady increase of G and E for the dry specimen with increasing pressure, indicative of progressive closure of the compliant intergranular contacts. Under argon- and water-saturated conditions, the measured moduli differ only marginally from those for dry conditions, without any significant stiffening or dispersion, suggesting that such measurements probe the saturated-isobaric regime. In marked contrast, glycerine saturation results in substantially higher and frequency-dependent moduli, along with frequency-dependent dissipation. We attribute this behaviour to the squirt flow transition with decreasing frequency from the saturated-isolated to the saturated-isobaric regime, modelled with a log-normal distribution of relaxation times (broader than the Debye peak of the standard anelastic solid) superimposed upon a monotonically frequency-dependent background. Although there are differences in detail, these findings corroborate those of Pimienta et al. for the same material tested in axial stress oscillation to higher frequencies under water-saturated conditions. Taken together, the two studies thus provide robust support for theoretical models of squirt flow dispersion and dissipation, occurring at frequencies between those of conventional ultrasonic wave-propagation laboratory methods and those of seismic exploration of the shallow crust.
Evaluating the Bouguer layer approximation method in modelling ocean effects on gravity changes induced by earthquakes
Authors: Zhao Xinyu , Zhou Xin
Published: January 2025

Ocean water mass redistributions triggered by earthquakes result in notable changes in the gravity potential field. These oceanic effects can be quantified using two primary methods: solving the sea level equation (SSLE) and the Bouguer layer approximation (BLA). The SSLE accounts for both the direct attraction and the elastic loading response induced by the perturbed ocean water during an earthquake. In contrast, the BLA disregards the elastic loading effect and utilizes the Bouguer correction formula to estimate the impact of direct attraction. In this study, we evaluate the effectiveness of the BLA by comparing it with the SSLE in estimating both coseismic and post-seismic gravity field changes from simulation test and three realistic events, the 2004 Sumatra Mw 9.2, the 2011 Tohoku-Oki Mw 9.0 and the 2014 Iquique Mw 8.1. Our simulations involve a thrust fault and a strike-slip fault beneath a uniform ocean covering, while the Sumatra, the Tohoku-Oki and the Iquique events are under realistic sea-land distribution. Our findings reveal minimal discrepancies between the BLA and SSLE, suggesting that the BLA is effective in correcting oceanic effects for gravity changes of both long and short wavelengths.