bluuebunny/crossref_metadata_2025_split huggingface dataset:
An audio-tactile interface based on dielectric elastomer actuators
Authors: Gratz-Kelly Sebastian , Krüger Tim , Rizzello Gianluca , Seelecke Stefan , Moretti Giacomo 
Published: January 2023

Abstract
This paper presents a concept of a dielectric elastomer actuator (DEA) user interface (smart button) that can sense a user’s touch and provide multi-sensory tactile and acoustic feedbacks through a single electrical input signal. The DEA relies on a multi-layer layout, in which a layer detects user-driven deformations (touches) via custom-built capacitance sensing electronics, and the remaining layers are used to provide actuation (audio-tactile feedbacks). Building upon a recently presented principle, combined tactile and acoustic feedbacks are produced by concurrently exciting different vibration modes of the same active membrane over different frequency ranges. An integrated demonstrator setup is presented, which includes a DEA, an acoustic enclosure, compact sensing and driving electronics. A characterization of the prototype is conducted, including an analysis of the sound pressure level, the force/stroke output at lower working frequencies, the ability to sense deformations with different profiles and produce combined audio-tactile outputs. Compared to previous works on multi-function DEAs, the system presented in this paper provides largely improved sensing performance (with lower working voltage) and features a deeper level of integration (with small-scale custom sensing electronics, and logics embedded onto scalable microcontrollers) and is thus specifically optimised for user-interaction applications. On this end, tests with users are presented here for the first time, which allowed evaluating the subjective perception of the interface’s feedbacks. By means of further optimisation and miniaturisation of the power/sensing electronics and structural components, the layout and multifunction DEA principle presented here might lead, in the future, to the development of DEA-based smart buttons for active surfaces, or portable/wearable user interfaces and communicators.
Closed-loop vasculature network design for bioprinting large, solid tissue scaffolds
Authors: Kumar Hitendra , Dixit Kartikeya , Sharma Rohan , MacDonald M Ethan , Sinha Niraj , Kim Keekyoung 
Published: January 2023

Abstract
Vascularization is an indispensable requirement for fabricating large solid tissues and organs. The natural vasculature derived from medical imaging modalities for large tissues and organs are highly complex and convoluted. However, the present bioprinting capabilities limit the fabrication of such complex natural vascular networks. Simplified bioprinted vascular networks, on the other hand, lack the capability to sustain large solid tissues. This work proposes a generalized and adaptable numerical model to design the vasculature by utilizing the tissue/organ anatomy. Starting with processing the patient’s medical images, organ structure, tissue-specific cues, and key vasculature tethers are determined. An open-source abdomen magnetic resonance image dataset was used in this work. The extracted properties and cues are then used in a mathematical model for guiding the vascular network formation comprising arterial and venous networks. Next, the generated three-dimensional networks are used to simulate the nutrient transport and consumption within the organ over time and the regions deprived of the nutrients are identified. These regions provide cues to evolve and optimize the vasculature in an iterative manner to ensure the availability of the nutrient transport throughout the bioprinted scaffolds. The mass transport of six components of cell culture media—glucose, glycine, glutamine, riboflavin, human serum albumin, and oxygen was studied within the organ with designed vasculature. As the vascular structure underwent iterations, the organ regions deprived of these key components decreased significantly highlighting the increase in structural complexity and efficacy of the designed vasculature. The numerical method presented in this work offers a valuable tool for designing vascular scaffolds to guide the cell growth and maturation of the bioprinted tissues for faster regeneration post bioprinting.
Three-dimensional bioprinted BMSCs-laden highly adhesive artificial periosteum containing gelatin-dopamine and graphene oxide nanosheets promoting bone defect repair
Authors: Sun Xin , Yang Jin , Ma Jie , Wang Tianchang , Zhao Xue , Zhu Dan , Jin Wenjie , Zhang Kai , Sun Xuzhou , Shen Yuling , Xie Neng , Yang Fei , Shang Xiushuai , Li Shuai , Zhou Xiaojun , He Chuanglong , Zhang Deteng , Wang Jinwu 
Published: January 2023

Abstract
The periosteum is a connective tissue membrane adhering to the surface of bone tissue that primarily provides nutrients and regulates osteogenesis during bone development and injury healing. However, building an artificial periosteum with good adhesion properties and satisfactory osteogenesis for bone defect repair remains a challenge, especially using three-dimensional (3D) bioprinting. In this study, dopamine was first grafted onto the molecular chain of gelatin using N-(3-dimethylaminopropyl)-N′-ethylcarbodiimide hydrochloride and N-hydroxysuccinimide (NHS) to activate the carboxyl group and produce modified gelatin-dopamine (GelDA). Next, a methacrylated gelatin, methacrylated silk fibroin, GelDA, and graphene oxide nanosheet composite bioink loaded with bone marrow mesenchymal stem cells was prepared and used for bioprinting. The physicochemical properties, biocompatibility, and osteogenic roles of the bioink and 3D bioprinted artificial periosteum were then systematically evaluated. The results showed that the developed bioink showed good thermosensitivity and printability and could be used to build 3D bioprinted artificial periosteum with satisfactory cell viability and high adhesion. Finally, the 3D bioprinted artificial periosteum could effectively enhance osteogenesis both in vitro and in vivo. Thus, the developed 3D bioprinted artificial periosteum can prompt new bone formation and provides a promising strategy for bone defect repair.
Effects of three patterns of elevated CO2 in single and multiple generations on photosynthesis and stomatal features in rice
Authors: Yang Kai , Huang Yao , Yang Jingrui , Lv Chunhua , Hu Zhenghua , Yu Lingfei , Sun Wenjuan 
Published: January 2023

AbstractBackground and AimsEffects of elevated CO2 (E) within a generation on photosynthesis and stomatal features have been well documented in crops; however, long-term responses to gradually elevated CO2 (Eg) and abruptly elevated CO2 (Ea) over multiple generations remain scarce.MethodsJaponica rice plants grown in open-top chambers were tested in the first generation (F1) under Ea and in the fifth generation (F5) under Eg and Ea, as follows: Ea in F1: ambient CO2 (A) + 200 μmol mol−1; Eg in F5: an increase of A + 40 μmol mol−1 year−1 until A + 200 μmol mol−1 from 2016 to 2020; Ea in F5: A + 200 μmol mol−1 from 2016 to 2020. For multigenerational tests, the harvested seeds were grown continuously in the following year in the respective CO2 environments.Key ResultsThe responses to Ea in F1 were consistent with the previous consensus, such as the occurrence of photosynthetic acclimation, stimulation of photosynthesis, and downregulation of photosynthetic physiological parameters and stomatal area. In contrast, multigenerational exposure to both Eg and Ea did not induce photosynthetic acclimation, but stimulated greater photosynthesis and had little effect on the photosynthetic physiology and stomatal traits. This suggests that E retained intergenerational effects on photosynthesis and stomatal features and that there were no multigenerational differences in the effects of Eg and Ea.ConclusionsThe present study demonstrated that projecting future changes induced by E based on the physiological responses of contemporary plants could be misleading. Thus, responses of plants to large and rapid environmental changes within a generation cannot predict the long-term response of plants to natural environmental changes over multiple generations, especially in annual herbs with short life cycles.
MFR-DTA: a multi-functional and robust model for predicting drug–target binding affinity and region
Authors: Hua Yang , Song Xiaoning , Feng Zhenhua , Wu Xiaojun 
Published: January 2023

Abstract

Motivation
Recently, deep learning has become the mainstream methodology for drug–target binding affinity prediction. However, two deficiencies of the existing methods restrict their practical applications. On the one hand, most existing methods ignore the individual information of sequence elements, resulting in poor sequence feature representations. On the other hand, without prior biological knowledge, the prediction of drug–target binding regions based on attention weights of a deep neural network could be difficult to verify, which may bring adverse interference to biological researchers.

Results
We propose a novel Multi-Functional and Robust Drug–Target binding Affinity prediction (MFR-DTA) method to address the above issues. Specifically, we design a new biological sequence feature extraction block, namely BioMLP, that assists the model in extracting individual features of sequence elements. Then, we propose a new Elem-feature fusion block to refine the extracted features. After that, we construct a Mix-Decoder block that extracts drug–target interaction information and predicts their binding regions simultaneously. Last, we evaluate MFR-DTA on two benchmarks consistently with the existing methods and propose a new dataset, sc-PDB, to better measure the accuracy of binding region prediction. We also visualize some samples to demonstrate the locations of their binding sites and the predicted multi-scale interaction regions. The proposed method achieves excellent performance on these datasets, demonstrating its merits and superiority over the state-of-the-art methods.

Availability and implementation
https://github.com/JU-HuaY/MFR.
The adapted Activity-By-Contact model for enhancer–gene assignment and its application to single-cell data
Authors: Hecker Dennis , Behjati Ardakani Fatemeh , Karollus Alexander , Gagneur Julien , Schulz Marcel H 
Published: January 2023

AbstractMotivationIdentifying regulatory regions in the genome is of great interest for understanding the epigenomic landscape in cells. One fundamental challenge in this context is to find the target genes whose expression is affected by the regulatory regions. A recent successful method is the Activity-By-Contact (ABC) model which scores enhancer–gene interactions based on enhancer activity and the contact frequency of an enhancer to its target gene. However, it describes regulatory interactions entirely from a gene’s perspective, and does not account for all the candidate target genes of an enhancer. In addition, the ABC model requires two types of assays to measure enhancer activity, which limits the applicability. Moreover, there is neither implementation available that could allow for an integration with transcription factor (TF) binding information nor an efficient analysis of single-cell data.ResultsWe demonstrate that the ABC score can yield a higher accuracy by adapting the enhancer activity according to the number of contacts the enhancer has to its candidate target genes and also by considering all annotated transcription start sites of a gene. Further, we show that the model is comparably accurate with only one assay to measure enhancer activity. We combined our generalized ABC model with TF binding information and illustrated an analysis of a single-cell ATAC-seq dataset of the human heart, where we were able to characterize cell type-specific regulatory interactions and predict gene expression based on TF affinities. All executed processing steps are incorporated into our new computational pipeline STARE.Availability and implementationThe software is available at https://github.com/schulzlab/STAREContactmarcel.schulz@em.uni-frankfurt.deSupplementary informationSupplementary data are available at Bioinformatics online.
Benchmarking tools for a priori identifiability analysis
Authors: Rey Barreiro Xabier , Villaverde Alejandro F 
Published: January 2023

Abstract

Motivation
The theoretical possibility of determining the state and parameters of a dynamic model by measuring its outputs is given by its structural identifiability and its observability. These properties should be analysed before attempting to calibrate a model, but their a priori analysis can be challenging, requiring symbolic calculations that often have a high computational cost. In recent years, a number of software tools have been developed for this task, mostly in the systems biology community. These tools have vastly different features and capabilities, and a critical assessment of their performance is still lacking.

Results
Here, we present a comprehensive study of the computational resources available for analysing structural identifiability. We consider 13 software tools developed in 7 programming languages and evaluate their performance using a set of 25 case studies created from 21 models. Our results reveal their strengths and weaknesses, provide guidelines for choosing the most appropriate tool for a given problem and highlight opportunities for future developments.

Availability and implementation
https://github.com/Xabo-RB/Benchmarking_files.
Ex vivoconfocal microscopy detects basic patterns of acute and chronic lesions using fresh kidney samples
Authors: Villarreal Jesús Z , Pérez-Anker Javiera , Puig Susana , Xipell Marc , Espinosa Gerard , Barnadas Esther , Larque Ana B , Malvehy J , Cervera Ricard , Pereira Arturo , Martinez-Pozo Antonio , Quintana Luis F , García-Herrera Adriana 
Published: January 2023

ABSTRACTBackgroundEx vivo confocal microscopy is a real-time technique that provides high-resolution images of fresh, non-fixed tissues, with an optical resolution comparable to conventional pathology. The objective of this study was to investigate the feasibility of using ex vivo confocal microscopy in fusion mode (FuCM) and the haematoxylin and eosin (H&E)-like digital staining that results for the analysis of basic patterns of lesion in nephropathology.MethodsForty-eight renal samples were scanned in a fourth-generation ex vivo confocal microscopy device. Samples were subjected to confocal microscopy imaging and were then processed using conventional pathology techniques. Concordance between the techniques was evaluated by means of the percentage of agreement and the κ index.ResultsAgreement between conventional microscopy and H&E-like digital staining was strong (κ = 0.88) in the evaluation of acute tubular damage and was substantial (κ = 0.79) in the evaluation of interstitial fibrosis, interstitial inflammation, arterial and arteriolar lesions. H&E-like digital staining also allows rapid identification of extracapillary proliferation (κ = 0.88), necrosis and segmental sclerosis (κ = .88) in the glomerular compartment, but the results reported here are limited because of the small number of cases with these glomerular findings.ConclusionsFuCM proved to be as effective as conventional techniques in evaluating the presence of acute tubular necrosis and interstitial fibrosis changes, but in fresh tissue. The ease of acquisition of ex vivo confocal microscopy images suggests that FuCM may be useful for rapid evaluation of kidney biopsies and to restructure the clinical workflow in renal histopathology.
The TANGO2 disease and the therapeutic challenge of acute arrhythmia management: a case report
Authors: Gomes Sílvia A , Laranjo Sérgio , Trigo Conceição , Pinto Fátima F 
Published: January 2023

AbstractBackgroundTANGO2-related metabolic encephalopathy and arrhythmia are a rare, newly recognized, and likely under-diagnosed condition. First described in 2016, it is characterized by developmental delay and recurrent metabolic crisis. During these episodes, patients may present QTc prolongation and ventricular arrhythmias.Case summaryA 13-year-old female, with developmental delay, presented with severe rhabdomyolysis and an initially normal electrocardiogram (ECG). Due to the worsening of rhabdomyolysis, QTc prolongation was identified (QTc 570 ms) and oral β-blocker therapy started. A non-sustained ventricular tachycardia developed, initially managed with magnesium and lidocaine. After a short period, an arrhythmic storm of polymorphic ventricular extrasystoles induced Torsade de Pointes (TdP) was triggered. A temporary percutaneous pacing lead was placed and esmolol infusion started. The electrical instability ran in parallel with the increasing severity of rhabdomyolysis and systolic ventricular function decline. Genetic testing identified a pathogenic variant in homozygosity in the TANGO2 gene. A stable sinus rhythm was achieved with metabolic and serum electrolytes optimization. ECG showed normalization of the QTc interval.DiscussionThe full TANGO2-related phenotype emerges over time and the prognosis is linked to the appearance of ECG abnormalities. QT interval prolongation can lead to life-threatening ventricular tachycardias. The arrhythmia mechanism seems to be secondary to metabolite build-up in cardiomyocytes, which can explain the cardiac phenotype during the crisis which subsides after their resolution. In these patients, avoiding bradycardia is fundamental, since long QT-related TdP seems to be triggered by bradycardia and short-long-short ventricular premature beats (VPB). During an acute metabolic crisis, the management of arrhythmias relies on metabolic control.
Simultaneous ST-elevation myocardial infarction in monozygotic twins: a case report of entangled twins
Authors: Kassab Kameel , Gupta Vishal 
Published: January 2023

AbstractBackgroundThe development of coronary artery disease (CAD) is strongly influenced by genetic and environmental factors. Monozygotic twins represent a unique population that provides insights into the interaction of genetic, environmental, and social factors and their effects on the development of CAD.Case summaryTwo 54-year-old identical twins presented to an outside hospital with acute chest pain. Twin B developed chest pain after witnessing Twin A in distress from an acute chest pain episode. Electrocardiogram performed on each of them was diagnostic of ST-elevation myocardial infarction. Upon arrival at the angioplasty centre, Twin A was taken for emergency coronary angiography yet his pain subsided on the way to the catheterization lab hence, Twin B was taken for angiography instead. Twin B angiography demonstrated acute occlusion of the proximal left anterior descending coronary artery and was treated with percutaneous coronary intervention. Twin A coronary angiogram demonstrated 60% ostial first diagonal branch stenosis with a normal distal flow. He was diagnosed with possible coronary vasospasm.ConclusionThis is the first report of a simultaneous presentation of monozygotic twins with ST-elevation acute coronary syndrome. While genetic and environmental contributions to the development of CAD have been described, this case highlights the strong social bond that exists between monozygotic twins. Once CAD is diagnosed in one twin, aggressive risk factor modification and screening should be implemented in the other.
Management of patients with chronic kidney disease: a French medical centre database analysis
Authors: Ariza Matthieu , Martin Steven , Dusenne Mikaël , Darmon David , Schuers Matthieu 
Published: January 2023

Abstract

Objective(s)
Chronic kidney disease (CKD) is an insidious disease that requires early nephroprotective measures to delay progression to end-stage kidney disease. The objective of this study was to describe the management of patients with CKD in primary care, including clinical and biological monitoring and prescribed treatments. A retrospective, single-centre study was conducted on adult patients who were treated in the Maison de Neufchâtel (France) between 2012 and 2017 at least once a year. The inclusion criteria were 2 estimated glomerular filtration rate (eGFR) measurements &lt;60 mL/min more than 3 months apart. Two subgroups were constituted according to whether CKD was coded in the electronic medical records (EMRs).

Results
A total of 291 (6.7%, CI95% 5.9–7.4) patients with CKD were included. The mean eGFR was 51.0 ± 16.4 mL/min. Hypertension was the most frequent health problem reported (n = 93, 32%). Nephrotective agents were prescribed in 194 (66.7%) patients, non-steroidal anti-inflammatory drugs (NSAIDs) in 22 (8%) patients, and proton-pump inhibitors (PPIs) in 147 (47%) patients. CKD coding in EMRs was associated with dosage of natraemia (n = 34, 100%, P &lt; 0.01), albuminuria (n = 20, 58%, P &lt; 0.01), vitamin D (n = 14, 41%, P &lt; 0.001), and phosphorus (n = 11, 32%, P &lt; 0.001). Eighty-one patients (31.5%) with low eGFR without an entered code for CKD were prescribed an albuminuria dosage. Clinical monitoring could not be analysed due to poor coding.

Conclusion
This pilot study reinforces the hypothesis that CKD is underscreened and undermanaged. More systematic coding of medical information in EMRs and further studies on medical centre databases should improve primary care practices.
Patient characteristics and factors contributing to recurrence of bacterial vaginosis presented in primary care
Authors: Delfstra Natasja S , Uijen Annemarie A , Vos M Caroline , Akkermans Reinier , Lagro-Janssen Antoine L , Teunissen Doreth A M 
Published: January 2023

Abstract

Background
Bacterial vaginosis (BV) is a common problem in primary care. BV symptoms often have a negative impact on patients’ quality of life and may predispose to gynaecological problems. Some patients experience recurring episodes of BV. This study’s objective is to identify possible factors that may be associated with BV recurrence and describe the characteristics of these patients and interventions performed by general practitioners.

Methods
In this retrospective cohort study, we used data from a primary care registration network in the Netherlands in the period 2015–2020. We analysed differences between patients with recurrent BV and patients with a single episode of BV in terms of characteristics and interventions performed by general practitioners.

Results
We found that patients with recently prescribed antibiotics, and a medical history of sexually transmitted infections and/or Candidiasis significantly more often presented with recurrent BV. Patients with recurrent BV had more remote consultations and less in-person consultations than single-episode patients. The reason for encounter was more often a request for medication. Regarding GPs’ diagnostic and therapeutic interventions, microbiological tests were more frequently performed in recurrent BV patients. Moreover, most patients in both groups were prescribed oral metronidazole most frequently.

Conclusions
Our findings might help GPs to better recognise patients at risk of recurrence. GPs could re-evaluate their approach to the diagnosis and treatment of recurrent BV, opting for in-person consultation and using standardised diagnostic criteria and microbiological testing in patients with recurrent complaints. Antibiotic use for other conditions in these patients may lead to new BV episodes.