bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fresh and frozen cardiac tissue are comparable in DNA methylation array β-values, but formalin-fixed, paraffin-embedded tissue may overestimate DNA methylation levels
Authors: Dupont Mikkel Eriksen , Jacobsen Stine Bøttcher , Christiansen Steffan Noe Niikanoff , Tfelt-Hansen Jacob , Smerup Morten Holdgaard , Andersen Jeppe Dyrberg , Morling Niels 
Published: September 2023

AbstractUntreated fresh cardiac tissue is the optimal tissue material for investigating DNA methylation patterns of cardiac biology and diseases. However, fresh tissue is difficult to obtain. Therefore, tissue stored as frozen or formalin-fixed, paraffin-embedded (FFPE) is widely used for DNA methylation studies. It is unknown whether storage conditions alter the DNA methylation in cardiac tissue. In this study, we compared the DNA methylation patterns of fresh, frozen, and FFPE cardiac tissue to investigate if the storage method affected the DNA methylation results. We used the Infinium MethylationEPIC assay to obtain genome-wide methylation levels in fresh, frozen, and FFPE tissues from nine individuals. We found that the DNA methylation levels of 21.4% of the examined CpG sites were overestimated in the FFPE samples compared to that of fresh and frozen tissue, whereas 5.7% were underestimated. Duplicate analyses of the DNA methylation patterns showed high reproducibility (precision) for frozen and FFPE tissues. In conclusion, we found that frozen and FFPE tissues gave reproducible DNA methylation results and that frozen and fresh tissues gave similar results.
“Redirecting an anti-IL-1β antibody to bind a new, unrelated and computationally predicted epitope on hIL-17A”
Authors: Fischman Sharon , Levin Itay , Rondeau Jean-Michel , Štrajbl Marek , Lehmann Sylvie , Huber Thomas , Nimrod Guy , Cebe Régis , Omer Dotan , Kovarik Jiri , Bernstein Shmuel , Sasson Yehezkel , Demishtein Alik , Shlamkovich Tomer , Bluvshtein Olga , Grossman Noam , Barak-Fuchs Reut , Zhenin Michael , Fastman Yair , Twito Shir , Vana Tal , Zur Nevet , Ofran Yanay 
Published: September 2023

AbstractAntibody engineering technology is at the forefront of therapeutic antibody development. The primary goal for engineering a therapeutic antibody is the generation of an antibody with a desired specificity, affinity, function, and developability profile. Mature antibodies are considered antigen specific, which may preclude their use as a starting point for antibody engineering. Here, we explore the plasticity of mature antibodies by engineering novel specificity and function to a pre-selected antibody template. Using a small, focused library, we engineered AAL160, an anti-IL-1β antibody, to bind the unrelated antigen IL-17A, with the introduction of seven mutations. The final redesigned antibody, 11.003, retains favorable biophysical properties, binds IL-17A with sub-nanomolar affinity, inhibits IL-17A binding to its cognate receptor and is functional in a cell-based assay. The epitope of the engineered antibody can be computationally predicted based on the sequence of the template antibody, as is confirmed by the crystal structure of the 11.003/IL-17A complex. The structures of the 11.003/IL-17A and the AAL160/IL-1β complexes highlight the contribution of germline residues to the paratopes of both the template and re-designed antibody. This case study suggests that the inherent plasticity of antibodies allows for re-engineering of mature antibodies to new targets, while maintaining desirable developability profiles.
Optimal tracking strategies in a turbulent flow
Authors: Calascibetta Chiara , Biferale Luca , Borra Francesco , Celani Antonio , Cencini Massimo 
Published: September 2023

AbstractPursuing a drifting target in a turbulent flow is an extremely difficult task whenever the searcher has limited propulsion and maneuvering capabilities. Even in the case when the relative distance between pursuer and target stays below the turbulent dissipative scale, the chaotic nature of the trajectory of the target represents a formidable challenge. Here, we show how to successfully apply optimal control theory to find navigation strategies that overcome chaotic dispersion and allow the searcher to reach the target in a minimal time. We contrast the results of optimal control – which requires perfect observability and full knowledge of the dynamics of the environment – with heuristic algorithms that are reactive – relying on local, instantaneous information about the flow. While the latter display worse performances, optimally controlled pursuers can track the target for times much longer than the typical inverse Lyapunov exponent and are considerably more robust.
Protéger les enfants du TSPT
Authors: Askenazy Florence , Fernandez Arnaud , Gindt Morgane 
Published: September 2023

Afin de protéger les enfants des effets traumatiques, il est très important que les parents comprennent les facteurs de risque associés. Le trouble de stress post-traumatique (TSPT) est un trouble psychiatrique reconnu chez les adultes et les enfants, qui survient après un événement potentiellement traumatique. Environ 15% des enfants de la population générale présentent un TSPT, et ce pourcentage peut être beaucoup plus élevé dans le contexte d’attaques terroristes. Le TSPT peut devenir chronique chez un nombre significatif d’enfants, ce qui entraîne des difficultés scolaires et des risques de désocialisation. À la suite de l’attaque terroriste de Nice le 14 juillet 2016, un centre spécialisé dans les soins psychothérapeutiques et l’évaluation des psychotraumatismes chez les enfants a été créé. L’équipe pluridisciplinaire du centre propose des soins intégratifs fondés sur différentes approches thérapeutiques. Un programme de recherche, appelé « programme 14-7 », a été mis en place pour étudier la prévalence du TSPT et des facteurs de risque associés chez les enfants et les parents exposés à l’attentat.
Les résultats préliminaires de l’étude ont montré un taux élevé de TSPT et de troubles anxieux chez les enfants. Les parents eux-mêmes sont également affectés par les événements traumatiques, ce qui rend plus difficile leur rôle de soutien envers leurs enfants. Divers facteurs environnementaux et familiaux peuvent influencer le développement du TSPT chez les enfants. Les réactions des parents et de l’environnement familial sont un des facteurs les plus importants. L’existence de pathologies parentales est également un facteur de risque important, car l’état mental des parents peut influencer celui de leurs enfants.
Dans la ville de Nice, un accompagnement familial systémique dans les domaines de la santé mentale, psychique, sociale et juridique est nécessaire pour prévenir les conséquences du TSPT et des troubles qui y sont associés. Les facteurs de risque tels que les réactions de l’environnement, le type d’attachement et les pathologies parentales doivent être pris en compte dans les décisions thérapeutiques. La littérature scientifique confirme ces constatations sur le terrain et souligne l’importance de l’implication des adultes et des pouvoirs publics dans le soutien aux familles impactées.
Prävention postoperativer Wundinfektionen
Authors: Utzolino Stefan , Eckmann Christian , Lock Johan Friso 
Published: September 2023

ZusammenfassungDie moderne Chirurgie ermöglicht immer komplexere operative Eingriffe bei immer älteren und komorbiden Patienten. Dies geht mit einem potenziell erhöhten Risiko für perioperative
Infektionen (SSI) einher. Für deren Vermeidung sind Sauberkeit, Händedesinfektion und steriles Arbeiten essenziell, während einige traditionelle Hygienemaßnahmen zur Prävention untauglich
sind. In diesem Beitrag werden Unterschiede der relevantesten Leitlinien zu SSI ggf. besonders herausgestellt.
Urgent Follow-up after Outpatient Nonstress Tests and the Potential for Fetal Monitoring at Home
Authors: Dangel Alissa , Shindgikar Priyanka , Polio Andrew , Breeze Janis L. , House Michael 
Published: September 2023

Objective This study aimed to measure the proportion of patients needing urgent clinical follow-up after an abnormal outpatient nonstress test (NST). We further sought to capture the patient perspective on the acceptability of performing NSTs at home.
Study Design A retrospective cohort study was performed over a 2-year period to determine the frequency of abnormal NSTs in a hospital-based, antepartum testing unit in patients greater than or equal to 32 weeks' gestation. The proportion of patients who delivered within 24 hours of an abnormal NST was also determined. A cross-sectional, web-based patient survey was conducted to obtain insight into the patient's comfort level with potentially performing NSTs at home.
Results The chart review yielded 665 patients who underwent 2,122 NSTs at greater than or equal to 32 weeks. Of the 2,122 NSTs, 111 were categorized as abnormal and required urgent clinical follow-up, or 5.2% (95% confidence interval [CI] 4.3, 6.3%). Of the 665 patients, 13 delivered within 24 hours of an abnormal NST, or 2.0% (95% CI 1.0, 3.3%). In the web-based survey, the proportion of respondents who would feel comfortable or very comfortable conducting NSTs at home was 87/125, or 69.6% (95% CI 60.9, 77.1%).
Conclusion This study revealed that 5.2% of NSTs performed in a hospital-based antepartum testing unit were abnormal and required urgent clinical follow-up. Of the patients being followed in the antepartum testing unit, 2.0% delivered within 24 hours of an abnormal NST. The majority of the survey respondents indicated they would feel comfortable performing NSTs at home. The present study adds important information regarding the risks and benefits of NSTs at home.
Key Points
On love
Authors: Kotthaus Jochem 
Published: September 2023

AbstractIn this paper, I will explore love as a universe of meaning constituted at the crossroads of cultural patterns and actors’ biographical experiences. Universes of meaning provide a structure of cognitive pre-selections. While the social in general is composed of a multitude of universes of meaning, they belong to the public. Romantic relationships are private and enable privacy. I will (1) propose a definition of love and a framework that serves to ensure its theoretical validity. I will then (2) analytically deconstruct the unity of communication, interaction, eroticism, and emotionality as love’s different media of experience and explore their self-referential functionality.
Lock-in photothermal method for in-plane thermal diffusivity measurements using arrayed temperature sensors on suspended SiNx membranes
Authors: Jiang Felix , Ryu Meguya , Pachauri Vivek , Ingebrandt Sven , Vu Xuan Thang , Morikawa Junko 
Published: September 2023

A device consisting of a line- or spiral-shaped temperature sensor array on a two-dimensional (2D) silicon nitride (SiNx) membrane of thickness 50 or 150 nm is developed for use in the lock-in photothermal method to determine the in-plane thermal diffusivity of SiNx membranes in air and in vacuum. The results of 2D heat diffusion are analyzed by the quadrupole method, and the system is approximated to the one-dimensional (1D) fin standing in a surrounding media (the fin approximation). The results show that 2D thermal diffusion on the membrane is affected not only by heat exchange with the surrounding environment but also by parallel thermal diffusion caused by heat conduction in the air along the membrane surface. The measurement using photothermal heating and contact detection of the temperature response enables the phenomenon to be detected consistently at a wide frequency range of temperature waves (50–1000 Hz). The measured thermal diffusivity values of the SiNx membrane are much smaller than those of bulk material, which can be reasonably considered an effect of the confined state of the phonon in the nanoscale geometry of the membrane.
MEMS audio speakers
*
Authors: Garud Meera , Pratap Rudra 
Published: September 2023

Abstract
Miniaturization of electro-mechanical sensors and actuators has benefited from an advancement in CMOS technology over the years. However, miniaturization of audio speakers has seen considerable development only in the recent times. This paper reviews the developments in micro-electro-mechanical-systems (MEMS) audio speaker research and the initial commercial products available in the market. At first glance, it appears that the relatively slow development of MEMS speakers can be attributed to the fact that the principle of actuation has remained unchanged for several decades. Unfortunately, the physics behind audible sound production holds us back from exclusively adopting miniaturized speakers—sound pressure level is directly proportional to the area of the sound radiating surface. Nevertheless, researchers are continuing to explore new avenues for designing and developing MEMS speakers, without limiting themselves to the existing actuation principles. With newly discovered materials and improving technology, the research in MEMS speakers is gaining attention and new products are emerging. A speaker design based on piezoelectric actuation or electrostatics actuation is favorable at MEMS scale. Indian research community is also contributing to advances in MEMS speakers and near-ultrasonic devices. This paper reviews the development in MEMS audio speakers in India and in the world. The tabulated review findings aim to offer readers an overview of the development of micro-speakers and to provide guidance for designing new micro-speakers.
Analyzing beam-gas interactions in an
H2+
cyclotron beam
Authors: Calvo Pedro , Winklehner Daniel , Oliver Concepción ,   on behalf of the IsoDAR collaboration
Published: September 2023

Abstract
For the Isotope Decay At Rest (IsoDAR) experiment in neutrino physics (searching for sterile neutrinos), we have developed a novel compact isochronous cyclotron with direct injection through an axially embedded RFQ. For IsoDAR to be decisive within five years of running, 10 mA of protons, cw at 80% duty factor are needed on a neutrino production target. To alleviate space charge in the cyclotron driver, we accelerate 5 mA of

H

2

+

, to be broken up into 10 mA of protons after extraction from the cyclotron. An open question that we are answering with this paper is whether the beam losses from gas-stripping (the removal of electrons from

H

2

+

through the interaction of the beam ions with the residual gas in the accelerator) are going to be a significant challenge. Using a newly added feature to the well-established Object-Oriented Parallel Accelerator Library code, we calculate gas-stripping losses in the IsoDAR cyclotron using realistic beam distributions, magnetic fields, gas composition, and pressure. We show that to maintain losses due to dissociation below 1% over the entire acceleration region, a vacuum of at least 6 × 10−7 mbar is required.
Dense speed-of-sound shift imaging for ultrasonic thermometry
Authors: Grutman Tal , Ilovitsh Tali 
Published: September 2023

Abstract

Objective. Develop a dense algorithm for calculating the speed-of-sound shift between consecutive acoustic acquisitions as a noninvasive means to evaluating temperature change during thermal ablation. Methods. An algorithm for dense speed-of-sound shift imaging (DSI) was developed to simultaneously incorporate information from the entire field of view using a combination of dense optical flow and inverse problem regularization, thus speeding up the calculation and introducing spatial agreement between pixels natively. Thermal ablation monitoring consisted of two main steps: pixel shift tracking using Farneback optical flow, and mathematical modeling of the relationship between the pixel displacement and temperature change as an inverse problem to find the speed-of-sound shift. A calibration constant translates from speed-of-sound shift to temperature change. The method performance was tested in ex vivo samples and compared to standard thermal strain imaging (TSI) methods. Main results. Thermal ablation at a frequency of 2 MHz was applied to an agarose phantom that created a speed-of-sound shift measured by an L12-5 imaging transducer. A focal spot was reconstructed by solving the inverse problem. Next, a thermocouple measured the temperature rise during thermal ablation of ex vivo chicken breast to calibrate the setup. Temperature changes between 3 °C and 15 °C was measured with high thermometry precision of less than 2 °C error for temperature changes as low as 8 °C. The DSI method outperformed standard TSI in both spatial coherence and runtime in high-intensity focused ultrasound-induced hyperthermia. Significance. Dense ultrasonic speed-of-sound shift imaging can successfully monitor the speed-of-sound shift introduced by thermal ablation. This technique is faster and more robust than current methods, and therefore can be used as a noninvasive, real time and cost-effective thermometry method, with high clinical applicability.
The first investigation of spot-scanning proton arc (SPArc) delivery time and accuracy with different delivery tolerance window settings
Authors: Liu Gang , Zhao Lewei , Liu Peilin , Dao Riao , Qian Yujia , Cong Xiaoda , Janssens Guillaume , Li Xiaoqiang , Ding Xuanfeng 
Published: September 2023

Abstract

Objective. To investigate the impact of various delivery tolerance window settings on the treatment delivery time and dosimetric accuracy of spot-scanning proton arc (SPArc) therapy. Approach. SPArc plans were generated for three representative disease sites (brain, lung, and liver cancer) with an angle sampling frequency of 2.5°. An in-house dynamic arc controller was used to simulate the arc treatment delivery with various tolerance windows (±0.25, ±0.5, ±1, and ±1.25°). The controller generates virtual logfiles during the arc delivery simulation, such as gantry speed, acceleration and deceleration, spot position, and delivery sequence, similar to machine logfiles. The virtual logfile was then imported to the treatment planning system to reconstruct the delivered dose distribution and compare it to the initial SPArc nominal plan. A three-dimensional gamma index was used to quantitatively assess delivery accuracy. Total treatment delivery time and relative lost time (dynamic arc delivery time—fix beam delivery time)/fix beam delivery time) were reported. Main Results. The 3D gamma passing rate (GPR) was greater than 99% for all cases when using 3%/3 mm and 2%/2 mm criteria and the GPR (1%/1 mm criteria) degraded as the tolerance window opens. The total delivery time for dynamic arc delivery increased with the decreasing delivery tolerance window length. The average delivery time and the relative lost time (%) were 630 ± 212 s (253% ± 68%), 322 ± 101 s (81% ± 31%), 225 ± 60 s (27% ± 16%), 196 ± 41 s (11% ± 6%), 187 ± 29 s (6% ± 1%) for tolerance windows ±0.25, ±0.5, ±1, and ±1.25° respectively. Significance. The study quantitatively analyzed the dynamic SPArc delivery time and accuracy with different delivery tolerance window settings, which offer a critical reference in the future SPArc plan optimization and delivery controller design.
Deep learning-based multi-stage postoperative type-b aortic dissection segmentation using global-local fusion learning
Authors: Zhang Xuyang , Cheng Guoliang , Han Xiaofeng , Li Shilong , Xiong Jiang , Wu Ziheng , Zhang Hongkun , Chen Duanduan 
Published: September 2023

Abstract

Objective. Type-b aortic dissection (AD) is a life-threatening cardiovascular disease and the primary treatment is thoracic endovascular aortic repair (TEVAR). Due to the lack of a rapid and accurate segmentation technique, the patient-specific postoperative AD model is unavailable in clinical practice, resulting in impracticable 3D morphological and hemodynamic analyses during TEVAR assessment. This work aims to construct a deep learning-based segmentation framework for postoperative type-b AD. Approach. The segmentation is performed in a two-stage manner. A multi-class segmentation of the contrast-enhanced aorta, thrombus (TH), and branch vessels (BV) is achieved in the first stage based on the cropped image patches. True lumen (TL) and false lumen (FL) are extracted from a straightened image containing the entire aorta in the second stage. A global-local fusion learning mechanism is designed to improve the segmentation of TH and BR by compensating for the missing contextual features of the cropped images in the first stage. Results. The experiments are conducted on a multi-center dataset comprising 133 patients with 306 follow-up images. Our framework achieves the state-of-the-art dice similarity coefficient (DSC) of 0.962, 0.921, 0.811, and 0.884 for TL, FL, TH, and BV, respectively. The global-local fusion learning mechanism increases the DSC of TH and BV by 2.3% (p < 0.05) and 1.4% (p < 0.05), respectively, based on the baseline. Segmenting TH in stage 1 can achieve significantly better DSC for FL (0.921 ± 0.055 versus 0.857 ± 0.220, p < 0.01) and TH (0.811 ± 0.137 versus 0.797 ± 0.146, p < 0.05) than in stage 2. Our framework supports more accurate vascular volume quantifications compared with previous segmentation model, especially for the patients with enlarged TH+FL after TEVAR, and shows good generalizability to different hospital settings. Significance. Our framework can quickly provide accurate patient-specific AD models, supporting the clinical practice of 3D morphological and hemodynamic analyses for quantitative and more comprehensive patient-specific TEVAR assessments.
Ferroelectric phase transitions of nanoislands based on transverse ising model
Authors: Chen Sheng , Mo Yixiang , Wu Yanyi 
Published: September 2023

Abstract
Based on the transverse field Ising model, the phase transition properties of nanoislands with a spin-1/2 are studied by using the usual decoupling approximation of Fermi-type Green’s function. The phase diagram indicates that the phase transition curve (J

S

/J = t

c
, Ω
S

/J ∼ t

c
) is highly sensitive to the interlayer exchange interaction (J

R

/J) and the ratio of surface to center transverse fields (Ω
S

/Ω). The polarization diagram reveals that the polarization curve exhibits steps attributed to spin inversion, and the temperature of the step point corresponds to the temperature at which spin configuration changes.
Water chemical treatment by photocatalytic activity of reduced graphene oxide-decorated zinc sulfide nanocomposite
Authors: Mosayebi Pegah , Dorranian Davoud , Sari Amirhossein , Behzad Kasra 
Published: September 2023

Abstract
The photocatalytic properties of reduced graphene oxide decorated ZnS nanocomposite was employed for photodegradation of phenol red as a chemical agent in water. ZnS nanocomposite was synthesized by hydrothermal method. Reduced graphene oxide decorated ZnS nanocomposite was produced by pulsed laser ablation of graphite bulk in the solution of ZnS nanocomposite. Variety of spectroscopic and imaging diagnostics including X-ray diffraction (XRD), UV–vis absorption spectroscopy, transmission electron microscopy (TEM), and scanning electron microscopy (SEM) were used to characterize the synthesized nanostructures. Water treatment was carried out in a closed handmade reactor. The concentration of the phenol red pollutant as the chemical agent, was extracted from the absorption spectra of treated water. Dependence of the behaviors of phenol red dye on the pH of the medium was studied in detail. Effects of UV radiation intensity, treatment time, pH of the polluted water, and aging on the efficiency of the treatment were investigated. Results show that even in the dark condition rGO-ZnS nanocomposite is an effective material to remove phenol red pollutant from water. The highest efficiency of treatment after 120 min was achieved in neutral pH water. Furthermore, after 7 days, with nanostructures and without UV radiation, the removal process in the polluted water was continued.