bluuebunny/crossref_metadata_2025_split huggingface dataset:
Learned adaptive multiphoton illumination microscopy for large-scale immune response imaging
Authors: Pinkard Henry , Baghdassarian Hratch , Mujal Adriana , Roberts Ed , Hu Kenneth H. , Friedman Daniel Haim , Malenica Ivana , Shagam Taylor , Fries Adam , Corbin Kaitlin , Krummel Matthew F. , Waller Laura 
Published: March 2021

AbstractMultiphoton microscopy is a powerful technique for deep in vivo imaging in scattering samples. However, it requires precise, sample-dependent increases in excitation power with depth in order to generate contrast in scattering tissue, while minimizing photobleaching and phototoxicity. We show here how adaptive imaging can optimize illumination power at each point in a 3D volume as a function of the sample’s shape, without the need for specialized fluorescent labeling. Our method relies on training a physics-based machine learning model using cells with identical fluorescent labels imaged in situ. We use this technique for in vivo imaging of immune responses in mouse lymph nodes following vaccination. We achieve visualization of physiologically realistic numbers of antigen-specific T cells (~2 orders of magnitude lower than previous studies), and demonstrate changes in the global organization and motility of dendritic cell networks during the early stages of the immune response. We provide a step-by-step tutorial for implementing this technique using exclusively open-source hardware and software.
DNA interstrand cross-links induced by the major oxidative adenine lesion 7,8-dihydro-8-oxoadenine
Authors: Rozelle Aaron L. , Cheun Young , Vilas Caroline K. , Koag Myong-Chul , Lee Seongmin 
Published: March 2021

AbstractOxidative damage to DNA generates 7,8-dihydro-8-oxoguanine (oxoG) and 7,8-dihydro-8-oxoadenine (oxoA) as two major lesions. Despite the comparable prevalence of these lesions, the biological effects of oxoA remain poorly characterized. Here we report the discovery of a class of DNA interstrand cross-links (ICLs) involving oxidized nucleobases. Under oxidative conditions, oxoA, but not oxoG, readily reacts with an opposite base to produce ICLs, highlighting a latent alkylating nature of oxoA. Reactive halogen species, one-electron oxidants, and the myeloperoxidase/H2O2/Cl− system induce oxoA ICLs, suggesting that oxoA-mediated cross-links may arise endogenously. Nucleobase analog studies suggest C2-oxoA is covalently linked to N2-guanine and N3-adenine for the oxoA-G and oxoA-A ICLs, respectively. The oxoA ICLs presumably form via the oxidative activation of oxoA followed by the nucleophilic attack by an opposite base. Our findings provide insights into oxoA-mediated mutagenesis and contribute towards investigations of oxidative stress-induced ICLs and oxoA-based latent alkylating agents.
Long-term and large-scale multispecies dataset tracking population changes of common European breeding birds
Authors: Brlík Vojtěch , Šilarová Eva , Škorpilová Jana , Alonso Hany , Anton Marc , Aunins Ainars , Benkö Zoltán , Biver Gilles , Busch Malte , Chodkiewicz Tomasz , Chylarecki Przemysław , Coombes Dick , de Carli Elisabetta , del Moral Juan C. , Derouaux Antoine , Escandell Virginia , Eskildsen Daniel P. , Fontaine Benoît , Foppen Ruud P. B. , Gamero Anna , Gregory Richard D. , Harris Sarah , Herrando Sergi , Hristov Iordan , Husby Magne , Ieronymidou Christina , Jiquet Frédéric , Kålås John A. , Kamp Johannes , Kmecl Primož , Kurlavičius Petras , Lehikoinen Aleksi , Lewis Lesley , Lindström Åke , Manolopoulos Aris , Martí David , Massimino Dario , Moshøj Charlotte , Nellis Renno , Noble David , Paquet Alain , Paquet Jean-Yves , Portolou Danae , Ramírez Iván , Redel Cindy , Reif Jiří , Ridzoň Jozef , Schmid Hans , Seaman Benjamin , Silva Laura , Soldaat Leo , Spasov Svetoslav , Staneva Anna , Szép Tibor , Florenzano Guido Tellini , Teufelbauer Norbert , Trautmann Sven , van der Meij Tom , van Strien Arco , van Turnhout Chris , Vermeersch Glenn , Vermouzek Zdeněk , Vikstrøm Thomas , Voříšek Petr , Weiserbs Anne , Klvaňová Alena 
Published: March 2021

AbstractAround fifteen thousand fieldworkers annually count breeding birds using standardized protocols in 28 European countries. The observations are collected by using country-specific and standardized protocols, validated, summarized and finally used for the production of continent-wide annual and long-term indices of population size changes of 170 species. Here, we present the database and provide a detailed summary of the methodology used for fieldwork and calculation of the relative population size change estimates. We also provide a brief overview of how the data are used in research, conservation and policy. We believe this unique database, based on decades of bird monitoring alongside the comprehensive summary of its methodology, will facilitate and encourage further use of the Pan-European Common Bird Monitoring Scheme results.
Discovering latent node Information by graph attention network
Authors: Gu Weiwei , Gao Fei , Lou Xiaodan , Zhang Jiang 
Published: March 2021

AbstractIn this paper, we propose graph attention based network representation (GANR) which utilizes the graph attention architecture and takes graph structure as the supervised learning information. Compared with node classification based representations, GANR can be used to learn representation for any given graph. GANR is not only capable of learning high quality node representations that achieve a competitive performance on link prediction, network visualization and node classification but it can also extract meaningful attention weights that can be applied in node centrality measuring task. GANR can identify the leading venture capital investors, discover highly cited papers and find the most influential nodes in Susceptible Infected Recovered Model. We conclude that link structures in graphs are not limited on predicting linkage itself, it is capable of revealing latent node information in an unsupervised way once a appropriate learning algorithm, like GANR, is provided.
Compound heterozygous mutations in TGFBI cause a severe phenotype of granular corneal dystrophy type 2
Authors: Jun Ikhyun , Ji Yong Woo , Choi Seung-il , Lee Bo Ram , Min Ji Sang , Kim Eung Kweon 
Published: March 2021

AbstractWe investigated the clinical and genetic features of patients with severe phenotype of granular corneal dystrophy type 2 (GCD2) associated with compound heterozygosity in the transforming growth factor-β-induced (TGFBI) gene. Patients with severe GCD2 underwent ophthalmic examination (best-corrected visual acuity test, intraocular pressure measurement, slit-lamp examination, and slit-lamp photograph analysis) and direct Sanger sequencing of whole-TGFBI. The patient’s family was tested to determine the pedigrees. Five novel mutations (p.(His174Asp), p.(Ile247Asn), p.(Tyr88Cys), p.(Arg257Pro), and p.(Tyr468*)) and two known mutations (p.(Asn544Ser) and p.(Arg179*)) in TGFBI were identified, along with p.(Arg124His), in the patients. Trans-phase of TGFBI second mutations was confirmed by pedigree analysis. Multiple, extensive discoid granular, and increased linear deposits were observed in the probands carrying p.(Arg124His) and other nonsense mutations. Some patients who had undergone phototherapeutic keratectomy experienced rapid recurrence (p.(Ile247Asn) and p.(Asn544Ser)); however, the cornea was well-maintained in a patient who underwent deep anterior lamellar keratoplasty (p.(Ile247Asn)). Thus, compound heterozygosity of TGFBI is associated with the phenotypic variability of TGFBI corneal dystrophies, suggesting that identifying TGFBI second mutations may be vital in patients with extraordinarily severe phenotypes. Our findings indicate the necessity for a more precise observation of genotype–phenotype correlation and additional care when treating TGFBI corneal dystrophies.
Field size effects on DNA damage and proliferation in normal human cell populations irradiated with X-ray microbeams
Authors: Ojima Mitsuaki , Ito Atsushi , Usami Noriko , Ohara Maki , Suzuki Keiji , Kai Michiaki 
Published: March 2021

AbstractTo clarify the health risks of internal radiation exposure, it is important to investigate the radiological effects of local exposure at cell levels from radioactive materials taken up by organs. Focusing on the response of cell populations post-irradiation, X-ray microbeams are very effective at reproducing the effects of local exposure within an internal exposure in vitro. The present study aims to clarify the effects of local exposure by investigating the response of normal human cell (MRC-5) populations irradiated with X-ray microbeams of different beam sizes to DNA damage. The populations of MRC-5 were locally irradiated with X-ray microbeams of 1 Gy at 0.02–1.89 mm2 field sizes, and analyzed whether the number of 53BP1 foci as DSB (DNA double strand break) per cell changed with the field size. We found that even at the same dose, the number of DSB per cell increased depending on the X-irradiated field size on the cell population. This result indicated that DNA damage repair of X-irradiated cells might be enhanced in small size fields surrounded by non-irradiated cells. This study suggests that X-irradiated cells received some signal (a rescue signal) from surrounding non-irradiated cells may be involved in the response of cell populations post-irradiation.
Predicting the membrane permeability of organic fluorescent probes by the deep neural network based lipophilicity descriptor DeepFl-LogP
Authors: Soliman Kareem , Grimm Florian , Wurm Christian A. , Egner Alexander 
Published: March 2021

AbstractLight microscopy has become an indispensable tool for the life sciences, as it enables the rapid acquisition of three-dimensional images from the interior of living cells/tissues. Over the last decades, super-resolution light microscopy techniques have been developed, which allow a resolution up to an order of magnitude higher than that of conventional light microscopy. Those techniques require labelling of cellular structures with fluorescent probes exhibiting specific properties, which are supplied from outside and therefore have to surpass cell membranes. Currently, major efforts are undertaken to develop probes which can surpass cell membranes and exhibit the photophysical properties required for super-resolution imaging. However, the process of probe development is still based on a tedious and time consuming manual screening. An accurate computer based model that enables the prediction of the cell permeability based on their chemical structure would therefore be an invaluable asset for the development of fluorescent probes. Unfortunately, current models, which are based on multiple molecular descriptors, are not well suited for this task as they require high effort in the usage and exhibit moderate accuracy in their prediction. Here, we present a novel fragment based lipophilicity descriptor DeepFL-LogP, which was developed on the basis of a deep neural network. DeepFL-LogP exhibits excellent correlation with the experimental partition coefficient reference data (R2 = 0.892 and MSE = 0.359) of drug-like substances. Further a simple threshold permeability model on the basis of this descriptor allows to categorize the permeability of fluorescent probes with 96% accuracy. This novel descriptor is expected to largely simplify and speed up the development process for novel cell permeable fluorophores.
Dicer increases the indication for trastuzumab treatment in gastric cancer patients via overexpression of human epidermal growth factor receptor 2
Authors: Wu Jianhua , Zhao Qun , Zhao Yue , Zhang Xiaoyun , Tian Yuan , Guo Zhanjun 
Published: March 2021

AbstractThe low proportion of gastric cancer (GC) patients with high HER2 expression limits the clinical application of trastuzumab, a humanized epidermal growth factor receptor 2 (HER2) antibody targeting for GC treatment. We found that Dicer was positively correlated with HER2 expression in GC tissue by immunostaining as well as induce HER2 overexpression without increasing invasiveness of GC cell. In addition, both the growth of GC referring to cell proliferation, invasion, migration and apoptosis was inhibited by Dicer overexpression. Moreover, the HER2 overexpression induced by Dicer provided more effective and additive target for trastuzumab to amplify the inhibition effect for GC cells in vitro and in vivo. Furthermore, as assessed in a subsequent experiment, calcitriol induced HER2 overexpression and amplified the inhibition effect of trastuzumab in GC cells referring to proliferation. Our finding demonstrated the calcitriol might increase indication of trastuzumab by inducing HER2 overexpression in GC patients. Dicer would be a potential target that extend the clinical indications of HER2 antibody in patients with low or negative HER2, who were not fit for HER2 antibody treatment before.
Free-water diffusion tensor imaging improves the accuracy and sensitivity of white matter analysis in Alzheimer’s disease
Authors: Bergamino Maurizio , Walsh Ryan R. , Stokes Ashley M. 
Published: March 2021

AbstractMagnetic resonance imaging (MRI) based diffusion tensor imaging (DTI) can assess white matter (WM) integrity through several metrics, such as fractional anisotropy (FA), axial/radial diffusivities (AxD/RD), and mode of anisotropy (MA). Standard DTI is susceptible to the effects of extracellular free water (FW), which can be removed using an advanced free-water DTI (FW-DTI) model. The purpose of this study was to compare standard and FW-DTI metrics in the context of Alzheimer’s disease (AD). Data were obtained from the Open Access Series of Imaging Studies (OASIS-3) database and included both healthy controls (HC) and mild-to-moderate AD. With both standard and FW-DTI, decreased FA was found in AD, mainly in the corpus callosum and fornix, consistent with neurodegenerative mechanisms. Widespread higher AxD and RD were observed with standard DTI; however, the FW index, indicative of AD-associated neurodegeneration, was significantly elevated in these regions in AD, highlighting the potential impact of free water contributions on standard DTI in neurodegenerative pathologies. Using FW-DTI, improved consistency was observed in FA, AxD, and RD, and the complementary FW index was higher in the AD group as expected. With both standard and FW-DTI, higher values of MA coupled with higher values of FA in AD were found in the anterior thalamic radiation and cortico-spinal tract, most likely arising from a loss of crossing fibers. In conclusion, FW-DTI better reflects the underlying pathology of AD and improves the accuracy of DTI metrics related to WM integrity in Alzheimer’s disease.
Changes in respiratory mechanics of artificial pneumothorax two-lung ventilation in video-assisted thoracoscopic esophagectomy in prone position
Authors: Tanigawa Yoshinori , Nakamura Kimihide , Yamashita Tomoko , Nakagawachi Akira , Sakaguchi Yoshiro 
Published: March 2021

AbstractWe aimed to clarify the changes in respiratory mechanics and factors associated with them in artificial pneumothorax two-lung ventilation in video-assisted thoracoscopic esophagectomy in the prone position (PP-VATS-E) for esophageal cancer. Data of patients with esophageal cancer, who underwent PP-VATs-E were retrospectively analyzed. Our primary outcome was the change in the respiratory mechanics after intubation (T1), in the prone position (T2), after initiation of the artificial pneumothorax two-lung ventilation (T3), at 1 and 2 h (T4 and T5), in the supine position (T6), and after laparoscopy (T7). The secondary outcome was identifying factors affecting the change in dynamic lung compliance (Cdyn). Sixty-seven patients were included. Cdyn values were significantly lower at T3, T4, and T5 than at T1 (p < 0.001). End-expiratory flow was significantly higher at T4 and T5 than at T1 (p < 0.05). Body mass index and preoperative FEV1.0% were found to significantly influence Cdyn reduction during artificial pneumothorax and two-lung ventilation (OR [95% CI]: 1.29 [1.03–2.24] and 0.20 (0.05–0.44); p = 0.010 and p = 0.034, respectively]. Changes in driving pressure were nonsignificant, and hypoxemia requiring treatment was not noted. This study suggests that in PP-VATs-E, artificial pneumothorax two-lung ventilation is safer for the management of anesthesia than conventional one-lung ventilation (UMIN Registry: 000042174).
Nanostructured metal nitrides for photocatalysts
Authors: Rao Tingke , Cai Wen , Zhang Han , Liao Wugang 
Published: March 2021

The morphology, size, defects and nanostructured construction of metal nitrides (MNs) are demonstrated to be critical factors in their catalytic efficiency for water spitting and CO2 reduction, emphasizing the importance of their synthetic methods.
Spatial Release From Masking in Pediatric Cochlear Implant Recipients With Single-Sided Deafness
Authors: Park Lisa R. , Dillon Margaret T. , Buss Emily , O'Connell Brendan P. , Brown Kevin D. 
Published: March 2021

Purpose
Children with single-sided deafness (SSD) experience difficulty understanding speech in multisource listening situations. Case reports and retrospective studies have indicated that a cochlear implant (CI) may improve masked speech recognition in children with SSD. This prospective study was conducted to determine whether providing a CI to children with SSD supports spatial release from masking (SRM), an improvement in speech recognition associated with separating the target and masker sources.

Method
Twenty children with at least a moderate-to-profound hearing loss in one ear and normal hearing in the contralateral ear underwent cochlear implantation. The average age of implantation was 5.5 years (range: 3.5–12.7). After 12 months of CI use, subjects completed a sentence recognition task in multitalker masker with and without the CI. The target was presented from the front, and the masker was either colocated with the target (0°) or from the side (+90° or −90°). A two-way repeated-measures analysis of variance was completed to investigate SRM with and without the CI.

Results
Pediatric CI recipients experienced significant SRM when the masker was directed to the normal-hearing ear or to the affected ear.

Conclusions
The results indicate that cochlear implantation in children with SSD supports binaural skills required for speech recognition in noise. These results are consistent with improved functional communication in multisource environments, like classrooms.
The Effect of Parkinson's Disease on Otoacoustic Emissions and Efferent Suppression of Transient Evoked Otoacoustic Emissions
Authors: De Groote Evelien , Bockstael Annelies , Botteldooren Dick , Santens Patrick , De Letter Miet 
Published: March 2021

Purpose
Several studies have demonstrated increased auditory thresholds in patients with Parkinson's disease (PD) based on subjective tonal audiometry. However, the pathophysiological mechanisms underlying auditory dysfunction in PD remain elusive. The primary aim of this study was to investigate cochlear and olivocochlear function in PD using objective measurements and to assess the effect of dopaminergic medication on auditory function.

Method
Eighteen patients with PD and 18 gender- and age-matched healthy controls (HCs) were included. Patients with PD participated in medication on and off conditions. Linear mixed models were used to determine the effect of PD on tonal audiometry, transient evoked and distortion product otoacoustic emissions (OAEs), and efferent suppression (ES).

Results
Tonal audiometry revealed normal auditory thresholds in patients with PD for their age across all frequencies. OAE signal amplitudes demonstrated a significant interaction effect between group (PD vs. HC) and frequency, indicating decreased OAEs at low frequencies and increased OAEs at high frequencies in patients with PD. No significant differences were found between patients with PD and HCs regarding ES. In addition, no significant effect of medication status was found on auditory measurements in patients with PD.

Conclusions
Altered OAEs support the hypothesis of cochlear alterations in PD. No evidence was found for the involvement of the medial olivocochlear system. Altogether, OAEs may provide an objective early indicator of auditory alterations in PD and should complement subjective tonal audiometry when assessing and monitoring auditory function in PD.
Second‐order SMO‐based sensorless control of IM drive: experimental investigations of observer sensitivity and system reconfiguration in postfault operation mode
Authors: Maamouri Rebah , Trabelsi Mohamed , Boussak Mohamed , M'Sahli Faouzi 
Published: March 2021

AbstractIn normal operation mode, sensorless speed‐controlled motor drives should be more reliable, less expensive and less bulky than their counterparts with a speed sensor. The sensorless drive structure allows avoiding the electromagnetic and vibratory sensitivity of the mechanical sensor, the additional connecting circuits, additional space for the sensor, its price and maintenance requirements. However, in postfault operation mode, the robustness of speed sensorless control strategies has been poorly addressed in the study. Accordingly, this study deals with an experimental study of the robustness and the availability of speed‐controlled induction motor (IM) drives without speed sensor in the presence of inverter open‐switches faults. For that purpose, a super twisting algorithm‐based observer for motor speed estimation is proposed for experimental investigation. Experimental results are performed upon 3‐kW IM drive by using dSPACE digital signal processing controller board. Experimental investigations evaluate the performances of the method used for the control without speed sensor in prefault, postfault and regeneration operation modes.
Application of simplified convolutional neural networks for initial stator winding fault detection of the PMSM drive using different raw signal data
Authors: Skowron Maciej , Orlowska‐Kowalska Teresa , Kowalski Czeslaw T. 
Published: March 2021

AbstractPermanent magnet synchronous motors (PMSM) have become one of the most substantial components of modern industrial drives. These motors, like all the others, can unfortunately undergo various failures, causing production line downtime and resulting losses. Accordingly, it is necessary to develop fault diagnostic techniques which detect the damages at the earliest possible stage. This study presents a method of detecting incipient faults of the PMSM stator windings using direct signal analysis and a convolutional neural network (CNN). During the tests, the structures of CNN were optimised to constitute a balance between the high efficiency of fault detection and a small number of network parameters. The effectiveness of the CNNs with inputs constituted by different electrical signals measured in the drive system is compared. Three raw data signals are tested as CNN inputs, namely: stator phase currents, phase‐to‐phase voltages and axial flux, without data preprocessing. The article aims to show the possibility of detecting the incipient interturn short circuits in the PMSM stator winding based on the information obtained directly from the measured signals as well as to present the influence of the drive operating conditions and the type of measurement signals used on the structure and performance of the developed CNNs.